From ac8cc57bb24da92878446cdc2138cd79245813b2 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Tue, 28 May 2024 11:46:47 -0400 Subject: [PATCH 01/14] Generating CDS template Fixes #396 --- cds-template.csv | 1 + 1 file changed, 1 insertion(+) create mode 100644 cds-template.csv diff --git a/cds-template.csv b/cds-template.csv new file mode 100644 index 00000000..932a2e3e --- /dev/null +++ b/cds-template.csv @@ -0,0 +1 @@ +Genomic Reference,Library layout,Data Type,Sequencing Platform,Library Selection Method,HTAN Data File ID,HTAN Parent Biospecimen ID,Filename,File Format \ No newline at end of file From 14cde7fdbff6e5d4adf48749d6eca680962b49e2 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 10:33:47 -0400 Subject: [PATCH 02/14] Adding CDS components to HTAN.model.csv --- HTAN.model.csv | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/HTAN.model.csv b/HTAN.model.csv index b2ffefbd..87d02c0c 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -7,6 +7,11 @@ Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organis File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, +CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,"hg19, hg38_long_polya, Release 31 (GRCh38.p12)",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, +CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,, +CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like +CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning @@ -1031,6 +1036,7 @@ Tile overlap Y,Percentage of image overlap to allow tile stitching in x directio Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophagus goblet cells.,"Yes, No",,,FALSE,Follow Up,,, Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,, +<<<<<<< Updated upstream Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, Microarray Platform ID,"The NCBI GEO Microarray Platform ID that links to the table containing the array definition",,,,TRUE,Microarray Level 1,,,regex match GPL\d+ Microarray Molecule,Microarray is measuring this kind of molecule,"DNA, RNA",,,TRUE,Microarray Level 1,,, @@ -1045,3 +1051,6 @@ Precancer Case,Yes/No indicator to designate the participant for whom precancero Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,, Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ +======= +Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, +>>>>>>> Stashed changes From 1379d9ccfe5638de3ae4b935a052313c0ffeb7f0 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 10:37:53 -0400 Subject: [PATCH 03/14] Revert "Adding CDS components to HTAN.model.csv" This reverts commit 14cde7fdbff6e5d4adf48749d6eca680962b49e2. --- HTAN.model.csv | 9 --------- 1 file changed, 9 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index 87d02c0c..b2ffefbd 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -7,11 +7,6 @@ Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organis File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, -CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,"hg19, hg38_long_polya, Release 31 (GRCh38.p12)",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, -CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,, -CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like -CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning @@ -1036,7 +1031,6 @@ Tile overlap Y,Percentage of image overlap to allow tile stitching in x directio Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophagus goblet cells.,"Yes, No",,,FALSE,Follow Up,,, Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,, -<<<<<<< Updated upstream Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, Microarray Platform ID,"The NCBI GEO Microarray Platform ID that links to the table containing the array definition",,,,TRUE,Microarray Level 1,,,regex match GPL\d+ Microarray Molecule,Microarray is measuring this kind of molecule,"DNA, RNA",,,TRUE,Microarray Level 1,,, @@ -1051,6 +1045,3 @@ Precancer Case,Yes/No indicator to designate the participant for whom precancero Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,, Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ -======= -Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, ->>>>>>> Stashed changes From b097a0c76b2cc7e1fd795703b3400ff630b81bcc Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 10:41:51 -0400 Subject: [PATCH 04/14] Adding CDS components to HTAN.model.cs --- HTAN.model.csv | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index b2ffefbd..a260a913 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -7,6 +7,11 @@ Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organis File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, +CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,"hg19, hg38_long_polya, Release 31 (GRCh38.p12)",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, +CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,, +CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like +CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning @@ -1032,7 +1037,7 @@ Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophag Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,, Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, -Microarray Platform ID,"The NCBI GEO Microarray Platform ID that links to the table containing the array definition",,,,TRUE,Microarray Level 1,,,regex match GPL\d+ +Microarray Platform ID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,,,,TRUE,Microarray Level 1,,,regex match GPL\d+ Microarray Molecule,Microarray is measuring this kind of molecule,"DNA, RNA",,,TRUE,Microarray Level 1,,, Microarray Label,Microarray used this kind of label,,,,TRUE,Microarray Level 1,,, Microarray Value Definition,What the provided value signifies,,,,TRUE,Microarray Level 1,,, @@ -1044,4 +1049,4 @@ Days to Vital Status Reference,Number of days between the date used for index an Precancer Case,Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).,"Yes - Precancer Case, No, Not Reported, unknown",,,TRUE,Patient,,, Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,, Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int -WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ +WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ \ No newline at end of file From 890993e6943669208f67cea32237d770b93d585e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 14:48:46 +0000 Subject: [PATCH 05/14] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 48375 ++++++++++++++++++++++---------------------- 1 file changed, 24443 insertions(+), 23932 deletions(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index f73558f7..c33b5b0e 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -2877,652 +2877,697 @@ "sms:validationRules": [] }, { - "@id": "bts:Checksum", + "@id": "bts:CDSGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "MD5 checksum of the BAM file", - "rdfs:label": "Checksum", + "rdfs:comment": "TBD", + "rdfs:label": "CDSGenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Checksum", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Hg19" + }, + { + "@id": "bts:Hg38LongPolya" + }, + { + "@id": "bts:Release31(GRCh38.p12)" + } + ], + "sms:displayName": "CDS Genomic Reference", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANDataFileID", + "@id": "bts:Hg19", "@type": "rdfs:Class", - "rdfs:comment": "Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANDataFileID", + "rdfs:comment": "TBD", + "rdfs:label": "Hg19", "rdfs:subClassOf": [ { - "@id": "bts:File" + "@id": "bts:CDSGenomicReference" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Data File ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:displayName": "hg19", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HTANBiospecimenID", + "@id": "bts:Hg38LongPolya", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANBiospecimenID", + "rdfs:comment": "TBD", + "rdfs:label": "Hg38LongPolya", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:CDSGenomicReference" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Biospecimen ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:displayName": "hg38_long_polya", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:Biospecimen", + "@id": "bts:Release31(GRCh38.p12)", "@type": "rdfs:Class", - "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", - "rdfs:label": "Biospecimen", + "rdfs:comment": "TBD", + "rdfs:label": "Release31(GRCh38.p12)", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:CDSGenomicReference" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen", + "sms:displayName": "Release 31 (GRCh38.p12)", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:CDSLibraryLayout", + "@type": "rdfs:Class", + "rdfs:comment": "The read strategy or method that was used for sequencing and analysis of a nucleotide library.", + "rdfs:label": "CDSLibraryLayout", + "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANBiospecimenID" - }, - { - "@id": "bts:SourceHTANBiospecimenID" - }, - { - "@id": "bts:HTANParentID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:CollectionDaysfromIndex" - }, - { - "@id": "bts:AdjacentBiospecimenIDs" - }, - { - "@id": "bts:BiospecimenType" - }, - { - "@id": "bts:AcquisitionMethodType" - }, - { - "@id": "bts:FixativeType" - }, - { - "@id": "bts:StorageMethod" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ProcessingDaysfromIndex" + "@id": "bts:PairedEnd" }, { - "@id": "bts:ProtocolLink" - }, + "@id": "bts:SingleRead" + } + ], + "sms:displayName": "CDS Library Layout", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PairedEnd", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "PairedEnd", + "rdfs:subClassOf": [ { - "@id": "bts:SiteDataSource" + "@id": "bts:CDSLibraryLayout" }, { - "@id": "bts:CollectionMedia" - }, + "@id": "bts:LibraryLayout" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Paired End", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SingleRead", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SingleRead", + "rdfs:subClassOf": [ { - "@id": "bts:MountingMedium" + "@id": "bts:CDSLibraryLayout" }, { - "@id": "bts:ProcessingLocation" - }, + "@id": "bts:LibraryLayout" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Single Read", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CDSDataType", + "@type": "rdfs:Class", + "rdfs:comment": "Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.", + "rdfs:label": "CDSDataType", + "rdfs:subClassOf": [ { - "@id": "bts:HistologyAssessmentBy" - }, + "@id": "bts:Publication" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HistologyAssessmentMedium" + "@id": "bts:10xVisiumSpatialTranscriptomics" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:BulkMethylation-seq" }, { - "@id": "bts:TumorInfiltratingLymphocytes" + "@id": "bts:BulkRNA-seq" }, { - "@id": "bts:DegreeofDysplasia" + "@id": "bts:BulkWES" }, { - "@id": "bts:DysplasiaFraction" + "@id": "bts:ElectronMicroscopy" }, { - "@id": "bts:NumberProliferatingCells" + "@id": "bts:ExSeq" }, { - "@id": "bts:PercentEosinophilInfiltration" + "@id": "bts:HI-C-seq" }, { - "@id": "bts:PercentGranulocyteInfiltration" + "@id": "bts:RPPA" }, { - "@id": "bts:PercentInflamInfiltration" + "@id": "bts:Imaging" }, { - "@id": "bts:PercentLymphocyteInfiltration" + "@id": "bts:MassSpectrometry" }, { - "@id": "bts:PercentMonocyteInfiltration" + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics" }, { - "@id": "bts:PercentNecrosis" + "@id": "bts:OtherAssay" }, { - "@id": "bts:PercentNeutrophilInfiltration" + "@id": "bts:SRRSImaging" }, { - "@id": "bts:PercentNormalCells" + "@id": "bts:Slide-seq" }, { - "@id": "bts:PercentStromalCells" + "@id": "bts:ScATAC-seq" }, { - "@id": "bts:PercentTumorCells" + "@id": "bts:ScDNA-seq" }, { - "@id": "bts:PercentTumorNuclei" + "@id": "bts:ScRNA-seq" }, { - "@id": "bts:FiducialMarker" + "@id": "bts:AccessoryManifest" }, { - "@id": "bts:SlicingMethod" - }, + "@id": "bts:OtherDataTypeSpecified" + } + ], + "sms:displayName": "CDS Data Type", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10xVisiumSpatialTranscriptomics", + "rdfs:subClassOf": [ { - "@id": "bts:LysisBuffer" + "@id": "bts:CDSDataType" }, { - "@id": "bts:MethodofNucleicAcidIsolation" + "@id": "bts:DataType" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANParentID", + "@id": "bts:BulkMethylation-seq", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", - "rdfs:label": "HTANParentID", + "rdfs:comment": "TBD", + "rdfs:label": "BulkMethylation-seq", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent ID", - "sms:required": "sms:true", + "sms:displayName": "Bulk Methylation-seq", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANParentBiospecimenID", + "@id": "bts:BulkRNA-seq", "@type": "rdfs:Class", - "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", - "rdfs:label": "HTANParentBiospecimenID", + "rdfs:comment": "TBD", + "rdfs:label": "BulkRNA-seq", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent Biospecimen ID", - "sms:required": "sms:true", + "sms:displayName": "Bulk RNA-seq", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANParentDataFileID", + "@id": "bts:BulkWES", "@type": "rdfs:Class", - "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", - "rdfs:label": "HTANParentDataFileID", + "rdfs:comment": "TBD", + "rdfs:label": "BulkWES", "rdfs:subClassOf": [ { - "@id": "bts:File" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent Data File ID", - "sms:required": "sms:true", + "sms:displayName": "Bulk WES", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClinicalDataTier2", + "@id": "bts:ElectronMicroscopy", "@type": "rdfs:Class", - "rdfs:comment": "Tier 2 Cancer Data", - "rdfs:label": "ClinicalDataTier2", + "rdfs:comment": "TBD", + "rdfs:label": "ElectronMicroscopy", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Clinical Data Tier 2", + "sms:displayName": "Electron Microscopy", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:SentinelLymphNodeCount" - }, - { - "@id": "bts:SentinelNodePositiveAssessmentCount" - }, - { - "@id": "bts:TumorExtranodalExtensionIndicator" - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:OtherBiopsyResectionSite" - }, - { - "@id": "bts:ExtentofTumorResection" - }, - { - "@id": "bts:PriorSitesofRadiation" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:ConcomitantMedicationReceivedType" - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator" - }, - { - "@id": "bts:COVID19OccurrenceIndicator" - }, - { - "@id": "bts:COVID19CurrentStatus" - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator" - }, - { - "@id": "bts:COVID19AntibodyTesting" - }, - { - "@id": "bts:COVID19ComplicationsSeverity" - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup" - }, - { - "@id": "bts:Ecigvapeuse" - }, - { - "@id": "bts:Ecigvape30dayusenum" - }, - { - "@id": "bts:Ecigvapetimesperday" - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears" - }, - { - "@id": "bts:Chewingtobaccodailyusecount" - }, - { - "@id": "bts:Secondhandsmokeexposureyears" - }, - { - "@id": "bts:KnownGeneticPredispositionMutation" - }, - { - "@id": "bts:HereditaryCancerPredispositionSyndrome" - }, - { - "@id": "bts:CancerAssociatedGeneMutations" - }, - { - "@id": "bts:MutationalSignatures" - }, - { - "@id": "bts:MismatchRepairSystemStatus" - }, - { - "@id": "bts:LabTestsforMMRStatus" - }, - { - "@id": "bts:ModeofCancerDetection" - }, - { - "@id": "bts:EducationLevel" - }, - { - "@id": "bts:CountryofBirth" - }, - { - "@id": "bts:MedicallyUnderservedArea" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:ExSeq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ExSeq", + "rdfs:subClassOf": [ { - "@id": "bts:RuralvsUrban" + "@id": "bts:CDSDataType" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:DataType" }, { - "@id": "bts:CancerIncidenceLocation" + "@id": "bts:ImagingAssayType" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ExSeq", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TimepointLabel", + "@id": "bts:HI-C-seq", "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", + "rdfs:comment": "TBD", + "rdfs:label": "HI-C-seq", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", + "sms:displayName": "HI-C-seq", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StartDaysfromIndex", + "@id": "bts:RPPA", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", - "rdfs:label": "StartDaysfromIndex", + "rdfs:comment": "TBD", + "rdfs:label": "RPPA", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Start Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "RPPA", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:StopDaysfromIndex", + "@id": "bts:Imaging", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", - "rdfs:label": "StopDaysfromIndex", + "rdfs:comment": "TBD", + "rdfs:label": "Imaging", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stop Days from Index", + "sms:displayName": "Imaging", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:SentinelLymphNodeCount", + "@id": "bts:MassSpectrometry", "@type": "rdfs:Class", - "rdfs:comment": "Numeric count of sentinel lymph nodes.", - "rdfs:label": "SentinelLymphNodeCount", + "rdfs:comment": "TBD", + "rdfs:label": "MassSpectrometry", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sentinel Lymph Node Count", + "sms:displayName": "Mass Spectrometry", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SentinelNodePositiveAssessmentCount", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics", "@type": "rdfs:Class", - "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", - "rdfs:label": "SentinelNodePositiveAssessmentCount", + "rdfs:comment": "TBD", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomics", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sentinel Node Positive Assessment Count", + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorExtranodalExtensionIndicator", + "@id": "bts:OtherAssay", "@type": "rdfs:Class", - "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", - "rdfs:label": "TumorExtranodalExtensionIndicator", + "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", + "rdfs:label": "OtherAssay", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Assay" + }, + { + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:NO" - }, + "sms:displayName": "Other Assay", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:YES" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Nosourcedocumentation" + "@id": "bts:Component" }, { - "@id": "bts:Notapplicable" + "@id": "bts:Filename" }, { - "@id": "bts:Notsampledordissected" + "@id": "bts:FileFormat" }, { - "@id": "bts:Present" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Present-extensive" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Present-minimal" - }, + "@id": "bts:AssayType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSImaging", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SRRSImaging", + "rdfs:subClassOf": [ { - "@id": "bts:UNKNOWN" + "@id": "bts:CDSDataType" }, { - "@id": "bts:Unspecified" + "@id": "bts:DataType" } ], - "sms:displayName": "Tumor Extranodal Extension Indicator", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Imaging", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SatelliteMetastasisPresentIndicator", + "@id": "bts:Slide-seq", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", - "rdfs:label": "SatelliteMetastasisPresentIndicator", + "rdfs:comment": "TBD", + "rdfs:label": "Slide-seq", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, + "sms:displayName": "Slide-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATAC-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ScATAC-seq", + "rdfs:subClassOf": [ { - "@id": "bts:No" + "@id": "bts:CDSDataType" }, { - "@id": "bts:Unknown" + "@id": "bts:DataType" } ], - "sms:displayName": "Satellite Metastasis Present Indicator", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATAC-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OtherBiopsyResectionSite", + "@id": "bts:ScDNA-seq", "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", - "rdfs:label": "OtherBiopsyResectionSite", + "rdfs:comment": "TBD", + "rdfs:label": "ScDNA-seq", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Biopsy Resection Site", + "sms:displayName": "scDNA-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExtentofTumorResection", + "@id": "bts:ScRNA-seq", "@type": "rdfs:Class", - "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", - "rdfs:label": "ExtentofTumorResection", + "rdfs:comment": "TBD", + "rdfs:label": "ScRNA-seq", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scRNA-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AccessoryManifest", + "@type": "rdfs:Class", + "rdfs:comment": "Accessory specific attributes", + "rdfs:label": "AccessoryManifest", + "rdfs:subClassOf": [ { - 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"@id": "bts:Urethra" + "@id": "bts:HysterectomyMarginsInvolved" }, { - "@id": "bts:UrinaryTract" + "@id": "bts:PregnancyOutcome" }, { - "@id": "bts:Uterus" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:Uvula" + "@id": "bts:HistoneFamily" }, { - "@id": "bts:Vagina" + "@id": "bts:TestAnalyteType" }, { - "@id": "bts:VasDeferens" + "@id": "bts:WHOCNSGrade" }, { - "@id": "bts:Vein" + "@id": "bts:Laterality" }, { - "@id": "bts:Venous" + "@id": "bts:VascularInvasionType" }, { - "@id": "bts:Vertebra" + "@id": "bts:LungTumorLobeBronchialLocation" }, { - "@id": "bts:Vulva" + "@id": "bts:AdditonalFindingsUninvolvedProstate" }, { - "@id": "bts:WhiteBloodCells" + "@id": "bts:SlicingMethod" }, { - "@id": "bts:Wrist" + "@id": "bts:Race" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Prior Sites of Radiation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Immunosuppression", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not immunosuppressive therapy was administered.", - "rdfs:label": "Immunosuppression", - "rdfs:subClassOf": [ + "@id": "bts:CDCHIVRiskFactors" + }, { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ImmunosuppressiveTreatmentType" + }, { - "@id": "bts:Yes" + "@id": "bts:TreatmentIntentType" }, { - "@id": "bts:No" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:Unknown" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Ploidy" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "Immunosuppression", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ConcomitantMedicationReceivedType", - "@type": "rdfs:Class", - "rdfs:comment": "An enumerated list of the type of concomitant medication received by the patient.", - "rdfs:label": "ConcomitantMedicationReceivedType", - "rdfs:subClassOf": [ + "@id": "bts:INSSStage" + }, { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - 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(Extension to GDC attributes in Family History Tier 1)", - "rdfs:label": "FamilyMemberVitalStatusIndicator", - "rdfs:subClassOf": [ + "@id": "bts:DiabetesTreatmentType" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:TreatmentFrequency" + }, { - "@id": "bts:VitalStatusAlive" + "@id": "bts:TumorGrade" }, { - "@id": "bts:VitalStatusDead" + "@id": "bts:OvarianCancerHistologicSubtype" }, { - "@id": "bts:Unknown" + "@id": "bts:PancreasPrecancerHistopathologicGrade" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Family Member Vital Status Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19OccurrenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", - "rdfs:label": "COVID19OccurrenceIndicator", - "rdfs:subClassOf": [ + "@id": "bts:CauseofDeath" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IRSGroup" + }, { - "@id": "bts:Yes" + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" }, { - "@id": "bts:No" + "@id": "bts:BreastCancerAllredEstrogenReceptorScore" }, { - "@id": "bts:Unknown" + "@id": "bts:CNSLeukemiaStatus" }, { - "@id": "bts:NotApplicable" + "@id": "bts:KarnofskyPerformanceStatus" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Occurrence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CurrentStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", - "rdfs:label": "COVID19CurrentStatus", - "rdfs:subClassOf": [ + "@id": "bts:TreatmentOutcome" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ECOGPerformanceStatus" + }, { - "@id": "bts:Patientcurrentlyhassymptoms" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" + "@id": "bts:TestResult" }, { - "@id": "bts:PatientneverhadanysymptomsofCOVID-19" + "@id": "bts:LungCancerParticipantProcedureHistory" }, { - "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" + "@id": "bts:LungAdjacentHistologyType" }, { - "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" + "@id": "bts:HistoneVariant" }, { - "@id": "bts:Statusunknownduetootherreasons" - } - ], - "sms:displayName": "COVID19 Current Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", - "rdfs:label": "COVID19PositiveLabTestIndicator", - "rdfs:subClassOf": [ + "@id": "bts:PreservationMethod" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StorageMethod" + }, { - "@id": "bts:Yes" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:No" + "@id": "bts:LocationExtentExtraprostaticExtension" }, { - "@id": "bts:Unknown" + "@id": "bts:FixativeType" }, { - "@id": "bts:NotApplicable" + "@id": "bts:HPVPositiveType" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Positive Lab Test Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19AntibodyTesting", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", - "rdfs:label": "COVID19AntibodyTesting", - "rdfs:subClassOf": [ + "@id": "bts:LymphNodeInvolvedSite" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ClinicalBiospecimenType" + }, { - "@id": "bts:SARS-CoV-2IgMantibodypositive" + "@id": "bts:VariantType" }, { - "@id": "bts:SARS-CoV-2IgGantibodypositive" + "@id": "bts:MethodofDiagnosis" }, { - "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" + "@id": "bts:AJCCClinicalN" }, { - "@id": "bts:SARS-CoV-2IgMantibodynegative" + "@id": "bts:AJCCPathologicN" }, { - "@id": "bts:SARS-CoV-2IgGantibodynegative" + "@id": "bts:Chromosome" }, { - "@id": "bts:SARS-CoV-2IgG/IgMantibodynegative" + "@id": "bts:LocationNaturePositiveMargins" }, { - "@id": "bts:Unknown" + "@id": "bts:ConcomitantMedicationReceivedType" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Antigen" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Antibody Testing", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19ComplicationsSeverity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.", - "rdfs:label": "COVID19ComplicationsSeverity", - "rdfs:subClassOf": [ + "@id": "bts:CurrentLungCancerSymptoms" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DiseaseResponse" + }, { - "@id": "bts:Cardiaccomplications" + "@id": "bts:AJCCClinicalStage" }, { - "@id": "bts:Pulmonarycomplications" + "@id": "bts:AJCCPathologicStage" }, { - "@id": "bts:Systemiccomplications" + "@id": "bts:MetastasisatDiagnosisSite" }, { - "@id": "bts:Other" + "@id": "bts:CDSSequencingPlatform" }, { - "@id": "bts:NotApplicable" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "COVID19 Complications Severity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder", - "rdfs:label": "COVID19CancerTreatmentFollowup", - "rdfs:subClassOf": [ + "@id": "bts:TypeofSmokeExposure" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AJCCClinicalT" + }, { - "@id": "bts:Yes" + "@id": "bts:AJCCPathologicT" }, { - "@id": "bts:No" + "@id": "bts:MutationalSignatures" }, { - "@id": "bts:Unknown" + "@id": "bts:LungCancerHarboringGenomicAberrations" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "COVID19 Cancer Treatment Followup", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapeuse", - "@type": "rdfs:Class", - "rdfs:comment": "Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)", - "rdfs:label": "Ecigvapeuse", - "rdfs:subClassOf": [ + "@id": "bts:HereditaryCancerPredispositionSyndrome" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LaboratoryTest" + }, { - "@id": "bts:Current" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:Former" + "@id": "bts:RelationshipPrimaryDiagnosis" }, { - "@id": "bts:Never" + "@id": "bts:TreatmentType" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ecig vape use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvape30dayusenum", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days e-cigarettes or vaping device was used in the last 30 days", - "rdfs:label": "Ecigvape30dayusenum", - "rdfs:subClassOf": [ + "@id": "bts:CancerAssociatedGeneMutations" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape 30 day use num", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapetimesperday", - "@type": "rdfs:Class", - "rdfs:comment": "e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)", - "rdfs:label": "Ecigvapetimesperday", - "rdfs:subClassOf": [ + "@id": "bts:LungTopography" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape times per day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", - "rdfs:label": "Typeofsmokeexposurecumulativeyears", - "rdfs:subClassOf": [ + "@id": "bts:RiskFactor" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Type of smoke exposure cumulative years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chewingtobaccodailyusecount", - "@type": "rdfs:Class", - "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", - "rdfs:label": "Chewingtobaccodailyusecount", - "rdfs:subClassOf": [ + "@id": "bts:RelationshipType" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Chewing tobacco daily use count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Secondhandsmokeexposureyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's exposure to second-hand cigarette smoke", - "rdfs:label": "Secondhandsmokeexposureyears", - "rdfs:subClassOf": [ + "@id": "bts:Comorbidity" + }, { - "@id": "bts:Exposure" + "@id": "bts:CountryofBirth" + }, + { + "@id": "bts:PriorSitesofRadiation" + }, + { + "@id": "bts:TopographyCode" + }, + { + "@id": "bts:ProgressionorRecurrenceAnatomicSite" + }, + { + "@id": "bts:TreatmentAnatomicSite" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:TissueorOrganofOrigin" + }, + { + "@id": "bts:PrimaryDiagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Second hand smoke exposure years", + "sms:displayName": "unknown", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:KnownGeneticPredispositionMutation", + "@id": "bts:NotReported", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", - "rdfs:label": "KnownGeneticPredispositionMutation", + "rdfs:comment": "TBD", + "rdfs:label": "NotReported", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SmokingExposure" + }, { - "@id": "bts:Yes" + "@id": "bts:AlcoholExposure" }, { - "@id": "bts:No" + "@id": "bts:SmokeExposureDuration" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Known Genetic Predisposition Mutation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HereditaryCancerPredispositionSyndrome", - 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"@id": "bts:Afghanistan" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Albania" + "@id": "bts:Component" }, { - "@id": "bts:Algeria" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:Andorra" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:Angola" + "@id": "bts:HTANParentID" }, { - "@id": "bts:Anguilla" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:Argentina" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:Armenia" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:Aruba" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:Australia" + "@id": "bts:FixativeType" }, { - "@id": "bts:Austria" + "@id": "bts:StorageMethod" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:Bahamas" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Bahrain" + "@id": "bts:SiteDataSource" }, { - "@id": "bts:Bangladesh" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:Barbados" + "@id": "bts:MountingMedium" }, { - "@id": "bts:Belarus" + "@id": "bts:ProcessingLocation" }, { - "@id": "bts:Belgium" + "@id": "bts:HistologyAssessmentBy" }, { - "@id": "bts:Belize" + "@id": "bts:HistologyAssessmentMedium" }, { - "@id": "bts:Benin" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:Bermuda" + "@id": "bts:TumorInfiltratingLymphocytes" }, { - "@id": "bts:Bhutan" + "@id": "bts:DegreeofDysplasia" }, { - "@id": "bts:Bolivia" + "@id": "bts:DysplasiaFraction" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:NumberProliferatingCells" }, { - "@id": "bts:Botswana" + "@id": "bts:PercentEosinophilInfiltration" }, { - "@id": "bts:Brazil" + "@id": "bts:PercentGranulocyteInfiltration" }, { - "@id": "bts:Brunei" + "@id": "bts:PercentInflamInfiltration" }, { - "@id": "bts:Bulgaria" + "@id": "bts:PercentLymphocyteInfiltration" }, { - "@id": "bts:BurkinaFaso" + "@id": "bts:PercentMonocyteInfiltration" }, { - "@id": "bts:Burundi" + "@id": "bts:PercentNecrosis" }, { - "@id": "bts:Cambodia" + "@id": "bts:PercentNeutrophilInfiltration" }, { - "@id": "bts:Cameroon" + "@id": "bts:PercentNormalCells" }, { - "@id": "bts:Canada" + "@id": "bts:PercentStromalCells" }, { - "@id": "bts:CapeVerde" + "@id": "bts:PercentTumorCells" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:PercentTumorNuclei" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:FiducialMarker" }, { - "@id": "bts:Chad" + "@id": "bts:SlicingMethod" }, { - "@id": "bts:Chile" + "@id": "bts:LysisBuffer" }, { - "@id": "bts:China" - }, + "@id": "bts:MethodofNucleicAcidIsolation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", + "rdfs:label": "HTANParentID", + "rdfs:subClassOf": [ { - "@id": "bts:Colombia" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", + "rdfs:label": "HTANParentBiospecimenID", + "rdfs:subClassOf": [ { - "@id": "bts:Comoros" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Biospecimen ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentDataFileID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", + "rdfs:label": "HTANParentDataFileID", + "rdfs:subClassOf": [ { - "@id": "bts:Congo" - }, + "@id": "bts:File" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Data File ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Tier 2 Cancer Data", + "rdfs:label": "ClinicalDataTier2", + "rdfs:subClassOf": [ { - "@id": "bts:CookIslands" + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:CostaRica" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Croatia" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Cuba" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Curacao" + "@id": "bts:SentinelLymphNodeCount" }, { - "@id": "bts:Cyprus" + "@id": "bts:SentinelNodePositiveAssessmentCount" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:TumorExtranodalExtensionIndicator" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:SatelliteMetastasisPresentIndicator" }, { - "@id": "bts:Denmark" + "@id": "bts:OtherBiopsyResectionSite" }, { - "@id": "bts:Djibouti" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:Dominica" + "@id": "bts:PriorSitesofRadiation" }, { - "@id": "bts:DominicanRepublic" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:Ecuador" + "@id": "bts:ConcomitantMedicationReceivedType" }, { - "@id": "bts:Egypt" + "@id": "bts:FamilyMemberVitalStatusIndicator" }, { - "@id": "bts:ElSalvador" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:COVID19CurrentStatus" }, { - "@id": "bts:Eritrea" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:Estonia" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:Eswatini" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:Ethiopia" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:Ecigvapeuse" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:Ecigvape30dayusenum" }, { - "@id": "bts:FederatedStatesofMicronesia" + "@id": "bts:Ecigvapetimesperday" }, { - "@id": "bts:Fiji" + "@id": "bts:Typeofsmokeexposurecumulativeyears" }, { - "@id": "bts:Finland" + "@id": "bts:Chewingtobaccodailyusecount" }, { - "@id": "bts:France" + "@id": "bts:Secondhandsmokeexposureyears" }, { - "@id": "bts:FrenchGuiana" + "@id": "bts:KnownGeneticPredispositionMutation" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:HereditaryCancerPredispositionSyndrome" }, { - "@id": "bts:Gabon" + "@id": "bts:CancerAssociatedGeneMutations" }, { - "@id": "bts:Gambia" + "@id": "bts:MutationalSignatures" }, { - "@id": "bts:Georgia" + "@id": "bts:MismatchRepairSystemStatus" }, { - "@id": "bts:Germany" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:Ghana" + "@id": "bts:ModeofCancerDetection" }, { - "@id": "bts:Gibraltar" + "@id": "bts:EducationLevel" }, { - "@id": "bts:Greece" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:Greenland" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:Grenada" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:Guadeloupe" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:Guam" + "@id": "bts:CancerIncidenceLocation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:TimepointLabel", + "@type": "rdfs:Class", + "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label": "TimepointLabel", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Timepoint Label", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:StartDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label": "StartDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:StopDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stop Days from Index", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SentinelLymphNodeCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric count of sentinel lymph nodes.", + "rdfs:label": "SentinelLymphNodeCount", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Lymph Node Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount", + "@type": "rdfs:Class", + "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", + "rdfs:label": "SentinelNodePositiveAssessmentCount", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Node Positive Assessment Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorExtranodalExtensionIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", + "rdfs:label": "TumorExtranodalExtensionIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" }, { - "@id": "bts:Guatemala" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Guernsey" + "@id": "bts:NO" }, { - "@id": "bts:Guinea" + "@id": "bts:YES" }, { - "@id": "bts:Guinea-Bissau" + "@id": "bts:Nosourcedocumentation" }, { - "@id": "bts:Guyana" + "@id": "bts:Notapplicable" }, { - "@id": "bts:Haiti" + "@id": "bts:Notsampledordissected" }, { - "@id": "bts:HolySee" + "@id": "bts:Present" }, { - "@id": "bts:Honduras" + "@id": "bts:Present-extensive" }, { - "@id": "bts:HongKong" + "@id": "bts:Present-minimal" }, { - "@id": "bts:Hungary" + "@id": "bts:UNKNOWN" }, { - "@id": "bts:Iceland" + "@id": "bts:Unspecified" + } + ], + "sms:displayName": "Tumor Extranodal Extension Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SatelliteMetastasisPresentIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", + "rdfs:label": "SatelliteMetastasisPresentIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:India" + "@id": "bts:No" }, { - "@id": "bts:Indonesia" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Satellite Metastasis Present Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OtherBiopsyResectionSite", + "@type": "rdfs:Class", + "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", + "rdfs:label": "OtherBiopsyResectionSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Other Biopsy Resection Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ExtentofTumorResection", + "@type": "rdfs:Class", + "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", + "rdfs:label": "ExtentofTumorResection", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GrossTotalResection" }, { - "@id": "bts:Iran" + "@id": "bts:OpenBiopsy" }, { - "@id": "bts:Iraq" + "@id": "bts:SubtotalResection" }, { - "@id": "bts:Ireland" + "@id": "bts:ExtensiveSubtotal" }, { - "@id": "bts:IsleofMan" + "@id": "bts:Minor" }, { - "@id": "bts:Israel" + "@id": "bts:Optimaldebulking" }, { - "@id": "bts:Italy" + "@id": "bts:Other" }, { - "@id": "bts:Jamaica" + "@id": "bts:Partialdebulking" }, { - "@id": "bts:Japan" + "@id": "bts:Segmental" }, { - "@id": "bts:Jersey" + "@id": "bts:Suboptimal" }, { - "@id": "bts:Jordan" + "@id": "bts:Suboptimaldebulking" }, { - "@id": "bts:Kazakhstan" + "@id": "bts:NTR" }, { - "@id": "bts:Kenya" + "@id": "bts:Unknown" }, { - "@id": "bts:Kiribati" + "@id": "bts:NotReported" }, { - "@id": "bts:Kosovo" + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Extent of Tumor Resection", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorSitesofRadiation", + "@type": "rdfs:Class", + "rdfs:comment": "The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.", + "rdfs:label": "PriorSitesofRadiation", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Abdomentotal" }, { - "@id": "bts:Kuwait" + "@id": "bts:AbdominalWall" }, { - "@id": "bts:Kyrgyzstan" + "@id": "bts:Acetabulum" }, { - "@id": "bts:Laos" + "@id": "bts:Adenoid" }, { - "@id": "bts:Latvia" + "@id": "bts:Adipose" }, { - "@id": "bts:Lebanon" + "@id": "bts:Adrenal" }, { - "@id": "bts:Lesotho" + "@id": "bts:AlveolarRidge" }, { - "@id": "bts:Liberia" + "@id": "bts:AmnioticFluid" }, { - "@id": "bts:Libya" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Liechtenstein" + "@id": "bts:AnalSphincter" }, { - "@id": "bts:Lithuania" + "@id": "bts:Ankle" }, { - "@id": "bts:Luxembourg" + "@id": "bts:Anorectum" }, { - "@id": "bts:Macau" + "@id": "bts:AntecubitalFossa" }, { - "@id": "bts:Madagascar" + "@id": "bts:Antrum" }, { - "@id": "bts:Malawi" + "@id": "bts:Anus" }, { - "@id": "bts:Malaysia" + "@id": "bts:Aorta" }, { - "@id": "bts:Maldives" + "@id": "bts:AorticBody" }, { - "@id": "bts:Mali" + "@id": "bts:Appendix" }, { - "@id": "bts:Malta" + "@id": "bts:AqueousFluid" }, { - "@id": "bts:MarshallIslands" + "@id": "bts:Arm" }, { - "@id": "bts:Martinique" + "@id": "bts:Artery" }, { - "@id": "bts:Mauritania" + "@id": "bts:AscendingColon" }, { - "@id": "bts:Mauritius" + "@id": "bts:AscendingColonHepaticFlexure" }, { - "@id": "bts:Mayotte" + "@id": "bts:Ascites" }, { - "@id": "bts:Mexico" + "@id": "bts:AuditoryCanal" }, { - "@id": "bts:Moldova" + "@id": "bts:AutonomicNervousSystem" }, { - "@id": "bts:Monaco" + "@id": "bts:Axilla" }, { - "@id": "bts:Mongolia" + "@id": "bts:Back" }, { - "@id": "bts:Montenegro" + "@id": "bts:BileDuct" }, { - "@id": "bts:Montserrat" + "@id": "bts:Bladder" }, { - "@id": "bts:Morocco" + "@id": "bts:Blood" }, { - "@id": "bts:Mozambique" + "@id": "bts:BloodVessel" }, { - "@id": "bts:Myanmar" + "@id": "bts:Bodytotal" }, { - "@id": "bts:Namibia" + "@id": "bts:Bone" }, { - "@id": "bts:Nauru" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:Nepal" + "@id": "bts:Bonenon-spine" }, { - "@id": "bts:Netherlands" + "@id": "bts:Bowel" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:Brain" }, { - "@id": "bts:NewZealand" + "@id": "bts:BrainStem" }, { - "@id": "bts:Nicaragua" + "@id": "bts:Breast" }, { - "@id": "bts:Niger" + "@id": "bts:BroadLigament" }, { - "@id": "bts:Nigeria" + "@id": "bts:Bronchiole" }, { - "@id": "bts:Niue" + "@id": "bts:Bronchus" }, { - "@id": "bts:NorthKorea" + "@id": "bts:Brow" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:BuccalCavity" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:BuccalMucosa" }, { - "@id": "bts:Norway" + "@id": "bts:Buttock" }, { - "@id": "bts:Oman" + "@id": "bts:Calf" }, { - "@id": "bts:Pakistan" + "@id": "bts:Capillary" }, { - "@id": "bts:Palau" + "@id": "bts:Cardia" }, { - "@id": "bts:Panama" + "@id": "bts:Carina" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:CarotidArtery" }, { - "@id": "bts:Paraguay" + "@id": "bts:CarotidBody" }, { - "@id": "bts:Peru" + "@id": "bts:Cartilage" }, { - "@id": "bts:Philippines" + "@id": "bts:Cecum" }, { - "@id": "bts:Poland" + "@id": "bts:Cell-Line" }, { - "@id": "bts:Portugal" + "@id": "bts:CentralNervousSystem" }, { - "@id": "bts:PuertoRico" + "@id": "bts:Cerebellum" }, { - "@id": "bts:Qatar" + "@id": "bts:CerebralCortex" }, { - "@id": "bts:Reunion" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:Romania" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Russia" + "@id": "bts:CervicalSpine" }, { - "@id": "bts:Rwanda" + "@id": "bts:Cervix" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Chest" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:ChestWall" }, { - "@id": "bts:SaintLucia" + "@id": "bts:Chin" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:Clavicle" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:Clitoris" }, { - "@id": "bts:Samoa" + "@id": "bts:Colon" }, { - "@id": "bts:SanMarino" + "@id": "bts:ColonMucosaOnly" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:CommonDuct" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:Senegal" + "@id": "bts:ConnectiveTissue" }, { - "@id": "bts:Serbia" + "@id": "bts:Dermal" }, { - "@id": "bts:Seychelles" + "@id": "bts:DescendingColon" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Diaphragm" }, { - "@id": "bts:Singapore" + "@id": "bts:DistantSite" }, { - "@id": "bts:Slovakia" + "@id": "bts:Duodenum" }, { - "@id": "bts:Slovenia" + "@id": "bts:Ear" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:EarCanal" }, { - "@id": "bts:Somalia" + "@id": "bts:EarPinna(External)" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:Elbow" }, { - "@id": "bts:SouthKorea" + "@id": "bts:EndocrineGland" }, { - "@id": "bts:SouthSudan" + "@id": "bts:Epididymis" }, { - "@id": "bts:Spain" + "@id": "bts:EpiduralSpace" }, { - "@id": "bts:SriLanka" + "@id": "bts:Epitrochlear" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:EsophagogastricJunction" }, { - "@id": "bts:Sudan" + "@id": "bts:Esophagus" }, { - "@id": "bts:Suriname" + "@id": "bts:EsophagusMucosaOnly" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:Eye" }, { - "@id": "bts:Sweden" + "@id": "bts:FallopianTube" }, { - "@id": "bts:Switzerland" + "@id": "bts:FemoralArtery" }, { - "@id": "bts:Syria" + "@id": "bts:FemoralVein" }, { - "@id": "bts:Taiwan" + "@id": "bts:Femur" }, { - "@id": "bts:Tajikistan" + "@id": "bts:Fibroblasts" }, { - "@id": "bts:Tanzania" + "@id": "bts:Fibula" }, { - "@id": "bts:Thailand" + "@id": "bts:Finger" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:FloorofMouth" }, { - "@id": "bts:Togo" + "@id": "bts:Fluid" }, { - "@id": "bts:Tokelau" + "@id": "bts:Foot" }, { - "@id": "bts:Tonga" + "@id": "bts:Forearm" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:Forehead" }, { - "@id": "bts:Tunisia" + "@id": "bts:Foreskin" }, { - "@id": "bts:Turkey" + "@id": "bts:FrontalCortex" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:FrontalLobe" }, { - "@id": "bts:Tuvalu" + "@id": "bts:FundusofStomach" }, { - "@id": "bts:Uganda" + "@id": "bts:Gallbladder" }, { - "@id": "bts:Ukraine" + "@id": "bts:Ganglia" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:GastroesophagealJunction" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:GastrointestinalTract" }, { - "@id": "bts:UnitedStates" + "@id": "bts:GastrointestinalIntestine" }, { - "@id": "bts:Uruguay" + "@id": "bts:GenitourinaryNOS" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:Groin" }, { - "@id": "bts:Vanuatu" + "@id": "bts:Gum" }, { - "@id": "bts:Venezuela" + "@id": "bts:Hand" }, { - "@id": "bts:Vietnam" + "@id": "bts:HardPalate" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:HeadFaceOrNeckNos" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:HeadandNeck" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:Heart" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Hepatic" }, { - "@id": "bts:Yemen" + "@id": "bts:HepaticDuct" }, { - "@id": "bts:Zambia" + "@id": "bts:HepaticVein" }, { - "@id": "bts:Zimbabwe" + "@id": "bts:Hilar" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Country of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedArea", - "@type": "rdfs:Class", - "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", - "rdfs:label": "MedicallyUnderservedArea", - "rdfs:subClassOf": [ + "@id": "bts:Hip" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hippocampus" + }, { - "@id": "bts:MedicallyUnderservedArea-Yes" + "@id": "bts:Humerus" }, { - "@id": "bts:MedicallyUnderservedArea-No" + "@id": "bts:Hypopharynx" }, { - "@id": "bts:MedicallyUnderservedArea-Unknown" - } - ], - "sms:displayName": "Medically Underserved Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RuralvsUrban", - "@type": "rdfs:Class", - "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", - "rdfs:label": "RuralvsUrban", - "rdfs:subClassOf": [ + "@id": "bts:IleocecalValve" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ileum" + }, { - "@id": "bts:UrbanPopulation(population>50000)" + "@id": "bts:Ilium" }, { - "@id": "bts:UrbanCluster(population2500-50000)" + "@id": "bts:IndexFinger" }, { - "@id": "bts:RuralPopulation(population<2500)" - } - ], - "sms:displayName": "Rural vs Urban", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidence", - "@type": "rdfs:Class", - "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", - "rdfs:label": "CancerIncidence", - "rdfs:subClassOf": [ + "@id": "bts:Ischium" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidenceLocation", - "@type": "rdfs:Class", - "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", - "rdfs:label": "CancerIncidenceLocation", - "rdfs:subClassOf": [ + "@id": "bts:IsletCells" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Cancer related clinical data specific to SRRS", - "rdfs:label": "SRRSClinicalDataTier2", - "rdfs:subClassOf": [ + "@id": "bts:Jaw" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Jejunum" + }, { - "@id": "bts:Component" + "@id": "bts:Joint" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Kidney" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Knee" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:LacrimalGland" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:LargeBowel" }, { - "@id": "bts:EducationLevel" + "@id": "bts:Laryngopharynx" }, { - "@id": "bts:CountryofBirth" + "@id": "bts:Larynx" }, { - "@id": "bts:MedicallyUnderservedArea" + "@id": "bts:Leg" }, { - "@id": "bts:RuralvsUrban" + "@id": "bts:Leptomeninges" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:Ligament" }, { - "@id": "bts:CancerIncidenceLocation" + "@id": "bts:Lip" }, { - "@id": "bts:Ethnicity" + "@id": "bts:Liver" }, { - "@id": "bts:Gender" + "@id": "bts:LumbarSpine" }, { - "@id": "bts:Race" + "@id": "bts:Lung" }, { - "@id": "bts:VitalStatus" + "@id": "bts:LymphNode" }, { - "@id": "bts:AgeatDiagnosis" + "@id": "bts:LymphNode(s)Axilla" }, { - "@id": "bts:DaystoLastFollowup" + "@id": "bts:LymphNode(s)Cervical" }, { - "@id": "bts:DaystoLastKnownDiseaseStatus" + "@id": "bts:LymphNode(s)Distant" }, { - "@id": "bts:DaystoRecurrence" + "@id": "bts:LymphNode(s)Epitrochlear" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:LymphNode(s)Femoral" }, { - "@id": "bts:Morphology" + "@id": "bts:LymphNode(s)Hilar" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:LymphNode(s)Iliac-Common" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:LymphNode(s)Iliac-External" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:LymphNode(s)Inguinal" }, { - "@id": "bts:TissueorOrganofOrigin" + "@id": "bts:LymphNode(s)InternalMammary" }, { - "@id": "bts:NCIAtlasCancerSite" + "@id": "bts:LymphNode(s)Mammary" }, { - "@id": "bts:TumorGrade" + "@id": "bts:LymphNode(s)Mediastinal" }, { - "@id": "bts:PackYearsSmoked" + "@id": "bts:LymphNode(s)Mesenteric" }, { - "@id": "bts:YearsSmoked" + "@id": "bts:LymphNode(s)Occipital" }, { - "@id": "bts:DaystoFollowUp" + "@id": "bts:LymphNode(s)Paraaortic" }, { - "@id": "bts:GeneSymbol" + "@id": "bts:LymphNode(s)Parotid" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:LymphNode(s)Pelvic" }, { - "@id": "bts:TestResult" + "@id": "bts:LymphNode(s)Popliteal" }, { - "@id": "bts:TreatmentType" + "@id": "bts:LymphNode(s)Regional" }, { - "@id": "bts:TumorLargestDimensionDiameter" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Ethnicity", - "@type": "rdfs:Class", - "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", - "rdfs:label": "Ethnicity", - "rdfs:subClassOf": [ + "@id": "bts:LymphNode(s)Retroperitoneal" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LymphNode(s)Scalene" + }, { - "@id": "bts:Hispanicorlatino" + "@id": "bts:LymphNode(s)Splenic" }, { - "@id": "bts:Nothispanicorlatino" + "@id": "bts:LymphNode(s)Subclavicular" }, { - "@id": "bts:Unknown" + "@id": "bts:LymphNode(s)Submandibular" }, { - "@id": "bts:NotReported" + "@id": "bts:LymphNode(s)Supraclavicular" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Ethnicity", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Gender", - "@type": "rdfs:Class", - "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", - "rdfs:label": "Gender", - "rdfs:subClassOf": [ + "@id": "bts:Mandible" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Mantle" + }, { - "@id": "bts:Female" + "@id": "bts:Maxilla" }, { - "@id": "bts:Male" + "@id": "bts:MediastinalSoftTissue" }, { - "@id": "bts:Unknown" + "@id": "bts:Mediastinum" }, { - "@id": "bts:Unspecified" + "@id": "bts:Mesentery" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Gender", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Race", - "@type": "rdfs:Class", - "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", - "rdfs:label": "Race", - "rdfs:subClassOf": [ + "@id": "bts:Mesothelium" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:MiddleFinger" + }, { - "@id": "bts:White" + "@id": "bts:Mitochondria" }, { - "@id": "bts:Americanindianoralaskanative" + "@id": "bts:Muscle" }, { - "@id": "bts:Blackorafricanamerican" + "@id": "bts:Nails" }, { - "@id": "bts:Asian" + "@id": "bts:NasalCavity" }, { - "@id": "bts:Nativehawaiianorotherpacificislander" + "@id": "bts:NasalSoftTissue" }, { - "@id": "bts:Other" + "@id": "bts:Nasopharynx" }, { - "@id": "bts:Unknown" + "@id": "bts:Neck" }, { - "@id": "bts:NotReported" + "@id": "bts:Nerve" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Race", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VitalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", - "rdfs:subClassOf": [ + "@id": "bts:Nerve(s)Cranial" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:OccipitalCortex" + }, { - "@id": "bts:Alive" + "@id": "bts:OcularOrbits" }, { - "@id": "bts:Dead" + "@id": "bts:Omentum" }, { - "@id": "bts:Unknown" + "@id": "bts:OralCavity" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vital Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", - "rdfs:label": "AgeatDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:OralCavityMucosaOnly" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Age at Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoLastFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastFollowup", - "rdfs:subClassOf": [ + "@id": "bts:Oropharynx" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Follow up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoLastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastKnownDiseaseStatus", - "rdfs:subClassOf": [ + "@id": "bts:Other" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoRecurrence", - "rdfs:subClassOf": [ + "@id": "bts:Ovary" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:LastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", - "rdfs:label": "LastKnownDiseaseStatus", - "rdfs:subClassOf": [ + "@id": "bts:Palate" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Pancreas" + }, { - "@id": "bts:Distantmetrecurrence/progression" + "@id": "bts:Parametrium" }, { - "@id": "bts:Loco-regionalrecurrence/progression" + "@id": "bts:ParaspinalGanglion" }, { - "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" + "@id": "bts:Parathyroid" }, { - "@id": "bts:Tumorfree" + "@id": "bts:ParotidGland" }, { - "@id": "bts:Unknowntumorstatus" + "@id": "bts:Patella" }, { - "@id": "bts:Withtumor" + "@id": "bts:Pelvis" }, { - "@id": "bts:NotReported" + "@id": "bts:Penis" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:Pericardium" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Morphology", - "@type": "rdfs:Class", - "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", - "rdfs:label": "Morphology", - "rdfs:subClassOf": [ + "@id": "bts:PeriorbitalSoftTissue" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Morphology", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PrimaryDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "PrimaryDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Acinarcellcarcinoma" + "@id": "bts:PeritonealCavity" }, { - "@id": "bts:Acutebasophilicleukaemia" + "@id": "bts:Peritoneum" }, { - "@id": "bts:AcuteleukemiaBurkitttype" + "@id": "bts:Pharynx" }, { - "@id": "bts:AcuteleukemiaNOS" + "@id": "bts:Pineal" }, { - "@id": "bts:Acutelymphaticleukemia" + "@id": "bts:PinealGland" }, { - "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" + "@id": "bts:PituitaryGland" }, { - "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" + "@id": "bts:Placenta" }, { - "@id": "bts:AcutelymphoblasticleukemiaNOS" + "@id": "bts:Pleura" }, { - "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" + "@id": "bts:PoplitealFossa" }, { - "@id": "bts:Acutelymphocyticleukemia" + "@id": "bts:Pouch" }, { - "@id": "bts:Acutelymphoidleukemia" + "@id": "bts:PrimaryTumorField" }, { - "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" + "@id": "bts:Primarytumorsite" }, { - "@id": "bts:AcutemyeloidleukemiaMLL" + "@id": "bts:Prostate" }, { - "@id": "bts:AcutemyeloidleukemiaNOS" + "@id": "bts:ProstateBed" }, { - "@id": "bts:Acutemyelomonocyticleukemia" + "@id": "bts:ProstateSeminalVesiclesandLymphNodes" }, { - "@id": "bts:AcutepromyelocyticleukemiaNOS" + "@id": "bts:Pylorus" }, { - "@id": "bts:Adenocarcinoidtumor" + "@id": "bts:RectosigmoidJunction" }, { - "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" + "@id": "bts:Rectum" }, { - "@id": "bts:AdenocarcinomainapolypNOS" + "@id": "bts:RegionalSite" }, { - "@id": "bts:Adenocarcinomainadenomatouspolyp" + "@id": "bts:Retina" }, { - "@id": "bts:Adenocarcinomainpolypoidadenoma" + "@id": "bts:Retro-OrbitalRegion" }, { - "@id": "bts:AdenocarcinomainsituinapolypNOS" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" + "@id": "bts:Rib" }, { - "@id": "bts:Adenocarcinomainsituintubularadenoma" + "@id": "bts:RingFinger" }, { - "@id": "bts:Adenocarcinomainsitumucinous" + "@id": "bts:RoundLigament" }, { - "@id": "bts:Adenocarcinomainsitunon-mucinous" + "@id": "bts:Sacrum" }, { - "@id": "bts:AdenocarcinomainsituNOS" + "@id": "bts:SalivaryGland" }, { - "@id": "bts:Adenocarcinomaintubularadenoma" + "@id": "bts:Scalp" }, { - "@id": "bts:Adenocarcinomainvillousadenoma" + "@id": "bts:Scapula" }, { - "@id": "bts:Adenocarcinomaofanalducts" + "@id": "bts:SciaticNerve" }, { - "@id": "bts:Adenocarcinomaofanalglands" + "@id": "bts:Scrotum" }, { - "@id": "bts:Adenocarcinomadiffusetype" + "@id": "bts:SeminalVesicle" }, { - "@id": "bts:Adenocarcinomaendocervicaltype" + "@id": "bts:Shoulder" }, { - "@id": "bts:Adenocarcinomaintestinaltype" + "@id": "bts:SigmoidColon" }, { - "@id": "bts:AdenocarcinomametastaticNOS" + "@id": "bts:Sinus" }, { - "@id": "bts:AdenocarcinomaNOS" + "@id": "bts:Sinus(es)Maxillary" }, { - "@id": "bts:Adenocarcinomapancreatobiliarytype" + "@id": "bts:SkeletalMuscle" }, { - "@id": "bts:Adultrhabdomyoma" + "@id": "bts:Skin" }, { - "@id": "bts:AdultT-celllymphoma" + "@id": "bts:Skinlowerextremitylocal" }, { - "@id": "bts:AdultT-celllymphoma/leukemia" + "@id": "bts:Skintotal" }, { - "@id": "bts:Astrocytomaanaplastic" + "@id": "bts:Skintrunklocal" }, { - "@id": "bts:Astrocytomalowgrade" + "@id": "bts:Skinupperextremitylocal" }, { - "@id": "bts:AstrocytomaNOS" + "@id": "bts:Skull" }, { - "@id": "bts:BcelllymphomaNOS" + "@id": "bts:SmallBowel" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + "@id": "bts:SmallBowelMucosaOnly" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + "@id": "bts:SmallFinger" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" + "@id": "bts:SoftTissue" }, { - "@id": "bts:B-ALL" + "@id": "bts:SpinalColumn" }, { - "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" + "@id": "bts:SpinalCord" }, { - "@id": "bts:Basalcelladenocarcinoma" + "@id": "bts:Spine" }, { - "@id": "bts:Basalcelladenoma" + "@id": "bts:Spleen" }, { - "@id": "bts:BasalcellcarcinomaNOS" + "@id": "bts:SplenicFlexure" }, { - "@id": "bts:Basalcellepithelioma" + "@id": "bts:Sternum" }, { - "@id": "bts:Basalcelltumor" + "@id": "bts:Stomach" }, { - "@id": "bts:Basophiladenocarcinoma" + "@id": "bts:StomachMucosaOnly" }, { - "@id": "bts:Basophiladenoma" + "@id": "bts:SubcutaneousTissue" }, { - "@id": "bts:Basophilcarcinoma" + "@id": "bts:Synovium" }, { - "@id": "bts:Bileductadenocarcinoma" + "@id": "bts:TemporalCortex" }, { - "@id": "bts:Bileductadenoma" + "@id": "bts:Tendon" }, { - "@id": "bts:Bileductcarcinoma" + "@id": "bts:Testis" }, { - "@id": "bts:Bileductcystadenocarcinoma" + "@id": "bts:Thigh" }, { - "@id": "bts:Bileductcystadenoma" + "@id": "bts:ThoracicSpine" }, { - "@id": "bts:Bronchialadenomacarcinoid" + "@id": "bts:Thorax" }, { - "@id": "bts:Bronchialadenomacylindroid" + "@id": "bts:Throat" }, { - "@id": "bts:BronchialadenomaNOS" + "@id": "bts:Thumb" }, { - "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" + "@id": "bts:Thymus" }, { - "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + "@id": "bts:Thyroid" }, { - "@id": "bts:Bronchio-alveolarcarcinomamucinous" + "@id": "bts:Tibia" }, { - "@id": "bts:Bronchiolaradenocarcinoma" + "@id": "bts:Tongue" }, { - "@id": "bts:Bronchiolarcarcinoma" + "@id": "bts:Tonsil" }, { - "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" + "@id": "bts:Tonsil(Pharyngeal)" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" + "@id": "bts:Trachea/MajorBronchi" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + "@id": "bts:TransverseColon" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" + "@id": "bts:Trunk" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + "@id": "bts:UmbilicalCord" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + "@id": "bts:Unknown" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" + "@id": "bts:Ureter" }, { - "@id": "bts:Burkittcellleukemia" + "@id": "bts:Urethra" }, { - "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" + "@id": "bts:UrinaryTract" }, { - "@id": "bts:Burkitttumor" + "@id": "bts:Uterus" }, { - "@id": "bts:Burkitt-likelymphoma" + "@id": "bts:Uvula" }, { - "@id": "bts:C-ALL" + "@id": "bts:Vagina" }, { - "@id": "bts:Cancer" + "@id": "bts:VasDeferens" }, { - "@id": "bts:Capillaryhemangioma" + "@id": "bts:Vein" }, { - "@id": "bts:Capillarylymphangioma" + "@id": "bts:Venous" }, { - "@id": "bts:CarcinomainapolypNOS" + "@id": "bts:Vertebra" }, { - "@id": "bts:Carcinomainadenomatouspolyp" + "@id": "bts:Vulva" }, { - "@id": "bts:Carcinomainpleomorphicadenoma" + "@id": "bts:WhiteBloodCells" }, { - "@id": "bts:CarcinomainsituinapolypNOS" + "@id": "bts:Wrist" }, { - "@id": "bts:Carcinomainsituinadenomatouspolyp" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Prior Sites of Radiation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Immunosuppression", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not immunosuppressive therapy was administered.", + "rdfs:label": "Immunosuppression", + "rdfs:subClassOf": [ { - "@id": "bts:CarcinomainsituNOS" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:CarcinomaanaplasticNOS" + "@id": "bts:Yes" }, { - "@id": "bts:Carcinomadiffusetype" + "@id": "bts:No" }, { - "@id": "bts:Carcinomaintestinaltype" + "@id": "bts:Unknown" }, { - "@id": "bts:CarcinomametastaticNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:CarcinomaNOS" - }, + "@id": "bts:NotDone" + } + ], + "sms:displayName": "Immunosuppression", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ConcomitantMedicationReceivedType", + "@type": "rdfs:Class", + "rdfs:comment": "An enumerated list of the type of concomitant medication received by the patient.", + "rdfs:label": "ConcomitantMedicationReceivedType", + "rdfs:subClassOf": [ { - "@id": "bts:CarcinosarcomaNOS" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:CarcinomaundifferentiatedNOS" + "@id": "bts:Anticoagulantagents" }, { - "@id": "bts:CementomaNOS" + "@id": "bts:Anticonvulsant" }, { - "@id": "bts:Centralneuroblastoma" + "@id": "bts:Antifungal" }, { - "@id": "bts:Centralneurocytoma" + "@id": "bts:Antiplateletagents" }, { - "@id": "bts:Cerebellarliponeurocytoma" + "@id": "bts:Antidepressants-ModerateCYP2D6inhibitors" }, { - "@id": "bts:CerebellarsarcomaNOS" + "@id": "bts:Antidepressants-StrongCYP2D6inhibitors" }, { - "@id": "bts:CervicalintraepithelialneoplasiagradeIII" + "@id": "bts:Antidepressants-weakCYP2D2inhibitorsornon-inhibitors" }, { - "@id": "bts:Cervicalintraepithelialneoplasialowgrade" + "@id": "bts:Anxiolyticsorsedatives" }, { - "@id": "bts:ChondromaNOS" + "@id": "bts:Aspirin" }, { - "@id": "bts:Chondrosarcomagrade2/3" + "@id": "bts:Bisphosphonatesfortreatment/preventionofboneloss" }, { - "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" + "@id": "bts:Corticosteroid" }, { - "@id": "bts:ChronicgranulocyticleukemiaNOS" + "@id": "bts:COX-2inhibitor" }, { - "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:Decadron" }, { - "@id": "bts:ChronicleukemiaNOS" + "@id": "bts:Diabetes-Insulin" }, { - "@id": "bts:Chroniclymphaticleukemia" + "@id": "bts:Diabetes-Metformincontainingagents" }, { - "@id": "bts:Chroniclymphocyticleukemia" + "@id": "bts:Growthfactor" }, { - "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" + "@id": "bts:Intravaginalestrogenpreparations" }, { - "@id": "bts:Chroniclymphoidleukemia" + "@id": "bts:Lipid-loweringdrugs" }, { - "@id": "bts:Chronicmonocyticleukemia" + "@id": "bts:Non-prescriptionsupplementsformemory" }, { - "@id": "bts:ChronicmyelocyticleukemiaNOS" + "@id": "bts:Non-prescriptionsupplementsforreliefofhotflashes" }, { - "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" + "@id": "bts:Non-steroidalanti-inflammatoryagents" }, { - "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:Opioids" }, { - "@id": "bts:ChronicmyeloidleukemiaNOS" + "@id": "bts:Other" }, { - "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" + "@id": "bts:Prescriptionmedicationsformemory" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaNOS" + "@id": "bts:Prescriptionmedicationsforreliefofhotflashes" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaType1" + "@id": "bts:Prophylacticantiplatelettherapy" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" + "@id": "bts:Tricyclicantidepressants" }, { - "@id": "bts:ChronicmyeloproliferativediseaseNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Chronicmyeloproliferativedisorder" + "@id": "bts:Unknown" }, { - "@id": "bts:Chronicneutrophilicleukemia" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Concomitant Medication Received Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyMemberVitalStatusIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", + "rdfs:label": "FamilyMemberVitalStatusIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" - }, + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" + "@id": "bts:VitalStatusAlive" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + "@id": "bts:VitalStatusDead" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" + "@id": "bts:Unknown" }, { - "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Family Member Vital Status Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19OccurrenceIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", + "rdfs:label": "COVID19OccurrenceIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + "@id": "bts:Yes" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + "@id": "bts:No" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" - }, + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Occurrence Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CurrentStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", + "rdfs:label": "COVID19CurrentStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Combinedsmallcellcarcinoma" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Combinedsmallcell-adenocarcinoma" + "@id": "bts:Patientcurrentlyhassymptoms" }, { - "@id": "bts:Combinedsmallcell-largecarcinoma" + "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" }, { - "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" + "@id": "bts:PatientneverhadanysymptomsofCOVID-19" }, { - "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" + "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" }, { - "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" + "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" }, { - "@id": "bts:Dermalnevus" - }, + "@id": "bts:Statusunknownduetootherreasons" + } + ], + "sms:displayName": "COVID19 Current Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19PositiveLabTestIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", + "rdfs:label": "COVID19PositiveLabTestIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:DermatofibromaNOS" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DiffuseastrocytomaIDH-mutant" + "@id": "bts:Yes" }, { - "@id": "bts:DiffuseastrocytomaIDH-wildtype" + "@id": "bts:No" }, { - "@id": "bts:Diffuseastrocytomalowgrade" + "@id": "bts:Unknown" }, { - "@id": "bts:DiffuselargeB-celllymphomaNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Diffusemelanocytosis" - }, + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Positive Lab Test Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19AntibodyTesting", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", + "rdfs:label": "COVID19AntibodyTesting", + "rdfs:subClassOf": [ { - "@id": "bts:DuctadenocarcinomaNOS" + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:SARS-CoV-2IgMantibodypositive" }, { - 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"@id": "bts:No" + "@id": "bts:Montserrat" }, { - "@id": "bts:Unknown" + "@id": "bts:Morocco" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Progression or Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteofResectionorBiopsy", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "SiteofResectionorBiopsy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" + "@id": "bts:Mozambique" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:Myanmar" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:Namibia" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:Nauru" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:Nepal" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:Netherlands" }, { - "@id": "bts:Analcanal" + "@id": "bts:NewCaledonia" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:NewZealand" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:Nicaragua" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:Niger" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:Nigeria" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:Niue" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:NorthKorea" }, { - "@id": "bts:AnusNOS" + "@id": "bts:NorthMacedonia" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:NorthernMarianaIslands" }, { - "@id": "bts:Appendix" + "@id": "bts:Norway" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:Oman" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:Pakistan" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:Palau" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:Panama" }, { - "@id": "bts:Bladderneck" + "@id": "bts:PapuaNewGuinea" }, { - "@id": "bts:BladderNOS" + "@id": "bts:Paraguay" }, { - "@id": "bts:Blood" + "@id": "bts:Peru" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:Philippines" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:Poland" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:Portugal" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:PuertoRico" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:Qatar" }, { - "@id": "bts:BoneNOS" + "@id": "bts:Reunion" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:Romania" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:Russia" }, { - "@id": "bts:Brainstem" + "@id": "bts:Rwanda" }, { - "@id": "bts:BrainNOS" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:BreastNOS" + "@id": "bts:SaintLucia" }, { - "@id": "bts:Broadligament" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:Carotidbody" + "@id": "bts:Samoa" }, { - "@id": "bts:Caudaequina" + "@id": "bts:SanMarino" }, { - "@id": "bts:Cecum" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:Senegal" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:Serbia" }, { - "@id": "bts:Cerebrum" + "@id": "bts:Seychelles" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:SierraLeone" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:Singapore" }, { - "@id": "bts:Choroid" + "@id": "bts:Slovakia" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:Slovenia" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:ColonNOS" + "@id": "bts:Somalia" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:SouthKorea" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:SouthSudan" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:Spain" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:SriLanka" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:Sudan" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:Suriname" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:Sweden" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:Switzerland" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:Syria" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:Taiwan" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:Tajikistan" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:Tanzania" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:Thailand" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:Togo" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Tokelau" }, { - "@id": "bts:Duodenum" + "@id": "bts:Tonga" }, { - "@id": "bts:Endocervix" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:Tunisia" }, { - "@id": "bts:Endometrium" + "@id": "bts:Turkey" }, { - "@id": "bts:Epididymis" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:Tuvalu" }, { - "@id": "bts:Ethmoidsinus" + "@id": "bts:Uganda" }, { - "@id": "bts:Exocervix" + "@id": "bts:Ukraine" }, { - "@id": "bts:Externalear" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:UnitedStates" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:Uruguay" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:EyeNOS" + "@id": "bts:Vanuatu" }, { - "@id": "bts:Eyelid" + "@id": "bts:Venezuela" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:Vietnam" }, { - "@id": "bts:FemalegenitaltractNOS" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:Frontallobe" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:WesternSahara" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:Yemen" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:Zambia" }, { - "@id": "bts:Gallbladder" + "@id": "bts:Zimbabwe" }, { - "@id": "bts:Gastricantrum" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Country of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea", + "@type": "rdfs:Class", + "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", + "rdfs:label": "MedicallyUnderservedArea", + "rdfs:subClassOf": [ { - "@id": "bts:GastrointestinaltractNOS" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Glanspenis" + "@id": "bts:MedicallyUnderservedArea-Yes" }, { - "@id": "bts:Glottis" + "@id": "bts:MedicallyUnderservedArea-No" }, { - "@id": "bts:GreatercurvatureofstomachNOS" - }, + "@id": "bts:MedicallyUnderservedArea-Unknown" + } + ], + "sms:displayName": "Medically Underserved Area", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RuralvsUrban", + "@type": "rdfs:Class", + "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", + "rdfs:label": "RuralvsUrban", + "rdfs:subClassOf": [ { - "@id": "bts:GumNOS" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Hardpalate" + "@id": "bts:UrbanPopulation(population>50000)" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:UrbanCluster(population2500-50000)" }, { - "@id": "bts:HeadfaceorneckNOS" - }, + "@id": "bts:RuralPopulation(population<2500)" + } + ], + "sms:displayName": "Rural vs Urban", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidence", + "@type": "rdfs:Class", + "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", + "rdfs:label": "CancerIncidence", + "rdfs:subClassOf": [ { - "@id": "bts:Heart" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidenceLocation", + "@type": "rdfs:Class", + "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", + "rdfs:label": "CancerIncidenceLocation", + "rdfs:subClassOf": [ { - "@id": "bts:HematopoieticsystemNOS" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Cancer related clinical data specific to SRRS", + "rdfs:label": "SRRSClinicalDataTier2", + "rdfs:subClassOf": [ { - "@id": "bts:Hepaticflexureofcolon" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:Component" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Ileum" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:EducationLevel" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:Isthmusuteri" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:Jejunum" + "@id": "bts:CancerIncidenceLocation" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:Ethnicity" }, { - "@id": "bts:Labiummajus" + "@id": "bts:Gender" }, { - "@id": "bts:Labiumminus" + "@id": "bts:Race" }, { - "@id": "bts:Lacrimalgland" + "@id": "bts:VitalStatus" }, { - "@id": "bts:Laryngealcartilage" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:LarynxNOS" + "@id": "bts:DaystoLastFollowup" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:DaystoLastKnownDiseaseStatus" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:DaystoRecurrence" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:Morphology" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:PrimaryDiagnosis" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:LipNOS" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:Liver" + "@id": "bts:TissueorOrganofOrigin" }, { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + "@id": "bts:NCIAtlasCancerSite" }, { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + "@id": "bts:TumorGrade" }, { - "@id": "bts:Lowergum" + "@id": "bts:PackYearsSmoked" }, { - "@id": "bts:LowerlimbNOS" + "@id": "bts:YearsSmoked" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:DaystoFollowUp" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:GeneSymbol" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:TestResult" }, { - "@id": "bts:LungNOS" + "@id": "bts:TreatmentType" }, { - "@id": "bts:LymphnodeNOS" - }, + "@id": "bts:TumorLargestDimensionDiameter" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Ethnicity", + "@type": "rdfs:Class", + "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "rdfs:label": "Ethnicity", + "rdfs:subClassOf": [ { - "@id": "bts:Lymphnodesofaxillaorarm" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Lymphnodesofheadfaceandneck" + "@id": "bts:Hispanicorlatino" }, { - "@id": "bts:Lymphnodesofinguinalregionorleg" + "@id": "bts:Nothispanicorlatino" }, { - "@id": "bts:Lymphnodesofmultipleregions" + "@id": "bts:Unknown" }, { - "@id": "bts:Mainbronchus" + "@id": "bts:NotReported" }, { - "@id": "bts:MajorsalivaryglandNOS" - }, + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Ethnicity", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Gender", + "@type": "rdfs:Class", + "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "rdfs:label": "Gender", + "rdfs:subClassOf": [ { - "@id": "bts:MalegenitalorgansNOS" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Mandible" + "@id": "bts:Female" }, { - "@id": "bts:Maxillarysinus" + "@id": "bts:Male" }, { - "@id": "bts:Meckeldiverticulum" + "@id": "bts:Unknown" }, { - "@id": "bts:MediastinumNOS" + "@id": "bts:Unspecified" }, { - "@id": "bts:Medullaofadrenalgland" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Gender", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Race", + "@type": "rdfs:Class", + "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "rdfs:label": "Race", + "rdfs:subClassOf": [ { - "@id": "bts:MeningesNOS" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Middleear" + "@id": "bts:White" }, { - "@id": "bts:Middlelobelung" + "@id": "bts:Americanindianoralaskanative" }, { - "@id": "bts:Middlethirdofesophagus" + "@id": "bts:Blackorafricanamerican" }, { - "@id": "bts:MouthNOS" + "@id": "bts:Asian" }, { - "@id": "bts:MucosaoflipNOS" + "@id": "bts:Nativehawaiianorotherpacificislander" }, { - "@id": "bts:Mucosaoflowerlip" + "@id": "bts:Other" }, { - "@id": "bts:Mucosaofupperlip" + "@id": "bts:Unknown" }, { - "@id": "bts:Myometrium" + "@id": "bts:NotReported" }, { - "@id": "bts:Nasalcavity" - }, + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Race", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:VitalStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", + "rdfs:subClassOf": [ { - "@id": "bts:NasopharynxNOS" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NervoussystemNOS" + "@id": "bts:Alive" }, { - "@id": "bts:Nipple" + "@id": "bts:Dead" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:Unknown" }, { - "@id": "bts:Olfactorynerve" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Vital Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label": "AgeatDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:Opticnerve" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Age at Diagnosis", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoLastFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastFollowup", + "rdfs:subClassOf": [ { - "@id": "bts:OrbitNOS" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Follow up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:OropharynxNOS" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoRecurrence", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoRecurrence", + "rdfs:subClassOf": [ { - "@id": "bts:Otherill-definedsites" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:LastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", + "rdfs:label": "LastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + "@id": "bts:Distantmetrecurrence/progression" }, { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:Loco-regionalrecurrence/progression" }, { - "@id": "bts:Ovary" + "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:Tumorfree" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:Unknowntumorstatus" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:Withtumor" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id": "bts:NotReported" }, { - "@id": "bts:Overlappinglesionofbrain" + "@id": "bts:NotAllowedToCollect" }, { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Morphology", + "@type": "rdfs:Class", + "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", + "rdfs:label": "Morphology", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofbreast" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Morphology", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "PrimaryDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofcervixuteri" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:Acinarcellcarcinoma" }, { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + "@id": "bts:Acutebasophilicleukaemia" }, { - "@id": "bts:Overlappinglesionofcorpusuteri" + "@id": "bts:AcuteleukemiaBurkitttype" }, { - "@id": "bts:Overlappinglesionofdigestivesystem" + "@id": "bts:AcuteleukemiaNOS" }, { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + "@id": "bts:Acutelymphaticleukemia" }, { - "@id": "bts:Overlappinglesionofesophagus" + "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" }, { - "@id": "bts:Overlappinglesionofeyeandadnexa" + "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" }, { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" + "@id": "bts:AcutelymphoblasticleukemiaNOS" }, { - "@id": "bts:Overlappinglesionoffloorofmouth" + "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" }, { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + "@id": "bts:Acutelymphocyticleukemia" }, { - "@id": "bts:Overlappinglesionofhypopharynx" + "@id": "bts:Acutelymphoidleukemia" }, { - "@id": "bts:Overlappinglesionofill-definedsites" + "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" }, { - "@id": "bts:Overlappinglesionoflarynx" + "@id": "bts:AcutemyeloidleukemiaMLL" }, { - "@id": "bts:Overlappinglesionoflip" + "@id": "bts:AcutemyeloidleukemiaNOS" }, { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + "@id": "bts:Acutemyelomonocyticleukemia" }, { - "@id": "bts:Overlappinglesionoflung" + "@id": "bts:AcutepromyelocyticleukemiaNOS" }, { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" + "@id": "bts:Adenocarcinoidtumor" }, { - "@id": "bts:Overlappinglesionofmalegenitalorgans" + "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" }, { - "@id": "bts:Overlappinglesionofnasopharynx" + "@id": "bts:AdenocarcinomainapolypNOS" }, { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + "@id": "bts:Adenocarcinomainadenomatouspolyp" }, { - "@id": "bts:Overlappinglesionofpalate" + "@id": "bts:Adenocarcinomainpolypoidadenoma" }, { - "@id": "bts:Overlappinglesionofpancreas" + "@id": "bts:AdenocarcinomainsituinapolypNOS" }, { - "@id": "bts:Overlappinglesionofpenis" + "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" }, { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + "@id": "bts:Adenocarcinomainsituintubularadenoma" }, { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + "@id": "bts:Adenocarcinomainsitumucinous" }, { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + "@id": "bts:Adenocarcinomainsitunon-mucinous" }, { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + "@id": "bts:AdenocarcinomainsituNOS" }, { - "@id": "bts:Overlappinglesionofskin" + "@id": "bts:Adenocarcinomaintubularadenoma" }, { - "@id": "bts:Overlappinglesionofsmallintestine" + "@id": "bts:Adenocarcinomainvillousadenoma" }, { - "@id": "bts:Overlappinglesionofstomach" + "@id": "bts:Adenocarcinomaofanalducts" }, { - "@id": "bts:Overlappinglesionoftongue" + "@id": "bts:Adenocarcinomaofanalglands" }, { - "@id": "bts:Overlappinglesionoftonsil" + "@id": "bts:Adenocarcinomadiffusetype" }, { - "@id": "bts:Overlappinglesionofurinaryorgans" + "@id": "bts:Adenocarcinomaendocervicaltype" }, { - "@id": "bts:Overlappinglesionofvulva" + "@id": "bts:Adenocarcinomaintestinaltype" }, { - "@id": "bts:Overlappinglesionsoforopharynx" + "@id": "bts:AdenocarcinomametastaticNOS" }, { - "@id": "bts:PalateNOS" + "@id": "bts:AdenocarcinomaNOS" }, { - "@id": "bts:PancreasNOS" + "@id": "bts:Adenocarcinomapancreatobiliarytype" }, { - "@id": "bts:Pancreaticduct" + "@id": "bts:Adultrhabdomyoma" }, { - "@id": "bts:Parametrium" + "@id": "bts:AdultT-celllymphoma" }, { - "@id": "bts:Paraspinal" + "@id": "bts:AdultT-celllymphoma/leukemia" }, { - "@id": "bts:Parathyroidgland" + "@id": "bts:Astrocytomaanaplastic" }, { - "@id": "bts:Paraurethralgland" + "@id": "bts:Astrocytomalowgrade" }, { - "@id": "bts:Parietallobe" + "@id": "bts:AstrocytomaNOS" }, { - "@id": "bts:Parotidgland" + "@id": "bts:BcelllymphomaNOS" }, { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" }, { - "@id": "bts:Pelviclymphnodes" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" }, { - "@id": "bts:PelvisNOS" + "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" }, { - "@id": "bts:PenisNOS" + "@id": "bts:B-ALL" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + "@id": "bts:Basalcelladenocarcinoma" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + "@id": "bts:Basalcelladenoma" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + "@id": "bts:BasalcellcarcinomaNOS" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + "@id": "bts:Basalcellepithelioma" }, { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + "@id": "bts:Basalcelltumor" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + "@id": "bts:Basophiladenocarcinoma" }, { - "@id": "bts:PeritoneumNOS" + "@id": "bts:Basophiladenoma" }, { - "@id": "bts:PharynxNOS" + "@id": "bts:Basophilcarcinoma" }, { - "@id": "bts:Pinealgland" + "@id": "bts:Bileductadenocarcinoma" }, { - "@id": "bts:Pituitarygland" + "@id": "bts:Bileductadenoma" }, { - "@id": "bts:Placenta" + "@id": "bts:Bileductcarcinoma" }, { - "@id": "bts:PleuraNOS" + "@id": "bts:Bileductcystadenocarcinoma" }, { - "@id": "bts:Postcricoidregion" + "@id": "bts:Bileductcystadenoma" }, { - "@id": "bts:Posteriormediastinum" + "@id": "bts:Bronchialadenomacarcinoid" }, { - "@id": "bts:Posteriorwallofbladder" + "@id": "bts:Bronchialadenomacylindroid" }, { - "@id": "bts:Posteriorwallofhypopharynx" + "@id": "bts:BronchialadenomaNOS" }, { - "@id": "bts:Posteriorwallofnasopharynx" + "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:Posteriorwalloforopharynx" + "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" }, { - "@id": "bts:Prepuce" + "@id": "bts:Bronchio-alveolarcarcinomamucinous" }, { - "@id": "bts:Prostategland" + "@id": "bts:Bronchiolaradenocarcinoma" }, { - "@id": "bts:Pylorus" + "@id": "bts:Bronchiolarcarcinoma" }, { - "@id": "bts:Pyriformsinus" + "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" }, { - "@id": "bts:Rectosigmoidjunction" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" }, { - "@id": "bts:RectumNOS" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" }, { - "@id": "bts:Renalpelvis" + "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" }, { - "@id": "bts:ReticuloendothelialsystemNOS" + "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" }, { - "@id": "bts:Retina" + "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" }, { - "@id": "bts:Retromolararea" + "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" }, { - "@id": "bts:Retroperitoneum" + "@id": "bts:Burkittcellleukemia" }, { - "@id": "bts:Ribsternumclavicleandassociatedjoints" + "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" }, { - "@id": "bts:Roundligament" + "@id": "bts:Burkitttumor" }, { - "@id": "bts:ScrotumNOS" + "@id": "bts:Burkitt-likelymphoma" }, { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + "@id": "bts:C-ALL" }, { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:Cancer" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:Capillaryhemangioma" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:Capillarylymphangioma" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:CarcinomainapolypNOS" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:Carcinomainadenomatouspolyp" }, { - "@id": "bts:Skinofscalpandneck" + "@id": "bts:Carcinomainpleomorphicadenoma" }, { - "@id": "bts:Skinoftrunk" + "@id": "bts:CarcinomainsituinapolypNOS" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:Carcinomainsituinadenomatouspolyp" }, { - "@id": "bts:SkinNOS" + "@id": "bts:CarcinomainsituNOS" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:CarcinomaanaplasticNOS" }, { - "@id": "bts:SoftpalateNOS" + "@id": "bts:Carcinomadiffusetype" }, { - "@id": "bts:Specifiedpartsofperitoneum" + "@id": "bts:Carcinomaintestinaltype" }, { - "@id": "bts:Spermaticcord" + "@id": "bts:CarcinomametastaticNOS" }, { - "@id": "bts:Sphenoidsinus" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:Spinalcord" + "@id": "bts:CarcinosarcomaNOS" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:CarcinomaundifferentiatedNOS" }, { - "@id": "bts:Spleen" + "@id": "bts:CementomaNOS" }, { - "@id": "bts:Splenicflexureofcolon" + "@id": "bts:Centralneuroblastoma" }, { - "@id": "bts:StomachNOS" + "@id": "bts:Centralneurocytoma" }, { - "@id": "bts:Subglottis" + "@id": "bts:Cerebellarliponeurocytoma" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:CerebellarsarcomaNOS" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:CervicalintraepithelialneoplasiagradeIII" }, { - "@id": "bts:Superiorwallofnasopharynx" + "@id": "bts:Cervicalintraepithelialneoplasialowgrade" }, { - "@id": "bts:Supraglottis" + "@id": "bts:ChondromaNOS" }, { - "@id": "bts:Tailofpancreas" + "@id": "bts:Chondrosarcomagrade2/3" }, { - "@id": "bts:Temporallobe" + "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" }, { - "@id": "bts:TestisNOS" + "@id": "bts:ChronicgranulocyticleukemiaNOS" }, { - "@id": "bts:Thoracicesophagus" + "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id": "bts:ThoraxNOS" + "@id": "bts:ChronicleukemiaNOS" }, { - "@id": "bts:Thymus" + "@id": "bts:Chroniclymphaticleukemia" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:Chroniclymphocyticleukemia" }, { - "@id": "bts:TongueNOS" + "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:Chroniclymphoidleukemia" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:Chronicmonocyticleukemia" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:ChronicmyelocyticleukemiaNOS" }, { - "@id": "bts:Trachea" + "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" }, { - "@id": "bts:Transversecolon" + "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:ChronicmyeloidleukemiaNOS" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:ChronicmyelomonocyticleukemiaNOS" }, { - "@id": "bts:Uppergum" + "@id": "bts:ChronicmyelomonocyticleukemiaType1" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:ChronicmyeloproliferativediseaseNOS" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:Chronicmyeloproliferativedisorder" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:Chronicneutrophilicleukemia" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" }, { - "@id": "bts:Urachus" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" }, { - "@id": "bts:Ureter" + "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" }, { - "@id": "bts:Urethra" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" }, { - "@id": "bts:UterusNOS" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" }, { - "@id": "bts:Uvula" + "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" }, { - "@id": "bts:Vallecula" + "@id": "bts:Combinedsmallcellcarcinoma" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:Combinedsmallcell-adenocarcinoma" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:Combinedsmallcell-largecarcinoma" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:Dermalnevus" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:DermatofibromaNOS" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:DiffuseastrocytomaIDH-mutant" }, { - "@id": "bts:Clitoris" + "@id": "bts:DiffuseastrocytomaIDH-wildtype" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:Diffuseastrocytomalowgrade" }, { - "@id": "bts:Unknown" + "@id": "bts:DiffuselargeB-celllymphomaNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Site of Resection or Biopsy", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TissueorOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "TissueorOrganofOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Diffusemelanocytosis" + }, { - "@id": "bts:AbdomenNOS" + "@id": "bts:DuctadenocarcinomaNOS" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:DuctadenomaNOS" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:Ductcarcinomadesmoplastictype" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:DuctcarcinomaNOS" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:Ductcellcarcinoma" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:DuctalcarcinomainsituNOS" }, { - "@id": "bts:Analcanal" + "@id": "bts:DuctalcarcinomaNOS" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:Dysplasticnevus" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:EndometrialsarcomaNOS" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:EndometrioidadenocarcinomaNOS" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:EndometrioidadenofibromaNOS" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:EndometrioidadenomaNOS" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:EndometrioidcarcinomaNOS" }, { - "@id": "bts:AnusNOS" + "@id": "bts:Eosinophiladenocarcinoma" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:Eosinophiladenoma" }, { - "@id": "bts:Appendix" + "@id": "bts:Eosinophilcarcinoma" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:Eosinophilicgranuloma" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:Eosinophilicleukemia" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:EpendymomaNOS" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:EpidermoidcarcinomainsituNOS" }, { - "@id": "bts:Bladderneck" + "@id": "bts:EpidermoidcarcinomaNOS" }, { - "@id": "bts:BladderNOS" + "@id": "bts:Epithelialtumorbenign" }, { - "@id": "bts:Blood" + "@id": "bts:Epithelialtumormalignant" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" }, { - "@id": "bts:BoneNOS" + "@id": "bts:Ewingsarcoma" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:GangliogliomaNOS" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:Familialadenomatouspolyposis" }, { - "@id": "bts:Brainstem" + "@id": "bts:Gastrincelltumor" }, { - "@id": "bts:BrainNOS" + "@id": "bts:Gastrincelltumormalignant" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:Gastrinomamalignant" }, { - "@id": "bts:BreastNOS" + "@id": "bts:GastrinomaNOS" }, { - "@id": "bts:Broadligament" + "@id": "bts:Gastrointestinalstromaltumormalignant" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:Glioblastoma" }, { - "@id": "bts:Carotidbody" + "@id": "bts:Gliomamalignant" }, { - "@id": "bts:Caudaequina" + "@id": "bts:GliomaNOS" }, { - "@id": "bts:Cecum" + "@id": "bts:Haemangioblastoma" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:Haemangiosarcoma" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:Hepatocarcinoma" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:Hepatocellularadenoma" }, { - "@id": "bts:Cerebrum" + "@id": "bts:HepatocellularcarcinomaNOS" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:Hepatocholangiocarcinoma" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:Hepatoidadenocarcinoma" }, { - "@id": "bts:Choroid" + "@id": "bts:Hepatoidcarcinoma" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:HodgkindiseaseNOS" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:Hodgkingranuloma" }, { - "@id": "bts:ColonNOS" + "@id": "bts:HodgkinlymphomamixedcellularityNOS" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:HodgkinlymphomanodularsclerosisNOS" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:HodgkinlymphomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:HodgkinparagranulomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:Hodgkinsarcoma" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:InfiltratingbasalcellcarcinomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:InfiltratingductcarcinomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:Infiltratingductandcolloidcarcinoma" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:Infiltratingductandcribriformcarcinoma" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:Inflammatoryadenocarcinoma" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:Inflammatorycarcinoma" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:Interstitialcelltumorbenign" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:Interstitialcelltumormalignant" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:InterstitialcelltumorNOS" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:Intracysticpapilloma" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:Intradermalnevus" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:Intraductalandlobularcarcinoma" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Intraductalcarcinomaclinging" }, { - "@id": "bts:Duodenum" + "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" }, { - "@id": "bts:Endocervix" + "@id": "bts:IntraductalcarcinomaNOS" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:Intraductalcarcinomasolidtype" }, { - "@id": "bts:Endometrium" + "@id": "bts:Intraductalmicropapillarycarcinoma" }, { - "@id": "bts:Epididymis" + "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" }, { - "@id": "bts:Ethmoidsinus" + "@id": "bts:Intraductalpapillarycarcinoma" }, { - "@id": "bts:Exocervix" + "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" }, { - "@id": "bts:Externalear" + "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:Intraductaltubulopapillaryneoplasm" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:IntraepidermalcarcinomaNOS" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:IntravascularB-celllymphoma" }, { - "@id": "bts:EyeNOS" + "@id": "bts:Juvenilemyelomonocyticleukemia" }, { - "@id": "bts:Eyelid" + "@id": "bts:Kaposisarcoma" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:LargecellcarcinomaNOS" }, { - "@id": "bts:FemalegenitaltractNOS" + "@id": "bts:Liposarcomadifferentiated" }, { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:LiposarcomaNOS" }, { - "@id": "bts:Frontallobe" + "@id": "bts:Liposarcomawelldifferentiated" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:Livercelladenoma" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:Livercellcarcinoma" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:Lobularadenocarcinoma" }, { - "@id": "bts:Gallbladder" + "@id": "bts:Lobularandductalcarcinoma" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:LobularcarcinomainsituNOS" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:Lobularcarcinomanoninfiltrating" }, { - "@id": "bts:Glanspenis" + "@id": "bts:LobularcarcinomaNOS" }, { - "@id": "bts:Glottis" + "@id": "bts:LymphaticleukemicNOS" }, { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:LymphoblasticleukemiaNOS" }, { - "@id": "bts:GumNOS" + "@id": "bts:Lymphoblastoma" }, { - "@id": "bts:Hardpalate" + "@id": "bts:LymphocyticleukemiaNOS" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:LymphomaNOS" }, { - "@id": "bts:HeadfaceorneckNOS" + "@id": "bts:Malignancy" }, { - "@id": "bts:Heart" + "@id": "bts:MalignantlymphomadiffuseNOS" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:MalignantlymphomaHodgkin" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:MalignantlymphomaimmunoblasticNOS" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:MalignantlymphomalargeB-cellNOS" }, { - "@id": "bts:Ileum" + "@id": "bts:MalignantlymphomalargecellNOS" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:MalignantlymphomalymphoblasticNOS" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:MalignantlymphomalymphocyticdiffuseNOS" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:MalignantlymphomalymphocyticnodularNOS" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:MalignantlymphomalymphocyticNOS" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:Malignantlymphomamixedcelltypediffuse" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:Malignantlymphomamixedcelltypefollicular" }, { - "@id": "bts:Isthmusuteri" + "@id": "bts:Malignantlymphomamixedcelltypenodular" }, { - "@id": "bts:Jejunum" + "@id": "bts:MalignantlymphomanodularNOS" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:Malignantlymphomanon-HodgkinNOS" }, { - "@id": "bts:Labiummajus" + "@id": "bts:MalignantlymphomaNOS" }, { - "@id": "bts:Labiumminus" + "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" }, { - "@id": "bts:Lacrimalgland" + "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" }, { - "@id": "bts:Laryngealcartilage" + "@id": "bts:Malignantmelanomaingiantpigmentednevus" }, { - "@id": "bts:LarynxNOS" + "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:Malignantmelanomainjunctionalnevus" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:Malignantmelanomainprecancerousmelanosis" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:MalignantmelanomaNOS" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:Malignantmelanomaregressing" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:Mammarycarcinomainsitu" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:Medullaryadenocarcinoma" }, { - "@id": "bts:LipNOS" + "@id": "bts:MedullarycarcinomaNOS" }, { - "@id": "bts:Liver" + "@id": "bts:Medullaryosteosarcoma" }, { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + "@id": "bts:MedulloblastomaNOS" }, { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + "@id": "bts:Melanoameloblastoma" }, { - "@id": "bts:Lowergum" + "@id": "bts:Melanocyticnevus" }, { - "@id": "bts:LowerlimbNOS" + "@id": "bts:Melanocytomaeyeball" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:MelanocytomaNOS" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:Melanomainsitu" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:Melanomamalignantofsoftparts" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:MelanomaNOS" }, { - "@id": "bts:LungNOS" + "@id": "bts:Melanoticmedulloblastoma" }, { - "@id": "bts:LymphnodeNOS" + "@id": "bts:MelanoticMPNST" }, { - "@id": "bts:Lymphnodesofaxillaorarm" + "@id": "bts:Melanoticneuroectodermaltumor" }, { - "@id": "bts:Lymphnodesofheadfaceandneck" + "@id": "bts:Melanoticneurofibroma" }, { - "@id": "bts:Lymphnodesofinguinalregionorleg" + "@id": "bts:Melanoticprogonoma" }, { - "@id": "bts:Lymphnodesofmultipleregions" + "@id": "bts:MelanoticpsammomatousMPNST" }, { - "@id": "bts:Mainbronchus" + "@id": "bts:Melanoticschwannoma" }, { - "@id": "bts:MajorsalivaryglandNOS" + "@id": "bts:Meningealmelanocytoma" }, { - "@id": "bts:MalegenitalorgansNOS" + "@id": "bts:Meningealmelanoma" }, { - "@id": "bts:Mandible" + "@id": "bts:Meningiomaanaplastic" }, { - "@id": "bts:Maxillarysinus" + "@id": "bts:Meningiomamalignant" }, { - "@id": "bts:Meckeldiverticulum" + "@id": "bts:MeningiomaNOS" }, { - "@id": "bts:MediastinumNOS" + "@id": "bts:MicropapillarycarcinomaNOS" }, { - "@id": "bts:Medullaofadrenalgland" + "@id": "bts:Mixedadenocarcinomaandepidermoidcarcinoma" }, { - "@id": "bts:MeningesNOS" + "@id": "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" }, { - "@id": "bts:Middleear" + "@id": "bts:Mixedmedullary-follicularcarcinoma" }, { - "@id": "bts:Middlelobelung" + "@id": "bts:Mixedmedullary-papillarycarcinoma" }, { - "@id": "bts:Middlethirdofesophagus" + "@id": "bts:Mixedpancreaticendocrineandexocrinetumormalignant" }, { - "@id": "bts:MouthNOS" + "@id": "bts:Mixedpinealtumor" }, { - "@id": "bts:MucosaoflipNOS" + "@id": "bts:Mixedsmallcellcarcinoma" }, { - "@id": "bts:Mucosaoflowerlip" + "@id": "bts:Mixedsquamouscellandglandularpapilloma" }, { - "@id": "bts:Mucosaofupperlip" + "@id": "bts:MixedtumormalignantNOS" }, { - "@id": "bts:Myometrium" + "@id": "bts:MixedtumorNOS" }, { - "@id": "bts:Nasalcavity" + "@id": "bts:MonocyticleukemiaNOS" }, { - "@id": "bts:NasopharynxNOS" + "@id": "bts:Mucosal-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:NervoussystemNOS" + "@id": "bts:Mucousadenocarcinoma" }, { - "@id": "bts:Nipple" + "@id": "bts:Multiplemyeloma" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:MyelocyticleukemiaNOS" }, { - "@id": "bts:Olfactorynerve" + "@id": "bts:MyeloidleukemiaNOS" }, { - "@id": "bts:Opticnerve" + "@id": "bts:MyelomaNOS" }, { - "@id": "bts:OrbitNOS" + "@id": "bts:Myoepithelioma" }, { - "@id": "bts:OropharynxNOS" + "@id": "bts:Neoplasmbenign" }, { - "@id": "bts:Otherill-definedsites" + "@id": "bts:Neoplasmmalignant" }, { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + "@id": "bts:Neoplasmmalignantuncertainwhetherprimaryormetastatic" }, { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + "@id": "bts:Neoplasmmetastatic" }, { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:NeoplasmNOS" }, { - "@id": "bts:Ovary" + "@id": "bts:Neoplasmsecondary" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:Neoplasmuncertainwhetherbenignormalignant" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:NephroblastomaNOS" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:NeuroblastomaNOS" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id": "bts:NeuroendocrinecarcinomaNOS" }, { - "@id": "bts:Overlappinglesionofbrain" + "@id": "bts:NeuroepitheliomaNOS" }, { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + "@id": "bts:NeurofibromaNOS" }, { - "@id": "bts:Overlappinglesionofbreast" + "@id": "bts:NeurofibromatosisNOS" }, { - "@id": "bts:Overlappinglesionofcervixuteri" + "@id": "bts:Neurofibrosarcoma" }, { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:Neurosarcoma" }, { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + "@id": "bts:NevusNOS" }, { - "@id": "bts:Overlappinglesionofcorpusuteri" + "@id": "bts:Non-HodgkinlymphomaNOS" }, { - "@id": "bts:Overlappinglesionofdigestivesystem" + "@id": "bts:Non-invasivelowgradeserouscarcinoma" }, { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + "@id": "bts:Non-lymphocyticleukemiaNOS" }, { - "@id": "bts:Overlappinglesionofesophagus" + "@id": "bts:Non-smallcellcarcinoma" }, { - "@id": "bts:Overlappinglesionofeyeandadnexa" + "@id": "bts:Nonpigmentednevus" }, { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" + "@id": "bts:NotReported" }, { - "@id": "bts:Overlappinglesionoffloorofmouth" + "@id": "bts:Oatcellcarcinoma" }, { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + "@id": "bts:Osteoblastomamalignant" }, { - "@id": "bts:Overlappinglesionofhypopharynx" + "@id": "bts:OsteoblastomaNOS" }, { - "@id": "bts:Overlappinglesionofill-definedsites" + "@id": "bts:OsteosarcomaNOS" }, { - "@id": "bts:Overlappinglesionoflarynx" + "@id": "bts:Pagetdiseaseandinfiltratingductcarcinomaofbreast" }, { - "@id": "bts:Overlappinglesionoflip" + "@id": "bts:Pagetdiseaseandintraductalcarcinomaofbreast" }, { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + "@id": "bts:Pagetdiseaseofbreast" }, { - "@id": "bts:Overlappinglesionoflung" + "@id": "bts:Pagetdiseaseextramammary" }, { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" + "@id": "bts:Pagetdiseasemammary" }, { - "@id": "bts:Overlappinglesionofmalegenitalorgans" + "@id": "bts:Pagetoidreticulosis" }, { - "@id": "bts:Overlappinglesionofnasopharynx" + "@id": "bts:Pancreaticendocrinetumorbenign" }, { - 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"@id": "bts:Non-Hodgkin'sLymphoma" + "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" }, { - "@id": "bts:OralCavityAndPharynx" + "@id": "bts:Undifferentiatedleukaemia" }, { - "@id": "bts:Ovary" + "@id": "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id": "bts:Pancreas" + "@id": "bts:Undifferentiatedroundcellsarcoma" }, { - "@id": "bts:ProstateGland" + "@id": "bts:Undifferentiatedsarcoma" }, { - "@id": "bts:Stomach" + "@id": "bts:Undifferentiatedspindlecellsarcoma" }, { - "@id": "bts:ThyroidGland" + "@id": "bts:Undifferentiateduterinesarcoma" }, { - "@id": "bts:Uterus" + "@id": "bts:Unknown" } ], - "sms:displayName": "NCI Atlas Cancer Site", - "sms:required": "sms:false", + "sms:displayName": "Primary Diagnosis", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TumorGrade", + "@id": "bts:ProgressionorRecurrence", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", - 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If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoFollowUp", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Follow Up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:GeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "GeneSymbol", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gene Symbol", + "sms:displayName": "Progression or Recurrence", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MolecularAnalysisMethod", + "@id": "bts:SiteofResectionorBiopsy", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularAnalysisMethod", + "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "SiteofResectionorBiopsy", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -10702,1297 +11520,1017 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ComparativeGenomicHybridization" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:CytogeneticsNOS" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:FISH" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:FlowCytometry" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:IHC" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:ISH" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Karyotype" + "@id": "bts:Analcanal" }, { - "@id": "bts:Microarray" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:MicrosatelliteAnalysis" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:NuclearStaining" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Other" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:RNASequencing" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:RT-PCR" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:SequencingNOS" + "@id": "bts:AnusNOS" }, { - "@id": "bts:SouthernBlotting" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:TargetedSequencing" + "@id": "bts:Appendix" }, { - "@id": "bts:WGS" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:WXS" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:NotReported" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Molecular Analysis Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TestResult", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestResult", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbnormalNOS" + "@id": "bts:Bladderneck" }, { - "@id": "bts:CopyNumberReported" + "@id": "bts:BladderNOS" }, { - "@id": "bts:Equivocal" + "@id": "bts:Blood" }, { - "@id": "bts:High" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:Intermediate" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:LossofExpression" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:Low" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Negative" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:Normal" + "@id": "bts:BoneNOS" }, { - "@id": "bts:Overexpressed" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:Positive" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:TestValueReported" + "@id": "bts:Brainstem" }, { - "@id": "bts:Unknown" + "@id": "bts:BrainNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Test Result", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of treatment administered.", - "rdfs:label": "TreatmentType", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AblationCryo" + "@id": "bts:BreastNOS" }, { - "@id": "bts:AblationEthanolInjection" + "@id": "bts:Broadligament" }, { - "@id": "bts:AblationMicrowave" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:AblationNOS" + "@id": "bts:Carotidbody" }, { - "@id": "bts:AblationRadiofrequency" + "@id": "bts:Caudaequina" }, { - "@id": "bts:AblationRadiosurgical" + "@id": "bts:Cecum" }, { - "@id": "bts:AncillaryTreatment" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:AntiseizureTreatment" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:BisphosphonateTherapy" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:BlindedStudyTreatmentunknown" + "@id": "bts:Cerebrum" }, { - "@id": "bts:BrachytherapyHighDose" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:BrachytherapyLowDose" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:BrachytherapyNOS" + "@id": "bts:Choroid" }, { - "@id": "bts:Chemoembolization" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:Chemoprotectant" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:Chemotherapy" + "@id": "bts:ColonNOS" }, { - "@id": "bts:ConcurrentChemoradiation" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:Cryoablation" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:Embolization" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:EthanolInjectionAblation" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:ExternalBeamRadiation" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:HormoneTherapy" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:I-131RadiationTherapy" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:InternalRadiation" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Immunotherapy(IncludingVaccines)" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:IsolatedLimbPerfusion(ILP)" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:OrganTransplantation" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:Other" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:PharmaceuticalTherapyNOS" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:Pleurodesis" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:Radiation2DConventional" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Radiation3DConformal" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:RadiationCombination" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:RadiationCyberknife" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:RadiationExternalBeam" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:RadiationImplants" + "@id": "bts:Duodenum" }, { - "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" + "@id": "bts:Endocervix" }, { - "@id": "bts:RadiationInternal" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:RadiationProtonBeam" + "@id": "bts:Endometrium" }, { - "@id": "bts:RadiationRadioisotope" + "@id": "bts:Epididymis" }, { - "@id": "bts:RadiationStereotactic/GammaKnife/SRS" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:RadiationSystemic" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:RadiationTherapyNOS" + "@id": "bts:Exocervix" }, { - "@id": "bts:RadioactiveIodineTherapy" + "@id": "bts:Externalear" }, { - "@id": "bts:Radioembolization" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:RadiosensitizingAgent" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:StemCellTreatment" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:StemCellTransplantationAutologous" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:StemCellTransplantationDoubleAutologous" + "@id": "bts:EyeNOS" }, { - "@id": "bts:StemCellTransplantationAllogeneic" + "@id": "bts:Eyelid" }, { - "@id": "bts:StemCellTransplantationNon-Myeloablative" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:StemCellTransplantationSyngenic" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:StemCellTransplantationHaploidentical" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:StemCellTransplantationNOS" + "@id": "bts:Frontallobe" }, { - "@id": "bts:StereotacticRadiosurgery" + "@id": "bts:Frontalsinus" }, { - "@id": "bts:SteroidTherapy" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:Surgery" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:TargetedMolecularTherapy" + "@id": "bts:Gallbladder" }, { - "@id": "bts:Unknown" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] - }, - { - "@id": "bts:TumorLargestDimensionDiameter", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", - "rdfs:label": "TumorLargestDimensionDiameter", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Largest Dimension Diameter", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "LungCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lung Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Glanspenis" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Glottis" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:GumNOS" }, { - "@id": "bts:LungCancerDetectionMethodType" + "@id": "bts:Hardpalate" }, { - "@id": "bts:LungCancerParticipantProcedureHistory" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:LungAdjacentHistologyType" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:LungTumorLocationAnatomicSite" + "@id": "bts:Heart" }, { - "@id": "bts:LungTumorLobeBronchialLocation" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:CurrentLungCancerSymptoms" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:LungTopography" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:LungCancerHarboringGenomicAberrations" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", - "rdfs:label": "LungCancerDetectionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LowDoseComputedTomography(LDCT)" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:ChestX-ray" + "@id": "bts:Ileum" }, { - "@id": "bts:ChestCT" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:Unknown" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Lung Cancer Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerParticipantProcedureHistory", - "@type": "rdfs:Class", - "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", - "rdfs:label": "LungCancerParticipantProcedureHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LobectomyBilateral" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:LobectomyLeft" + "@id": "bts:Intrathoraciclymphnodes" }, { - "@id": "bts:LobectomyRight" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:LungWedgeResectionBilateral" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:LungWedgeResectionLeft" + "@id": "bts:Jejunum" }, { - "@id": "bts:LungWedgeResectionMultiple" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:LungWedgeResectionRight" + "@id": "bts:Labiummajus" }, { - "@id": "bts:PneumonectomyLeft" + "@id": "bts:Labiumminus" }, { - "@id": "bts:PneumonectomyRight" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:Endobronchialbiopsy" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:Mediastinoscopy" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:VATSSclerosis" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:Brainresection" + "@id": "bts:Lateralwallofbladder" }, { - "@id": "bts:Segmentectomy" + "@id": "bts:Lateralwallofnasopharynx" }, { - "@id": "bts:Unknown" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:Other" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Cancer Participant Procedure History", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungAdjacentHistologyType", - "@type": "rdfs:Class", - "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", - "rdfs:label": "LungAdjacentHistologyType", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Lungadenocarcinoma" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:Adenosquamouscarcinoma" + "@id": "bts:LipNOS" }, { - "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" + "@id": "bts:Liver" }, { - "@id": "bts:Lungadenocarcinomainsitu" + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:Largecelllungcarcinoma" + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" }, { - "@id": "bts:Largecellneuroendocrinecarcinoma" + "@id": "bts:Lowergum" }, { - "@id": "bts:Lunglymphoepithelioma-likecarcinoma" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:Bronchioalveolarcarcinoma" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:ThoracicNUTcarcinoma" + "@id": "bts:Lowerthirdofesophagus" }, { - "@id": "bts:Sarcomatoidcarcinoma" + "@id": "bts:Lower-innerquadrantofbreast" }, { - "@id": "bts:Smallcelllungcarcinoma" + "@id": "bts:Lower-outerquadrantofbreast" }, { - "@id": "bts:Squamouscelllungcarcinoma" + "@id": "bts:LungNOS" }, { - "@id": "bts:Lungsquamouscellcarcinomainsitu" + "@id": "bts:LymphnodeNOS" }, { - "@id": "bts:Other" + "@id": "bts:Lymphnodesofaxillaorarm" }, { - "@id": "bts:Unknown" + "@id": "bts:Lymphnodesofheadfaceandneck" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Adjacent Histology Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungTumorLocationAnatomicSite", - "@type": "rdfs:Class", - "rdfs:comment": "Anatomic location of the tumor inside the lung", - "rdfs:label": "LungTumorLocationAnatomicSite", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Maincarina" + "@id": "bts:Lymphnodesofinguinalregionorleg" }, { - "@id": "bts:Left" + "@id": "bts:Lymphnodesofmultipleregions" }, { - "@id": "bts:Right" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:Unknown" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Tumor Location Anatomic Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungTumorLobeBronchialLocation", - "@type": "rdfs:Class", - "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", - "rdfs:label": "LungTumorLobeBronchialLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Upperlobe" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:Middlelobe" + "@id": "bts:Mandible" }, { - "@id": "bts:Lowerlobe" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:Stump" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:Bronchus" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Tumor Lobe Bronchial Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CurrentLungCancerSymptoms", - "@type": "rdfs:Class", - "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", - "rdfs:label": "CurrentLungCancerSymptoms", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Asbestosis" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:Productivecough" + "@id": "bts:Middleear" }, { - "@id": "bts:Non-productivecough" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:Wheezing" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:Rhonci" + "@id": "bts:MouthNOS" }, { - "@id": "bts:Crackles" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:Hemoptysis" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:Dyspnea" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:Unexplainedweightloss" + "@id": "bts:Myometrium" }, { - "@id": "bts:Unexplainedlossofenergy/fatigue" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:Chestpainordiscomfort" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:Dysphagia" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Nipple" }, { - "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" + "@id": "bts:Occipitallobe" }, { - 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"@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ColorectalCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:Upper-innerquadrantofbreast" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Urachus" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Ureter" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:ColorectalCancerDetectionMethodType" + "@id": "bts:Urethra" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:UterusNOS" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:Uvula" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:Vallecula" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:MLH1PromoterMethylationStatus" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:ColorectalPolypShape" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:SizeofPolypRemoved" + "@id": "bts:Clitoris" }, { - "@id": "bts:ColorectalPolypCount" + "@id": "bts:Overlappinglesionofbiliarytract" }, { - "@id": "bts:ColorectalPolypType" + "@id": "bts:Unknown" }, { - "@id": "bts:ColorectalPolypAdenomaType" + "@id": "bts:NotReported" } ], + "sms:displayName": "Site of Resection or Biopsy", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerDetectionMethodType", + "@id": "bts:TissueorOrganofOrigin", "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", - "rdfs:label": "ColorectalCancerDetectionMethodType", + "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "TissueorOrganofOrigin", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -12000,1837 +12538,1017 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Fecaloccultbloodtest" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:Sigmoidoscopy" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:Colonoscopy" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:Virtualcolonoscopy" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:DNAstooltest" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:Other" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Unknown" + "@id": "bts:Analcanal" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Colorectal Cancer Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofPriorColonPolyps", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "HistoryofPriorColonPolyps", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:No" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "History of Prior Colon Polyps", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyColonCancerHistoryIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", - "rdfs:label": "FamilyColonCancerHistoryIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:No" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Colon Cancer History Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:AnusNOS" }, { - "@id": "bts:No" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Appendix" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beforeage50" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Endometrial Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beforeage50" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:Bladderneck" }, { - "@id": "bts:Unknown" + "@id": "bts:BladderNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Ovarian Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", - "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-Crohn'sdisease" + "@id": "bts:Blood" }, { - "@id": "bts:Yes-Ulcerativecolitis" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:No" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:Unknown" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PatientColonoscopyPerformedIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", - "rdfs:label": "PatientColonoscopyPerformedIndicator", - "rdfs:subClassOf": [ + "@id": "bts:Bonemarrow" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BoneoflimbNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:BoneNOS" }, { - "@id": "bts:No" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Patient Colonoscopy Performed Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerTumorBorderConfiguration", - "@type": "rdfs:Class", - "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", - "rdfs:label": "ColorectalCancerTumorBorderConfiguration", - "rdfs:subClassOf": [ + "@id": "bts:Brainstem" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BrainNOS" + }, { - "@id": "bts:Indeterminate" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:Infiltrating" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Other" + "@id": "bts:Broadligament" }, { - "@id": "bts:Pushing" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Cancer Tumor Border Configuration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MLH1PromoterMethylationStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", - "rdfs:label": "MLH1PromoterMethylationStatus", - "rdfs:subClassOf": [ + "@id": "bts:Carotidbody" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Caudaequina" + }, { - "@id": "bts:Absent" + "@id": "bts:Cecum" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:NotAssessed" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:Present" - } - ], - "sms:displayName": "MLH1 Promoter Methylation Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerKRASIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", - "rdfs:label": "ColorectalCancerKRASIndicator", - "rdfs:subClassOf": [ + "@id": "bts:Cerebralmeninges" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Cerebrum" + }, { - "@id": "bts:Yes" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:No" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:Unknown" + "@id": "bts:Choroid" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Cancer KRAS Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColonPolypOccurenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "ColonPolypOccurenceIndicator", - "rdfs:subClassOf": [ + "@id": "bts:Ciliarybody" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Cloacogeniczone" + }, { - "@id": "bts:Yes" + "@id": "bts:ColonNOS" }, { - "@id": "bts:No" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:Unknown" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colon Polyp Occurence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyHistoryColorectalPolyp", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyHistoryColorectalPolyp", - "rdfs:subClassOf": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + }, { - "@id": "bts:Yes" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:No" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:Unknown" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Family History Colorectal Polyp", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypNewIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", - "rdfs:label": "ColorectalPolypNewIndicator", - "rdfs:subClassOf": [ + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + }, { - "@id": "bts:Yes" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:No" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp New Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypShape", - "@type": "rdfs:Class", - "rdfs:comment": "Shape of polyp identified in the participant", - "rdfs:label": "ColorectalPolypShape", - "rdfs:subClassOf": [ + "@id": "bts:Cortexofadrenalgland" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CranialnerveNOS" + }, { - "@id": "bts:Pedunculated" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Sessile" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:Flat" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Notstated" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Shape", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeofPolypRemoved", - "@type": "rdfs:Class", - "rdfs:comment": "Size of the polyp removed in cm", - "rdfs:label": "SizeofPolypRemoved", - "rdfs:subClassOf": [ + "@id": "bts:DorsalsurfaceoftongueNOS" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size of Polyp Removed", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypCount", - "@type": "rdfs:Class", - "rdfs:comment": "The total number of polyps detected", - "rdfs:label": "ColorectalPolypCount", - "rdfs:subClassOf": [ + "@id": "bts:Duodenum" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Polyp Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of polyp found in the participant", - "rdfs:label": "ColorectalPolypType", - "rdfs:subClassOf": [ + "@id": "bts:Endocervix" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:EndocrineglandNOS" + }, { - "@id": "bts:Adenoma" + "@id": "bts:Endometrium" }, { - "@id": "bts:Hyperplastic" + "@id": "bts:Epididymis" }, { - "@id": "bts:Mixed" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:Papillomatous" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:Normal" + "@id": "bts:Exocervix" }, { - "@id": "bts:Cancer" + "@id": "bts:Externalear" }, { - "@id": "bts:Other" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Colorectal Polyp Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypAdenomaType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of adenoma associated with the polyp", - "rdfs:label": "ColorectalPolypAdenomaType", - "rdfs:subClassOf": [ + "@id": "bts:Externallowerlip" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Externalupperlip" + }, { - "@id": "bts:Tubular" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:Villous" + "@id": "bts:EyeNOS" }, { - "@id": "bts:Tubulovillous" + "@id": "bts:Eyelid" }, { - "@id": "bts:Sessileserrated" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:Traditionalserrated" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:Serratednotspecified" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:Notstated" + "@id": "bts:Frontallobe" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Adenoma Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "BreastCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:Frontalsinus" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Fundusofstomach" + }, { - "@id": "bts:Component" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Gallbladder" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Glanspenis" }, { - "@id": "bts:BreastCarcinomaDetectionMethodType" + "@id": "bts:Glottis" }, { - "@id": "bts:BreastCarcinomaHistologyCategory" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + "@id": "bts:GumNOS" }, { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + "@id": "bts:Hardpalate" }, { - "@id": "bts:BreastBiopsyProcedureFindingType" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:BreastQuadrantSite" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:BreastCancerAssessmentTests" + "@id": "bts:Heart" }, { - "@id": "bts:BreastCancerGenomicTestPerformed" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:MammaprintRiskGroup" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:OncotypeRiskGroup" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" + "@id": "bts:Ileum" }, { - "@id": "bts:BreastCancerAllredEstrogenReceptorScore" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:PriorInvasiveBreastDisease" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:BreastCarcinomaERStatusPercentageValue" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:BreastCarcinomaPRStatusPercentageValue" + "@id": "bts:Intrahepaticbileduct" }, { - 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"@id": "bts:StopDaysfromIndex" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:CNSTumorPrimaryAnatomicSite" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:GliomaSpecificMetastasisSites" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:GliomaSpecificRadiationField" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus" + "@id": "bts:Cheekmucosa" + }, + { + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], + "sms:displayName": "Tissue or Organ of Origin", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CNSTumorPrimaryAnatomicSite", + "@id": "bts:NCIAtlasCancerSite", "@type": "rdfs:Class", - "rdfs:comment": "Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2", - "rdfs:label": "CNSTumorPrimaryAnatomicSite", + "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", + "rdfs:label": "NCIAtlasCancerSite", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -13838,72 +13556,84 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Thalamus" + "@id": "bts:Bladder" }, { - "@id": "bts:Ventricles" + "@id": "bts:BrainAndOtherNervousSystem" }, { - "@id": "bts:Intracranial/Leptomeningeal" + "@id": "bts:FemaleBreast" }, { - "@id": "bts:Suprasellar/Hypothalamic/Pituitary" + "@id": "bts:InsituFemaleBreast" }, { - "@id": "bts:Cerebellar/Posteriorfossa" + "@id": "bts:CervixUteri" }, { - "@id": "bts:Brainstem-Medulla" + "@id": "bts:LessThanAge" }, { - "@id": "bts:Brainstem-Midbrain/Tectum" + "@id": "bts:MalignantChildhoodNeoplasm" }, { - "@id": "bts:Brainstem-Pons" + "@id": "bts:ColonAndRectum" }, { - "@id": "bts:Spinalcord-Cervical" + "@id": "bts:Esophagus" }, { - "@id": "bts:Spinalcord-Thoracic" + "@id": "bts:KidneyAndRenalPelvis" }, { - "@id": "bts:Spinalcord-Lumbar" + "@id": "bts:Leukemia" }, { - "@id": "bts:Opticpathway" + "@id": "bts:LiverAndBileDuct" }, { - "@id": "bts:OtherlocationsNOS" + "@id": "bts:LungAndBronchus" }, { - "@id": "bts:Paraspinalganglion" + "@id": "bts:CutaneousMelanoma" }, { - "@id": "bts:Basalganglia" + "@id": "bts:Non-Hodgkin'sLymphoma" }, { - "@id": "bts:Hippocampus" + "@id": "bts:OralCavityAndPharynx" }, { - "@id": "bts:Meninges/Dura" + "@id": "bts:Ovary" }, { - "@id": "bts:Otherlymphnodes" + "@id": "bts:Pancreas" + }, + { + "@id": "bts:ProstateGland" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:ThyroidGland" + }, + { + "@id": "bts:Uterus" } ], - "sms:displayName": "CNS Tumor Primary Anatomic Site", + "sms:displayName": "NCI Atlas Cancer Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GliomaSpecificMetastasisSites", + "@id": "bts:TumorGrade", "@type": "rdfs:Class", - "rdfs:comment": "Evidence of active brain metastasis including leptomeningeal involvement", - "rdfs:label": "GliomaSpecificMetastasisSites", + "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", + "rdfs:label": "TumorGrade", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -13911,135 +13641,124 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CSF" + "@id": "bts:G1" }, { - "@id": "bts:Spine" + "@id": "bts:G2" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:G3" }, { - "@id": "bts:Brain" + "@id": "bts:G4" }, { - "@id": "bts:Other" + "@id": "bts:GX" }, { - "@id": "bts:Leptomeningeal" + "@id": "bts:GB" + }, + { + "@id": "bts:HighGrade" + }, + { + "@id": "bts:IntermediateGrade" + }, + { + "@id": "bts:LowGrade" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" }, { "@id": "bts:NotApplicable" } ], - "sms:displayName": "Glioma Specific Metastasis Sites", + "sms:displayName": "Tumor Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GliomaSpecificRadiationField", + "@id": "bts:PackYearsSmoked", "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the CNS where radiation was administered in a partcipant with glioma", - "rdfs:label": "GliomaSpecificRadiationField", + "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", + "rdfs:label": "PackYearsSmoked", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Craniospinal" - }, - { - "@id": "bts:Focal-tumorbed" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Pack Years Smoked", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:YearsSmoked", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", + "rdfs:label": "YearsSmoked", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:Exposure" } ], - "sms:displayName": "Glioma Specific Radiation Field", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Years Smoked", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:DaystoFollowUp", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a supra tentorial ependymoma", - "rdfs:label": "SupraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoFollowUp", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:ST-EPN-RELA" - }, - { - "@id": "bts:ST-EPN-YAP1" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Supra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Days to Follow Up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:GeneSymbol", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a infra tentorial ependymoma", - "rdfs:label": "InfraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "GeneSymbol", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:PF-EPN-A" - }, - { - "@id": "bts:PF-EPN-B" - }, - { - "@id": "bts:Myxopapillaryependymoma" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Infra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", + "sms:displayName": "Gene Symbol", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus", + "@id": "bts:MolecularAnalysisMethod", "@type": "rdfs:Class", - "rdfs:comment": "Neuroblastoma MYCN amplification or over-expression status", - "rdfs:label": "NeuroblastomaMYCNGeneAmplificationStatus", + "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularAnalysisMethod", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -14047,247 +13766,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Amplified" - }, - { - "@id": "bts:Notamplified" - }, - { - "@id": "bts:Notdone" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Neuroblastoma MYCN Gene Amplification Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3", - "rdfs:label": "AcuteLymphoblasticLeukemiaTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:SpecimenBlastCountPercentageValue" + "@id": "bts:ComparativeGenomicHybridization" }, { - "@id": "bts:NCIALLRiskGroup" + "@id": "bts:CytogeneticsNOS" }, { - "@id": "bts:MRDALLDiagnosticSensitivity" + "@id": "bts:FISH" }, { - "@id": "bts:CNSLeukemiaStatus" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SpecimenBlastCountPercentageValue", - "@type": "rdfs:Class", - "rdfs:comment": "The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis", - "rdfs:label": "SpecimenBlastCountPercentageValue", - "rdfs:subClassOf": [ - { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Specimen Blast Count Percentage Value", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NCIALLRiskGroup", - "@type": "rdfs:Class", - "rdfs:comment": "The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.", - "rdfs:label": "NCIALLRiskGroup", - "rdfs:subClassOf": [ - { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:NCIHighRisk" + "@id": "bts:FlowCytometry" }, { - "@id": "bts:NCIStandardRisk" + "@id": "bts:IHC" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "NCI ALL Risk Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MRDALLDiagnosticSensitivity", - "@type": "rdfs:Class", - "rdfs:comment": "The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.", - "rdfs:label": "MRDALLDiagnosticSensitivity", - "rdfs:subClassOf": [ - { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Optimal" + "@id": "bts:ISH" }, { - "@id": "bts:Suboptimal" + "@id": "bts:Karyotype" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Microarray" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "MRD ALL Diagnostic Sensitivity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CNSLeukemiaStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The status of central nervous system leukemia at the time of diagnosis.", - "rdfs:label": "CNSLeukemiaStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CNS1" + "@id": "bts:MicrosatelliteAnalysis" }, { - "@id": "bts:CNS2" + "@id": "bts:NuclearStaining" }, { - "@id": "bts:CNS3" + "@id": "bts:Other" }, { - "@id": "bts:CNS2a" + "@id": "bts:RNASequencing" }, { - "@id": "bts:CNS2b" + "@id": "bts:RT-PCR" }, { - "@id": "bts:CNS2c" + "@id": "bts:SequencingNOS" }, { - "@id": "bts:CNS3a" + "@id": "bts:SouthernBlotting" }, { - "@id": "bts:CNS3b" + "@id": "bts:TargetedSequencing" }, { - "@id": "bts:CNS3c" + "@id": "bts:WGS" }, { - "@id": "bts:Notevaluated" + "@id": "bts:WXS" }, { "@id": "bts:Unknown" - } - ], - "sms:displayName": "CNS Leukemia Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Ovarian cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "OvarianCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ovarian Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:OvarianCancerHistologicSubtype" - }, - { - "@id": "bts:OvarianCancerSurgicalOutcome" + "@id": "bts:NotReported" }, { - "@id": "bts:OvarianCancerPlatinumStatus" + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Molecular Analysis Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OvarianCancerHistologicSubtype", + "@id": "bts:TestResult", "@type": "rdfs:Class", - "rdfs:comment": "Text term to describe the histological subtype of ovarian cancer in the participant", - "rdfs:label": "OvarianCancerHistologicSubtype", + "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestResult", "rdfs:subClassOf": [ { - "@id": "bts:OvarianCancerTier3" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -14295,88 +13848,63 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:High-gradeserous" - }, - { - "@id": "bts:Low-gradeserous" + "@id": "bts:AbnormalNOS" }, { - "@id": "bts:High-gradeendometrioid" + "@id": "bts:CopyNumberReported" }, { - "@id": "bts:Low-gradeendometrioid" + "@id": "bts:Equivocal" }, { - "@id": "bts:Clearcell" + "@id": "bts:High" }, { - "@id": "bts:Mucinous" + "@id": "bts:Intermediate" }, { - "@id": "bts:Sex-cordstromal" + "@id": "bts:LossofExpression" }, { - "@id": "bts:Germcell" + "@id": "bts:Low" }, { - "@id": "bts:Other" + "@id": "bts:Negative" }, { - "@id": "bts:Unknown" + "@id": "bts:Normal" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Ovarian Cancer Histologic Subtype", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerSurgicalOutcome", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of surgical treatment administered.", - "rdfs:label": "OvarianCancerSurgicalOutcome", - "rdfs:subClassOf": [ - { - "@id": "bts:OvarianCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:R0resection" + "@id": "bts:Overexpressed" }, { - "@id": "bts:Optimalcytoreduction" + "@id": "bts:Positive" }, { - "@id": "bts:Sub-optimalcytoreduction" + "@id": "bts:TestValueReported" }, { - "@id": "bts:Other" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Ovarian Cancer Surgical Outcome", - "sms:required": "sms:false", + "sms:displayName": "Test Result", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OvarianCancerPlatinumStatus", + "@id": "bts:TreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", - "rdfs:label": "OvarianCancerPlatinumStatus", + "rdfs:comment": "Text term that describes the kind of treatment administered.", + "rdfs:label": "TreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:OvarianCancerTier3" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -14384,253 +13912,178 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Platinum-refractory" - }, - { - "@id": "bts:Platinum-sensitive" - }, - { - "@id": "bts:Platinum-resistant" - }, - { - "@id": "bts:Datanotavailable" + "@id": "bts:AblationCryo" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ovarian Cancer Platinum Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ProstateCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Prostate Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:AblationEthanolInjection" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:AblationMicrowave" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:AblationNOS" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:AblationRadiofrequency" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:AblationRadiosurgical" }, { - "@id": "bts:LocationExtentExtraprostaticExtension" + "@id": "bts:AncillaryTreatment" }, { - "@id": "bts:LocationNaturePositiveMargins" + "@id": "bts:AntiseizureTreatment" }, { - "@id": "bts:SeminalVesicleInvasion" + "@id": "bts:BisphosphonateTherapy" }, { - "@id": "bts:ProstateCarcinomaHistologicType" + "@id": "bts:BlindedStudyTreatmentunknown" }, { - "@id": "bts:ProstateCancerLocalExtent" + "@id": "bts:BrachytherapyHighDose" }, { - "@id": "bts:AdditonalFindingsUninvolvedProstate" + "@id": "bts:BrachytherapyLowDose" }, { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:LocationExtentExtraprostaticExtension", - "@type": "rdfs:Class", - "rdfs:comment": "Location and extent of extraprostatic extension", - "rdfs:label": "LocationExtentExtraprostaticExtension", - "rdfs:subClassOf": [ - { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LeftAnterior" + "@id": "bts:BrachytherapyNOS" }, { - "@id": "bts:LeftLateral" + "@id": "bts:Chemoembolization" }, { - "@id": "bts:LeftPosterolateral" + "@id": "bts:Chemoprotectant" }, { - "@id": "bts:LeftPosterior" + "@id": "bts:Chemotherapy" }, { - "@id": "bts:LeftApex" + "@id": "bts:ConcurrentChemoradiation" }, { - "@id": "bts:LeftMid" + "@id": "bts:Cryoablation" }, { - "@id": "bts:LeftBase" + "@id": "bts:Embolization" }, { - "@id": "bts:LeftFocal" + "@id": "bts:EthanolInjectionAblation" }, { - "@id": "bts:LeftNon-focal(established)" + "@id": "bts:ExternalBeamRadiation" }, { - "@id": "bts:RightAnterior" + "@id": "bts:HormoneTherapy" }, { - "@id": "bts:RightLateral" + "@id": "bts:I-131RadiationTherapy" }, { - "@id": "bts:RightPosterolateral" + "@id": "bts:InternalRadiation" }, { - "@id": "bts:RightPosterior" + "@id": "bts:Immunotherapy(IncludingVaccines)" }, { - "@id": "bts:RightApex" + "@id": "bts:IsolatedLimbPerfusion(ILP)" }, { - "@id": "bts:RightMid" + "@id": "bts:OrganTransplantation" }, { - "@id": "bts:RightBase" + "@id": "bts:Other" }, { - "@id": "bts:RightFocal" + "@id": "bts:PharmaceuticalTherapyNOS" }, { - "@id": "bts:RightNon-focal(established)" + "@id": "bts:Pleurodesis" }, { - "@id": "bts:Unknown" + "@id": "bts:Radiation2DConventional" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Location Extent Extraprostatic Extension", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LocationNaturePositiveMargins", - "@type": "rdfs:Class", - "rdfs:comment": "Location and nature of positive margins", - "rdfs:label": "LocationNaturePositiveMargins", - "rdfs:subClassOf": [ - { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LeftAnterior" + "@id": "bts:Radiation3DConformal" }, { - "@id": "bts:LeftLateral" + "@id": "bts:RadiationCombination" }, { - "@id": "bts:LeftPosterolateral" + "@id": "bts:RadiationCyberknife" }, { - "@id": "bts:LeftPosterior" + "@id": "bts:RadiationExternalBeam" }, { - "@id": "bts:LeftApex" + "@id": "bts:RadiationImplants" }, { - "@id": "bts:LeftMid" + "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" }, { - "@id": "bts:LeftBase" + "@id": "bts:RadiationInternal" }, { - "@id": "bts:LeftFocal" + "@id": "bts:RadiationProtonBeam" }, { - "@id": "bts:LeftExtensive" + "@id": "bts:RadiationRadioisotope" }, { - "@id": "bts:LeftPositiveinanareaofextraprostaticextension(EPE)" + "@id": "bts:RadiationStereotactic/GammaKnife/SRS" }, { - "@id": "bts:LeftPositiveinanareaofintraprostaticincision(II)" + "@id": "bts:RadiationSystemic" }, { - "@id": "bts:LeftPositivewhereitisdifficulttodistinguishEPEvsII" + "@id": "bts:RadiationTherapyNOS" }, { - "@id": "bts:RightAnterior" + "@id": "bts:RadioactiveIodineTherapy" }, { - "@id": "bts:RightLateral" + "@id": "bts:Radioembolization" }, { - "@id": "bts:RightPosterolateral" + "@id": "bts:RadiosensitizingAgent" }, { - "@id": "bts:RightPosterior" + "@id": "bts:StemCellTreatment" }, { - "@id": "bts:RightApex" + "@id": "bts:StemCellTransplantationAutologous" }, { - "@id": "bts:RightMid" + "@id": "bts:StemCellTransplantationDoubleAutologous" }, { - "@id": "bts:RightBase" + "@id": "bts:StemCellTransplantationAllogeneic" }, { - "@id": "bts:RightFocal" + "@id": "bts:StemCellTransplantationNon-Myeloablative" }, { - "@id": "bts:RightExtensive" + "@id": "bts:StemCellTransplantationSyngenic" }, { - "@id": "bts:RightPositiveinanareaofextraprostaticextension(EPE)" + "@id": "bts:StemCellTransplantationHaploidentical" }, { - "@id": "bts:RightPositiveinanareaofintraprostaticincision(II)" + "@id": "bts:StemCellTransplantationNOS" }, { - "@id": "bts:RightPositivewhereitisdifficulttodistinguishEPEvsII" + "@id": "bts:StereotacticRadiosurgery" }, { - "@id": "bts:Bladderneck(blockPUM)" + "@id": "bts:SteroidTherapy" }, { - "@id": "bts:Vasdeferens" + "@id": "bts:Surgery" }, { - "@id": "bts:Apicalmargin(blockDUM)" + "@id": "bts:TargetedMolecularTherapy" }, { "@id": "bts:Unknown" @@ -14639,104 +14092,95 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Location Nature Positive Margins", + "sms:displayName": "Treatment Type", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:SeminalVesicleInvasion", + "@id": "bts:TumorLargestDimensionDiameter", "@type": "rdfs:Class", - "rdfs:comment": "An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.", - "rdfs:label": "SeminalVesicleInvasion", + "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", + "rdfs:label": "TumorLargestDimensionDiameter", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:None" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Right" - }, - { - "@id": "bts:Bothsides" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Seminal Vesicle Invasion", + "sms:displayName": "Tumor Largest Dimension Diameter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProstateCarcinomaHistologicType", + "@id": "bts:LungCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "The diagnostic subclassification of an invasive prostate carcinoma.", - "rdfs:label": "ProstateCarcinomaHistologicType", + "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "LungCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Lung Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Prostaticadenocarcinoma(conventionalNOS)" + "@id": "bts:Component" }, { - "@id": "bts:Prostaticductadenocarcinoma" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Acinarprostatemucinous(colloid)adenocarcinoma" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Acinarprostateadenocarcinoma-signet-ringvariant" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Prostaticadenosquamouscarcinoma" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Acinarprostatemucinousadenocarcinoma" + "@id": "bts:LungCancerDetectionMethodType" }, { - "@id": "bts:Prostaticsmallcellcarcinoma" + "@id": "bts:LungCancerParticipantProcedureHistory" }, { - "@id": "bts:Acinarprostateadenocarcinoma-sarcomatoidvariant" + "@id": "bts:LungAdjacentHistologyType" }, { - "@id": "bts:UndifferentiatedcarcinomaNOS" + "@id": "bts:LungTumorLocationAnatomicSite" }, { - "@id": "bts:Other" + "@id": "bts:LungTumorLobeBronchialLocation" + }, + { + "@id": "bts:CurrentLungCancerSymptoms" + }, + { + "@id": "bts:LungTopography" + }, + { + "@id": "bts:LungCancerHarboringGenomicAberrations" } ], - "sms:displayName": "Prostate Carcinoma Histologic Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProstateCancerLocalExtent", + "@id": "bts:LungCancerDetectionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "The response used to categorize the local extent of disease for prostate cancer.", - "rdfs:label": "ProstateCancerLocalExtent", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", + "rdfs:label": "LungCancerDetectionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14744,30 +14188,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:OrganConfined" + "@id": "bts:LowDoseComputedTomography(LDCT)" }, { - "@id": "bts:Extraprostaticextension" + "@id": "bts:ChestX-ray" + }, + { + "@id": "bts:ChestCT" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Prostate Cancer Local Extent", + "sms:displayName": "Lung Cancer Detection Method Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdditonalFindingsUninvolvedProstate", + "@id": "bts:LungCancerParticipantProcedureHistory", "@type": "rdfs:Class", - "rdfs:comment": "Additional findings, uninvolved prostate", - "rdfs:label": "AdditonalFindingsUninvolvedProstate", + "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", + "rdfs:label": "LungCancerParticipantProcedureHistory", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14775,148 +14225,113 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:High-gradeprostaticintraepithelialneoplasia(PIN)" + "@id": "bts:LobectomyBilateral" }, { - "@id": "bts:Inflammation" + "@id": "bts:LobectomyLeft" }, { - "@id": "bts:Benignprostatichyperplasia(BPH)" + "@id": "bts:LobectomyRight" }, { - "@id": "bts:ProstaticIntraductaladenocarcinoma" + "@id": "bts:LungWedgeResectionBilateral" }, { - "@id": "bts:Other" + "@id": "bts:LungWedgeResectionLeft" }, { - "@id": "bts:Unknown" + "@id": "bts:LungWedgeResectionMultiple" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Additonal Findings Uninvolved Prostate", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes various morphological and cytological subtypes in protate tumors.", - "rdfs:label": "ProstateCancerCytologicMorphologicSubtypes", - "rdfs:subClassOf": [ + "@id": "bts:LungWedgeResectionRight" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PneumonectomyLeft" + }, { - "@id": "bts:Prostaticbasalcellhyperplasia" + "@id": "bts:PneumonectomyRight" }, { - "@id": "bts:Prostaticclearcellcribiformhyperplasia" + "@id": "bts:Endobronchialbiopsy" }, { - "@id": "bts:Prostaticatypicaladenomatoushyperplasia(adenosisorAAH)" + "@id": "bts:Mediastinoscopy" }, { - "@id": "bts:Lowgradeprostaticintraepithelialneoplasia(PIN)/(PINI)" + "@id": "bts:VATSSclerosis" }, { - "@id": "bts:Highgradeprostaticintraepithelialneoplasia(HGPIN)/(PINII&PINIII)" + "@id": "bts:Brainresection" }, { - "@id": "bts:Other" + "@id": "bts:Segmentectomy" }, { "@id": "bts:Unknown" }, + { + "@id": "bts:Other" + }, { "@id": "bts:NotReported" } ], - "sms:displayName": "Prostate Cancer Cytologic Morphologic Subtypes", + "sms:displayName": "Lung Cancer Participant Procedure History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SarcomaTier3", + "@id": "bts:LungAdjacentHistologyType", "@type": "rdfs:Class", - "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", - "rdfs:label": "SarcomaTier3", + "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", + "rdfs:label": "LungAdjacentHistologyType", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sarcoma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Lungadenocarcinoma" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Adenosquamouscarcinoma" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Lungadenocarcinomainsitu" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Largecelllungcarcinoma" }, { - "@id": "bts:SarcomaSubtype" + "@id": "bts:Largecellneuroendocrinecarcinoma" }, { - "@id": "bts:SarcomaDiagnosisClassificationCategory" + "@id": "bts:Lunglymphoepithelioma-likecarcinoma" }, { - "@id": "bts:SarcomaTumorExtensionType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SarcomaSubtype", - "@type": "rdfs:Class", - "rdfs:comment": "The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.", - "rdfs:label": "SarcomaSubtype", - "rdfs:subClassOf": [ - { - "@id": "bts:SarcomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" + "@id": "bts:Bronchioalveolarcarcinoma" }, { - "@id": "bts:Leiomyosarcoma(uterineorextra-uterine)" + "@id": "bts:ThoracicNUTcarcinoma" }, { - "@id": "bts:OtherSynovialSarcomaOrMalignantPeripheralNerveSheathTumorSarcoma" + "@id": "bts:Sarcomatoidcarcinoma" }, { - "@id": "bts:GastrointestinalStromalTumor" + "@id": "bts:Smallcelllungcarcinoma" }, { - "@id": "bts:Liposarcoma" + "@id": "bts:Squamouscelllungcarcinoma" }, { - "@id": "bts:Undifferentiatedpleomorphicsarcomaormalignantfibroushistiosarcoma" + "@id": "bts:Lungsquamouscellcarcinomainsitu" }, { "@id": "bts:Other" @@ -14928,18 +14343,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sarcoma Subtype", + "sms:displayName": "Lung Adjacent Histology Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SarcomaDiagnosisClassificationCategory", + "@id": "bts:LungTumorLocationAnatomicSite", "@type": "rdfs:Class", - "rdfs:comment": "High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.", - "rdfs:label": "SarcomaDiagnosisClassificationCategory", + "rdfs:comment": "Anatomic location of the tumor inside the lung", + "rdfs:label": "LungTumorLocationAnatomicSite", "rdfs:subClassOf": [ { - "@id": "bts:SarcomaTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14947,13 +14362,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BoneSarcoma" + "@id": "bts:Maincarina" }, { - "@id": "bts:MusculoskeletalSarcoma" + "@id": "bts:Left" }, { - "@id": "bts:SoftTissueSarcoma" + "@id": "bts:Right" }, { "@id": "bts:Unknown" @@ -14962,18 +14377,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sarcoma Diagnosis Classification Category", + "sms:displayName": "Lung Tumor Location Anatomic Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SarcomaTumorExtensionType", + "@id": "bts:LungTumorLobeBronchialLocation", "@type": "rdfs:Class", - "rdfs:comment": "The field to indicate the organs and structures to which the tumor has become adherent or has invaded.", - "rdfs:label": "SarcomaTumorExtensionType", + "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", + "rdfs:label": "LungTumorLobeBronchialLocation", "rdfs:subClassOf": [ { - "@id": "bts:SarcomaTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14981,22 +14396,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Extraosseous" - }, - { - "@id": "bts:Intracranial" + "@id": "bts:Upperlobe" }, { - "@id": "bts:Lymphnodes" + "@id": "bts:Middlelobe" }, { - "@id": "bts:Parameningeal" + "@id": "bts:Lowerlobe" }, { - "@id": "bts:Thoraciccavity" + "@id": "bts:Stump" }, { - "@id": "bts:Other" + "@id": "bts:Bronchus" }, { "@id": "bts:Unknown" @@ -15005,133 +14417,110 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sarcoma Tumor Extension Type", + "sms:displayName": "Lung Tumor Lobe Bronchial Location", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PancreaticCancerTier3", + "@id": "bts:CurrentLungCancerSymptoms", "@type": "rdfs:Class", - "rdfs:comment": "Pancreatic cancer specific attributes in Clinical Tier Data 3", - "rdfs:label": "PancreaticCancerTier3", + "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", + "rdfs:label": "CurrentLungCancerSymptoms", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pancreatic Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Asbestosis" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Productivecough" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Non-productivecough" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Wheezing" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Rhonci" }, { - "@id": "bts:PancreasPrecancerHistopathologicGrade" + "@id": "bts:Crackles" }, { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" + "@id": "bts:Hemoptysis" }, { - "@id": "bts:PancreaticDuctFinalPathologyType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PancreasPrecancerHistopathologicGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.", - "rdfs:label": "PancreasPrecancerHistopathologicGrade", - "rdfs:subClassOf": [ + "@id": "bts:Dyspnea" + }, { - "@id": "bts:PancreaticCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Unexplainedweightloss" + }, { - "@id": "bts:IPMN-Adenoma" + "@id": "bts:Unexplainedlossofenergy/fatigue" }, { - "@id": "bts:IPMN-Borderline" + "@id": "bts:Chestpainordiscomfort" }, { - "@id": "bts:IPMN-Carcinomainsitu" + "@id": "bts:Dysphagia" }, { - "@id": "bts:IPMN-Invasivecarcinoma" + "@id": "bts:Pneumonia" }, { - "@id": "bts:PanIN1" + "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" }, { - "@id": "bts:PanIN1A" + "@id": "bts:Airentrydecreased/fair/poor/diminished" }, { - "@id": "bts:PanIN1B" + "@id": "bts:Fair/pooraeration" }, { - "@id": "bts:PanIN2" + "@id": "bts:Shallowinspiration" }, { - "@id": "bts:PanIN3" + "@id": "bts:Breathsoundscoarse/diminished" }, { - "@id": "bts:Unknown" + "@id": "bts:Dullnesstopercussion" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreas Precancer Histopathologic Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype", - "@type": "rdfs:Class", - "rdfs:comment": "The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen", - "rdfs:label": "PancreaticIPMNPathologyEpithelialSubtype", - "rdfs:subClassOf": [ + "@id": "bts:Abnormalbreathsounds" + }, { - "@id": "bts:PancreaticCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Clearlungstoauscultationorpercussion" + }, { - "@id": "bts:GastricFoveolar" + "@id": "bts:Unlabored/normalbreathing" }, { - "@id": "bts:Intestinal" + "@id": "bts:Coldsymptoms/flu/sinus/nasalcongestion" }, { - "@id": "bts:IntraductalTubopapillary" + "@id": "bts:Sinuspain/infection" }, { - "@id": "bts:Pancreatobiliary" + "@id": "bts:Fingerclubbing" }, { - "@id": "bts:Oncocytic" + "@id": "bts:Noevidenceoflungcancerrecurrence" + }, + { + "@id": "bts:PatientisNED" + }, + { + "@id": "bts:Oxygensupplemental-portableO2atnightorcontinuous" + }, + { + "@id": "bts:Prolongedexpiration-long/forcedexpiratoryphase" }, { "@id": "bts:Other" @@ -15143,18 +14532,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", + "sms:displayName": "Current Lung Cancer Symptoms", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PancreaticDuctFinalPathologyType", + "@id": "bts:LungTopography", "@type": "rdfs:Class", - "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", - "rdfs:label": "PancreaticDuctFinalPathologyType", + "rdfs:comment": "Lung PCA specific topography (not covered in previous tiers)", + "rdfs:label": "LungTopography", "rdfs:subClassOf": [ { - "@id": "bts:PancreaticCancerTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -15162,143 +14551,279 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Side-Branch" + "@id": "bts:MC-Carinabetweenrightandleftlungs(maincarina)" }, { - "@id": "bts:MainDuct" + "@id": "bts:TR-Trachea(airwaywallbetweentracheo-esophagealbifurcationandmaincarina)" }, { - "@id": "bts:Mixed" + "@id": "bts:CarinaNOS(Carinanototherwisespecified)" }, { - "@id": "bts:NotSpecified" + "@id": "bts:LUDB-Carinabetweenthelingulaandupperdivisionleftupperlobe" }, { - "@id": "bts:None" + "@id": "bts:CarinabetweenLUDBorificeandlingulaorifice" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreatic Duct Final Pathology Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", - "rdfs:label": "MelanomaTier3", - "rdfs:subClassOf": [ + "@id": "bts:LUDB-orificeairwaywallbetweenLUDBandLB3(LB1+2carinae)" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Melanoma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:LingulaorificeairwaywallbetweenLUDBandLB4/5carinae" + }, { - "@id": "bts:Component" + "@id": "bts:RMB-Rightmainstembronchus(airwaywallbetweenMC&RULcarina)" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:LMB-Leftmainstembronchus(airwaywallbetweenMC&LULcarina)" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:RLNOS(Rightlungnototherwisespecified)" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:RB1/2-Carinabetweenapicalandposteriorsegmentsrightupperlobe(CarinabetweenRB1orificeandRB2orifice)" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:RB6A/B-CarinabetweenapicalandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" + "@id": "bts:RB6A/C-CarinabetweenapicalandmedialsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:CutaneousMelanomaTumorRegressionRange" + "@id": "bts:RB6B/C-CarinabetweenmedialandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:MelanomaSpecimenClarkLevelValue" + "@id": "bts:RB7A/B-CarinabetweenmedialandlateralsubsegmentsmedialbasalsegmentRLL" }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins" + "@id": "bts:RB8/9-CarinabetweenanteriorandlateralsegmentsRLL(CarinabetweenRB8orificeandRB9orifice)" }, { - "@id": "bts:MelanomaLesionSize" + "@id": "bts:RB8A/B-CarinabetweenmedialandlateralsubsegmentsanteriorsegmentRLL" }, { - "@id": "bts:HistoryofAtypicalNevi" + "@id": "bts:RB9/10-CarinabetweenlateralandposteriorsegmentsRLL" }, { - "@id": "bts:FitzpatrickSkinTone" + "@id": "bts:RB9A/B-CarinabetweenmedialandlateralsubsegmentslateralsegmentRLL" }, { - "@id": "bts:HistoryofChronicUVExposure" + "@id": "bts:RB10A/B-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:HistoryofBlisteringSunburn" + "@id": "bts:RB10A/C-CarinabetweenmedialandapicalsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:HistoryofTanningBedUse" + "@id": "bts:RB1A/B-CarinabetweenmedialandlateralsubsegmentsapicalsegmentRUL" }, { - "@id": "bts:ImmediateFamilyHistoryMelanoma" + "@id": "bts:RB10B/C-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:MelanomaBiopsyResectionSites" + "@id": "bts:RB6-CarinaofsuperiorsegmentRLL(CarinabetweenRB6orificeandlowerportionofRLLorifice)" }, { - "@id": "bts:CutaneousMelanomaUlceration" + "@id": "bts:RB6orificeAirwaywallbetweenRB6andRB6A/B/Ccarinae" }, { - "@id": "bts:CutaneousMelanomaAdditionalFindings" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes", - "@type": "rdfs:Class", - "rdfs:comment": "Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaTumorInfiltratingLymphocytes", - "rdfs:subClassOf": [ + "@id": "bts:BronchusIntermediusBronchus(airwaywall)betweenrightupperandrightmiddlelobes" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RB1/3-CarinabetweenapicalandanteriorsegmentsRUL(CarinabetweenRB1orificeandRB3orifice)" + }, { - "@id": "bts:Absent" + "@id": "bts:RB2/3-CarinabetweenanteriorandposteriorsegmentsRUL(CarinabetweenRB2orificeandRB3orifice)" }, { - "@id": "bts:Brisk" + "@id": "bts:RB2A/B-Carinabetweenthemedialandlateralsubsegmentsoftheposteriorsegment(RUL)" }, { - "@id": "bts:Nonbrisk" + "@id": "bts:RB3A/B-CarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentRUL" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, + "@id": "bts:RB4/5-Carinabetweenthelateralandmedialsegmentsrightmiddlelobe(CarinabetweenRB4orificeandRB5orifice)" + }, + { + "@id": "bts:RB4A/B-Carinabetweenthemedialandlateralsubsegmentsofthelateralsegmentoftherightmiddlelobe" + }, + { + "@id": "bts:RB5A/B-Carinabetweenthemedialandlateralsubsegmentsofthemedialsegmentoftherightmiddlelobe" + }, + { + "@id": "bts:RULCarinaebetweenRULorificeandbronchusintermedius" + }, + { + "@id": "bts:RULorificeAirwaywallbetweenRULandRB1/RB2/RB3" + }, + { + "@id": "bts:RB1orificeApicalsegment-rightupperlobe(airwaywallbetweenRB1andRB1A/Bcarinae)" + }, + { + "@id": "bts:RB2orificePosteriorsegment-rightupperlobe(airwaywallbetweenRB2andRB2A/Bcarinae)" + }, + { + "@id": "bts:RB3orificeAnteriorsegment-rightupperlobe(airwaywallbetweenRB3andRB3A/Bcarinae)" + }, + { + "@id": "bts:RML-CarinabetweenRMLorificeandRLLorifice" + }, + { + "@id": "bts:RMLorificeAirwaywallbetweenRMLandRB4/5" + }, + { + "@id": "bts:RB4orificeLateralsegmentrightmiddlelobe(airwaywallbetweenRB4andRB4A/Bcarinae)" + }, + { + "@id": "bts:RB5orificeMedialsegmentrightmiddlelobe(airwaywallbetweenRB5andRB5A/Bcarinae)" + }, + { + "@id": "bts:RLLorificeAirwaywallbetweenRMLandRB6-10carinae" + }, + { + "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" + }, + { + "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" + }, + { + "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" + }, + { + "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" + }, + { + "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" + }, + { + "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" + }, + { + "@id": "bts:LLNOS(Leftlungnototherwisespecified)" + }, + { + "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" + }, + { + "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" + }, + { + "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" + }, + { + "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" + }, + { + "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" + }, + { + "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" + }, + { + "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" + }, + { + "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" + }, + { + "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" + }, + { + "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" + }, + { + "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" + }, + { + "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" + }, + { + "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + }, + { + "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" + }, + { + "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + }, + { + "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" + }, + { + "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" + }, + { + "@id": "bts:LB6orificeAirwaywallbetweenLB6andLB6A/Bcarinae" + }, + { + "@id": "bts:LB1A/CCarinabetweentheapicalandlateralsubsegmentsoftheapicalsegmentleftupperlobe" + }, + { + "@id": "bts:LB1B/CCarinabetweenthemedialandlateralsubsegmentsoftheapicalsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LB2A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LB2A/CCarinabetweentheapicalandmedialsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LB2B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentleftupperlobe" + }, + { + "@id": "bts:LB1+2/3Carinabetweentheapico-posteriorandanteriorsegmentsoftheleftupperlobe(CarinabetweenLB1+2orificeandLB3orifice)" + }, + { + "@id": "bts:LB3A/BCarinabetweentheapicalandlateralsubsegmentsoftheanteriorsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LULCarinabetweentheLULorificeandLLLorifice(airways)" + }, + { + "@id": "bts:LULorificeAirwaywallbetweenLULandLUDB" + }, + { + "@id": "bts:LB3orificeAnteriorsegmentleftupperlobe(airwaywallbetweenLB3andLB3A/Bcarinae)" + }, + { + "@id": "bts:LB4orificeSuperiorsegmentlingula(airwaywallbetweenLB4andLB4A/Bcarinae)" + }, + { + "@id": "bts:LB5orificeInferiorsegmentlingula(airwaywallbetweenLB5andLB5A/Bcarinae)" + }, + { + "@id": "bts:LLLorificeAirwaywallbetweenLULcarinaandLB6-10carinae" + }, + { + "@id": "bts:LB9orificeLateralsegmentleftlowerlobe(airwaywallbetweenLB9andLB9A/Bcarinae)" + }, + { + "@id": "bts:LB8orificeAnteriorsegmentleftlowerlobe(airwaywallbetweenLB8andLB8A/Bcarinae)" + }, + { + "@id": "bts:LB10orificePosteriorsegmentleftlowerlobe(airwaywallbetweenLB10andLB10A/Bcarinae)" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lung Topography", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { - "@id": "bts:CutaneousMelanomaTumorRegressionRange", + "@id": "bts:LungCancerHarboringGenomicAberrations", "@type": "rdfs:Class", - "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", - "rdfs:label": "CutaneousMelanomaTumorRegressionRange", + "rdfs:comment": "Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)", + "rdfs:label": "LungCancerHarboringGenomicAberrations", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -15306,70 +14831,232 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:G12AKRASmutation" }, { - "@id": "bts:Presentinvolving75%ormore" + "@id": "bts:G12CKRASmutation" }, { - "@id": "bts:Presentinvolvinglessthan75%" + "@id": "bts:G12DKRASmutation" + }, + { + "@id": "bts:G12RKRASmutation" + }, + { + "@id": "bts:G12SKRASmutation" + }, + { + "@id": "bts:G12VKRASmutation" + }, + { + "@id": "bts:G13DKRASmutation" + }, + { + "@id": "bts:G13RKRASmutation" + }, + { + "@id": "bts:G13CKRASmutation" + }, + { + "@id": "bts:G13AKRASmutation" + }, + { + "@id": "bts:G13VKRASmutation" + }, + { + "@id": "bts:Q61LKRASmutation" + }, + { + "@id": "bts:Q61HKRASmutation" + }, + { + "@id": "bts:A146TKRASmutation" + }, + { + "@id": "bts:G719XEGFRmutation" + }, + { + "@id": "bts:T790MEGFRmutation" + }, + { + "@id": "bts:C797SEGFRmutation" + }, + { + "@id": "bts:L858REGFRmutation" + }, + { + "@id": "bts:L861QEGFRmutation" + }, + { + "@id": "bts:Exon19deletion" + }, + { + "@id": "bts:Exon20insertion" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant1" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant2" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant3" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant4" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant5" + }, + { + "@id": "bts:V600EBRAFmutation" + }, + { + "@id": "bts:V600DBRAFmutation" + }, + { + "@id": "bts:V600KBRAFmutation" + }, + { + "@id": "bts:V600RBRAFmutation" + }, + { + "@id": "bts:K601EBRAFmutation" + }, + { + "@id": "bts:D963spliceMETmutation" + }, + { + "@id": "bts:D1010NMETmutation" + }, + { + "@id": "bts:D1010spliceMETmutation" + }, + { + "@id": "bts:Intron13mutation" + }, + { + "@id": "bts:Intron14mutation" + }, + { + "@id": "bts:Exon14mutation" + }, + { + "@id": "bts:Exon14deletion" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", + "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MelanomaSpecimenClarkLevelValue", + "@id": "bts:ColorectalCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", - "rdfs:label": "MelanomaSpecimenClarkLevelValue", + "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ColorectalCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Colorectal Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:I" + "@id": "bts:Component" }, { - "@id": "bts:II" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:III" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:IV" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:V" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:NoSourceDocumentation" + "@id": "bts:ColorectalCancerDetectionMethodType" }, { - "@id": "bts:Unknown" + "@id": "bts:HistoryofPriorColonPolyps" + }, + { + "@id": "bts:FamilyColonCancerHistoryIndicator" + }, + { + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + }, + { + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + }, + { + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + }, + { + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + }, + { + "@id": "bts:PatientColonoscopyPerformedIndicator" + }, + { + "@id": "bts:ColorectalCancerTumorBorderConfiguration" + }, + { + "@id": "bts:MLH1PromoterMethylationStatus" + }, + { + "@id": "bts:ColorectalCancerKRASIndicator" + }, + { + "@id": "bts:ColonPolypOccurenceIndicator" + }, + { + "@id": "bts:FamilyHistoryColorectalPolyp" + }, + { + "@id": "bts:ColorectalPolypNewIndicator" + }, + { + "@id": "bts:ColorectalPolypShape" + }, + { + "@id": "bts:SizeofPolypRemoved" + }, + { + "@id": "bts:ColorectalPolypCount" + }, + { + "@id": "bts:ColorectalPolypType" + }, + { + "@id": "bts:ColorectalPolypAdenomaType" } ], - "sms:displayName": "Melanoma Specimen Clark Level Value", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins", + "@id": "bts:ColorectalCancerDetectionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate presence of tumor at resection margins", - "rdfs:label": "CutaneousMelanomaSurgicalMargins", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", + "rdfs:label": "ColorectalCancerDetectionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15377,47 +15064,73 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Positive" + "@id": "bts:Fecaloccultbloodtest" }, { - "@id": "bts:Negative" + "@id": "bts:Sigmoidoscopy" + }, + { + "@id": "bts:Colonoscopy" + }, + { + "@id": "bts:Virtualcolonoscopy" + }, + { + "@id": "bts:DNAstooltest" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Cutaneous Melanoma Surgical Margins", + "sms:displayName": "Colorectal Cancer Detection Method Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MelanomaLesionSize", + "@id": "bts:HistoryofPriorColonPolyps", "@type": "rdfs:Class", - "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", - "rdfs:label": "MelanomaLesionSize", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "HistoryofPriorColonPolyps", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Melanoma Lesion Size", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "History of Prior Colon Polyps", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofAtypicalNevi", + "@id": "bts:FamilyColonCancerHistoryIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Patient has a history of atypical nevi", - "rdfs:label": "HistoryofAtypicalNevi", + "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", + "rdfs:label": "FamilyColonCancerHistoryIndicator", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15425,33 +15138,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes(morethan50)" - }, - { - "@id": "bts:Yes(lessthan50)" + "@id": "bts:Yes" }, { "@id": "bts:No" }, { - "@id": "bts:Unknown" + "@id": "bts:NotApplicable" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "History of Atypical Nevi", + "sms:displayName": "Family Colon Cancer History Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FitzpatrickSkinTone", + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The Fitzpatrick classification of skin phototype", - "rdfs:label": "FitzpatrickSkinTone", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15459,42 +15169,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:I" - }, - { - "@id": "bts:II" - }, - { - "@id": "bts:III" - }, - { - "@id": "bts:IV" + "@id": "bts:Yes" }, { - "@id": "bts:V" + "@id": "bts:No" }, { - "@id": "bts:VI" + "@id": "bts:NotApplicable" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" } ], - "sms:displayName": "Fitzpatrick Skin Tone", + "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofChronicUVExposure", + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", "@type": "rdfs:Class", - "rdfs:comment": "History of chronic UV exposure", - "rdfs:label": "HistoryofChronicUVExposure", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15502,33 +15200,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Outdooroccupational" - }, - { - "@id": "bts:Outdoorrecreational" + "@id": "bts:Beforeage50" }, { - "@id": "bts:Therapeutic" + "@id": "bts:Notbeforeage50" }, { - "@id": "bts:None" + "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "History of Chronic UV Exposure", + "sms:displayName": "Immediate Family History Endometrial Cancer", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofBlisteringSunburn", + "@id": "bts:ImmediateFamilyHistoryOvarianCancer", "@type": "rdfs:Class", - "rdfs:comment": "Patient has history of blistering sunburn", - "rdfs:label": "HistoryofBlisteringSunburn", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15536,30 +15231,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Beforeage50" }, { - "@id": "bts:No" + "@id": "bts:Notbeforeage50" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "History of Blistering Sunburn", + "sms:displayName": "Immediate Family History Ovarian Cancer", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofTanningBedUse", + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", "@type": "rdfs:Class", - "rdfs:comment": "History of tanning bed use of the patient", - "rdfs:label": "HistoryofTanningBedUse", + "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", + "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15567,36 +15262,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Never" - }, - { - "@id": "bts:Lessthan10times" + "@id": "bts:Yes-Crohn'sdisease" }, { - "@id": "bts:10-50times" + "@id": "bts:Yes-Ulcerativecolitis" }, { - "@id": "bts:50-100times" + "@id": "bts:No" }, { - "@id": "bts:Morethan100times" + "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "History of Tanning Bed Use", + "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryMelanoma", + "@id": "bts:PatientColonoscopyPerformedIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryMelanoma", + "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", + "rdfs:label": "PatientColonoscopyPerformedIndicator", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15604,27 +15296,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Beforeage50" + "@id": "bts:Yes" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:No" + }, + { + "@id": "bts:NotApplicable" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Immediate Family History Melanoma", + "sms:displayName": "Patient Colonoscopy Performed Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MelanomaBiopsyResectionSites", + "@id": "bts:ColorectalCancerTumorBorderConfiguration", "@type": "rdfs:Class", - "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", - "rdfs:label": "MelanomaBiopsyResectionSites", + "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", + "rdfs:label": "ColorectalCancerTumorBorderConfiguration", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15632,84 +15327,126 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Skinofscalp" - }, - { - "@id": "bts:Skinofeyelid" - }, - { - "@id": "bts:Skinofnose" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Skinoflip" + "@id": "bts:Infiltrating" }, { - "@id": "bts:Skinofear" + "@id": "bts:Other" }, { - "@id": "bts:Skinofneck" + "@id": "bts:Pushing" }, { - "@id": "bts:Skinofotherpartsofface" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Cancer Tumor Border Configuration", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MLH1PromoterMethylationStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", + "rdfs:label": "MLH1PromoterMethylationStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofchest" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofback" + "@id": "bts:Absent" }, { - "@id": "bts:Skinofabdomen" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Skinoftrunk-other" + "@id": "bts:NotAssessed" }, { - "@id": "bts:Skinofbreast" - }, + "@id": "bts:Present" + } + ], + "sms:displayName": "MLH1 Promoter Methylation Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalCancerKRASIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", + "rdfs:label": "ColorectalCancerKRASIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofupperlimbandshoulder" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofpalm" + "@id": "bts:Yes" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:No" }, { - "@id": "bts:Skinofsole" + "@id": "bts:Unknown" }, { - "@id": "bts:Skinofpenis" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Cancer KRAS Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColonPolypOccurenceIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "ColonPolypOccurenceIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofscrotum" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofvulva" + "@id": "bts:Yes" }, { - "@id": "bts:Skinother" + "@id": "bts:No" }, { - "@id": "bts:SkinNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Melanoma Biopsy Resection Sites", + "sms:displayName": "Colon Polyp Occurence Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaUlceration", + "@id": "bts:FamilyHistoryColorectalPolyp", "@type": "rdfs:Class", - "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaUlceration", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyHistoryColorectalPolyp", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15717,30 +15454,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:Yes" }, { - "@id": "bts:Present" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Cutaneous Melanoma Ulceration", + "sms:displayName": "Family History Colorectal Polyp", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaAdditionalFindings", + "@id": "bts:ColorectalPolypNewIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaAdditionalFindings", + "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", + "rdfs:label": "ColorectalPolypNewIndicator", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15748,67 +15485,98 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ActinicKeratosis" + "@id": "bts:Yes" }, { - "@id": "bts:NevusRemnant" + "@id": "bts:No" }, { - "@id": "bts:SolarElastosis" + "@id": "bts:Unknown" }, { - "@id": "bts:FibrosingRegression" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp New Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypShape", + "@type": "rdfs:Class", + "rdfs:comment": "Shape of polyp identified in the participant", + "rdfs:label": "ColorectalPolypShape", + "rdfs:subClassOf": [ { - "@id": "bts:NestingMelanoma" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:PagetoidSpread" + "@id": "bts:Pedunculated" }, { - "@id": "bts:VascularProliferation" + "@id": "bts:Sessile" }, { - "@id": "bts:Other" + "@id": "bts:Flat" }, { - "@id": "bts:Unknown" + "@id": "bts:Notstated" }, { "@id": "bts:NotApplicable" } ], - "sms:displayName": "Cutaneous Melanoma Additional Findings", + "sms:displayName": "Colorectal Polyp Shape", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoBirth", + "@id": "bts:SizeofPolypRemoved", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoBirth", + "rdfs:comment": "Size of the polyp removed in cm", + "rdfs:label": "SizeofPolypRemoved", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Birth", + "sms:displayName": "Size of Polyp Removed", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:CountryofResidence", + "@id": "bts:ColorectalPolypCount", "@type": "rdfs:Class", - "rdfs:comment": "Country of Residence at enrollment", - "rdfs:label": "CountryofResidence", + "rdfs:comment": "The total number of polyps detected", + "rdfs:label": "ColorectalPolypCount", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Colorectal Polyp Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypType", + "@type": "rdfs:Class", + "rdfs:comment": "Type of polyp found in the participant", + "rdfs:label": "ColorectalPolypType", + "rdfs:subClassOf": [ + { + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15816,773 +15584,883 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Afghanistan" + "@id": "bts:Adenoma" }, { - "@id": "bts:Albania" + "@id": "bts:Hyperplastic" }, { - "@id": "bts:Algeria" + "@id": "bts:Mixed" }, { - "@id": "bts:Andorra" + "@id": "bts:Papillomatous" }, { - "@id": "bts:Angola" + "@id": "bts:Normal" }, { - "@id": "bts:Anguilla" + "@id": "bts:Cancer" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:Other" }, { - "@id": "bts:Argentina" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Colorectal Polyp Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypAdenomaType", + "@type": "rdfs:Class", + "rdfs:comment": "Type of adenoma associated with the polyp", + "rdfs:label": "ColorectalPolypAdenomaType", + "rdfs:subClassOf": [ { - "@id": "bts:Armenia" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Aruba" + "@id": "bts:Tubular" }, { - "@id": "bts:Australia" + "@id": "bts:Villous" }, { - "@id": "bts:Austria" + "@id": "bts:Tubulovillous" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:Sessileserrated" }, { - "@id": "bts:Bahamas" + "@id": "bts:Traditionalserrated" }, { - "@id": "bts:Bahrain" + "@id": "bts:Serratednotspecified" }, { - "@id": "bts:Bangladesh" + "@id": "bts:Notstated" }, { - "@id": "bts:Barbados" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp Adenoma Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "BreastCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:Belarus" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Belgium" + "@id": "bts:Component" }, { - "@id": "bts:Belize" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Benin" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Bermuda" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Bhutan" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Bolivia" + "@id": "bts:BreastCarcinomaDetectionMethodType" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:BreastCarcinomaHistologyCategory" }, { - "@id": "bts:Botswana" + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" }, { - "@id": "bts:Brazil" + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" }, { - "@id": "bts:Brunei" + "@id": "bts:BreastBiopsyProcedureFindingType" }, { - "@id": "bts:Bulgaria" + "@id": "bts:BreastQuadrantSite" }, { - "@id": "bts:BurkinaFaso" + "@id": "bts:BreastCancerAssessmentTests" }, { - "@id": "bts:Burundi" + "@id": "bts:BreastCancerGenomicTestPerformed" }, { - "@id": "bts:Cambodia" + "@id": "bts:MammaprintRiskGroup" }, { - "@id": "bts:Cameroon" + "@id": "bts:OncotypeRiskGroup" }, { - "@id": "bts:Canada" + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" }, { - "@id": "bts:CapeVerde" + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:BreastCancerAllredEstrogenReceptorScore" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:PriorInvasiveBreastDisease" }, { - "@id": "bts:Chad" + "@id": "bts:BreastCarcinomaERStatusPercentageValue" }, { - "@id": "bts:Chile" + "@id": "bts:BreastCarcinomaPRStatusPercentageValue" }, { - "@id": "bts:China" + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" }, { - "@id": "bts:Colombia" + "@id": "bts:BreastCarcinomaCentromere17CopyNumber" }, { - "@id": "bts:Comoros" + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" }, { - "@id": "bts:Congo" + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" }, { - "@id": "bts:CookIslands" + "@id": "bts:BreastCarcinomaSurgicalProcedureName" }, { - "@id": "bts:CostaRica" + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:BreastCarcinomaHER2Status" }, { - "@id": "bts:Croatia" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:Cuba" + "@id": "bts:BreastCarcinomaERStainingIntensity" }, { - "@id": "bts:Curacao" + "@id": "bts:BreastCarcinomaPRStainingIntensity" }, { - "@id": "bts:Cyprus" + "@id": "bts:OncotypeScore" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:BreastImagingPerformedType" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" }, { - "@id": "bts:Denmark" + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" }, { - "@id": "bts:Djibouti" - }, + "@id": "bts:BIRADSMammographyBreastDensityCategory" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaDetectionMethodType", + "@type": "rdfs:Class", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", + "rdfs:label": "BreastCarcinomaDetectionMethodType", + "rdfs:subClassOf": [ { - "@id": "bts:Dominica" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DominicanRepublic" + "@id": "bts:ClinicalExam" }, { - "@id": "bts:Ecuador" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Egypt" + "@id": "bts:NippleDischarge" }, { - "@id": "bts:ElSalvador" + "@id": "bts:Other" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:ScreeningMammography" }, { - "@id": "bts:Eritrea" + "@id": "bts:ScreeningMRI" }, { - "@id": "bts:Estonia" + "@id": "bts:Selfexam" }, { - "@id": "bts:Eswatini" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Detection Method Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHistologyCategory", + "@type": "rdfs:Class", + "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", + "rdfs:label": "BreastCarcinomaHistologyCategory", + "rdfs:subClassOf": [ { - "@id": "bts:Ethiopia" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:Infiltratingductalcarcinoma" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:Infiltratinglobularcarcinoma" }, { - "@id": "bts:FederatedStatesofMicronesia" + "@id": "bts:InvasivemammarycarcinomaNOS" }, { - "@id": "bts:Fiji" + "@id": "bts:Invasivemixedductalandlobularcarcinoma" }, { - "@id": "bts:Finland" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Carcinoma Histology Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", + "@type": "rdfs:Class", + "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", + "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", + "rdfs:subClassOf": [ { - "@id": "bts:France" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:FrenchGuiana" + "@id": "bts:Alveolartype" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:Classicaltype" }, { - "@id": "bts:Gabon" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Gambia" + "@id": "bts:Pleomorphictype" }, { - "@id": "bts:Georgia" - }, - { - "@id": "bts:Germany" - }, - { - "@id": "bts:Ghana" - }, - { - "@id": "bts:Gibraltar" - }, - { - "@id": "bts:Greece" - }, - { - "@id": "bts:Greenland" - }, - { - "@id": "bts:Grenada" - }, - { - "@id": "bts:Guadeloupe" - }, - { - "@id": "bts:Guam" - }, - { - "@id": "bts:Guatemala" - }, - { - "@id": "bts:Guernsey" - }, - { - "@id": "bts:Guinea" - }, - { - "@id": "bts:Guinea-Bissau" - }, - { - "@id": "bts:Guyana" - }, - { - "@id": "bts:Haiti" - }, - { - "@id": "bts:HolySee" - }, - { - "@id": "bts:Honduras" - }, - { - "@id": "bts:HongKong" - }, - { - "@id": "bts:Hungary" - }, - { - "@id": "bts:Iceland" - }, - { - "@id": "bts:India" - }, - { - "@id": "bts:Indonesia" - }, - { - "@id": "bts:Iran" - }, - { - "@id": "bts:Iraq" - }, - { - "@id": "bts:Ireland" - }, - { - "@id": "bts:IsleofMan" - }, - { - "@id": "bts:Israel" - }, - { - "@id": "bts:Italy" - }, - { - "@id": "bts:Jamaica" - }, - { - "@id": "bts:Japan" - }, - { - "@id": "bts:Jersey" - }, - { - "@id": "bts:Jordan" - }, - { - "@id": "bts:Kazakhstan" - }, - { - "@id": "bts:Kenya" - }, - { - "@id": "bts:Kiribati" - }, - { - "@id": "bts:Kosovo" - }, - { - "@id": "bts:Kuwait" - }, - { - "@id": "bts:Kyrgyzstan" - }, - { - "@id": "bts:Laos" - }, - { - "@id": "bts:Latvia" - }, - { - "@id": "bts:Lebanon" - }, - { - "@id": "bts:Lesotho" - }, - { - "@id": "bts:Liberia" - }, - { - "@id": "bts:Libya" - }, - { - "@id": "bts:Liechtenstein" - }, - { - "@id": "bts:Lithuania" - }, - { - "@id": "bts:Luxembourg" - }, - { - "@id": "bts:Macau" - }, - { - "@id": "bts:Madagascar" - }, - { - "@id": "bts:Malawi" - }, - { - "@id": "bts:Malaysia" - }, - { - "@id": "bts:Maldives" - }, - { - "@id": "bts:Mali" - }, - { - "@id": "bts:Malta" - }, - { - "@id": "bts:MarshallIslands" - }, - { - "@id": "bts:Martinique" - }, - { - "@id": "bts:Mauritania" - }, - { - "@id": "bts:Mauritius" - }, - { - "@id": "bts:Mayotte" - }, - { - "@id": "bts:Mexico" - }, - { - "@id": "bts:Moldova" - }, - { - "@id": "bts:Monaco" - }, - { - "@id": "bts:Mongolia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", + "@type": "rdfs:Class", + "rdfs:comment": "The histologic subtype for the most common type of invasive breast carcinoma.", + "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", + "rdfs:subClassOf": [ { - "@id": "bts:Montenegro" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Montserrat" + "@id": "bts:Classicaltype" }, { - "@id": "bts:Morocco" + "@id": "bts:Invasivecarcinoma-typecannotbedetermined" }, { - "@id": "bts:Mozambique" + "@id": "bts:Invasivecribriformcarcinoma" }, { - "@id": "bts:Myanmar" + "@id": "bts:Invasivemicropapillarycarcinoma" }, { - "@id": "bts:Namibia" + "@id": "bts:Invasivepapillarycarcinoma" }, { - "@id": "bts:Nauru" + "@id": "bts:Invasivetubularcarcinoma" }, { - "@id": "bts:Nepal" + "@id": "bts:Medullarycarcinoma" }, { - "@id": "bts:Netherlands" + "@id": "bts:Mucinouscarcinoma" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:Tubulolobularcarcinoma" }, { - "@id": "bts:NewZealand" + "@id": "bts:Other" }, { - "@id": "bts:Nicaragua" + "@id": "bts:Unknown" }, { - "@id": "bts:Niger" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Invasive Ductal Breast Carcinoma Histologic Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastBiopsyProcedureFindingType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.", + "rdfs:label": "BreastBiopsyProcedureFindingType", + "rdfs:subClassOf": [ { - "@id": "bts:Nigeria" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Niue" + "@id": "bts:Atypicalhyperplasia" }, { - "@id": "bts:NorthKorea" + "@id": "bts:DCIS" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:LCIS" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:Cancer" }, { - "@id": "bts:Norway" + "@id": "bts:Nocancer" }, { - "@id": "bts:Oman" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Biopsy Procedure Finding Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastQuadrantSite", + "@type": "rdfs:Class", + "rdfs:comment": "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", + "rdfs:label": "BreastQuadrantSite", + "rdfs:subClassOf": [ { - "@id": "bts:Pakistan" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Palau" + "@id": "bts:Upperouterquadrant" }, { - "@id": "bts:Panama" + "@id": "bts:Lowerouterquadrant" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:Upperinnerquadrant" }, { - "@id": "bts:Paraguay" + "@id": "bts:Lowerinnerquadrant" }, { - "@id": "bts:Peru" + "@id": "bts:Central" }, { - "@id": "bts:Philippines" + "@id": "bts:Nipple" }, { - "@id": "bts:Poland" + "@id": "bts:Unknown" }, { - "@id": "bts:Portugal" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Quadrant Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAssessmentTests", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", + "rdfs:label": "BreastCancerAssessmentTests", + "rdfs:subClassOf": [ { - "@id": "bts:PuertoRico" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Qatar" + "@id": "bts:EstrogenreceptorIHC" }, { - "@id": "bts:Reunion" + "@id": "bts:ProgesteronereceptorIHC" }, { - "@id": "bts:Romania" + "@id": "bts:HER2IHC" }, { - "@id": "bts:Russia" + "@id": "bts:HER2FISH-CISH" }, { - "@id": "bts:Rwanda" + "@id": "bts:HER2FISH" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Other" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:Unknown" }, { - "@id": "bts:SaintLucia" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Cancer Assessment Tests", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerGenomicTestPerformed", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", + "rdfs:label": "BreastCancerGenomicTestPerformed", + "rdfs:subClassOf": [ { - "@id": "bts:SaintPierreandMiquelon" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:Oncotype" }, { - "@id": "bts:Samoa" + "@id": "bts:MammaPrint" }, { - "@id": "bts:SanMarino" + "@id": "bts:Other" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:Unknown" }, { - "@id": "bts:Senegal" - }, + "@id": "bts:Notperformed" + } + ], + "sms:displayName": "Breast Cancer Genomic Test Performed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MammaprintRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "rdfs:label": "MammaprintRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:Serbia" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Seychelles" + "@id": "bts:Highrisk" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:Singapore" + "@id": "bts:Lowrisk" }, { - "@id": "bts:Slovakia" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Slovenia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Mammaprint Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OncotypeRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "rdfs:label": "OncotypeRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:SolomonIslands" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Somalia" + "@id": "bts:Highrisk" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:SouthKorea" + "@id": "bts:Lowrisk" }, { - "@id": "bts:SouthSudan" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Spain" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Oncotype Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaEstrogenReceptorStatus", + "rdfs:subClassOf": [ { - "@id": "bts:SriLanka" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StateofPalestine" + "@id": "bts:Borderline" }, { - "@id": "bts:Sudan" + "@id": "bts:Equivocal" }, { - "@id": "bts:Suriname" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:Negative" }, { - "@id": "bts:Sweden" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Switzerland" + "@id": "bts:PerformedbutNotAvailable" }, { - "@id": "bts:Syria" + "@id": "bts:Positive" }, { - "@id": "bts:Taiwan" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Estrogen Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Tajikistan" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Tanzania" + "@id": "bts:Borderline" }, { - "@id": "bts:Thailand" + "@id": "bts:Equivocal" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Togo" + "@id": "bts:Negative" }, { - "@id": "bts:Tokelau" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Tonga" + "@id": "bts:PerformedbutNotAvailable" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:Positive" }, { - "@id": "bts:Tunisia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAllredEstrogenReceptorScore", + "@type": "rdfs:Class", + "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "rdfs:label": "BreastCancerAllredEstrogenReceptorScore", + "rdfs:subClassOf": [ { - "@id": "bts:Turkey" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Turkmenistan" + "@id": "bts:0" }, { - "@id": "bts:Tuvalu" + "@id": "bts:1" }, { - "@id": "bts:Uganda" + "@id": "bts:2" }, { - "@id": "bts:Ukraine" + "@id": "bts:3" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:4" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:5" }, { - "@id": "bts:UnitedStates" + "@id": "bts:6" }, { - "@id": "bts:Uruguay" + "@id": "bts:7" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:8" }, { - "@id": "bts:Vanuatu" + "@id": "bts:10" }, { - "@id": "bts:Venezuela" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Cancer Allred Estrogen Receptor Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorInvasiveBreastDisease", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate prior invasive breast condition in the participant", + "rdfs:label": "PriorInvasiveBreastDisease", + "rdfs:subClassOf": [ { - "@id": "bts:Vietnam" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:DCIS" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:LCIS" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Other" }, { - "@id": "bts:Yemen" + "@id": "bts:Unknown" }, { - "@id": "bts:Zambia" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Prior Invasive Breast Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaERStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStatusPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:Zimbabwe" + "@id": "bts:BreastCancerTier3" } ], - "sms:displayName": "Country of Residence", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma ER Status Percentage Value", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AgeIsObfuscated", + "@id": "bts:BreastCarcinomaPRStatusPercentageValue", "@type": "rdfs:Class", - "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "rdfs:label": "AgeIsObfuscated", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStatusPercentageValue", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label": "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:subClassOf": [ { - "@id": "bts:True" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaCentromere17CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", + "rdfs:label": "BreastCarcinomaCentromere17CopyNumber", + "rdfs:subClassOf": [ { - "@id": "bts:False" + "@id": "bts:BreastCancerTier3" } ], - "sms:displayName": "Age Is Obfuscated", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearOfBirth", + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label": "YearOfBirth", + "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year Of Birth", + "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OccupationDurationYears", + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", + "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Occupation Duration Years", + "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrematureAtBirth", + "@id": "bts:BreastCarcinomaSurgicalProcedureName", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", + "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "rdfs:label": "BreastCarcinomaSurgicalProcedureName", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16590,47 +16468,62 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Lumpectomy" }, { - "@id": "bts:No" + "@id": "bts:Radicalmastectomy" }, { - "@id": "bts:Unknown" + "@id": "bts:Modifiedradicalmastectomy" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" + }, + { + "@id": "bts:Partialmastectomy" + }, + { + "@id": "bts:Re-excision" + }, + { + "@id": "bts:Simplemastectomy" + }, + { + "@id": "bts:Surgerynotperformed" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Premature At Birth", + "sms:displayName": "Breast Carcinoma Surgical Procedure Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WeeksGestationatBirth", + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", + "rdfs:comment": "HER2 ratio of the participant at diagnosis", + "rdfs:label": "BreastCarcinomaHER2RatioDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Weeks Gestation at Birth", + "sms:displayName": "Breast Carcinoma HER2 Ratio Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelativewithCancerHistory", + "@id": "bts:BreastCarcinomaHER2Status", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", + "rdfs:comment": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Status", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16638,30 +16531,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-CancerHistoryRelative" + "@id": "bts:Positive" }, { - "@id": "bts:None" + "@id": "bts:Negative" }, { - "@id": "bts:Unknown" + "@id": "bts:Amplified" }, { - "@id": "bts:NotReported" + "@id": "bts:Non-amplified" + }, + { + "@id": "bts:Equivocal" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Relative with Cancer History", + "sms:displayName": "Breast Carcinoma HER2 Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SmokingExposure", + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", + "rdfs:comment": "Did the patient receive hormonal therapy for prevention of breast cancer?", + "rdfs:label": "HormoneTherapyBreastCancerPreventionIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16669,27 +16574,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-SmokingExposure" + "@id": "bts:Yes" }, { - "@id": "bts:No-SmokingExposure" + "@id": "bts:No" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", + "sms:displayName": "Hormone Therapy Breast Cancer Prevention Indicator", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholExposure", + "@id": "bts:BreastCarcinomaERStainingIntensity", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", + "rdfs:comment": "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStainingIntensity", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16697,27 +16605,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AlcoholExposure" + "@id": "bts:Strong" }, { - "@id": "bts:No-AlcoholExposure" + "@id": "bts:Moderate" }, { - "@id": "bts:NotReported" + "@id": "bts:Weak" + }, + { + "@id": "bts:Weak-Moderate" + }, + { + "@id": "bts:Moderate-Strong" + }, + { + "@id": "bts:Weak-Strong" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", + "sms:displayName": "Breast Carcinoma ER Staining Intensity", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AsbestosExposure", + "@id": "bts:BreastCarcinomaPRStainingIntensity", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", + "rdfs:comment": "Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStainingIntensity", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16725,30 +16648,59 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Strong" }, { - "@id": "bts:No" + "@id": "bts:Moderate" }, { - "@id": "bts:Unknown" + "@id": "bts:Weak" }, { - "@id": "bts:NotReported" + "@id": "bts:Weak-Moderate" + }, + { + "@id": "bts:Moderate-Strong" + }, + { + "@id": "bts:Weak-Strong" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Asbestos Exposure", + "sms:displayName": "Breast Carcinoma PR Staining Intensity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CoalDustExposure", + "@id": "bts:OncotypeScore", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", + "rdfs:comment": "OncotypeDX recurrence score", + "rdfs:label": "OncotypeScore", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Oncotype Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastImagingPerformedType", + "@type": "rdfs:Class", + "rdfs:comment": "The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).", + "rdfs:label": "BreastImagingPerformedType", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16756,27 +16708,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Mammogram" }, { - "@id": "bts:No" + "@id": "bts:Ultrasound" + }, + { + "@id": "bts:MRI" + }, + { + "@id": "bts:PET/CT" + }, + { + "@id": "bts:CT" + }, + { + "@id": "bts:Multipleimagingmodalities" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Coal Dust Exposure", + "sms:displayName": "Breast Imaging Performed Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.", + "rdfs:label": "MultifocalBreastCarcinomaPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16791,20 +16758,23 @@ }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", + "sms:displayName": "Multifocal Breast Carcinoma Present Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RadonExposure", + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", + "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.", + "rdfs:label": "MulticentricBreastCarcinomaPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16821,21 +16791,21 @@ "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Radon Exposure", + "sms:displayName": "Multicentric Breast Carcinoma Present Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RespirableCrystallineSilicaExposure", + "@id": "bts:BIRADSMammographyBreastDensityCategory", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:comment": "The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.", + "rdfs:label": "BIRADSMammographyBreastDensityCategory", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16843,5783 +16813,6015 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Predominantlyfatty" }, { - "@id": "bts:No" + "@id": "bts:Scatteredfibroglandulardensities" + }, + { + "@id": "bts:Heterogeneouslydense" + }, + { + "@id": "bts:Extremelydense" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:displayName": "BIRADS Mammography Breast Density Category", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdverseEvent", + "@id": "bts:NeuroblastomaandGliomaTier3", "@type": "rdfs:Class", - "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", - "rdfs:label": "AdverseEvent", + "rdfs:comment": "Brain cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "NeuroblastomaandGliomaTier3", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdominalDistension" - }, + "sms:displayName": "Neuroblastoma and Glioma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:AbdominalInfection" + "@id": "bts:Component" }, { - "@id": "bts:AbdominalPain" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:AbdominalSoftTissueNecrosis" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:AbducensNerveDisorder" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:AccessoryNerveDisorder" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Acidosis" + "@id": "bts:CNSTumorPrimaryAnatomicSite" }, { - "@id": "bts:AcousticNerveDisorderNOS" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:AcuteCoronarySyndrome" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:AcuteKidneyInjury" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:AdrenalInsufficiency" - }, + "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CNSTumorPrimaryAnatomicSite", + "@type": "rdfs:Class", + "rdfs:comment": "Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2", + "rdfs:label": "CNSTumorPrimaryAnatomicSite", + "rdfs:subClassOf": [ { - "@id": "bts:AdultRespiratoryDistressSyndrome" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - 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"@id": "bts:AnalStenosis" + "@id": "bts:Hippocampus" }, { - "@id": "bts:AnalUlcer" + "@id": "bts:Meninges/Dura" }, { - "@id": "bts:Anaphylaxis" - }, - { - "@id": "bts:Anemia" - }, + "@id": "bts:Otherlymphnodes" + } + ], + "sms:displayName": "CNS Tumor Primary Anatomic Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GliomaSpecificMetastasisSites", + "@type": "rdfs:Class", + "rdfs:comment": "Evidence of active brain metastasis including leptomeningeal involvement", + "rdfs:label": "GliomaSpecificMetastasisSites", + "rdfs:subClassOf": [ { - "@id": "bts:AnkleFracture" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:AnorectalInfection" + "@id": "bts:CSF" }, { - "@id": "bts:Anorexia" + "@id": "bts:Spine" }, { - "@id": "bts:Anorgasmia" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Anxiety" + "@id": "bts:Brain" }, { - "@id": "bts:AorticInjury" + "@id": "bts:Other" }, { - 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"@id": "bts:Kyphosis" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Melanoma Biopsy Resection Sites", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaUlceration", + "@type": "rdfs:Class", + "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaUlceration", + "rdfs:subClassOf": [ { - "@id": "bts:LactationDisorder" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LargeIntestinalAnastomoticLeak" + "@id": "bts:Absent" }, { - "@id": "bts:LaryngealEdema" + "@id": "bts:Present" }, { - "@id": "bts:LaryngealFistula" + "@id": "bts:Unknown" }, { - "@id": "bts:LaryngealHemorrhage" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cutaneous Melanoma Ulceration", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaAdditionalFindings", + "@type": "rdfs:Class", + "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaAdditionalFindings", + "rdfs:subClassOf": [ { - 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoBirth", + "rdfs:subClassOf": [ { - "@id": "bts:Leukoencephalopathy" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Birth", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:CountryofResidence", + "@type": "rdfs:Class", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", + "rdfs:subClassOf": [ { - "@id": "bts:LibidoDecreased" + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Afghanistan" }, { - "@id": "bts:LibidoIncreased" + "@id": "bts:Albania" }, { - "@id": "bts:LipInfection" + "@id": "bts:Algeria" }, { - "@id": "bts:LipPain" + "@id": "bts:Andorra" }, { - "@id": "bts:LipaseIncreased" + "@id": "bts:Angola" }, { - 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"@id": "bts:Nausea" + "@id": "bts:Dominica" }, { - "@id": "bts:NeckEdema" + "@id": "bts:DominicanRepublic" }, { - "@id": "bts:NeckPain" + "@id": "bts:Ecuador" }, { - "@id": "bts:NeckSoftTissueNecrosis" + "@id": "bts:Egypt" }, { - "@id": "bts:NeoplasmsBenign" + "@id": "bts:ElSalvador" }, { - "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" + "@id": "bts:EquatorialGuinea" }, { - "@id": "bts:NervousSystemDisordersOther" + "@id": "bts:Eritrea" }, { - "@id": "bts:Neuralgia" + "@id": "bts:Estonia" }, { - "@id": "bts:NeutrophilCountDecreased" + "@id": "bts:Eswatini" }, { - "@id": "bts:NightBlindness" + "@id": "bts:Ethiopia" }, { - "@id": "bts:NippleDeformity" + "@id": "bts:FalklandIslands(Malvinas)" }, { - "@id": "bts:Non-CardiacChestPain" + "@id": "bts:FaroeIslands" }, { - "@id": "bts:Nystagmus" + "@id": "bts:FederatedStatesofMicronesia" }, { - "@id": "bts:Obesity" + "@id": "bts:Fiji" }, { - "@id": "bts:ObstructionGastric" + "@id": "bts:Finland" }, { - "@id": "bts:OculomotorNerveDisorder" + "@id": "bts:France" }, { - 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"@id": "bts:PainofSkin" + "@id": "bts:Guyana" }, { - "@id": "bts:Palmar-PlantarErythrodysesthesiaSyndrome" + "@id": "bts:Haiti" }, { - "@id": "bts:Palpitations" + "@id": "bts:HolySee" }, { - "@id": "bts:PancreasInfection" + "@id": "bts:Honduras" }, { - "@id": "bts:PancreaticAnastomoticLeak" + "@id": "bts:HongKong" }, { - "@id": "bts:PancreaticDuctStenosis" + "@id": "bts:Hungary" }, { - "@id": "bts:PancreaticEnzymesDecreased" + "@id": "bts:Iceland" }, { - "@id": "bts:PancreaticFistula" + "@id": "bts:India" }, { - "@id": "bts:PancreaticHemorrhage" + "@id": "bts:Indonesia" }, { - "@id": "bts:PancreaticNecrosis" + "@id": "bts:Iran" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:Iraq" }, { - "@id": "bts:Papilledema" + "@id": "bts:Ireland" }, { - "@id": "bts:PapulopustularRash" + "@id": "bts:IsleofMan" }, { - "@id": "bts:Paresthesia" + "@id": "bts:Israel" }, { - "@id": "bts:Paronychia" + "@id": "bts:Italy" }, { - "@id": "bts:ParoxysmalAtrialTachycardia" + "@id": "bts:Jamaica" }, { - "@id": "bts:PelvicFloorMuscleWeakness" + "@id": "bts:Japan" }, { - "@id": "bts:PelvicInfection" + "@id": "bts:Jersey" }, { - "@id": "bts:PelvicPain" + "@id": "bts:Jordan" }, { - "@id": "bts:PelvicSoftTissueNecrosis" + "@id": "bts:Kazakhstan" }, { - "@id": "bts:PenileInfection" + "@id": "bts:Kenya" }, { - "@id": "bts:PenilePain" + "@id": "bts:Kiribati" }, { - "@id": "bts:PerforationBileDuct" + "@id": "bts:Kosovo" }, { - "@id": "bts:PericardialEffusion" + "@id": "bts:Kuwait" }, { - "@id": "bts:PericardialTamponade" + "@id": "bts:Kyrgyzstan" }, { - "@id": "bts:Pericarditis" + "@id": "bts:Laos" }, { - "@id": "bts:PerinealPain" + "@id": "bts:Latvia" }, { - "@id": "bts:PeriodontalDisease" + "@id": "bts:Lebanon" }, { - "@id": "bts:PeriorbitalEdema" + "@id": "bts:Lesotho" }, { - "@id": "bts:PeriorbitalInfection" + "@id": "bts:Liberia" }, { - "@id": "bts:PeripheralIschemia" + "@id": "bts:Libya" }, { - "@id": "bts:PeripheralMotorNeuropathy" + "@id": "bts:Liechtenstein" }, { - "@id": "bts:PeripheralNerveInfection" + "@id": "bts:Lithuania" }, { - "@id": "bts:PeripheralSensoryNeuropathy" + "@id": "bts:Luxembourg" }, { - 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"@id": "bts:Presyncope" + "@id": "bts:NorthernMarianaIslands" }, { - "@id": "bts:Proctitis" + "@id": "bts:Norway" }, { - "@id": "bts:ProductiveCough" + "@id": "bts:Oman" }, { - "@id": "bts:ProlapseofIntestinalStoma" + "@id": "bts:Pakistan" }, { - "@id": "bts:ProlapseofUrostomy" + "@id": "bts:Palau" }, { - "@id": "bts:ProstateInfection" + "@id": "bts:Panama" }, { - "@id": "bts:ProstaticHemorrhage" + "@id": "bts:PapuaNewGuinea" }, { - "@id": "bts:ProstaticObstruction" + "@id": "bts:Paraguay" }, { - "@id": "bts:ProstaticPain" + "@id": "bts:Peru" }, { - "@id": "bts:Proteinuria" + "@id": "bts:Philippines" }, { - "@id": "bts:Pruritus" + "@id": "bts:Poland" }, { - "@id": "bts:PsychiatricDisordersOther" + "@id": "bts:Portugal" }, { - "@id": "bts:Psychosis" + "@id": "bts:PuertoRico" }, { - "@id": "bts:PulmonaryEdema" + "@id": "bts:Qatar" }, { - "@id": "bts:PulmonaryFibrosis" + "@id": "bts:Reunion" }, { - "@id": "bts:PulmonaryFistula" + "@id": "bts:Romania" }, { - "@id": "bts:PulmonaryHypertension" + "@id": "bts:Russia" }, { - "@id": "bts:PulmonaryValveDisease" + "@id": "bts:Rwanda" }, { - "@id": "bts:Purpura" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:PyramidalTractSyndrome" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:RadiationRecallReaction(Dermatologic)" + "@id": "bts:SaintLucia" }, { - "@id": "bts:Radiculitis" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:RashAcneiform" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:RashMaculo-Papular" + "@id": "bts:Samoa" }, { - "@id": "bts:RashPustular" + "@id": "bts:SanMarino" }, { - "@id": "bts:RectalAnastomoticLeak" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:RectalFistula" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:RectalHemorrhage" + "@id": "bts:Senegal" }, { - "@id": "bts:RectalMucositis" + "@id": "bts:Serbia" }, { - "@id": "bts:RectalNecrosis" + "@id": "bts:Seychelles" }, { - "@id": "bts:RectalObstruction" + "@id": "bts:SierraLeone" }, { - "@id": "bts:RectalPain" + "@id": "bts:Singapore" }, { - "@id": "bts:RectalPerforation" + "@id": "bts:Slovakia" }, { - "@id": "bts:RectalStenosis" + "@id": "bts:Slovenia" }, { - "@id": "bts:RectalUlcer" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:RecurrentLaryngealNervePalsy" + "@id": "bts:Somalia" }, { - "@id": "bts:RenalandUrinaryDisordersOther" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:RenalCalculi" + "@id": "bts:SouthKorea" }, { - "@id": "bts:RenalColic" + "@id": "bts:SouthSudan" }, { - "@id": "bts:RenalHemorrhage" + "@id": "bts:Spain" }, { - "@id": "bts:ReproductiveSystemandBreastDisordersOther" + "@id": "bts:SriLanka" }, { - "@id": "bts:RespiratoryFailure" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:Respiratory" + "@id": "bts:Sudan" }, { - "@id": "bts:ThoracicandMediastinalDisordersOther" + "@id": "bts:Suriname" }, { - "@id": "bts:Restlessness" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:RestrictiveCardiomyopathy" + "@id": "bts:Sweden" }, { - "@id": "bts:RetinalDetachment" + "@id": "bts:Switzerland" }, { - "@id": "bts:RetinalTear" + "@id": "bts:Syria" }, { - "@id": "bts:RetinalVascularDisorder" + "@id": "bts:Taiwan" }, { - "@id": "bts:RetinoicAcidSyndrome" + "@id": "bts:Tajikistan" }, { - "@id": "bts:Retinopathy" + "@id": "bts:Tanzania" }, { - "@id": "bts:RetroperitonealHemorrhage" + "@id": "bts:Thailand" }, { - "@id": "bts:ReversiblePosteriorLeukoencephalopathySyndrome" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:RhinitisInfective" + "@id": "bts:Togo" }, { - "@id": "bts:RightVentricularDysfunction" + "@id": "bts:Tokelau" }, { - "@id": "bts:SalivaryDuctInflammation" + "@id": "bts:Tonga" }, { - "@id": "bts:SalivaryGlandFistula" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:SalivaryGlandInfection" + "@id": "bts:Tunisia" }, { - "@id": "bts:ScalpPain" + "@id": "bts:Turkey" }, { - "@id": "bts:ScleralDisorder" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:Scoliosis" + "@id": "bts:Tuvalu" }, { - "@id": "bts:ScrotalInfection" + "@id": "bts:Uganda" }, { - "@id": "bts:ScrotalPain" + "@id": "bts:Ukraine" }, { - "@id": "bts:Seizure" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:Sepsis" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:Seroma" + "@id": "bts:UnitedStates" }, { - "@id": "bts:SerumAmylaseIncreased" + "@id": "bts:Uruguay" }, { - "@id": "bts:SerumSickness" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:SickSinusSyndrome" + "@id": "bts:Vanuatu" }, { - "@id": "bts:SinusBradycardia" + "@id": "bts:Venezuela" }, { - "@id": "bts:SinusDisorder" + "@id": "bts:Vietnam" }, { - "@id": "bts:SinusPain" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:SinusTachycardia" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:Sinusitis" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:SkinandSubcutaneousTissueDisordersOther" + "@id": "bts:WesternSahara" }, { - "@id": "bts:SkinAtrophy" + "@id": "bts:Yemen" }, { - "@id": "bts:SkinHyperpigmentation" + "@id": "bts:Zambia" }, { - "@id": "bts:SkinHypopigmentation" - }, + "@id": "bts:Zimbabwe" + } + ], + "sms:displayName": "Country of Residence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeIsObfuscated", + "@type": "rdfs:Class", + "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "rdfs:label": "AgeIsObfuscated", + "rdfs:subClassOf": [ { - "@id": "bts:SkinInduration" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SkinInfection" + "@id": "bts:True" }, { - "@id": "bts:SkinUlceration" - }, + "@id": "bts:False" + } + ], + "sms:displayName": "Age Is Obfuscated", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:YearOfBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label": "YearOfBirth", + "rdfs:subClassOf": [ { - "@id": "bts:SleepApnea" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Year Of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OccupationDurationYears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of years a patient worked in a specific occupation.", + "rdfs:label": "OccupationDurationYears", + "rdfs:subClassOf": [ { - "@id": "bts:SmallIntestinalAnastomoticLeak" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Occupation Duration Years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrematureAtBirth", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", + "rdfs:label": "PrematureAtBirth", + "rdfs:subClassOf": [ { - "@id": "bts:SmallIntestinalMucositis" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SmallIntestinalObstruction" + "@id": "bts:Yes" }, { - "@id": "bts:SmallIntestinalPerforation" + "@id": "bts:No" }, { - "@id": "bts:SmallIntestinalStenosis" + "@id": "bts:Unknown" }, { - "@id": "bts:SmallIntestineInfection" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Premature At Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WeeksGestationatBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", + "rdfs:label": "WeeksGestationatBirth", + "rdfs:subClassOf": [ { - "@id": "bts:SmallIntestineUlcer" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Weeks Gestation at Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RelativewithCancerHistory", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "rdfs:label": "RelativewithCancerHistory", + "rdfs:subClassOf": [ { - "@id": "bts:Sneezing" - }, + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SocialCircumstancesOther" + "@id": "bts:Yes-CancerHistoryRelative" }, { - "@id": "bts:SoftTissueInfection" + "@id": "bts:None" }, { - "@id": "bts:SoftTissueNecrosisLowerLimb" + "@id": "bts:Unknown" }, { - "@id": "bts:SoftTissueNecrosisUpperLimb" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Relative with Cancer History", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SmokingExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if individual has smoking exposure", + "rdfs:label": "SmokingExposure", + "rdfs:subClassOf": [ { - "@id": "bts:Somnolence" + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-SmokingExposure" }, { - "@id": "bts:SoreThroat" + "@id": "bts:No-SmokingExposure" }, { - "@id": "bts:Spasticity" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Smoking Exposure", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AlcoholExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if individual has alcohol exposure", + "rdfs:label": "AlcoholExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AlcoholExposure" }, { - "@id": "bts:SpermaticCordAnastomoticLeak" + "@id": "bts:No-AlcoholExposure" }, { - "@id": "bts:SpermaticCordHemorrhage" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Alcohol Exposure", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AsbestosExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", + "rdfs:label": "AsbestosExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SpermaticCordObstruction" + "@id": "bts:No" }, { - "@id": "bts:SpinalFracture" + "@id": "bts:Unknown" }, { - "@id": "bts:SpleenDisorder" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Asbestos Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CoalDustExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", + "rdfs:label": "CoalDustExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SplenicInfection" + "@id": "bts:No" }, { - "@id": "bts:StenosisofGastrointestinalStoma" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Coal Dust Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", + "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Stevens-JohnsonSyndrome" + "@id": "bts:No" }, { - "@id": "bts:StomaSiteInfection" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Environmental Tobacco Smoke Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RadonExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", + "rdfs:label": "RadonExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:StomachPain" + "@id": "bts:No" }, { - "@id": "bts:StomalUlcer" + "@id": "bts:Unknown" }, { - "@id": "bts:Stridor" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Radon Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RespirableCrystallineSilicaExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", + "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Stroke" + "@id": "bts:No" }, { - "@id": "bts:SuddenDeathNOS" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdverseEvent", + "@type": "rdfs:Class", + "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", + "rdfs:label": "AdverseEvent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdominalDistension" }, { - "@id": "bts:SuicidalIdeation" + "@id": "bts:AbdominalInfection" }, { - "@id": "bts:SuicideAttempt" + "@id": "bts:AbdominalPain" }, { - "@id": "bts:SuperficialSoftTissueFibrosis" + "@id": "bts:AbdominalSoftTissueNecrosis" }, { - "@id": "bts:SuperficialThrombophlebitis" + "@id": "bts:AbducensNerveDisorder" }, { - "@id": "bts:SuperiorVenaCavaSyndrome" + "@id": "bts:AccessoryNerveDisorder" }, { - "@id": "bts:SupraventricularTachycardia" + "@id": "bts:Acidosis" }, { - "@id": "bts:SurgicalandMedicalProceduresOther" + "@id": "bts:AcousticNerveDisorderNOS" }, { - "@id": "bts:Syncope" + "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" }, { - "@id": "bts:Telangiectasia" + "@id": "bts:AcuteCoronarySyndrome" }, { - "@id": "bts:TesticularDisorder" + "@id": "bts:AcuteKidneyInjury" }, { - "@id": "bts:TesticularHemorrhage" + "@id": "bts:AdrenalInsufficiency" }, { - "@id": "bts:TesticularPain" + "@id": "bts:AdultRespiratoryDistressSyndrome" }, { - "@id": "bts:ThromboembolicEvent" + "@id": "bts:Agitation" }, { - "@id": "bts:ThromboticThrombocytopenicPurpura" + "@id": "bts:Akathisia" }, { - "@id": "bts:Tinnitus" + "@id": "bts:AlanineAminotransferaseIncreased" }, { - "@id": "bts:ToothDevelopmentDisorder" + "@id": "bts:AlcoholIntolerance" }, { - "@id": "bts:ToothDiscoloration" + "@id": "bts:AlkalinePhosphataseIncreased" }, { - "@id": "bts:ToothInfection" + "@id": "bts:Alkalosis" }, { - "@id": "bts:Toothache" + "@id": "bts:AllergicReaction" }, { - "@id": "bts:ToxicEpidermalNecrolysis" + "@id": "bts:AllergicRhinitis" }, { - "@id": "bts:TrachealFistula" + "@id": "bts:Alopecia" }, { - "@id": "bts:TrachealHemorrhage" + "@id": "bts:Amnesia" }, { - "@id": "bts:TrachealMucositis" + "@id": "bts:AnalFistula" }, { - "@id": "bts:TrachealObstruction" + "@id": "bts:AnalHemorrhage" }, { - "@id": "bts:TrachealStenosis" + "@id": "bts:AnalMucositis" }, { - "@id": "bts:Tracheitis" + "@id": "bts:AnalNecrosis" }, { - "@id": "bts:TracheostomySiteBleeding" + "@id": "bts:AnalPain" }, { - "@id": "bts:TransientIschemicAttacks" + "@id": "bts:AnalStenosis" }, { - "@id": "bts:TreatmentRelatedSecondaryMalignancy" + "@id": "bts:AnalUlcer" }, { - "@id": "bts:Tremor" + "@id": "bts:Anaphylaxis" }, { - "@id": "bts:TricuspidValveDisease" + "@id": "bts:Anemia" }, { - "@id": "bts:TrigeminalNerveDisorder" + "@id": "bts:AnkleFracture" }, { - "@id": "bts:Trismus" + "@id": "bts:AnorectalInfection" }, { - "@id": "bts:TumorLysisSyndrome" + "@id": "bts:Anorexia" }, { - "@id": "bts:TumorPain" + "@id": "bts:Anorgasmia" }, { - "@id": "bts:Typhlitis" + "@id": "bts:Anxiety" }, { - "@id": "bts:UnequalLimbLength" + "@id": "bts:AorticInjury" }, { - "@id": "bts:UnintendedPregnancy" + "@id": "bts:AorticValveDisease" }, { - "@id": "bts:UpperGastrointestinalHemorrhage" + "@id": "bts:Aphonia" }, { - "@id": "bts:UpperRespiratoryInfection" + "@id": "bts:Apnea" }, { - "@id": "bts:UretericAnastomoticLeak" + "@id": "bts:Appendicitis" }, { - "@id": "bts:UrethralAnastomoticLeak" + "@id": "bts:AppendicitisPerforated" }, { - "@id": "bts:UrethralInfection" + "@id": "bts:Arachnoiditis" }, { - "@id": "bts:UrinaryFistula" + "@id": "bts:ArterialInjury" }, { - "@id": "bts:UrinaryFrequency" + "@id": "bts:ArteritisInfective" }, { - "@id": "bts:UrinaryIncontinence" + "@id": "bts:Arthralgia" }, { - "@id": "bts:UrinaryRetention" + "@id": "bts:Arthritis" }, { - "@id": "bts:UrinaryTractInfection" + "@id": "bts:Ascites" }, { - "@id": "bts:UrinaryTractObstruction" + "@id": "bts:AspartateAminotransferaseIncreased" }, { - "@id": "bts:UrinaryTractPain" + "@id": "bts:Aspiration" }, { - "@id": "bts:UrinaryUrgency" + "@id": "bts:Asystole" }, { - "@id": "bts:UrineDiscoloration" + "@id": "bts:Ataxia" }, { - "@id": "bts:UrineOutputDecreased" + "@id": "bts:Atelectasis" }, { - "@id": "bts:UrostomyLeak" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:UrostomyObstruction" + "@id": "bts:AtrialFlutter" }, { - "@id": "bts:UrostomySiteBleeding" + "@id": "bts:AtrioventricularBlockComplete" }, { - "@id": "bts:UrostomyStenosis" + "@id": "bts:AtrioventricularBlockFirstDegree" }, { - "@id": "bts:Urticaria" + "@id": "bts:AutoimmuneDisorder" }, { - "@id": "bts:UterineAnastomoticLeak" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:UterineFistula" + "@id": "bts:Azoospermia" }, { - "@id": "bts:UterineHemorrhage" + "@id": "bts:BackPain" }, { - "@id": "bts:UterineInfection" + "@id": "bts:BileDuctStenosis" }, { - "@id": "bts:UterineObstruction" + "@id": "bts:BiliaryAnastomoticLeak" }, { - "@id": "bts:UterinePain" + "@id": "bts:BiliaryFistula" }, { - "@id": "bts:UterinePerforation" + "@id": "bts:BiliaryTractInfection" }, { - "@id": "bts:Uveitis" + "@id": "bts:BladderAnastomoticLeak" }, { - "@id": "bts:VaginalAnastomoticLeak" + "@id": "bts:BladderInfection" }, { - "@id": "bts:VaginalDischarge" + "@id": "bts:BladderPerforation" }, { - "@id": "bts:VaginalDryness" + "@id": "bts:BladderSpasm" }, { - "@id": "bts:VaginalFistula" + "@id": "bts:Bloating" }, { - "@id": "bts:VaginalHemorrhage" + "@id": "bts:BloodandLymphaticSystemDisordersOther" }, { - "@id": "bts:VaginalInfection" + "@id": "bts:BloodAntidiureticHormoneAbnormal" }, { - "@id": "bts:VaginalInflammation" + "@id": "bts:BloodBilirubinIncreased" }, { - "@id": "bts:VaginalObstruction" + "@id": "bts:BloodCorticotrophinDecreased" }, { - "@id": "bts:VaginalPain" + "@id": "bts:BloodGonadotrophinAbnormal" }, { - "@id": "bts:VaginalPerforation" + "@id": "bts:BloodProlactinAbnormal" }, { - "@id": "bts:VaginalStricture" + "@id": "bts:BlurredVision" }, { - "@id": "bts:Vaginismus" + "@id": "bts:BodyOdor" }, { - "@id": "bts:VagusNerveDisorder" + "@id": "bts:BoneInfection" }, { - "@id": "bts:VasDeferensAnastomoticLeak" + "@id": "bts:BoneMarrowHypocellular" }, { - "@id": "bts:VascularAccessComplication" + "@id": "bts:BonePain" }, { - "@id": "bts:VascularDisordersOther" + "@id": "bts:BrachialPlexopathy" }, { - "@id": "bts:Vasculitis" + "@id": "bts:BreastAtrophy" }, { - "@id": "bts:VasovagalReaction" + "@id": "bts:BreastInfection" }, { - "@id": "bts:VenousInjury" + "@id": "bts:BreastPain" }, { - "@id": "bts:VentricularArrhythmia" + "@id": "bts:BronchialFistula" }, { - "@id": "bts:VentricularFibrillation" + "@id": "bts:BronchialInfection" }, { - "@id": "bts:VentricularTachycardia" + "@id": "bts:BronchialObstruction" }, { - "@id": "bts:Vertigo" + "@id": "bts:BronchialStricture" }, { - "@id": "bts:VestibularDisorder" + "@id": "bts:BronchopleuralFistula" }, { - "@id": "bts:Virilization" + "@id": "bts:BronchopulmonaryHemorrhage" }, { - "@id": "bts:VisceralArterialIschemia" + "@id": "bts:Bronchospasm" }, { - "@id": "bts:VitalCapacityAbnormal" + "@id": "bts:Bruising" }, { - "@id": "bts:VitreousHemorrhage" + "@id": "bts:BullousDermatitis" }, { - "@id": "bts:VoiceAlteration" + "@id": "bts:Burn" }, { - "@id": "bts:Vomiting" + "@id": "bts:ButtockPain" }, { - "@id": "bts:VulvalInfection" + "@id": "bts:CapillaryLeakSyndrome" }, { - "@id": "bts:WateringEyes" + "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" }, { - "@id": "bts:WeightGain" + "@id": "bts:CardiacArrest" }, { - "@id": "bts:WeightLoss" + "@id": "bts:CardiacDisordersOther" }, { - "@id": "bts:Wheezing" + "@id": "bts:CardiacTroponinIIncreased" }, { - "@id": "bts:WhiteBloodCellDecreased" + "@id": "bts:CardiacTroponinTIncreased" }, { - "@id": "bts:Wolff-Parkinson-WhiteSyndrome" + "@id": "bts:Cataract" }, { - "@id": "bts:WoundComplication" + "@id": "bts:CatheterRelatedInfection" }, { - "@id": "bts:WoundDehiscence" + "@id": "bts:CD4LymphocytesDecreased" }, { - "@id": "bts:WoundInfection" + "@id": "bts:CecalHemorrhage" }, { - "@id": "bts:WristFracture" - } - ], - "sms:displayName": "Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BarrettsEsophagusGobletCellsPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", - "rdfs:label": "BarrettsEsophagusGobletCellsPresent", - "rdfs:subClassOf": [ + "@id": "bts:CecalInfection" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CentralNervousSystemNecrosis" + }, { - "@id": "bts:Yes" + "@id": "bts:CerebrospinalFluidLeakage" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Barretts Esophagus Goblet Cells Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BMI", - "@type": "rdfs:Class", - "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", - "rdfs:label": "BMI", - "rdfs:subClassOf": [ + "@id": "bts:CervicitisInfection" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "BMI", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CauseofResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", - "rdfs:label": "CauseofResponse", - "rdfs:subClassOf": [ + "@id": "bts:Cheilitis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cause of Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Comorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", - "rdfs:label": "Comorbidity", - "rdfs:subClassOf": [ + "@id": "bts:ChestPainCardiac" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ChestWallPain" + }, { - "@id": "bts:AcuteRenalFailure" + "@id": "bts:Chills" }, { - "@id": "bts:Adenocarcinoma" + "@id": "bts:Cholecystitis" }, { - "@id": "bts:AdrenocorticalInsufficiency" + "@id": "bts:CholesterolHigh" }, { - "@id": "bts:AdenomatousPolyposisColi" + "@id": "bts:ChronicKidneyDisease" }, { - "@id": "bts:Allergies" + "@id": "bts:Chylothorax" }, { - "@id": "bts:Alpha-1Antitrypsin" + "@id": "bts:CognitiveDisturbance" }, { - "@id": "bts:Anemia" + "@id": "bts:Colitis" }, { - "@id": "bts:Anxiety" + "@id": "bts:ColonicFistula" }, { - "@id": "bts:Arrhythmia" + "@id": "bts:ColonicHemorrhage" }, { - "@id": "bts:Arthritis" + "@id": "bts:ColonicObstruction" }, { - "@id": "bts:Asthma" + "@id": "bts:ColonicPerforation" }, { - "@id": "bts:AtrialFibrillation" + "@id": "bts:ColonicStenosis" }, { - "@id": "bts:AvascularNecrosis" + "@id": "bts:ColonicUlcer" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:ConcentrationImpairment" }, { - "@id": "bts:BasalCellCarcinoma" + "@id": "bts:ConductionDisorder" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:Confusion" }, { - "@id": "bts:Behcet'sDisease" + "@id": "bts:Congenital" }, { - "@id": "bts:BiliaryDisorder" + "@id": "bts:FamilialandGeneticDisordersOther" }, { - "@id": "bts:BloodClots" + "@id": "bts:Conjunctivitis" }, { - "@id": "bts:BoneFracture(s)" + "@id": "bts:ConjunctivitisInfective" }, { - "@id": "bts:Bronchitis" + "@id": "bts:Constipation" }, { - "@id": "bts:CalciumChannelBlockers" + "@id": "bts:ConstrictivePericarditis" }, { - "@id": "bts:Cancer" + "@id": "bts:CornealInfection" }, { - "@id": "bts:Cataracts" + "@id": "bts:CornealUlcer" }, { - "@id": "bts:CeliacDisease" + "@id": "bts:Cough" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:CPKIncreased" }, { - "@id": "bts:UnknownEtiology" + "@id": "bts:CranialNerveInfection" }, { - "@id": "bts:CerebrovascularDisease" + "@id": "bts:CreatinineIncreased" }, { - "@id": "bts:Cholelithiasis" + "@id": "bts:Cushingoid" }, { - "@id": "bts:ChronicRenalFailure" + "@id": "bts:CystitisNoninfective" }, { - "@id": "bts:ColonPolyps" + "@id": "bts:CytokineReleaseSyndrome" }, { - "@id": "bts:CommonVariableImmunodeficiency" + "@id": "bts:DeathNeonatal" }, { - "@id": "bts:CongestiveHeartFailure(CHF)" + "@id": "bts:DeathNOS" }, { - "@id": "bts:ConnectiveTissueDisorder" + "@id": "bts:Dehydration" }, { - "@id": "bts:COPD" + "@id": "bts:DelayedOrgasm" }, { - "@id": "bts:CoronaryArteryDisease" + "@id": "bts:DelayedPuberty" }, { - "@id": "bts:Crohn'sDisease" + "@id": "bts:Delirium" }, { - "@id": "bts:CryptogenicOrganizingPneumonia" + "@id": "bts:Delusions" }, { - "@id": "bts:DeepVeinThrombosis/Thromboembolism" + "@id": "bts:DentalCaries" }, { - "@id": "bts:Denys-DrashSyndrome" + "@id": "bts:DepressedLevelofConsciousness" }, { "@id": "bts:Depression" }, { - "@id": "bts:Diabetes" + "@id": "bts:DermatitisRadiation" }, { - "@id": "bts:TypeII" + "@id": "bts:DeviceRelatedInfection" }, { - "@id": "bts:DiabeticNeuropathy" + "@id": "bts:Diarrhea" }, { - "@id": "bts:DietControlledDiabetes" + "@id": "bts:DisseminatedIntravascularCoagulation" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:Dizziness" }, { - "@id": "bts:DVT/PE" + "@id": "bts:DryEye" }, { - "@id": "bts:Dyslipidemia" + "@id": "bts:DryMouth" }, { - "@id": "bts:Epilepsy" + "@id": "bts:DrySkin" }, { - "@id": "bts:Eczema" + "@id": "bts:DuodenalFistula" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:DuodenalHemorrhage" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:DuodenalInfection" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:DuodenalObstruction" }, { - "@id": "bts:Fibrosis" + "@id": "bts:DuodenalPerforation" }, { - "@id": "bts:GastroesophagealRefluxDisease" + "@id": "bts:DuodenalStenosis" }, { - "@id": "bts:GERD" + "@id": "bts:DuodenalUlcer" }, { - "@id": "bts:Glaucoma" + "@id": "bts:Dysarthria" }, { - "@id": "bts:GlycogenStorageDisease" + "@id": "bts:Dysesthesia" }, { - "@id": "bts:Gout" + "@id": "bts:Dysgeusia" }, { - "@id": "bts:GonadalDysfunction" + "@id": "bts:Dysmenorrhea" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:Dyspareunia" }, { - "@id": "bts:H.pyloriInfection" + "@id": "bts:Dyspepsia" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:Dysphagia" }, { - "@id": "bts:Headache" + "@id": "bts:Dysphasia" }, { - "@id": "bts:HeartDisease" + "@id": "bts:Dyspnea" }, { - "@id": "bts:Hemihypertrophy" + "@id": "bts:EarandLabyrinthDisordersOther" }, { - "@id": "bts:HemorrhagicCystitis" + "@id": "bts:EarPain" }, { - "@id": "bts:Hepatitis" + "@id": "bts:EdemaCerebral" }, { - "@id": "bts:HepatitisAInfection" + "@id": "bts:EdemaFace" }, { - "@id": "bts:HepatitisBInfection" + "@id": "bts:EdemaLimbs" }, { - "@id": "bts:HepatitisCInfection" + "@id": "bts:EdemaTrunk" }, { - "@id": "bts:ChronicHepatitis" + "@id": "bts:EjaculationDisorder" }, { - "@id": "bts:HereditaryNon-polyposisColonCancer" + "@id": "bts:EjectionFractionDecreased" }, { - "@id": "bts:Herpes" + "@id": "bts:ElectrocardiogramQTCorrectedIntervalProlonged" }, { - "@id": "bts:HighGradeLiverDysplasticNodule" + "@id": "bts:EncephalitisInfection" }, { - "@id": "bts:HIV/AIDS" + "@id": "bts:EncephalomyelitisInfection" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:Encephalopathy" }, { - "@id": "bts:HUS/TTP" + "@id": "bts:EndocarditisInfective" }, { - "@id": "bts:Hypercholesterolemia" + "@id": "bts:EndocrineDisordersOther" }, { - "@id": "bts:Hypercalcemia" + "@id": "bts:Endophthalmitis" }, { - "@id": "bts:Hyperglycemia" + "@id": "bts:Enterocolitis" }, { - "@id": "bts:Hyperlipidemia" + "@id": "bts:EnterocolitisInfectious" }, { - "@id": "bts:Hypertension" + "@id": "bts:EnterovesicalFistula" }, { - "@id": "bts:Hypospadias" + "@id": "bts:Epistaxis" }, { - "@id": "bts:Hypothyroidism" + "@id": "bts:ErectileDysfunction" }, { - "@id": "bts:InflammatoryBowelDisease" + "@id": "bts:ErythemaMultiforme" }, { - "@id": "bts:InsulinControlledDiabetes" + "@id": "bts:Erythroderma" }, { - "@id": "bts:InterstitialPneumontisorARDS" + "@id": "bts:EsophagealAnastomoticLeak" }, { - "@id": "bts:IntraductalPapillaryMucinousNeoplasm" + "@id": "bts:EsophagealFistula" }, { - "@id": "bts:IronOverload" + "@id": "bts:EsophagealHemorrhage" }, { - "@id": "bts:IschemicHeartDisease" + "@id": "bts:EsophagealInfection" }, { - "@id": "bts:ITP" + "@id": "bts:EsophagealNecrosis" }, { - "@id": "bts:JointReplacement" + "@id": "bts:EsophagealObstruction" }, { - "@id": "bts:KidneyDisease" + "@id": "bts:EsophagealPain" }, { - "@id": "bts:LiverCirrhosis(LiverDisease)" + "@id": "bts:EsophagealPerforation" }, { - "@id": "bts:LiverToxicity(Non-Infectious)" + "@id": "bts:EsophagealStenosis" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:EsophagealUlcer" }, { - "@id": "bts:LowGradeLiverDysplasticNodule" + "@id": "bts:EsophagealVaricesHemorrhage" }, { - "@id": "bts:Lupus" + "@id": "bts:Esophagitis" }, { - "@id": "bts:LynchSyndrome" + "@id": "bts:Euphoria" }, { - "@id": "bts:MAI" + "@id": "bts:Exostosis" }, { - "@id": "bts:MyastheniaGravis" + "@id": "bts:ExternalEarInflammation" }, { - "@id": "bts:MyocardialInfarction" + "@id": "bts:ExternalEarPain" }, { - "@id": "bts:NeuroendocrineTumor" + "@id": "bts:ExtraocularMuscleParesis" }, { - "@id": "bts:NonalcoholicSteatohepatitis" + "@id": "bts:ExtrapyramidalDisorder" }, { - "@id": "bts:Obesity" + "@id": "bts:EyeDisordersOther" }, { - "@id": "bts:Organtransplant(site)" + "@id": "bts:EyeInfection" }, { - "@id": "bts:Osteoarthritis" + "@id": "bts:EyePain" }, { - "@id": "bts:OsteoporosisorOsteopenia" + "@id": "bts:EyelidFunctionDisorder" }, { - "@id": "bts:Other" + "@id": "bts:FacialMuscleWeakness" }, { - "@id": "bts:OtherCancerWithin5Years" + "@id": "bts:FacialNerveDisorder" }, { - "@id": "bts:OtherNonmalignantSystemicDisease" + "@id": "bts:FacialPain" }, { - "@id": "bts:OtherPulmonaryComplications" + "@id": "bts:Fall" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:FallopianTubeAnastomoticLeak" }, { - "@id": "bts:Pain(Various)" + "@id": "bts:FallopianTubeObstruction" }, { - "@id": "bts:PepticUlcer(Ulcer)" + "@id": "bts:FallopianTubePerforation" }, { - "@id": "bts:PeripheralNeuropathy" + "@id": "bts:FallopianTubeStenosis" }, { - "@id": "bts:PeripheralVascularDisease" + "@id": "bts:FatAtrophy" }, { - "@id": "bts:Peutz-JeghersDisease" + "@id": "bts:Fatigue" }, { - "@id": "bts:PregnancyinPatientorPartner" + "@id": "bts:FebrileNeutropenia" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:FecalIncontinence" }, { - "@id": "bts:Psoriasis" + "@id": "bts:FemaleGenitalTractFistula" }, { - "@id": "bts:PulmonaryFibrosis" + "@id": "bts:FeminizationAcquired" }, { - "@id": "bts:PulmonaryHemorrhage" + "@id": "bts:FetalDeath" }, { - "@id": "bts:RenalFailure(RequiringDialysis)" + "@id": "bts:FetalGrowthRetardation" }, { - "@id": "bts:RenalDialysis" + "@id": "bts:Fever" }, { - "@id": "bts:RenalInsufficiency" + "@id": "bts:FibrinogenDecreased" }, { - "@id": "bts:RheumatologicDisease" + "@id": "bts:FibrosisDeepConnectiveTissue" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:FlankPain" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:FlashingLights" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:Flatulence" }, { - "@id": "bts:Seizure" + "@id": "bts:Floaters" }, { - "@id": "bts:Sleepapnea" + "@id": "bts:FluLikeSymptoms" }, { - "@id": "bts:Smoking" + "@id": "bts:Flushing" }, { - "@id": "bts:Steatosis" + "@id": "bts:ForcedExpiratoryVolumeDecreased" }, { - "@id": "bts:Stroke" + "@id": "bts:Fracture" }, { - "@id": "bts:TransientIschemicAttack" + "@id": "bts:GaitDisturbance" }, { - "@id": "bts:Tuberculosis" + "@id": "bts:GallbladderFistula" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:GallbladderInfection" }, { - "@id": "bts:Tyrosinemia" + "@id": "bts:GallbladderNecrosis" }, { - "@id": "bts:UlcerativeColitis" + "@id": "bts:GallbladderObstruction" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:GallbladderPain" }, { - "@id": "bts:Unknown" + "@id": "bts:GallbladderPerforation" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ComorbidityMethodofDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", - "rdfs:label": "ComorbidityMethodofDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Histology" + "@id": "bts:GastricAnastomoticLeak" }, { - "@id": "bts:Pathology" + "@id": "bts:GastricFistula" }, { - "@id": "bts:Radiology" + "@id": "bts:GastricHemorrhage" }, { - "@id": "bts:Unknown" + "@id": "bts:GastricNecrosis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity Method of Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoAdverseEvent", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoAdverseEvent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoComorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoComorbidity", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DiabetesTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", - "rdfs:label": "DiabetesTreatmentType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:GastricPerforation" + }, { - "@id": "bts:Alpha-GlucosidaseInhibitor" + "@id": "bts:GastricStenosis" }, { - "@id": "bts:Biguanide" + "@id": "bts:GastricUlcer" }, { - "@id": "bts:Diet" + "@id": "bts:Gastritis" }, { - "@id": "bts:InjectedInsulin" + "@id": "bts:GastroesophagealRefluxDisease" }, { - "@id": "bts:Insulin" + "@id": "bts:GastrointestinalAnastomoticLeak" }, { - "@id": "bts:OralHypoglycemic" + "@id": "bts:GastrointestinalDisordersOther" }, { - "@id": "bts:Sulfonylurea" + "@id": "bts:GastrointestinalFistula" }, { - "@id": "bts:Thiazolidinedione" + "@id": "bts:GastrointestinalPain" }, { - "@id": "bts:Other" + "@id": "bts:GastrointestinalStomaNecrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:Gastroparesis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Diabetes Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DiseaseResponse", - "@type": "rdfs:Class", - "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", - "rdfs:label": "DiseaseResponse", - "rdfs:subClassOf": [ + "@id": "bts:GeneralDisordersandAdministrationSiteConditionsOther" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:GeneralizedMuscleWeakness" + }, { - "@id": "bts:AJ-AdjuvantTherapy" + "@id": "bts:GenitalEdema" }, { - "@id": "bts:BED-BiochemicalEvidenceofDisease" + "@id": "bts:GGTIncreased" }, { - "@id": "bts:CPD-ClinicalProgression" + "@id": "bts:GingivalPain" }, { - "@id": "bts:CR-CompleteResponse" + "@id": "bts:Glaucoma" }, { - "@id": "bts:CRU-CompleteResponseUnconfirmed" + "@id": "bts:GlossopharyngealNerveDisorder" }, { - "@id": "bts:DU-DiseaseUnchanged" + "@id": "bts:GlucoseIntolerance" }, { - "@id": "bts:IMR-Immunoresponse" + "@id": "bts:GrowthAccelerated" }, { - "@id": "bts:IPD-Immunoprogression" + "@id": "bts:GrowthHormoneAbnormal" }, { - "@id": "bts:MR-Minimal/Marginalresponse" + "@id": "bts:GrowthSuppression" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:GumInfection" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:Gynecomastia" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:Hallucinations" }, { - "@id": "bts:NR-NoResponse" + "@id": "bts:HaptoglobinDecreased" }, { - "@id": "bts:PA-PalliativeTherapy" + "@id": "bts:HeadSoftTissueNecrosis" }, { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:Headache" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:HearingImpaired" }, { - "@id": "bts:PDM-PersistentDistantMetastasis" + "@id": "bts:HeartFailure" }, { - "@id": "bts:PLD-PersistentLocoregionalDisease" + "@id": "bts:Hematoma" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:Hematosalpinx" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:Hematuria" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:HemoglobinIncreased" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:Hemoglobinuria" }, { - "@id": "bts:RP-Response" + "@id": "bts:Hemolysis" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:HemolyticUremicSyndrome" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:HemorrhoidalHemorrhage" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:Hemorrhoids" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:HepaticFailure" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:HepaticHemorrhage" }, { - "@id": "bts:TF-TumorFree" + "@id": "bts:HepaticInfection" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:HepaticNecrosis" }, { - "@id": "bts:WT-WithTumor" + "@id": "bts:HepaticPain" }, { - "@id": "bts:Unknown" + "@id": "bts:HepatitisViral" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Disease Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DLCORefPredictivePercent", - "@type": "rdfs:Class", - "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", - "rdfs:label": "DLCORefPredictivePercent", - "rdfs:subClassOf": [ + "@id": "bts:HepatobiliaryDisordersOther" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DLCO Ref Predictive Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ECOGPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The ECOG functional performance status of the patient/participant.", - "rdfs:label": "ECOGPerformanceStatus", - "rdfs:subClassOf": [ + "@id": "bts:Hiccups" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HipFracture" + }, { - "@id": "bts:\"0\"" + "@id": "bts:Hirsutism" }, { - "@id": "bts:\"1\"" + "@id": "bts:Hoarseness" }, { - "@id": "bts:\"2\"" + "@id": "bts:HotFlashes" }, { - "@id": "bts:\"3\"" + "@id": "bts:Hydrocephalus" }, { - "@id": "bts:\"4\"" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:\"5\"" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:\"0.0\"" + "@id": "bts:Hyperhidrosis" }, { - "@id": "bts:\"1.0\"" + "@id": "bts:Hyperkalemia" }, { - "@id": "bts:\"2.0\"" + "@id": "bts:Hypermagnesemia" }, { - "@id": "bts:\"3.0\"" + "@id": "bts:Hypernatremia" }, { - "@id": "bts:\"4.0\"" + "@id": "bts:Hyperparathyroidism" }, { - "@id": "bts:\"5.0\"" + "@id": "bts:Hypersomnia" }, { - "@id": "bts:Unknown" + "@id": "bts:Hypertension" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "ECOG Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", - "rdfs:label": "FEV1FVCPostBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hyperthyroidism" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 FVC Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", - "rdfs:label": "FEV1FVCPreBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hypertrichosis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV 1 FVC Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", - "rdfs:label": "FEV1RefPostBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hypertriglyceridemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", - "rdfs:label": "FEV1RefPreBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hyperuricemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Height", - "@type": "rdfs:Class", - "rdfs:comment": "The height of the patient in centimeters.", - "rdfs:label": "Height", - "rdfs:subClassOf": [ + "@id": "bts:Hypoalbuminemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Height", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "HepatitisSustainedVirologicalResponse", - "rdfs:subClassOf": [ + "@id": "bts:Hypocalcemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HypoglossalNerveDisorder" + }, { - "@id": "bts:Yes" + "@id": "bts:Hypoglycemia" }, { - "@id": "bts:No" + "@id": "bts:Hypohidrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:Hypokalemia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hepatitis Sustained Virological Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HPVPositiveType", - "@type": "rdfs:Class", - "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", - "rdfs:label": "HPVPositiveType", - "rdfs:subClassOf": [ + "@id": "bts:Hypomagnesemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hyponatremia" + }, { - "@id": "bts:\"16\"" + "@id": "bts:Hypoparathyroidism" }, { - "@id": "bts:\"18\"" + "@id": "bts:Hypophosphatemia" }, { - "@id": "bts:\"26\"" + "@id": "bts:Hypotension" }, { - "@id": "bts:\"31\"" + "@id": "bts:Hypothermia" }, { - "@id": "bts:\"33\"" + "@id": "bts:Hypothyroidism" }, { - "@id": "bts:\"35\"" + "@id": "bts:Hypoxia" }, { - "@id": "bts:\"39\"" + "@id": "bts:IlealFistula" }, { - "@id": "bts:\"45\"" + "@id": "bts:IlealHemorrhage" }, { - "@id": "bts:\"51\"" + "@id": "bts:IlealObstruction" }, { - "@id": "bts:\"52\"" + "@id": "bts:IlealPerforation" }, { - "@id": "bts:\"53\"" + "@id": "bts:IlealStenosis" }, { - "@id": "bts:\"56\"" + "@id": "bts:IlealUlcer" }, { - "@id": "bts:\"58\"" + "@id": "bts:Ileus" }, { - "@id": "bts:\"59\"" + "@id": "bts:ImmuneSystemDisordersOther" }, { - "@id": "bts:\"63\"" + "@id": "bts:InfectionsandInfestationsOther" }, { - "@id": "bts:\"66\"" + "@id": "bts:InfectiveMyositis" }, { - "@id": "bts:\"68\"" + "@id": "bts:InfusionRelatedReaction" }, { - "@id": "bts:\"70\"" + "@id": "bts:InfusionSiteExtravasation" }, { - "@id": "bts:\"73\"" + "@id": "bts:InjectionSiteReaction" }, { - "@id": "bts:\"82\"" + "@id": "bts:InjurytoCarotidArtery" }, { - "@id": "bts:Other" + "@id": "bts:InjurytoInferiorVenaCava" }, { - "@id": "bts:Unknown" + "@id": "bts:InjurytoJugularVein" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "HPV Positive Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KarnofskyPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", - "rdfs:label": "KarnofskyPerformanceStatus", - "rdfs:subClassOf": [ + "@id": "bts:InjurytoSuperiorVenaCava" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Injury" + }, { - "@id": "bts:\"0\"" + "@id": "bts:PoisoningandProceduralComplicationsOther" }, { - "@id": "bts:\"10\"" + "@id": "bts:INRIncreased" }, { - "@id": "bts:\"20\"" + "@id": "bts:Insomnia" }, { - "@id": "bts:\"30\"" + "@id": "bts:IntestinalStomaLeak" }, { - "@id": "bts:\"40\"" + "@id": "bts:IntestinalStomaObstruction" }, { - "@id": "bts:\"50\"" + "@id": "bts:IntestinalStomaSiteBleeding" }, { - "@id": "bts:\"60\"" + "@id": "bts:Intra-AbdominalHemorrhage" }, { - "@id": "bts:\"70\"" + "@id": "bts:IntracranialHemorrhage" }, { - "@id": "bts:\"80\"" + "@id": "bts:IntraoperativeArterialInjury" }, { - "@id": "bts:\"90\"" + "@id": "bts:IntraoperativeBreastInjury" }, { - "@id": "bts:\"100\"" + "@id": "bts:IntraoperativeCardiacInjury" }, { - "@id": "bts:Unknown" + "@id": "bts:IntraoperativeEarInjury" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Karnofsky Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MenopauseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's menopause status.", - "rdfs:label": "MenopauseStatus", - "rdfs:subClassOf": [ + "@id": "bts:IntraoperativeEndocrineInjury" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IntraoperativeGastrointestinalInjury" + }, { - "@id": "bts:Premenopausal" + "@id": "bts:IntraoperativeHeadandNeckInjury" }, { - "@id": "bts:Perimenopausal" + "@id": "bts:IntraoperativeHemorrhage" }, { - "@id": "bts:Postmenopausal" + "@id": "bts:IntraoperativeHepatobiliaryInjury" }, { - "@id": "bts:Unknown" + "@id": "bts:IntraoperativeMusculoskeletalInjury" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Menopause Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreatitisOnsetYear", - "@type": "rdfs:Class", - "rdfs:comment": "Date of onset of pancreatitis.", - "rdfs:label": "PancreatitisOnsetYear", - "rdfs:subClassOf": [ + "@id": "bts:IntraoperativeNeurologicalInjury" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pancreatitis Onset Year", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:RefluxTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", - "rdfs:label": "RefluxTreatmentType", - "rdfs:subClassOf": [ + "@id": "bts:IntraoperativeOcularInjury" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IntraoperativeRenalInjury" + }, { - "@id": "bts:Antacids" + "@id": "bts:IntraoperativeReproductiveTractInjury" }, { - "@id": "bts:H2Blockers" + "@id": "bts:IntraoperativeRespiratoryInjury" }, { - "@id": "bts:MedicallyTreated" + "@id": "bts:IntraoperativeSkinInjury" }, { - "@id": "bts:NoTreatment" + "@id": "bts:IntraoperativeSplenicInjury" }, { - "@id": "bts:NotApplicable" + "@id": "bts:IntraoperativeUrinaryInjury" }, { - "@id": "bts:NotReported" + "@id": "bts:IntraoperativeVenousInjury" }, { - "@id": "bts:ProtonPumpInhibitors" + "@id": "bts:InvestigationsOther" }, { - "@id": "bts:SurgicallyTreated" + "@id": "bts:IronOverload" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Reflux Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RiskFactor", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactor", - "rdfs:subClassOf": [ + "@id": "bts:IrregularMenstruation" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Irritability" + }, { - "@id": "bts:AlcoholConsumption" + "@id": "bts:IschemiaCerebrovascular" }, { - "@id": "bts:AlcoholicLiverDisease" + "@id": "bts:IVthNerveDisorder" }, { - "@id": "bts:AllergyAnimalNOS" + "@id": "bts:JejunalFistula" }, { - "@id": "bts:AllergyAnt" + "@id": "bts:JejunalHemorrhage" }, { - "@id": "bts:AllergyBee" + "@id": "bts:JejunalObstruction" }, { - "@id": "bts:AllergyCat" + "@id": "bts:JejunalPerforation" }, { - "@id": "bts:AllergyDairyorLactose" + "@id": "bts:JejunalStenosis" }, { - "@id": "bts:AllergyDog" + "@id": "bts:JejunalUlcer" }, { - "@id": "bts:AllergyEggs" + "@id": "bts:JointEffusion" }, { - "@id": "bts:AllergyFoodNOS" + "@id": "bts:JointInfection" }, { - "@id": "bts:AllergyFruit" + "@id": "bts:JointRangeofMotionDecreased" }, { - "@id": "bts:AllergyMeat" + "@id": "bts:JointRangeofMotionDecreasedCervicalSpine" }, { - "@id": "bts:AllergyMoldorDust" + "@id": "bts:JointRangeofMotionDecreasedLumbarSpine" }, { - "@id": "bts:AllergyNuts" + "@id": "bts:Keratitis" }, { - "@id": "bts:AllergyProcessedFoods" + "@id": "bts:KidneyAnastomoticLeak" }, { - "@id": "bts:AllergySeafood" + "@id": "bts:KidneyInfection" }, { - "@id": "bts:AllergyWasp" + "@id": "bts:Kyphosis" }, { - "@id": "bts:Alpha-1AntitrypsinDeficiency" + "@id": "bts:LactationDisorder" }, { - "@id": "bts:AutoimmuneAtrophicChronicGastritis" + "@id": "bts:LargeIntestinalAnastomoticLeak" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:LaryngealEdema" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:LaryngealFistula" }, { - "@id": "bts:Behcet'sDisease" + "@id": "bts:LaryngealHemorrhage" }, { - "@id": "bts:Cancer" + "@id": "bts:LaryngealInflammation" }, { - "@id": "bts:Cholelithiasis" + "@id": "bts:LaryngealMucositis" }, { - "@id": "bts:ChronicHepatitis" + "@id": "bts:LaryngealObstruction" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:LaryngealStenosis" }, { - "@id": "bts:ColonPolyps" + "@id": "bts:Laryngitis" }, { - "@id": "bts:Commonvariableimmunedeficiency(CVID)" + "@id": "bts:LaryngopharyngealDysesthesia" }, { - "@id": "bts:Denys-DrashSyndrome" + "@id": "bts:Laryngospasm" }, { - "@id": "bts:DiabetesNOS" + "@id": "bts:LeftVentricularSystolicDysfunction" }, { - "@id": "bts:DiabetesTypeI" + "@id": "bts:Lethargy" }, { - "@id": "bts:DiabetesTypeII" + "@id": "bts:LeukemiaSecondarytoOncologyChemotherapy" }, { - "@id": "bts:Diet" + "@id": "bts:Leukocytosis" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:Leukoencephalopathy" }, { - "@id": "bts:Endometriosis" + "@id": "bts:LibidoDecreased" }, { - "@id": "bts:Endosalpingiosis" + "@id": "bts:LibidoIncreased" }, { - "@id": "bts:Eczema" + "@id": "bts:LipInfection" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:LipPain" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:LipaseIncreased" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:Lipohypertrophy" }, { - "@id": "bts:Fibrosis" + "@id": "bts:LocalizedEdema" }, { - "@id": "bts:GastricPolyp(s)" + "@id": "bts:Lordosis" }, { - "@id": "bts:Gilbert'sSyndrome" + "@id": "bts:LowerGastrointestinalHemorrhage" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:LungInfection" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:LymphGlandInfection" }, { - "@id": "bts:HayFever" + "@id": "bts:LymphLeakage" }, { - "@id": "bts:Headache" + "@id": "bts:LymphNodePain" }, { - "@id": "bts:HelicobacterPylori-AssociatedGastritis" + "@id": "bts:Lymphedema" }, { - "@id": "bts:HematologicDisorderNOS" + "@id": "bts:Lymphocele" }, { - "@id": "bts:Hemihypertrophy" + "@id": "bts:LymphocyteCountDecreased" }, { - "@id": "bts:Hemochromatosis" + "@id": "bts:LymphocyteCountIncreased" }, { - "@id": "bts:HepaticEncephalopathy" + "@id": "bts:Malabsorption" }, { - "@id": "bts:HepatitisBInfection" + "@id": "bts:Malaise" }, { - "@id": "bts:HepatitisCInfection" + "@id": "bts:Mania" }, { - "@id": "bts:HepatitisNOS" + "@id": "bts:MediastinalHemorrhage" }, { - "@id": "bts:HighGradeDysplasia" + "@id": "bts:MediastinalInfection" }, { - "@id": "bts:HIV" + "@id": "bts:MemoryImpairment" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:Meningismus" }, { - "@id": "bts:Hypospadias" + "@id": "bts:Meningitis" }, { - "@id": "bts:IntestinalMetaplasia" + "@id": "bts:Menopause" }, { - "@id": "bts:IronOverload" + "@id": "bts:Menorrhagia" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:MetabolismandNutritionDisordersOther" }, { - "@id": "bts:LowGradeDysplasia" + "@id": "bts:MiddleEarInflammation" }, { - "@id": "bts:LymphocyticThyroiditis" + "@id": "bts:MitralValveDisease" }, { - "@id": "bts:LynchSyndrome" + "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" }, { - "@id": "bts:MyastheniaGravis" + "@id": "bts:MobitzTypeI" }, { - "@id": "bts:NonalcoholicFattyLiverDisease" + "@id": "bts:MovementsInvoluntary" }, { - "@id": "bts:NonalcoholicSteatohepatitis" + "@id": "bts:MucosalInfection" }, { - "@id": "bts:Obesity" + "@id": "bts:MucositisOral" }, { - "@id": "bts:OralContraceptives" + "@id": "bts:Multi-OrganFailure" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:MuscleWeaknessLeft-Sided" }, { - "@id": "bts:ParasiticDiseaseofBiliaryTract" + "@id": "bts:MuscleWeaknessLowerLimb" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:MuscleWeaknessRight-Sided" }, { - "@id": "bts:RecurrentPyogenicCholangitis" + "@id": "bts:MuscleWeaknessTrunk" }, { - "@id": "bts:RefluxDisease" + "@id": "bts:MuscleWeaknessUpperLimb" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:MusculoskeletalandConnectiveTissueDisordersOther" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:MusculoskeletalDeformity" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:Myalgia" }, { - "@id": "bts:Seizure" + "@id": "bts:Myelitis" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:MyelodysplasticSyndrome" }, { - "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:Steatosis" + "@id": "bts:Myocarditis" }, { - "@id": "bts:Tattoo" + "@id": "bts:Myositis" }, { - "@id": "bts:ThyroidNodularHyperplasia" + "@id": "bts:NailDiscoloration" }, { - "@id": "bts:TobaccoNOS" + "@id": "bts:NailInfection" }, { - "@id": "bts:TobaccoSmokeless" + "@id": "bts:NailLoss" }, { - "@id": "bts:TobaccoSmoking" + "@id": "bts:NailRidging" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:NasalCongestion" }, { - "@id": "bts:UndescendedTestis" + "@id": "bts:Nausea" }, { - "@id": "bts:VisionChanges" + "@id": "bts:NeckEdema" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:NeckPain" }, { - "@id": "bts:Unknown" + "@id": "bts:NeckSoftTissueNecrosis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Risk Factor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RiskFactorTreatment", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactorTreatment", - "rdfs:subClassOf": [ + "@id": "bts:NeoplasmsBenign" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" + }, { - "@id": "bts:Yes" + "@id": "bts:NervousSystemDisordersOther" }, { - "@id": "bts:No" + "@id": "bts:Neuralgia" }, { - "@id": "bts:Unknown" + "@id": "bts:NeutrophilCountDecreased" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Risk Factor Treatment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ViralHepatitisSerologies", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", - "rdfs:label": "ViralHepatitisSerologies", - "rdfs:subClassOf": [ + "@id": "bts:NightBlindness" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:NippleDeformity" + }, { - "@id": "bts:HBVCoreAntibody" + "@id": "bts:Non-CardiacChestPain" }, { - "@id": "bts:HBVDNA" + "@id": "bts:Nystagmus" }, { - "@id": "bts:HBVGenotype" + "@id": "bts:Obesity" }, { - "@id": "bts:HBVSurfaceAntibody" + "@id": "bts:ObstructionGastric" }, { - "@id": "bts:HCVGenotype" + "@id": "bts:OculomotorNerveDisorder" }, { - "@id": "bts:HepatitisBSurfaceAntigen" + "@id": "bts:OlfactoryNerveDisorder" }, { - "@id": "bts:HepatitisCAntibody" + "@id": "bts:Oligospermia" }, { - "@id": "bts:HepatitisCVirusRNA" + "@id": "bts:OpticNerveDisorder" }, { - "@id": "bts:Unknown" + "@id": "bts:OralCavityFistula" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Viral Hepatitis Serologies", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Weight", - "@type": "rdfs:Class", - "rdfs:comment": "The weight of the patient measured in kilograms.", - "rdfs:label": "Weight", - "rdfs:subClassOf": [ + "@id": "bts:OralDysesthesia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdverseEventGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "AdverseEventGrade", - "rdfs:subClassOf": [ + "@id": "bts:OralHemorrhage" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:OralPain" + }, { - "@id": "bts:Grade1" + "@id": "bts:OsteonecrosisofJaw" }, { - "@id": "bts:Grade2" + "@id": "bts:Osteoporosis" }, { - "@id": "bts:Grade3" + "@id": "bts:OtitisExterna" }, { - "@id": "bts:Grade4" + "@id": "bts:OtitisMedia" }, { - "@id": "bts:Grade5" - } - ], - "sms:displayName": "Adverse Event Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AIDSRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", - "rdfs:label": "AIDSRiskFactors", - "rdfs:subClassOf": [ + "@id": "bts:OvarianHemorrhage" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:OvarianInfection" + }, { - "@id": "bts:Candidiasis" + "@id": "bts:OvarianRupture" }, { - "@id": "bts:Coccidioidomycosis" + "@id": "bts:OvulationPain" }, { - "@id": "bts:Cryptococcosis" + "@id": "bts:Pain" }, { - "@id": "bts:Cytomegalovirus" + "@id": "bts:PaininExtremity" }, { - "@id": "bts:Encephalopathy" + "@id": "bts:PainofSkin" }, { - "@id": "bts:HerpesSimplexVirus" + "@id": "bts:Palmar-PlantarErythrodysesthesiaSyndrome" }, { - "@id": "bts:Histoplasmosis" + "@id": "bts:Palpitations" }, { - "@id": "bts:Isosporiasis" + "@id": "bts:PancreasInfection" }, { - "@id": "bts:MycobacteriumaviumComplex" + "@id": "bts:PancreaticAnastomoticLeak" }, { - "@id": "bts:Mycobacteriumtuberculosis" + "@id": "bts:PancreaticDuctStenosis" }, { - "@id": "bts:Mycobacterium" + "@id": "bts:PancreaticEnzymesDecreased" }, { - "@id": "bts:NOS" + "@id": "bts:PancreaticFistula" }, { - "@id": "bts:Nocardiosis" + "@id": "bts:PancreaticHemorrhage" }, { - "@id": "bts:PneumocystisPneumonia" + "@id": "bts:PancreaticNecrosis" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" + "@id": "bts:Papilledema" }, { - "@id": "bts:SalmonellaSepticemia" + "@id": "bts:PapulopustularRash" }, { - "@id": "bts:Toxoplasmosis" + "@id": "bts:Paresthesia" }, { - "@id": "bts:WastingSyndrome" - } - ], - "sms:displayName": "AIDS Risk Factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BodySurfaceArea", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", - "rdfs:label": "BodySurfaceArea", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Body Surface Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CD4Count", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", - "rdfs:label": "CD4Count", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "CD4 Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CDCHIVRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", - "rdfs:label": "CDCHIVRiskFactors", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Hemophiliac" - }, - { - "@id": "bts:HeterosexualContact" - }, - { - "@id": "bts:HomosexualContact" - }, - { - "@id": "bts:IntravenousDrugUser" - }, - { - "@id": "bts:None" + "@id": "bts:Paronychia" }, { - "@id": "bts:TransfusionRecipient" + "@id": "bts:ParoxysmalAtrialTachycardia" }, { - "@id": "bts:Unknown" + "@id": "bts:PelvicFloorMuscleWeakness" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "CDC HIV Risk Factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoImaging", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoImaging", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Imaging", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:EvidenceofRecurrenceType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", - "rdfs:label": "EvidenceofRecurrenceType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BiopsywithHistologicConfirmation" + "@id": "bts:PelvicInfection" }, { - "@id": "bts:ConvincingImageSource" + "@id": "bts:PelvicPain" }, { - "@id": "bts:PositiveBiomarkers" - } - ], - "sms:displayName": "Evidence of Recurrence Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HAARTTreatmentIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", - "rdfs:label": "HAARTTreatmentIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:PelvicSoftTissueNecrosis" }, { - "@id": "bts:No" + "@id": "bts:PenileInfection" }, { - "@id": "bts:Unknown" + "@id": "bts:PenilePain" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "HAART Treatment Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HIVViralLoad", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", - "rdfs:label": "HIVViralLoad", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HIV Viral Load", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HormonalContraceptiveUse", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", - "rdfs:label": "HormonalContraceptiveUse", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CurrentUser" + "@id": "bts:PerforationBileDuct" }, { - "@id": "bts:FormerUser" + "@id": "bts:PericardialEffusion" }, { - "@id": "bts:NeverUsed" + "@id": "bts:PericardialTamponade" }, { - "@id": "bts:Unknown" + "@id": "bts:Pericarditis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hormonal Contraceptive Use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HysterectomyMarginsInvolved", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", - "rdfs:label": "HysterectomyMarginsInvolved", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bladder" + "@id": "bts:PerinealPain" }, { - "@id": "bts:MacroscopicParametrium" + "@id": "bts:PeriodontalDisease" }, { - "@id": "bts:MicroscopicParametrium" + "@id": "bts:PeriorbitalEdema" }, { - "@id": "bts:None" + "@id": "bts:PeriorbitalInfection" }, { - "@id": "bts:Vagina" + "@id": "bts:PeripheralIschemia" }, { - "@id": "bts:Unknown" + "@id": "bts:PeripheralMotorNeuropathy" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hysterectomy Margins Involved", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HysterectomyType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", - "rdfs:label": "HysterectomyType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:HysterectomyNOS" + "@id": "bts:PeripheralNerveInfection" }, { - "@id": "bts:Notperformed" + "@id": "bts:PeripheralSensoryNeuropathy" }, { - "@id": "bts:RadicalHysterectomy" + "@id": "bts:PeritonealInfection" }, { - "@id": "bts:SimpleHysterectomy" + "@id": "bts:PeritonealNecrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:PersonalityChange" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hysterectomy Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingResult", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", - "rdfs:label": "ImagingResult", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Positive" + "@id": "bts:PhantomPain" }, { - "@id": "bts:Indeterminate" + "@id": "bts:PharyngealAnastomoticLeak" }, { - "@id": "bts:Negative" + "@id": "bts:PharyngealFistula" }, { - "@id": "bts:NotPerformed" + "@id": "bts:PharyngealHemorrhage" }, { - "@id": "bts:Unknown" + "@id": "bts:PharyngealMucositis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Imaging Result", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", - "rdfs:label": "ImagingType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - 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"@id": "bts:LowerlimbNOS" + "@id": "bts:Typhlitis" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:UnequalLimbLength" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:UnintendedPregnancy" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:UpperGastrointestinalHemorrhage" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:UpperRespiratoryInfection" }, { - "@id": "bts:LungNOS" + "@id": "bts:UretericAnastomoticLeak" }, { - "@id": "bts:LymphnodeNOS" + "@id": "bts:UrethralAnastomoticLeak" }, { - "@id": "bts:Lymphnodesofaxillaorarm" + "@id": "bts:UrethralInfection" }, { - "@id": "bts:Lymphnodesofheadfaceandneck" + "@id": "bts:UrinaryFistula" }, { - "@id": "bts:Lymphnodesofinguinalregionorleg" + "@id": "bts:UrinaryFrequency" }, { - "@id": "bts:Lymphnodesofmultipleregions" + "@id": "bts:UrinaryIncontinence" }, { - "@id": "bts:Mainbronchus" + "@id": "bts:UrinaryRetention" }, { - "@id": "bts:MajorsalivaryglandNOS" + "@id": "bts:UrinaryTractInfection" }, { - "@id": "bts:MalegenitalorgansNOS" + "@id": "bts:UrinaryTractObstruction" }, { - 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"@id": "bts:NasopharynxNOS" + "@id": "bts:UterinePerforation" }, { - "@id": "bts:NervoussystemNOS" + "@id": "bts:Uveitis" }, { - "@id": "bts:Nipple" + "@id": "bts:VaginalAnastomoticLeak" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:VaginalDischarge" }, { - "@id": "bts:Olfactorynerve" + "@id": "bts:VaginalDryness" }, { - "@id": "bts:Opticnerve" + "@id": "bts:VaginalFistula" }, { - "@id": "bts:OrbitNOS" + "@id": "bts:VaginalHemorrhage" }, { - "@id": "bts:OropharynxNOS" + "@id": "bts:VaginalInfection" }, { - "@id": "bts:Otherill-definedsites" + "@id": "bts:VaginalInflammation" }, { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + "@id": "bts:VaginalObstruction" }, { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + "@id": "bts:VaginalPain" }, { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:VaginalPerforation" }, { - "@id": "bts:Ovary" + "@id": "bts:VaginalStricture" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:Vaginismus" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:VagusNerveDisorder" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:VasDeferensAnastomoticLeak" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id": "bts:VascularAccessComplication" }, { - "@id": "bts:Overlappinglesionofbrain" + "@id": "bts:VascularDisordersOther" }, { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + "@id": "bts:Vasculitis" }, { - "@id": "bts:Overlappinglesionofbreast" + "@id": "bts:VasovagalReaction" }, { - "@id": "bts:Overlappinglesionofcervixuteri" + "@id": "bts:VenousInjury" }, { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:VentricularArrhythmia" }, { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + "@id": "bts:VentricularFibrillation" }, { - "@id": "bts:Overlappinglesionofcorpusuteri" + "@id": "bts:VentricularTachycardia" }, { - "@id": "bts:Overlappinglesionofdigestivesystem" + "@id": "bts:Vertigo" }, { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + "@id": "bts:VestibularDisorder" }, { - "@id": "bts:Overlappinglesionofesophagus" + "@id": "bts:Virilization" }, { - "@id": "bts:Overlappinglesionofeyeandadnexa" + "@id": "bts:VisceralArterialIschemia" }, { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" + "@id": "bts:VitalCapacityAbnormal" }, { - "@id": "bts:Overlappinglesionoffloorofmouth" + "@id": "bts:VitreousHemorrhage" }, { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + "@id": "bts:VoiceAlteration" }, { - "@id": "bts:Overlappinglesionofhypopharynx" + "@id": "bts:Vomiting" }, { - "@id": "bts:Overlappinglesionofill-definedsites" + "@id": "bts:VulvalInfection" }, { - "@id": "bts:Overlappinglesionoflarynx" + "@id": "bts:WateringEyes" }, { - "@id": "bts:Overlappinglesionoflip" + "@id": "bts:WeightGain" }, { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + "@id": "bts:WeightLoss" }, { - "@id": "bts:Overlappinglesionoflung" + "@id": "bts:Wheezing" }, { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" + "@id": "bts:WhiteBloodCellDecreased" }, { - "@id": "bts:Overlappinglesionofmalegenitalorgans" + "@id": "bts:Wolff-Parkinson-WhiteSyndrome" }, { - "@id": "bts:Overlappinglesionofnasopharynx" + "@id": "bts:WoundComplication" }, { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + "@id": "bts:WoundDehiscence" }, { - "@id": "bts:Overlappinglesionofpalate" + "@id": "bts:WoundInfection" }, { - "@id": "bts:Overlappinglesionofpancreas" - }, + "@id": "bts:WristFracture" + } + ], + "sms:displayName": "Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", + "rdfs:label": "BarrettsEsophagusGobletCellsPresent", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofpenis" + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + "@id": "bts:No" + } + ], + "sms:displayName": "Barretts Esophagus Goblet Cells Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BMI", + "@type": "rdfs:Class", + "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", + "rdfs:label": "BMI", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "BMI", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CauseofResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", + "rdfs:label": "CauseofResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cause of Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Comorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", + "rdfs:label": "Comorbidity", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AcuteRenalFailure" }, { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + "@id": "bts:Adenocarcinoma" }, { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + "@id": "bts:AdrenocorticalInsufficiency" }, { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + "@id": "bts:AdenomatousPolyposisColi" }, { - "@id": "bts:Overlappinglesionofskin" + "@id": "bts:Allergies" }, { - "@id": "bts:Overlappinglesionofsmallintestine" + "@id": "bts:Alpha-1Antitrypsin" }, { - "@id": "bts:Overlappinglesionofstomach" + "@id": "bts:Anemia" }, { - "@id": "bts:Overlappinglesionoftongue" + "@id": "bts:Anxiety" }, { - "@id": "bts:Overlappinglesionoftonsil" + "@id": "bts:Arrhythmia" }, { - "@id": "bts:Overlappinglesionofurinaryorgans" + "@id": "bts:Arthritis" }, { - "@id": "bts:Overlappinglesionofvulva" + "@id": "bts:Asthma" }, { - "@id": "bts:Overlappinglesionsoforopharynx" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:PalateNOS" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:PancreasNOS" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:Pancreaticduct" + "@id": "bts:BasalCellCarcinoma" }, { - "@id": "bts:Parametrium" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:Parathyroidgland" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:Paraurethralgland" + "@id": "bts:BiliaryDisorder" }, { - "@id": "bts:Parietallobe" + "@id": "bts:BloodClots" }, { - "@id": "bts:Parotidgland" + "@id": "bts:BoneFracture(s)" }, { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + "@id": "bts:Bronchitis" }, { - "@id": "bts:Pelviclymphnodes" + "@id": "bts:CalciumChannelBlockers" }, { - "@id": "bts:PelvisNOS" + "@id": "bts:Cancer" }, { - "@id": "bts:PenisNOS" + "@id": "bts:Cataracts" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + "@id": "bts:CeliacDisease" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + "@id": "bts:UnknownEtiology" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + "@id": "bts:CerebrovascularDisease" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + "@id": "bts:ChronicRenalFailure" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:PeritoneumNOS" + "@id": "bts:CommonVariableImmunodeficiency" }, { - "@id": "bts:PharynxNOS" + "@id": "bts:CongestiveHeartFailure(CHF)" }, { - "@id": "bts:Pinealgland" + "@id": "bts:ConnectiveTissueDisorder" }, { - "@id": "bts:Pituitarygland" + "@id": "bts:COPD" }, { - "@id": "bts:Placenta" + "@id": "bts:CoronaryArteryDisease" }, { - "@id": "bts:PleuraNOS" + "@id": "bts:Crohn'sDisease" }, { - "@id": "bts:Postcricoidregion" + "@id": "bts:CryptogenicOrganizingPneumonia" }, { - "@id": "bts:Posteriormediastinum" + "@id": "bts:DeepVeinThrombosis/Thromboembolism" }, { - "@id": "bts:Posteriorwallofbladder" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:Posteriorwallofhypopharynx" + "@id": "bts:Depression" }, { - "@id": "bts:Posteriorwallofnasopharynx" + "@id": "bts:Diabetes" }, { - "@id": "bts:Posteriorwalloforopharynx" + "@id": "bts:TypeII" }, { - "@id": "bts:Prepuce" + "@id": "bts:DiabeticNeuropathy" }, { - "@id": "bts:Prostategland" + "@id": "bts:DietControlledDiabetes" }, { - "@id": "bts:Pylorus" + "@id": "bts:Diverticulitis" }, { - "@id": "bts:Pyriformsinus" + "@id": "bts:DVT/PE" }, { - "@id": "bts:Rectosigmoidjunction" + "@id": "bts:Dyslipidemia" }, { - "@id": "bts:RectumNOS" + "@id": "bts:Epilepsy" }, { - "@id": "bts:Renalpelvis" + "@id": "bts:Eczema" }, { - "@id": "bts:ReticuloendothelialsystemNOS" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:Retina" + "@id": "bts:FamilialAdenomatousPolyposis" }, { - "@id": "bts:Retromolararea" + "@id": "bts:FanconiAnemia" }, { - "@id": "bts:Retroperitoneum" + "@id": "bts:Fibrosis" }, { - "@id": "bts:Ribsternumclavicleandassociatedjoints" + "@id": "bts:GastroesophagealRefluxDisease" }, { - "@id": "bts:Roundligament" + "@id": "bts:GERD" }, { - "@id": "bts:ScrotumNOS" + "@id": "bts:Glaucoma" }, { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + "@id": "bts:GlycogenStorageDisease" }, { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:Gout" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:GonadalDysfunction" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:GorlinSyndrome" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:H.pyloriInfection" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:Hashimoto'sThyroiditis" }, { - "@id": "bts:Skinofscalpandneck" + "@id": "bts:Headache" }, { - "@id": "bts:Skinoftrunk" + "@id": "bts:HeartDisease" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:Hemihypertrophy" }, { - "@id": "bts:SkinNOS" + "@id": "bts:HemorrhagicCystitis" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:Hepatitis" }, { - "@id": "bts:SoftpalateNOS" + "@id": "bts:HepatitisAInfection" }, { - "@id": "bts:Specifiedpartsofperitoneum" + "@id": "bts:HepatitisBInfection" }, { - "@id": "bts:Spermaticcord" + "@id": "bts:HepatitisCInfection" }, { - "@id": "bts:Sphenoidsinus" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:Spinalcord" + "@id": "bts:HereditaryNon-polyposisColonCancer" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:Herpes" }, { - "@id": "bts:Spleen" + "@id": "bts:HighGradeLiverDysplasticNodule" }, { - "@id": "bts:Splenicflexureofcolon" + "@id": "bts:HIV/AIDS" }, { - "@id": "bts:StomachNOS" + "@id": "bts:HumanPapillomavirusInfection" }, { - "@id": "bts:Subglottis" + "@id": "bts:HUS/TTP" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:Hypercholesterolemia" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:Superiorwallofnasopharynx" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:Supraglottis" + "@id": "bts:Hyperlipidemia" }, { - "@id": "bts:Tailofpancreas" + "@id": "bts:Hypertension" }, { - "@id": "bts:Temporallobe" + "@id": "bts:Hypospadias" }, { - "@id": "bts:TestisNOS" + "@id": "bts:Hypothyroidism" }, { - "@id": "bts:Thoracicesophagus" + "@id": "bts:InflammatoryBowelDisease" }, { - "@id": "bts:ThoraxNOS" + "@id": "bts:InsulinControlledDiabetes" }, { - "@id": "bts:Thymus" + "@id": "bts:InterstitialPneumontisorARDS" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:IntraductalPapillaryMucinousNeoplasm" }, { - "@id": "bts:TongueNOS" + "@id": "bts:IronOverload" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:IschemicHeartDisease" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:ITP" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:JointReplacement" }, { - "@id": "bts:Trachea" + "@id": "bts:KidneyDisease" }, { - "@id": "bts:Transversecolon" + "@id": "bts:LiverCirrhosis(LiverDisease)" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:LiverToxicity(Non-Infectious)" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:Li-FraumeniSyndrome" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:LowGradeLiverDysplasticNodule" }, { - "@id": "bts:Uppergum" + "@id": "bts:Lupus" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:LynchSyndrome" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:MAI" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:MyastheniaGravis" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:NeuroendocrineTumor" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:NonalcoholicSteatohepatitis" }, { - "@id": "bts:Urachus" + "@id": "bts:Obesity" }, { - "@id": "bts:Ureter" + "@id": "bts:Organtransplant(site)" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:Osteoarthritis" }, { - "@id": "bts:Urethra" + "@id": "bts:OsteoporosisorOsteopenia" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:Other" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:OtherCancerWithin5Years" }, { - "@id": "bts:UterusNOS" + "@id": "bts:OtherNonmalignantSystemicDisease" }, { - "@id": "bts:Uvula" + "@id": "bts:OtherPulmonaryComplications" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:Vallecula" + "@id": "bts:Pain(Various)" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:PepticUlcer(Ulcer)" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:PeripheralNeuropathy" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:PeripheralVascularDisease" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:Peutz-JeghersDisease" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:PregnancyinPatientorPartner" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:PrimarySclerosingCholangitis" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:Psoriasis" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:PulmonaryFibrosis" }, { - "@id": "bts:Clitoris" + "@id": "bts:PulmonaryHemorrhage" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:RenalFailure(RequiringDialysis)" + }, + { + "@id": "bts:RenalDialysis" + }, + { + "@id": "bts:RenalInsufficiency" + }, + { + "@id": "bts:RheumatologicDisease" + }, + { + "@id": "bts:RheumatoidArthritis" + }, + { + "@id": "bts:Rubinstein-TaybiSyndrome" + }, + { + "@id": "bts:Sarcoidosis" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:Sleepapnea" + }, + { + "@id": "bts:Smoking" + }, + { + "@id": "bts:Steatosis" + }, + { + "@id": "bts:Stroke" + }, + { + "@id": "bts:TransientIschemicAttack" + }, + { + "@id": "bts:Tuberculosis" + }, + { + "@id": "bts:TurcotSyndrome" + }, + { + "@id": "bts:Tyrosinemia" + }, + { + "@id": "bts:UlcerativeColitis" + }, + { + "@id": "bts:WagrSyndrome" }, { "@id": "bts:Unknown" @@ -22628,37 +22830,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Anatomic Site", + "sms:displayName": "Comorbidity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoTreatmentStart", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoTreatmentStart", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Treatment Start", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:InitialDiseaseStatus", + "@id": "bts:ComorbidityMethodofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", - "rdfs:label": "InitialDiseaseStatus", + "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", + "rdfs:label": "ComorbidityMethodofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22666,16 +22849,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:InitialDiagnosis" - }, - { - "@id": "bts:ProgressiveDisease" + "@id": "bts:Histology" }, { - "@id": "bts:RecurrentDisease" + "@id": "bts:Pathology" }, { - "@id": "bts:ResidualDisease" + "@id": "bts:Radiology" }, { "@id": "bts:Unknown" @@ -22684,52 +22864,56 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Initial Disease Status", + "sms:displayName": "Comorbidity Method of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RegimenorLineofTherapy", + "@id": "bts:DaystoAdverseEvent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the regimen or line of therapy.", - "rdfs:label": "RegimenorLineofTherapy", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoAdverseEvent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Regimen or Line of Therapy", + "sms:displayName": "Days to Adverse Event", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:TherapeuticAgents", + "@id": "bts:DaystoComorbidity", "@type": "rdfs:Class", - "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", - "rdfs:label": "TherapeuticAgents", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoComorbidity", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Therapeutic Agents", + "sms:displayName": "Days to Comorbidity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:TreatmentIntentType", + "@id": "bts:DiabetesTreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", - "rdfs:label": "TreatmentIntentType", + "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", + "rdfs:label": "DiabetesTreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22737,22 +22921,31 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Adjuvant" + "@id": "bts:Alpha-GlucosidaseInhibitor" }, { - "@id": "bts:CancerControl" + "@id": "bts:Biguanide" }, { - "@id": "bts:Cure" + "@id": "bts:Diet" }, { - "@id": "bts:Neoadjuvant" + "@id": "bts:InjectedInsulin" }, { - "@id": "bts:Palliative" + "@id": "bts:Insulin" }, { - "@id": "bts:Prevention" + "@id": "bts:OralHypoglycemic" + }, + { + "@id": "bts:Sulfonylurea" + }, + { + "@id": "bts:Thiazolidinedione" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -22761,18 +22954,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Intent Type", + "sms:displayName": "Diabetes Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChemoConcurrenttoRadiation", + "@id": "bts:DiseaseResponse", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", - "rdfs:label": "ChemoConcurrenttoRadiation", + "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", + "rdfs:label": "DiseaseResponse", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22780,10 +22973,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:No" + "@id": "bts:BED-BiochemicalEvidenceofDisease" + }, + { + "@id": "bts:CPD-ClinicalProgression" + }, + { + "@id": "bts:CR-CompleteResponse" + }, + { + "@id": "bts:CRU-CompleteResponseUnconfirmed" + }, + { + "@id": "bts:DU-DiseaseUnchanged" + }, + { + "@id": "bts:IMR-Immunoresponse" + }, + { + "@id": "bts:IPD-Immunoprogression" + }, + { + "@id": "bts:MR-Minimal/Marginalresponse" + }, + { + "@id": "bts:MX-MixedResponse" + }, + { + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + }, + { + "@id": "bts:NPB-NoPalliativeBenefit" + }, + { + "@id": "bts:NR-NoResponse" + }, + { + "@id": "bts:PA-PalliativeTherapy" + }, + { + "@id": "bts:PB-PalliativeBenefit" + }, + { + "@id": "bts:PD-ProgressiveDisease" + }, + { + "@id": "bts:PDM-PersistentDistantMetastasis" + }, + { + "@id": "bts:PLD-PersistentLocoregionalDisease" + }, + { + "@id": "bts:PPD-Pseudoprogression" + }, + { + "@id": "bts:PR-PartialResponse" + }, + { + "@id": "bts:PSR-Pseudoresponse" + }, + { + "@id": "bts:RD-ResponsiveDisease" + }, + { + "@id": "bts:RP-Response" + }, + { + "@id": "bts:RPD-RadiographicProgressiveDisease" + }, + { + "@id": "bts:SCR-StringentCompleteResponse" + }, + { + "@id": "bts:SD-StableDisease" + }, + { + "@id": "bts:SPD-SurgicalProgression" + }, + { + "@id": "bts:TE-TooEarly" + }, + { + "@id": "bts:TF-TumorFree" + }, + { + "@id": "bts:VGPR-VeryGoodPartialResponse" + }, + { + "@id": "bts:WT-WithTumor" }, { "@id": "bts:Unknown" @@ -22792,35 +23072,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Chemo Concurrent to Radiation", + "sms:displayName": "Disease Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NumberofCycles", + "@id": "bts:DLCORefPredictivePercent", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", - "rdfs:label": "NumberofCycles", + "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", + "rdfs:label": "DLCORefPredictivePercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Cycles", + "sms:displayName": "DLCO Ref Predictive Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReasonTreatmentEnded", + "@id": "bts:ECOGPerformanceStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", - "rdfs:label": "ReasonTreatmentEnded", + "rdfs:comment": "The ECOG functional performance status of the patient/participant.", + "rdfs:label": "ECOGPerformanceStatus", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22828,137 +23108,145 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AdverseTherapyEvent" + "@id": "bts:\"0\"" }, { - "@id": "bts:CourseofTherapyCompleted" + "@id": "bts:\"1\"" }, { - "@id": "bts:Death" + "@id": "bts:\"2\"" }, { - "@id": "bts:DiseaseProgression" + "@id": "bts:\"3\"" }, { - "@id": "bts:Other" + "@id": "bts:\"4\"" }, { - "@id": "bts:WithdrawalbySubject" + "@id": "bts:\"5\"" + }, + { + "@id": "bts:\"0.0\"" + }, + { + "@id": "bts:\"1.0\"" + }, + { + "@id": "bts:\"2.0\"" + }, + { + "@id": "bts:\"3.0\"" + }, + { + "@id": "bts:\"4.0\"" + }, + { + "@id": "bts:\"5.0\"" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Reason Treatment Ended", + "sms:displayName": "ECOG Performance Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentArm", + "@id": "bts:FEV1FVCPostBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", - "rdfs:label": "TreatmentArm", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", + "rdfs:label": "FEV1FVCPostBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:A081105" - }, - { - "@id": "bts:E4512" - }, - { - "@id": "bts:EA5142" - } - ], - "sms:displayName": "Treatment Arm", + "sms:displayName": "FEV1 FVC Post Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDose", + "@id": "bts:FEV1FVCPreBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", - "rdfs:label": "TreatmentDose", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", + "rdfs:label": "FEV1FVCPreBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Treatment Dose", + "sms:displayName": "FEV 1 FVC Pre Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDoseUnits", + "@id": "bts:FEV1RefPostBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", - "rdfs:label": "TreatmentDoseUnits", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", + "rdfs:label": "FEV1RefPostBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CGy" - }, - { - "@id": "bts:Gy" - } - ], - "sms:displayName": "Treatment Dose Units", + "sms:displayName": "FEV1 Ref Post Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentEffectIndicator", + "@id": "bts:FEV1RefPreBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", - "rdfs:label": "TreatmentEffectIndicator", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", + "rdfs:label": "FEV1RefPreBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:NotReported" - }, + "sms:displayName": "FEV1 Ref Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Height", + "@type": "rdfs:Class", + "rdfs:comment": "The height of the patient in centimeters.", + "rdfs:label": "Height", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:FollowUp" } ], - "sms:displayName": "Treatment Effect Indicator", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Height", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentFrequency", + "@id": "bts:HepatitisSustainedVirologicalResponse", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", - "rdfs:label": "TreatmentFrequency", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "HepatitisSustainedVirologicalResponse", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22966,31 +23254,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EveryHour" - }, - { - "@id": "bts:FiveTimesDaily" - }, - { - "@id": "bts:FourTimesDaily" - }, - { - "@id": "bts:ThreeTimesDaily" - }, - { - "@id": "bts:TwiceDaily" - }, - { - "@id": "bts:Every24Hours" - }, - { - "@id": "bts:EveryOtherDay" - }, - { - "@id": "bts:TwiceWeekly" + "@id": "bts:Yes" }, { - "@id": "bts:OnceWeekly" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -22999,35 +23266,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Frequency", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:YearofDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", - "rdfs:label": "YearofDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Year of Diagnosis", + "sms:displayName": "Hepatitis Sustained Virological Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrecancerousConditionType", + "@id": "bts:HPVPositiveType", "@type": "rdfs:Class", - "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", - "rdfs:label": "PrecancerousConditionType", + "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", + "rdfs:label": "HPVPositiveType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23035,132 +23285,87 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DuctalCarcinomaInSitu" - }, - { - "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" - }, - { - "@id": "bts:AtypicalAdenomatousLungHyperplasia" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:PancreaticIntraepithelialNeoplasia" - }, - { - "@id": "bts:ProstaticIntraepithelialNeoplasia" - }, - { - "@id": "bts:Melanocytichyperplasia" - }, - { - "@id": "bts:Atypicalmelanocyticproliferation" - }, - { - "@id": "bts:Melanomainsitu" - }, - { - "@id": "bts:Superficialspreading" - }, - { - "@id": "bts:Lentigomalignatype" - }, - { - "@id": "bts:Acral-lentiginous" - }, - { - "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" - }, - { - "@id": "bts:Persistentmelanomainsitu" - }, - { - "@id": "bts:Melanomainsitunototherwiseclassified" - }, - { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:\"16\"" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:\"18\"" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:\"26\"" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:\"31\"" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:\"33\"" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:\"35\"" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:\"39\"" }, { - "@id": "bts:Invasivemelanoma" + "@id": "bts:\"45\"" }, { - "@id": "bts:NormalWDA" + "@id": "bts:\"51\"" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:\"52\"" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:\"53\"" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:\"56\"" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:\"58\"" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:\"59\"" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:\"63\"" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:\"66\"" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:\"68\"" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:\"70\"" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:\"73\"" }, { - "@id": "bts:Hamartoma" + "@id": "bts:\"82\"" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Other" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Precancerous Condition Type", + "sms:displayName": "HPV Positive Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofDiagnosis", + "@id": "bts:KarnofskyPerformanceStatus", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", - "rdfs:label": "MethodofDiagnosis", + "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", + "rdfs:label": "KarnofskyPerformanceStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23168,73 +23373,37 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" - }, - { - "@id": "bts:BloodDraw" - }, - { - "@id": "bts:BoneMarrowAspirate" - }, - { - "@id": "bts:CoreBiopsy" - }, - { - "@id": "bts:Cytology" - }, - { - "@id": "bts:Cystoscopy" - }, - { - "@id": "bts:Debulking" - }, - { - "@id": "bts:DiagnosticImaging" - }, - { - "@id": "bts:DilationandCurettageProcedure" - }, - { - "@id": "bts:Enucleation" - }, - { - "@id": "bts:ExcisionalBiopsy" - }, - { - "@id": "bts:FineNeedleAspiration" + "@id": "bts:\"0\"" }, { - "@id": "bts:IncisionalBiopsy" + "@id": "bts:\"10\"" }, { - "@id": "bts:Laparoscopy" + "@id": "bts:\"20\"" }, { - "@id": "bts:Laparotomy" + "@id": "bts:\"30\"" }, { - "@id": "bts:Other" + "@id": "bts:\"40\"" }, { - "@id": "bts:PapSmear" + "@id": "bts:\"50\"" }, { - "@id": "bts:PhysicalExam" + "@id": "bts:\"60\"" }, { - "@id": "bts:PathologicReview" + "@id": "bts:\"70\"" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:\"80\"" }, { - "@id": "bts:Thoracentesis" + "@id": "bts:\"90\"" }, { - "@id": "bts:UltrasoundGuidedBiopsy" + "@id": "bts:\"100\"" }, { "@id": "bts:Unknown" @@ -23243,18 +23412,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Method of Diagnosis", + "sms:displayName": "Karnofsky Performance Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorMalignancy", + "@id": "bts:MenopauseStatus", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", - "rdfs:label": "PriorMalignancy", + "rdfs:comment": "Text term used to describe the patient's menopause status.", + "rdfs:label": "MenopauseStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23262,33 +23431,52 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Premenopausal" }, { - "@id": "bts:No" + "@id": "bts:Perimenopausal" }, { - "@id": "bts:Unknown" + "@id": "bts:Postmenopausal" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:NotReported" } ], - "sms:displayName": "Prior Malignancy", + "sms:displayName": "Menopause Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorTreatment", + "@id": "bts:PancreatitisOnsetYear", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", - "rdfs:label": "PriorTreatment", + "rdfs:comment": "Date of onset of pancreatitis.", + "rdfs:label": "PancreatitisOnsetYear", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatitis Onset Year", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:RefluxTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", + "rdfs:label": "RefluxTreatmentType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23296,33 +23484,45 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Antacids" }, { - "@id": "bts:No" + "@id": "bts:H2Blockers" }, { - "@id": "bts:Unknown" + "@id": "bts:MedicallyTreated" + }, + { + "@id": "bts:NoTreatment" + }, + { + "@id": "bts:NotApplicable" }, { "@id": "bts:NotReported" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:ProtonPumpInhibitors" + }, + { + "@id": "bts:SurgicallyTreated" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Prior Treatment", + "sms:displayName": "Reflux Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MetastasisatDiagnosis", + "@id": "bts:RiskFactor", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", - "rdfs:label": "MetastasisatDiagnosis", + "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactor", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23330,134 +23530,277 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DistantMetastasis" + "@id": "bts:AlcoholConsumption" }, { - "@id": "bts:MetastasisNOS" + "@id": "bts:AlcoholicLiverDisease" }, { - "@id": "bts:NoMetastasis" + "@id": "bts:AllergyAnimalNOS" }, { - "@id": "bts:RegionalMetastasis" + "@id": "bts:AllergyAnt" }, { - "@id": "bts:Unknown" + "@id": "bts:AllergyBee" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Metastasis at Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MetastasisatDiagnosisSite", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", - "rdfs:label": "MetastasisatDiagnosisSite", - "rdfs:subClassOf": [ + "@id": "bts:AllergyCat" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AllergyDairyorLactose" + }, { - "@id": "bts:Abdomen" + "@id": "bts:AllergyDog" }, { - "@id": "bts:AdrenalGland" + "@id": "bts:AllergyEggs" }, { - "@id": "bts:Ascites" + "@id": "bts:AllergyFoodNOS" }, { - "@id": "bts:Bone" + "@id": "bts:AllergyFruit" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:AllergyMeat" }, { - "@id": "bts:Brain" + "@id": "bts:AllergyMoldorDust" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:AllergyNuts" }, { - "@id": "bts:CentralNervousSystem" + "@id": "bts:AllergyProcessedFoods" }, { - "@id": "bts:Colon" + "@id": "bts:AllergySeafood" }, { - "@id": "bts:DistantNodes" + "@id": "bts:AllergyWasp" }, { - "@id": "bts:DistantOrgan" + "@id": "bts:Alpha-1AntitrypsinDeficiency" }, { - "@id": "bts:Groin" + "@id": "bts:AutoimmuneAtrophicChronicGastritis" }, { - "@id": "bts:Kidney" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:Liver" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:Lung" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:LymphNode" + "@id": "bts:Cancer" }, { - "@id": "bts:Axillary" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:Inguinal" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:LymphNodeNOS" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:Mediastinum" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:Omentum" + "@id": "bts:Commonvariableimmunedeficiency(CVID)" }, { - "@id": "bts:Ovary" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:Pelvis" + "@id": "bts:DiabetesNOS" }, { - "@id": "bts:PeritonealCavity" + "@id": "bts:DiabetesTypeI" }, { - "@id": "bts:Peritoneum" + "@id": "bts:DiabetesTypeII" }, { - "@id": "bts:Pleura" + "@id": "bts:Diet" }, { - "@id": "bts:Scalp" + "@id": "bts:Diverticulitis" }, { - "@id": "bts:Skin" + "@id": "bts:Endometriosis" }, { - "@id": "bts:SmallIntestine" + "@id": "bts:Endosalpingiosis" }, { - "@id": "bts:SoftTissue" + "@id": "bts:Eczema" }, { - "@id": "bts:SpinalCord" + "@id": "bts:Epstein-BarrVirus" + }, + { + "@id": "bts:FamilialAdenomatousPolyposis" + }, + { + "@id": "bts:FanconiAnemia" + }, + { + "@id": "bts:Fibrosis" + }, + { + "@id": "bts:GastricPolyp(s)" + }, + { + "@id": "bts:Gilbert'sSyndrome" + }, + { + "@id": "bts:GorlinSyndrome" + }, + { + "@id": "bts:Hashimoto'sThyroiditis" + }, + { + "@id": "bts:HayFever" + }, + { + "@id": "bts:Headache" + }, + { + "@id": "bts:HelicobacterPylori-AssociatedGastritis" + }, + { + "@id": "bts:HematologicDisorderNOS" + }, + { + "@id": "bts:Hemihypertrophy" + }, + { + "@id": "bts:Hemochromatosis" + }, + { + "@id": "bts:HepaticEncephalopathy" + }, + { + "@id": "bts:HepatitisBInfection" + }, + { + "@id": "bts:HepatitisCInfection" + }, + { + "@id": "bts:HepatitisNOS" + }, + { + "@id": "bts:HighGradeDysplasia" + }, + { + "@id": "bts:HIV" + }, + { + "@id": "bts:HumanPapillomavirusInfection" + }, + { + "@id": "bts:Hypospadias" + }, + { + "@id": "bts:IntestinalMetaplasia" + }, + { + "@id": "bts:IronOverload" + }, + { + "@id": "bts:Li-FraumeniSyndrome" + }, + { + "@id": "bts:LowGradeDysplasia" + }, + { + "@id": "bts:LymphocyticThyroiditis" + }, + { + "@id": "bts:LynchSyndrome" + }, + { + "@id": "bts:MyastheniaGravis" + }, + { + "@id": "bts:NonalcoholicFattyLiverDisease" + }, + { + "@id": "bts:NonalcoholicSteatohepatitis" + }, + { + "@id": "bts:Obesity" + }, + { + "@id": "bts:OralContraceptives" + }, + { + "@id": "bts:Pancreatitis" + }, + { + "@id": "bts:ParasiticDiseaseofBiliaryTract" + }, + { + "@id": "bts:PrimarySclerosingCholangitis" + }, + { + "@id": "bts:RecurrentPyogenicCholangitis" + }, + { + "@id": "bts:RefluxDisease" + }, + { + "@id": "bts:RheumatoidArthritis" + }, + { + "@id": "bts:Rubinstein-TaybiSyndrome" + }, + { + "@id": "bts:Sarcoidosis" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + }, + { + "@id": "bts:Steatosis" + }, + { + "@id": "bts:Tattoo" + }, + { + "@id": "bts:ThyroidNodularHyperplasia" + }, + { + "@id": "bts:TobaccoNOS" + }, + { + "@id": "bts:TobaccoSmokeless" + }, + { + "@id": "bts:TobaccoSmoking" + }, + { + "@id": "bts:TurcotSyndrome" + }, + { + "@id": "bts:UndescendedTestis" + }, + { + "@id": "bts:VisionChanges" + }, + { + "@id": "bts:WagrSyndrome" }, { "@id": "bts:Unknown" @@ -23466,18 +23809,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Metastasis at Diagnosis Site", + "sms:displayName": "Risk Factor", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FirstSymptomPriortoDiagnosis", + "@id": "bts:RiskFactorTreatment", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", - "rdfs:label": "FirstSymptomPriortoDiagnosis", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactorTreatment", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23485,22 +23828,59 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AlteredMentalStatus" + "@id": "bts:Yes" }, { - "@id": "bts:Headaches" + "@id": "bts:No" }, { - "@id": "bts:MotororMovementChanges" + "@id": "bts:Unknown" }, { - "@id": "bts:Seizures" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Risk Factor Treatment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ViralHepatitisSerologies", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", + "rdfs:label": "ViralHepatitisSerologies", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:HBVCoreAntibody" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:HBVDNA" }, { - "@id": "bts:VisualChanges" + "@id": "bts:HBVGenotype" + }, + { + "@id": "bts:HBVSurfaceAntibody" + }, + { + "@id": "bts:HCVGenotype" + }, + { + "@id": "bts:HepatitisBSurfaceAntigen" + }, + { + "@id": "bts:HepatitisCAntibody" + }, + { + "@id": "bts:HepatitisCVirusRNA" }, { "@id": "bts:Unknown" @@ -23509,57 +23889,69 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "First Symptom Prior to Diagnosis", + "sms:displayName": "Viral Hepatitis Serologies", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoDiagnosis", + "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDiagnosis", + "rdfs:comment": "The weight of the patient measured in kilograms.", + "rdfs:label": "Weight", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Diagnosis", + "sms:displayName": "Weight", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:PercentTumorInvasion", + "@id": "bts:AdverseEventGrade", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "AdverseEventGrade", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Invasion", + "schema:rangeIncludes": [ + { + "@id": "bts:Grade1" + }, + { + "@id": "bts:Grade2" + }, + { + "@id": "bts:Grade3" + }, + { + "@id": "bts:Grade4" + }, + { + "@id": "bts:Grade5" + } + ], + "sms:displayName": "Adverse Event Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ResidualDisease", + "@id": "bts:AIDSRiskFactors", "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", + "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", + "rdfs:label": "AIDSRiskFactors", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" - }, - { - "@id": "bts:InitialDiseaseStatus" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23567,67 +23959,109 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:R0" + "@id": "bts:Candidiasis" }, { - "@id": "bts:R1" + "@id": "bts:Coccidioidomycosis" }, { - "@id": "bts:R2" + "@id": "bts:Cryptococcosis" }, { - "@id": "bts:RX" + "@id": "bts:Cytomegalovirus" }, { - "@id": "bts:Unknown" + "@id": "bts:Encephalopathy" }, { - "@id": "bts:NotReported" + "@id": "bts:HerpesSimplexVirus" + }, + { + "@id": "bts:Histoplasmosis" + }, + { + "@id": "bts:Isosporiasis" + }, + { + "@id": "bts:MycobacteriumaviumComplex" + }, + { + "@id": "bts:Mycobacteriumtuberculosis" + }, + { + "@id": "bts:Mycobacterium" + }, + { + "@id": "bts:NOS" + }, + { + "@id": "bts:Nocardiosis" + }, + { + "@id": "bts:PneumocystisPneumonia" + }, + { + "@id": "bts:Pneumonia" + }, + { + "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" + }, + { + "@id": "bts:SalmonellaSepticemia" + }, + { + "@id": "bts:Toxoplasmosis" + }, + { + "@id": "bts:WastingSyndrome" } ], - "sms:displayName": "Residual Disease", + "sms:displayName": "AIDS Risk Factors", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SynchronousMalignancy", + "@id": "bts:BodySurfaceArea", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", + "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", + "rdfs:label": "BodySurfaceArea", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Body Surface Area", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CD4Count", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", + "rdfs:label": "CD4Count", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:FollowUp" } ], - "sms:displayName": "Synchronous Malignancy", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CD4 Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorConfinedtoOrganofOrigin", + "@id": "bts:CDCHIVRiskFactors", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", + "rdfs:label": "CDCHIVRiskFactors", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23635,10 +24069,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Hemophiliac" }, { - "@id": "bts:No" + "@id": "bts:HeterosexualContact" + }, + { + "@id": "bts:HomosexualContact" + }, + { + "@id": "bts:IntravenousDrugUser" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:TransfusionRecipient" }, { "@id": "bts:Unknown" @@ -23647,83 +24093,113 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Tumor Confined to Organ of Origin", + "sms:displayName": "CDC HIV Risk Factors", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorFocality", + "@id": "bts:DaystoImaging", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", - "rdfs:label": "TumorFocality", + "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoImaging", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Days to Imaging", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:EvidenceofRecurrenceType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", + "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:subClassOf": [ { - "@id": "bts:Multifocal" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Unifocal" + "@id": "bts:BiopsywithHistologicConfirmation" }, { - "@id": "bts:Unknown" + "@id": "bts:ConvincingImageSource" }, { - "@id": "bts:NotReported" + "@id": "bts:PositiveBiomarkers" } ], - "sms:displayName": "Tumor Focality", + "sms:displayName": "Evidence of Recurrence Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GrossTumorWeight", + "@id": "bts:HAARTTreatmentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", - "rdfs:label": "GrossTumorWeight", + "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", + "rdfs:label": "HAARTTreatmentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gross Tumor Weight", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HAART Treatment Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreslowThickness", + "@id": "bts:HIVViralLoad", "@type": "rdfs:Class", - "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", - "rdfs:label": "BreslowThickness", + "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", + "rdfs:label": "HIVViralLoad", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breslow Thickness", + "sms:displayName": "HIV Viral Load", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionPresent", + "@id": "bts:HormonalContraceptiveUse", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", - "rdfs:label": "VascularInvasionPresent", + "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", + "rdfs:label": "HormonalContraceptiveUse", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23731,33 +24207,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-VascularInvasionPresent" + "@id": "bts:CurrentUser" }, { - "@id": "bts:No" + "@id": "bts:FormerUser" }, { - "@id": "bts:Unknown" + "@id": "bts:NeverUsed" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:NotReported" } ], - "sms:displayName": "Vascular Invasion Present", + "sms:displayName": "Hormonal Contraceptive Use", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionType", + "@id": "bts:HysterectomyMarginsInvolved", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", + "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", + "rdfs:label": "HysterectomyMarginsInvolved", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23765,19 +24241,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Extramural" + "@id": "bts:Bladder" }, { - "@id": "bts:Intramural" + "@id": "bts:MacroscopicParametrium" }, { - "@id": "bts:Macro" + "@id": "bts:MicroscopicParametrium" }, { - "@id": "bts:Micro" + "@id": "bts:None" }, { - "@id": "bts:NoVascularInvasion" + "@id": "bts:Vagina" }, { "@id": "bts:Unknown" @@ -23786,18 +24262,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Vascular Invasion Type", + "sms:displayName": "Hysterectomy Margins Involved", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AnaplasiaPresent", + "@id": "bts:HysterectomyType", "@type": "rdfs:Class", - "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", - "rdfs:label": "AnaplasiaPresent", + "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", + "rdfs:label": "HysterectomyType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23805,10 +24281,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AnaplasiaPresent" + "@id": "bts:HysterectomyNOS" }, { - "@id": "bts:No" + "@id": "bts:Notperformed" + }, + { + "@id": "bts:RadicalHysterectomy" + }, + { + "@id": "bts:SimpleHysterectomy" }, { "@id": "bts:Unknown" @@ -23817,18 +24299,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Anaplasia Present", + "sms:displayName": "Hysterectomy Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AnaplasiaPresentType", + "@id": "bts:ImagingResult", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", - "rdfs:label": "AnaplasiaPresentType", + "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", + "rdfs:label": "ImagingResult", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23836,22 +24318,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" - }, - { - "@id": "bts:Diffuse" - }, - { - "@id": "bts:Equivocal" + "@id": "bts:Positive" }, { - "@id": "bts:Focal" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Present" + "@id": "bts:Negative" }, { - "@id": "bts:Sclerosis" + "@id": "bts:NotPerformed" }, { "@id": "bts:Unknown" @@ -23860,18 +24336,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Anaplasia Present Type", + "sms:displayName": "Imaging Result", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Laterality", + "@id": "bts:ImagingType", "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", - "rdfs:label": "Laterality", + "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", + "rdfs:label": "ImagingType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23879,39 +24355,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Bilateral" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Midline" - }, - { - "@id": "bts:Right" + "@id": "bts:99mTcBoneScintigraphy" }, { - "@id": "bts:Unilateral" + "@id": "bts:CTScan" }, { - "@id": "bts:Unknown" + "@id": "bts:MRI" }, { - "@id": "bts:NotReported" + "@id": "bts:PET" } ], - "sms:displayName": "Laterality", + "sms:displayName": "Imaging Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PerineuralInvasionPresent", + "@id": "bts:ImmunosuppressiveTreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", + "rdfs:comment": "The text term used to describe the type of immunosuppresive treatment the patient received.", + "rdfs:label": "ImmunosuppressiveTreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23919,10 +24386,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Anti-TNFTherapy" }, { - "@id": "bts:No" + "@id": "bts:Azathioprine" + }, + { + "@id": "bts:Cyclophosphamide" + }, + { + "@id": "bts:Methotrexate" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -23931,18 +24410,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Perineural Invasion Present", + "sms:displayName": "Immunosuppressive Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphaticInvasionPresent", + "@id": "bts:NadirCD4Count", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", - "rdfs:label": "LymphaticInvasionPresent", + "rdfs:comment": "Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).", + "rdfs:label": "NadirCD4Count", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nadir CD4 Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnancyOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of pregnancy the patient had", + "rdfs:label": "PregnancyOutcome", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23950,10 +24446,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:EctopicPregnancy" }, { - "@id": "bts:No" + "@id": "bts:InducedAbortion" + }, + { + "@id": "bts:LiveBirth" + }, + { + "@id": "bts:Miscarriage" + }, + { + "@id": "bts:Stillbirth" }, { "@id": "bts:Unknown" @@ -23962,52 +24467,52 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lymphatic Invasion Present", + "sms:displayName": "Pregnancy Outcome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesPositive", + "@id": "bts:RecistTargetedRegionsNumber", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", - "rdfs:label": "LymphNodesPositive", + "rdfs:comment": "Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria", + "rdfs:label": "RecistTargetedRegionsNumber", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Positive", + "sms:displayName": "Recist Targeted Regions Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesTested", + "@id": "bts:RecistTargetedRegionsSum", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", - "rdfs:label": "LymphNodesTested", + "rdfs:comment": "Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.", + "rdfs:label": "RecistTargetedRegionsSum", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Tested", + "sms:displayName": "Recist Targeted Regions Sum", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeritonealFluidCytologicalStatus", + "@id": "bts:ScanTracerUsed", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", + "rdfs:comment": "The text term used to describe the type of tracer used during the imaging or scan of the patient.", + "rdfs:label": "ScanTracerUsed", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -24015,36 +24520,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Atypical" - }, - { - "@id": "bts:Malignant" + "@id": "bts:Acetate" }, { - "@id": "bts:Non-Malignant" + "@id": "bts:Axumin" }, { - "@id": "bts:Unsatisfactory" + "@id": "bts:Choline" }, { - "@id": "bts:Unknown" + "@id": "bts:PSMA" }, { - "@id": "bts:NotReported" + "@id": "bts:SodiumFluoride" } ], - "sms:displayName": "Peritoneal Fluid Cytological Status", + "sms:displayName": "Scan Tracer Used", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClassificationofTumor", + "@id": "bts:TreatmentorTherapy", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", - "rdfs:label": "ClassificationofTumor", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.", + "rdfs:label": "TreatmentorTherapy", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -24052,39 +24554,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Primary" - }, - { - "@id": "bts:Metastasis" - }, - { - "@id": "bts:Recurrence" + "@id": "bts:Yes" }, { - "@id": "bts:Other" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" } ], - "sms:displayName": "Classification of Tumor", + "sms:displayName": "Treatment or Therapy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BestOverallResponse", + "@id": "bts:TreatmentEffect", "@type": "rdfs:Class", - "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", - "rdfs:label": "BestOverallResponse", + "rdfs:comment": "The text term used to describe the pathologic effect a treatment(s) had on the tumor.", + "rdfs:label": "TreatmentEffect", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -24092,113 +24585,110 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AJ-AdjuvantTherapy" - }, - { - "@id": "bts:CPD-ClinicalProgression" - }, - { - "@id": "bts:CR-CompleteResponse" - }, - { - "@id": "bts:CRU-CompleteResponseUnconfirmed" - }, - { - "@id": "bts:DU-DiseaseUnchanged" - }, - { - "@id": "bts:IMR-Immunoresponse" - }, - { - "@id": "bts:IPD-Immunoprogression" - }, - { - "@id": "bts:MR-Minimal/MarginalResponse" + "@id": "bts:CompleteNecrosis(NoViableTumor)" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:IncompleteNecrosis(ViableTumorPresent)" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:NoNecrosis" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:Unknown" }, { - "@id": "bts:NR-NoResponse" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Effect", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the patient's final outcome after the treatment was administered.", + "rdfs:label": "TreatmentOutcome", + "rdfs:subClassOf": [ { - "@id": "bts:PA-PalliativeTherapy" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:CompleteResponse" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:MixedResponse" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:NoMeasurableDisease" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:NoResponse" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:PartialResponse" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:PersistentDisease" }, { - "@id": "bts:RP-Response" + "@id": "bts:ProgressiveDisease" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:StableDisease" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:TreatmentOngoing" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:TreatmentStoppedDuetoToxicity" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:VeryGoodPartialResponse" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:Unknown" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:NotReported" } ], - "sms:displayName": "Best Overall Response", + "sms:displayName": "Treatment Outcome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitoticCount", + "@id": "bts:DaystoTreatmentEnd", "@type": "rdfs:Class", - "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", + "rdfs:comment": "Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentEnd", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mitotic Count", + "sms:displayName": "Days to Treatment End", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:AJCCClinicalM", + "@id": "bts:TreatmentAnatomicSite", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalM", + "rdfs:comment": "The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment", + "rdfs:label": "TreatmentAnatomicSite", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -24206,1389 +24696,994 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:M0" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:M1" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:M1a" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:M1b" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:M1c" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:MX" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:Analcanal" }, { - "@id": "bts:Unknown" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical M", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalN", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalN", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:N0" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:N0(i+)" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:N0(i-)" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:N0(mol+)" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:N1" + "@id": "bts:AnusNOS" }, { - "@id": "bts:N1a" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:N1b" + "@id": "bts:Appendix" }, { - "@id": "bts:N1bI" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:N1bII" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:N1bIII" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:N1bIV" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:N1c" + "@id": "bts:Bladderneck" }, { - "@id": "bts:N1mi" + "@id": "bts:BladderNOS" }, { - "@id": "bts:N2" + "@id": "bts:Blood" }, { - "@id": "bts:N2a" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:N2b" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:N2c" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:N3" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:N3a" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:N3b" + "@id": "bts:BoneNOS" }, { - "@id": "bts:N3c" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:N4" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:NX" + "@id": "bts:Brainstem" }, { - "@id": "bts:Unknown" + "@id": "bts:BrainNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical N", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalStage", - "@type": "rdfs:Class", - "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", - "rdfs:label": "AJCCClinicalStage", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Stage0" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:Stage0a" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Stage0is" + "@id": "bts:Broadligament" }, { - "@id": "bts:StageI" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:StageIA" + "@id": "bts:Carotidbody" }, { - "@id": "bts:StageIA1" + "@id": "bts:Caudaequina" }, { - "@id": "bts:StageIA2" + "@id": "bts:Cecum" }, { - "@id": "bts:StageIB" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:StageIB1" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:StageIB2" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:StageIC" + "@id": "bts:Cerebrum" }, { - "@id": "bts:StageII" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:StageIIA" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:StageIIA1" + "@id": "bts:Choroid" }, { - "@id": "bts:StageIIA2" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:StageIIB" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:StageIIC" + "@id": "bts:ColonNOS" }, { - "@id": "bts:StageIIC1" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:StageIII" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:StageIIIA" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:StageIIIB" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:StageIIIC" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:StageIS" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:StageIV" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:StageIVA" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:StageIVB" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:StageIVC" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:StageTis" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:StageX" + "@id": "bts:CranialnerveNOS" }, { - 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Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "GleasonGradeGroup", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + }, { - "@id": "bts:Group1" + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" }, { - "@id": "bts:Group2" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:Group3" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:Group4" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:Group5" - } - ], - "sms:displayName": "Gleason Grade Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GleasonGradeTertiary", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", - "rdfs:label": "GleasonGradeTertiary", - "rdfs:subClassOf": [ + "@id": "bts:Pinealgland" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Pituitarygland" + }, { - "@id": "bts:Pattern4" + "@id": "bts:Placenta" }, { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Gleason Grade Tertiary", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GleasonPatternsPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", - "rdfs:label": "GleasonPatternsPercent", - "rdfs:subClassOf": [ + "@id": "bts:PleuraNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gleason Patterns Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GreatestTumorDimension", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", - "rdfs:label": "GreatestTumorDimension", - "rdfs:subClassOf": [ + "@id": "bts:Postcricoidregion" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Greatest Tumor Dimension", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:IGCCCGStage", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", - "rdfs:label": "IGCCCGStage", - "rdfs:subClassOf": [ + "@id": "bts:Posteriormediastinum" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Posteriorwallofbladder" + }, { - "@id": "bts:GoodPrognosis" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:IntermediatePrognosis" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:PoorPrognosis" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:Unknown" + "@id": "bts:Prepuce" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "IGCCCG Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:INPCGrade", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", - "rdfs:label": "INPCGrade", - "rdfs:subClassOf": [ + "@id": "bts:Prostategland" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Pylorus" + }, { - "@id": "bts:Differentiating" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:PoorlyDifferentiated" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:Undifferentiated" + "@id": "bts:RectumNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INPC Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:INPCHistologicGroup", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", - "rdfs:label": "INPCHistologicGroup", - "rdfs:subClassOf": [ + "@id": "bts:ReticuloendothelialsystemNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Retina" + }, { - "@id": "bts:Favorable" + "@id": "bts:Retromolararea" }, { - "@id": "bts:Unfavorable" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:Unknown" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INPC Histologic Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:INRGStage", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", - "rdfs:label": "INRGStage", - "rdfs:subClassOf": [ + "@id": "bts:Roundligament" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ScrotumNOS" + }, { - "@id": "bts:L1" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:L2" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:M" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:Ms" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INRG Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:INSSStage", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", - "rdfs:label": "INSSStage", - "rdfs:subClassOf": [ + "@id": "bts:Skinofotherandunspecifiedpartsofface" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Skinofscalpandneck" + }, { - "@id": "bts:Stage1" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:Stage2A" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:Stage2B" + "@id": "bts:SkinNOS" }, { - "@id": "bts:Stage3" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:Stage4" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:Stage4S" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:Unknown" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INSS Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InternationalPrognosticIndex", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.", - "rdfs:label": "InternationalPrognosticIndex", - "rdfs:subClassOf": [ + "@id": "bts:Sphenoidsinus" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Spinalcord" + }, { - "@id": "bts:LowRisk" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:Low-IntermediateRisk" + "@id": "bts:Spleen" }, { - "@id": "bts:High-IntermediateRisk" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:HighRisk" - } - ], - "sms:displayName": "International Prognostic Index", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:IRSGroup", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", - "rdfs:label": "IRSGroup", - "rdfs:subClassOf": [ + "@id": "bts:StomachNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Subglottis" + }, { - "@id": "bts:GroupI" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:GroupIa" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:GroupIb" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:GroupII" + "@id": "bts:Supraglottis" }, { - "@id": "bts:GroupIIa" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:GroupIIc" + "@id": "bts:Temporallobe" }, { - "@id": "bts:GroupIII" + "@id": "bts:TestisNOS" }, { - "@id": "bts:GroupIIIa" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:GroupIIIb" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:GroupIV" + "@id": "bts:Thymus" }, { - "@id": "bts:Unknown" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "IRS Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:IRSStage", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", - "rdfs:label": "IRSStage", - "rdfs:subClassOf": [ + "@id": "bts:TongueNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:TonsilNOS" + }, { - "@id": "bts:1" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:2" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:3" + "@id": "bts:Trachea" }, { - "@id": "bts:4" + "@id": "bts:Transversecolon" }, { - "@id": "bts:Unknown" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "IRS Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ISSStage", - "@type": "rdfs:Class", - "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", - "rdfs:label": "ISSStage", - "rdfs:subClassOf": [ + "@id": "bts:Undescendedtestis" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Unknownprimarysite" + }, { - "@id": "bts:I" + "@id": "bts:Uppergum" }, { - "@id": "bts:II" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:III" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:NotReported" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "ISS Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphNodeInvolvedSite", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", - "rdfs:label": "LymphNodeInvolvedSite", - "rdfs:subClassOf": [ + "@id": "bts:Upperthirdofesophagus" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Upper-innerquadrantofbreast" + }, { - "@id": "bts:Axillary" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:Cervical" + "@id": "bts:Urachus" }, { - "@id": "bts:Epitrochlear" + "@id": "bts:Ureter" }, { - "@id": "bts:Femoral" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:Hilar" + "@id": "bts:Urethra" }, { - "@id": "bts:Iliac-common" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:Iliac-external" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:Iliac" + "@id": "bts:UterusNOS" }, { - "@id": "bts:NOS" + "@id": "bts:Uvula" }, { - "@id": "bts:Inguinal" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:Mediastinal" + "@id": "bts:Vallecula" }, { - "@id": "bts:Mesenteric" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:None" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:Occipital" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:Paraaortic" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:Parotid" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:Popliteal" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:Retroperitoneal" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:Splenic" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:Submandibular" + "@id": "bts:Clitoris" }, { - "@id": "bts:Supraclavicular" + "@id": "bts:Overlappinglesionofbiliarytract" }, { "@id": "bts:Unknown" @@ -25597,35 +25692,37 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lymph Node Involved Site", + "sms:displayName": "Treatment Anatomic Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MarginDistance", + "@id": "bts:DaystoTreatmentStart", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", - "rdfs:label": "MarginDistance", + "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentStart", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Margin Distance", + "sms:displayName": "Days to Treatment Start", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:MarginsInvolvedSite", + "@id": "bts:InitialDiseaseStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", - "rdfs:label": "MarginsInvolvedSite", + "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", + "rdfs:label": "InitialDiseaseStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25633,110 +25730,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GerotaFascia" - }, - { - "@id": "bts:Parenchyma" - }, - { - "@id": "bts:PerinephricFat" + "@id": "bts:InitialDiagnosis" }, { - "@id": "bts:Renal" + "@id": "bts:ProgressiveDisease" }, { - "@id": "bts:RenalCapsule" + "@id": "bts:RecurrentDisease" }, { - "@id": "bts:RenalSinus" + "@id": "bts:ResidualDisease" }, { - "@id": "bts:RenalVein" + "@id": "bts:Unknown" }, { - "@id": "bts:Ureter" + "@id": "bts:NotReported" } ], - "sms:displayName": "Margins Involved Site", + "sms:displayName": "Initial Disease Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedulloblastomaMolecularClassification", + "@id": "bts:RegimenorLineofTherapy", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", - "rdfs:label": "MedulloblastomaMolecularClassification", + "rdfs:comment": "The text term used to describe the regimen or line of therapy.", + "rdfs:label": "RegimenorLineofTherapy", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NotDetermined" - }, - { - "@id": "bts:Non-WNT/non-SHHActivated" - }, - { - "@id": "bts:SHH-Activated" - }, - { - "@id": "bts:WNT-Activated" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Medulloblastoma Molecular Classification", + "sms:displayName": "Regimen or Line of Therapy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicropapillaryFeatures", + "@id": "bts:TherapeuticAgents", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", - "rdfs:label": "MicropapillaryFeatures", + "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", + "rdfs:label": "TherapeuticAgents", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Micropapillary Features", + "sms:displayName": "Therapeutic Agents", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitosisKaryorrhexisIndex", + "@id": "bts:TreatmentIntentType", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", - "rdfs:label": "MitosisKaryorrhexisIndex", + "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", + "rdfs:label": "TreatmentIntentType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25744,47 +25801,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:High" - }, - { - "@id": "bts:Intermediate" + "@id": "bts:Adjuvant" }, { - "@id": "bts:Low" + "@id": "bts:CancerControl" }, { - "@id": "bts:Unknown" + "@id": "bts:Cure" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mitosis Karyorrhexis Index", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NonNodalRegionalDisease", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", - "rdfs:label": "NonNodalRegionalDisease", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" + "@id": "bts:Neoadjuvant" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Palliative" }, { - "@id": "bts:Present" + "@id": "bts:Prevention" }, { "@id": "bts:Unknown" @@ -25793,18 +25825,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Non Nodal Regional Disease", + "sms:displayName": "Treatment Intent Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NonNodalTumorDeposits", + "@id": "bts:ChemoConcurrenttoRadiation", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", - "rdfs:label": "NonNodalTumorDeposits", + "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", + "rdfs:label": "ChemoConcurrenttoRadiation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25824,52 +25856,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Non Nodal Tumor Deposits", + "sms:displayName": "Chemo Concurrent to Radiation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OvarianSpecimenStatus", + "@id": "bts:NumberofCycles", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", - "rdfs:label": "OvarianSpecimenStatus", + "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", + "rdfs:label": "NumberofCycles", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:OvarianCapsuleIntact" - }, - { - "@id": "bts:OvarianCapsuleRuptured" - }, - { - "@id": "bts:OvarianCapsuleFragmented" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Ovarian Specimen Status", + "sms:displayName": "Number of Cycles", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OvarianSurfaceInvolvement", + "@id": "bts:ReasonTreatmentEnded", "@type": "rdfs:Class", - "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", - "rdfs:label": "OvarianSurfaceInvolvement", + "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", + "rdfs:label": "ReasonTreatmentEnded", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25877,33 +25892,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:AdverseTherapyEvent" }, { - "@id": "bts:Present" + "@id": "bts:CourseofTherapyCompleted" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Death" }, { - "@id": "bts:Unknown" + "@id": "bts:DiseaseProgression" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" + }, + { + "@id": "bts:WithdrawalbySubject" } ], - "sms:displayName": "Ovarian Surface Involvement", + "sms:displayName": "Reason Treatment Ended", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PregnantatDiagnosis", + "@id": "bts:TreatmentArm", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", - "rdfs:label": "PregnantatDiagnosis", + "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", + "rdfs:label": "TreatmentArm", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25911,64 +25929,44 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" + "@id": "bts:A081105" }, { - "@id": "bts:Unknown" + "@id": "bts:E4512" }, { - "@id": "bts:NotReported" + "@id": "bts:EA5142" } ], - "sms:displayName": "Pregnant at Diagnosis", + "sms:displayName": "Treatment Arm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrimaryGleasonGrade", + "@id": "bts:TreatmentDose", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "PrimaryGleasonGrade", + "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", + "rdfs:label": "TreatmentDose", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pattern1" - }, - { - "@id": "bts:Pattern2" - }, - { - "@id": "bts:Pattern3" - }, - { - "@id": "bts:Pattern4" - }, - { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Primary Gleason Grade", + "sms:displayName": "Treatment Dose", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SecondaryGleasonGrade", + "@id": "bts:TreatmentDoseUnits", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "SecondaryGleasonGrade", + "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", + "rdfs:label": "TreatmentDoseUnits", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25976,33 +25974,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pattern1" - }, - { - "@id": "bts:Pattern2" - }, - { - "@id": "bts:Pattern3" - }, - { - "@id": "bts:Pattern4" + "@id": "bts:CGy" }, { - "@id": "bts:Pattern5" + "@id": "bts:Gy" } ], - "sms:displayName": "Secondary Gleason Grade", + "sms:displayName": "Treatment Dose Units", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SupratentorialLocalization", + "@id": "bts:TreatmentEffectIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", - "rdfs:label": "SupratentorialLocalization", + "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", + "rdfs:label": "TreatmentEffectIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -26010,53 +25999,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CerebralCortex" - }, - { - "@id": "bts:DeepGray" + "@id": "bts:Yes" }, { - "@id": "bts:SpinalCord" + "@id": "bts:No" }, { - "@id": "bts:WhiteMatter" + "@id": "bts:NotReported" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Supratentorial Localization", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorDepth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", - "rdfs:label": "TumorDepth", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Depth", + "sms:displayName": "Treatment Effect Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WHOCNSGrade", + "@id": "bts:TreatmentFrequency", "@type": "rdfs:Class", - "rdfs:comment": "WHO CNS Grade", - "rdfs:label": "WHOCNSGrade", + "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", + "rdfs:label": "TreatmentFrequency", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -26064,56 +26030,31 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GradeI" - }, - { - "@id": "bts:GradeII" + "@id": "bts:EveryHour" }, { - "@id": "bts:GradeIII" + "@id": "bts:FiveTimesDaily" }, { - "@id": "bts:GradeIV" + "@id": "bts:FourTimesDaily" }, { - "@id": "bts:GradeNotAssigned" + "@id": "bts:ThreeTimesDaily" }, { - "@id": "bts:Unknown" + "@id": "bts:TwiceDaily" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "WHO CNS Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WHONTEGrade", - "@type": "rdfs:Class", - "rdfs:comment": "WHO NTE Grade", - "rdfs:label": "WHONTEGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:G1" + "@id": "bts:Every24Hours" }, { - "@id": "bts:G2" + "@id": "bts:EveryOtherDay" }, { - "@id": "bts:G3" + "@id": "bts:TwiceWeekly" }, { - "@id": "bts:GX" + "@id": "bts:OnceWeekly" }, { "@id": "bts:Unknown" @@ -26122,35 +26063,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "WHO NTE Grade", + "sms:displayName": "Treatment Frequency", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AAChange", + "@id": "bts:YearofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "AAChange", + "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", + "rdfs:label": "YearofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "AA Change", + "sms:displayName": "Year of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Antigen", + "@id": "bts:PrecancerousConditionType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Antigen", + "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", + "rdfs:label": "PrecancerousConditionType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26158,108 +26099,132 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BCL6" + "@id": "bts:DuctalCarcinomaInSitu" }, { - "@id": "bts:CA-125" + "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" }, { - "@id": "bts:CA19-9" + "@id": "bts:AtypicalAdenomatousLungHyperplasia" }, { - "@id": "bts:CCND1" + "@id": "bts:Other" }, { - "@id": "bts:CD10" + "@id": "bts:PancreaticIntraepithelialNeoplasia" }, { - "@id": "bts:CD117" + "@id": "bts:ProstaticIntraepithelialNeoplasia" }, { - "@id": "bts:CD138" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:CD14" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:CD15" + "@id": "bts:Melanomainsitu" }, { - "@id": "bts:CD19" + "@id": "bts:Superficialspreading" }, { - "@id": "bts:CD20" + "@id": "bts:Lentigomalignatype" }, { - "@id": "bts:CD22" + "@id": "bts:Acral-lentiginous" }, { - "@id": "bts:CD23" + "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" }, { - "@id": "bts:CD25" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:CD3" + "@id": "bts:Melanomainsitunototherwiseclassified" }, { - "@id": "bts:CD30" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:CD33" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:CD34" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:CD45" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:CD5" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:CD56" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:CD7" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:CD79A" + "@id": "bts:Invasivemelanoma" }, { - "@id": "bts:CEA" + "@id": "bts:NormalWDA" }, { - "@id": "bts:HLA-DR" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:Mesothelin" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:NSE" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:SquamousCellCarcinomaAntigen" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:Unknown" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:NotReported" + "@id": "bts:Severedysplasia" + }, + { + "@id": "bts:Atypicaladenomatoushyperplasia" + }, + { + "@id": "bts:Adenocarcinomainsitu-nonmucinous" + }, + { + "@id": "bts:Adenocarcinomainsitu-mucinous" + }, + { + "@id": "bts:BenigntumorNOS" + }, + { + "@id": "bts:Hamartoma" + }, + { + "@id": "bts:CarcinomaNOS" + }, + { + "@id": "bts:Nodiagnosispossible" + }, + { + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Antigen", + "sms:displayName": "Precancerous Condition Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClinicalBiospecimenType", + "@id": "bts:MethodofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "ClinicalBiospecimenType", + "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", + "rdfs:label": "MethodofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26267,70 +26232,73 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Blood" + "@id": "bts:Autopsy" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:Biopsy" }, { - "@id": "bts:BuccalMucosa" + "@id": "bts:BloodDraw" }, { - "@id": "bts:BuffyCoat" + "@id": "bts:BoneMarrowAspirate" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:CoreBiopsy" }, { - "@id": "bts:ConnectiveTissue" + "@id": "bts:Cytology" }, { - "@id": "bts:EmbryonicFluid" + "@id": "bts:Cystoscopy" }, { - "@id": "bts:EmbryonicTissue" + "@id": "bts:Debulking" }, { - "@id": "bts:Feces" + "@id": "bts:DiagnosticImaging" }, { - "@id": "bts:Granulocyte" + "@id": "bts:DilationandCurettageProcedure" }, { - "@id": "bts:MuscleTissue" + "@id": "bts:Enucleation" }, { - "@id": "bts:NerveTissue" + "@id": "bts:ExcisionalBiopsy" }, { - "@id": "bts:PeritonealFluid" + "@id": "bts:FineNeedleAspiration" }, { - "@id": "bts:Plasma" + "@id": "bts:IncisionalBiopsy" }, { - "@id": "bts:PleuralFluid" + "@id": "bts:Laparoscopy" }, { - "@id": "bts:Saliva" + "@id": "bts:Laparotomy" }, { - "@id": "bts:Serum" + "@id": "bts:Other" }, { - "@id": "bts:Skin" + "@id": "bts:PapSmear" }, { - "@id": "bts:SoftTissue" + "@id": "bts:PhysicalExam" }, { - "@id": "bts:TissueNOS" + "@id": "bts:PathologicReview" }, { - "@id": "bts:UninvolvedTissueNOS" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:Urine" + "@id": "bts:Thoracentesis" + }, + { + "@id": "bts:UltrasoundGuidedBiopsy" }, { "@id": "bts:Unknown" @@ -26339,69 +26307,123 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Clinical Biospecimen Type", + "sms:displayName": "Method of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BloodTestNormalRangeUpper", + "@id": "bts:PriorMalignancy", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeUpper", + "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", + "rdfs:label": "PriorMalignancy", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Test Normal Range Upper", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Malignancy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BloodTestNormalRangeLower", + "@id": "bts:PriorTreatment", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", + "rdfs:label": "PriorTreatment", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Test Normal Range Lower", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Treatment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellCount", + "@id": "bts:MetastasisatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CellCount", + "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", + "rdfs:label": "MetastasisatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Count", + "schema:rangeIncludes": [ + { + "@id": "bts:DistantMetastasis" + }, + { + "@id": "bts:MetastasisNOS" + }, + { + "@id": "bts:NoMetastasis" + }, + { + "@id": "bts:RegionalMetastasis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Metastasis at Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Chromosome", + "@id": "bts:MetastasisatDiagnosisSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Chromosome", + "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", + "rdfs:label": "MetastasisatDiagnosisSite", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26409,82 +26431,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Chr1" + "@id": "bts:Abdomen" }, { - "@id": "bts:Chr2" + "@id": "bts:AdrenalGland" }, { - "@id": "bts:Chr3" + "@id": "bts:Ascites" }, { - "@id": "bts:Chr4" + "@id": "bts:Bone" }, { - "@id": "bts:Chr5" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:Chr6" + "@id": "bts:Brain" }, { - "@id": "bts:Chr7" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:Chr8" + "@id": "bts:CentralNervousSystem" }, { - "@id": "bts:Chr9" + "@id": "bts:Colon" }, { - "@id": "bts:Chr10" + "@id": "bts:DistantNodes" }, { - "@id": "bts:Chr11" + "@id": "bts:DistantOrgan" }, { - "@id": "bts:Chr12" + "@id": "bts:Groin" }, { - "@id": "bts:Chr13" + "@id": "bts:Kidney" }, { - "@id": "bts:Chr14" + "@id": "bts:Liver" }, { - "@id": "bts:Chr15" + "@id": "bts:Lung" }, { - "@id": "bts:Chr16" + "@id": "bts:LymphNode" }, { - "@id": "bts:Chr17" + "@id": "bts:Axillary" }, { - "@id": "bts:Chr18" + "@id": "bts:Inguinal" }, { - "@id": "bts:Chr19" + "@id": "bts:LymphNodeNOS" }, { - "@id": "bts:Chr20" + "@id": "bts:Mediastinum" }, { - "@id": "bts:Chr21" + "@id": "bts:Omentum" }, { - "@id": "bts:Chr22" + "@id": "bts:Ovary" }, { - "@id": "bts:Chr23" + "@id": "bts:Pelvis" }, { - "@id": "bts:ChrM" + "@id": "bts:PeritonealCavity" }, { - "@id": "bts:ChrX" + "@id": "bts:Peritoneum" }, { - "@id": "bts:ChrY" + "@id": "bts:Pleura" + }, + { + "@id": "bts:Scalp" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:SmallIntestine" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:SpinalCord" }, { "@id": "bts:Unknown" @@ -26493,18 +26530,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Chromosome", + "sms:displayName": "Metastasis at Diagnosis Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clonality", + "@id": "bts:FirstSymptomPriortoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Clonality", + "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", + "rdfs:label": "FirstSymptomPriortoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26512,75 +26549,118 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Clonal" + "@id": "bts:AlteredMentalStatus" }, { - "@id": "bts:Non-clonal" + "@id": "bts:Headaches" + }, + { + "@id": "bts:MotororMovementChanges" + }, + { + "@id": "bts:Seizures" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:VisualChanges" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Clonality", + "sms:displayName": "First Symptom Prior to Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CopyNumber", + "@id": "bts:DaystoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CopyNumber", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Copy Number", + "sms:displayName": "Days to Diagnosis", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:Cytoband", + "@id": "bts:PercentTumorInvasion", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Cytoband", + "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", + "rdfs:label": "PercentTumorInvasion", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cytoband", + "sms:displayName": "Percent Tumor Invasion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Exon", + "@id": "bts:ResidualDisease", "@type": "rdfs:Class", - "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Exon", + "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", + "rdfs:label": "ResidualDisease", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:InitialDiseaseStatus" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Exon", + "schema:rangeIncludes": [ + { + "@id": "bts:R0" + }, + { + "@id": "bts:R1" + }, + { + "@id": "bts:R2" + }, + { + "@id": "bts:RX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Residual Disease", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoneFamily", + "@id": "bts:SynchronousMalignancy", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", - "rdfs:label": "HistoneFamily", + "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", + "rdfs:label": "SynchronousMalignancy", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26588,19 +26668,41 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:H1" + "@id": "bts:Yes" }, { - "@id": "bts:H2A" + "@id": "bts:No" }, { - "@id": "bts:H2B" + "@id": "bts:Unknown" }, { - "@id": "bts:H3" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Synchronous Malignancy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorConfinedtoOrganofOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", + "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:H4" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -26609,18 +26711,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Histone Family", + "sms:displayName": "Tumor Confined to Organ of Origin", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoneVariant", + "@id": "bts:TumorFocality", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "HistoneVariant", + "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", + "rdfs:label": "TumorFocality", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26628,55 +26730,118 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CENP-A" + "@id": "bts:Multifocal" }, { - "@id": "bts:H2A-Bbd" + "@id": "bts:Unifocal" }, { - "@id": "bts:H2A.X" + "@id": "bts:Unknown" }, { - "@id": "bts:H2A.Z" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Focality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GrossTumorWeight", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", + "rdfs:label": "GrossTumorWeight", + "rdfs:subClassOf": [ { - "@id": "bts:H2A.Z.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gross Tumor Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreslowThickness", + "@type": "rdfs:Class", + "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", + "rdfs:label": "BreslowThickness", + "rdfs:subClassOf": [ { - "@id": "bts:H2A.Z.2" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breslow Thickness", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", + "rdfs:label": "VascularInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:H2A.Z.2.2" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:H3.1" + "@id": "bts:Yes-VascularInvasionPresent" }, { - "@id": "bts:H3.2" + "@id": "bts:No" }, { - "@id": "bts:H3.3" + "@id": "bts:Unknown" }, { - "@id": "bts:H3.5" + "@id": "bts:NotReported" }, { - "@id": "bts:H3.X" - }, + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Vascular Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", + "rdfs:label": "VascularInvasionType", + "rdfs:subClassOf": [ { - "@id": "bts:H3.Y" + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Extramural" }, { - "@id": "bts:H3t(H3.4)" + "@id": "bts:Intramural" }, { - "@id": "bts:MH2A" + "@id": "bts:Macro" }, { - "@id": "bts:MH2A.1" + "@id": "bts:Micro" }, { - "@id": "bts:MH2A.2" + "@id": "bts:NoVascularInvasion" }, { "@id": "bts:Unknown" @@ -26685,35 +26850,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Histone Variant", + "sms:displayName": "Vascular Invasion Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Intron", + "@id": "bts:AnaplasiaPresent", "@type": "rdfs:Class", - "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", - "rdfs:label": "Intron", + "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", + "rdfs:label": "AnaplasiaPresent", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Intron", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AnaplasiaPresent" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LaboratoryTest", + "@id": "bts:AnaplasiaPresentType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", - "rdfs:label": "LaboratoryTest", + "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", + "rdfs:label": "AnaplasiaPresentType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26721,139 +26900,93 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbsoluteNeutrophil" + "@id": "bts:Absent" }, { - "@id": "bts:Albumin" + "@id": "bts:Diffuse" }, { - "@id": "bts:AlphaFetoprotein" + "@id": "bts:Equivocal" }, { - "@id": "bts:B-cellgenotyping" + "@id": "bts:Focal" }, { - "@id": "bts:Basophil" + "@id": "bts:Present" }, { - "@id": "bts:Beta2Microglobulin" + "@id": "bts:Sclerosis" }, { - "@id": "bts:BloodUreaNitrogen" + "@id": "bts:Unknown" }, { - "@id": "bts:C-ReactiveProtein" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Laterality", + "@type": "rdfs:Class", + "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", + "rdfs:label": "Laterality", + "rdfs:subClassOf": [ { - "@id": "bts:Calcium" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Cellularity" + "@id": "bts:Bilateral" }, { - "@id": "bts:CirculatingTumorCells" + "@id": "bts:Left" }, { - "@id": "bts:Creatinine" + "@id": "bts:Midline" }, { - "@id": "bts:Eosinophil" + "@id": "bts:Right" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:Unilateral" }, { - "@id": "bts:Glucose" + "@id": "bts:Unknown" }, { - "@id": "bts:Hematocrit" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laterality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerineuralInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", + "rdfs:label": "PerineuralInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:Hemoglobin" - }, - { - "@id": "bts:HPV-E6/E7" - }, - { - "@id": "bts:HumanChorionicGonadotropin" - }, - { - "@id": "bts:HumanPapillomavirus" - }, - { - "@id": "bts:ImmunoglobulinA" - }, - { - "@id": "bts:ImmunoglobulinG" - }, - { - "@id": "bts:ImmunoglobulinM" - }, - { - "@id": "bts:LactateDehydrogenase" - }, - { - "@id": "bts:Leukocytes" - }, - { - "@id": "bts:LuteinizingHormone" - }, - { - "@id": "bts:Lymphoblasts" - }, - { - "@id": "bts:Lymphocytes" - }, - { - "@id": "bts:MProtein" - }, - { - "@id": "bts:Metamyelocytes" - }, - { - "@id": "bts:Myeloblasts" - }, - { - "@id": "bts:Myelocytes" - }, - { - "@id": "bts:NeutrophilBands" - }, - { - "@id": "bts:Platelets" - }, - { - "@id": "bts:Prolymphocytes" - }, - { - "@id": "bts:Promonocytes" - }, - { - "@id": "bts:Promyelocytes" - }, - { - "@id": "bts:SegmentedNeutrophil" - }, - { - "@id": "bts:SerumFreeImmunoglobulinLightChain" - }, - { - "@id": "bts:Kappa" - }, - { - "@id": "bts:Lambda" - }, - { - "@id": "bts:NOS" - }, - { - "@id": "bts:Testosterone" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:TotalBilirubin" + "@id": "bts:Yes" }, { - "@id": "bts:TotalProtein" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -26862,69 +26995,83 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Laboratory Test", + "sms:displayName": "Perineural Invasion Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LociAbnormalCount", + "@id": "bts:LymphaticInvasionPresent", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", - "rdfs:label": "LociAbnormalCount", + "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", + "rdfs:label": "LymphaticInvasionPresent", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loci Abnormal Count", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lymphatic Invasion Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LociCount", + "@id": "bts:LymphNodesPositive", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci tested.", - "rdfs:label": "LociCount", + "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", + "rdfs:label": "LymphNodesPositive", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loci Count", + "sms:displayName": "Lymph Nodes Positive", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Locus", + "@id": "bts:LymphNodesTested", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", - "rdfs:label": "Locus", + "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", + "rdfs:label": "LymphNodesTested", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Locus", + "sms:displayName": "Lymph Nodes Tested", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MismatchRepairMutation", + "@id": "bts:PeritonealFluidCytologicalStatus", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MismatchRepairMutation", + "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", + "rdfs:label": "PeritonealFluidCytologicalStatus", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26932,10 +27079,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Atypical" }, { - "@id": "bts:No" + "@id": "bts:Malignant" + }, + { + "@id": "bts:Non-Malignant" + }, + { + "@id": "bts:Unsatisfactory" }, { "@id": "bts:Unknown" @@ -26944,18 +27097,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Mismatch Repair Mutation", + "sms:displayName": "Peritoneal Fluid Cytological Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MolecularConsequence", + "@id": "bts:ClassificationofTumor", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularConsequence", + "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", + "rdfs:label": "ClassificationofTumor", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26963,157 +27116,153 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:3PrimeUTRVariant" - }, - { - "@id": "bts:5PrimeUTRVariant" + "@id": "bts:Primary" }, { - "@id": "bts:CodingSequenceVariant" + "@id": "bts:Metastasis" }, { - "@id": "bts:DownstreamGeneVariant" + "@id": "bts:Recurrence" }, { - "@id": "bts:FeatureElongation" + "@id": "bts:Other" }, { - "@id": "bts:FeatureTruncation" + "@id": "bts:Unknown" }, { - "@id": "bts:FrameshiftVariant" + "@id": "bts:NotReported" }, { - "@id": "bts:IncompleteTerminalCodonVariant" - }, + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Classification of Tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BestOverallResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", + "rdfs:label": "BestOverallResponse", + "rdfs:subClassOf": [ { - "@id": "bts:InframeDeletion" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:InframeInsertion" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:IntergenicVariant" + "@id": "bts:CPD-ClinicalProgression" }, { - "@id": "bts:IntronVariant" + "@id": "bts:CR-CompleteResponse" }, { - "@id": "bts:MaturemiRNAVariant" + "@id": "bts:CRU-CompleteResponseUnconfirmed" }, { - "@id": "bts:MissenseVariant" + "@id": "bts:DU-DiseaseUnchanged" }, { - "@id": "bts:NMDTranscriptVariant" + "@id": "bts:IMR-Immunoresponse" }, { - "@id": "bts:Non-codingTranscriptExonVariant" + "@id": "bts:IPD-Immunoprogression" }, { - "@id": "bts:Non-codingTranscriptVariant" + "@id": "bts:MR-Minimal/MarginalResponse" }, { - "@id": "bts:ProteinAlteringVariant" + "@id": "bts:MX-MixedResponse" }, { - "@id": "bts:RegulatoryRegionAblation" + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" }, { - "@id": "bts:RegulatoryRegionAmplification" + "@id": "bts:NPB-NoPalliativeBenefit" }, { - "@id": "bts:RegulatoryRegionVariant" + "@id": "bts:NR-NoResponse" }, { - "@id": "bts:SpliceAcceptorVariant" + "@id": "bts:PA-PalliativeTherapy" }, { - "@id": "bts:SpliceDonorVariant" + "@id": "bts:PB-PalliativeBenefit" }, { - "@id": "bts:SpliceRegionVariant" + "@id": "bts:PD-ProgressiveDisease" }, { - "@id": "bts:StartLost" + "@id": "bts:PPD-Pseudoprogression" }, { - "@id": "bts:StopGain" + "@id": "bts:PR-PartialResponse" }, { - "@id": "bts:StopLost" + "@id": "bts:PSR-Pseudoresponse" }, { - "@id": "bts:StopRetainedVariant" + "@id": "bts:RD-ResponsiveDisease" }, { - "@id": "bts:SynonymousVariant" + "@id": "bts:RP-Response" }, { - "@id": "bts:TFBindingSiteVariant" + "@id": "bts:RPD-RadiographicProgressiveDisease" }, { - "@id": "bts:TFBSAblation" + "@id": "bts:SCR-StringentCompleteResponse" }, { - "@id": "bts:TFBSAmplification" + "@id": "bts:SD-StableDisease" }, { - "@id": "bts:TranscriptAblation" + "@id": "bts:SPD-SurgicalProgression" }, { - "@id": "bts:TranscriptAmplification" + "@id": "bts:TE-TooEarly" }, { - "@id": "bts:UpstreamGeneVariant" + "@id": "bts:VGPR-VeryGoodPartialResponse" } ], - "sms:displayName": "Molecular Consequence", + "sms:displayName": "Best Overall Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pathogenicity", + "@id": "bts:MitoticCount", "@type": "rdfs:Class", - "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", - "rdfs:label": "Pathogenicity", + "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", + "rdfs:label": "MitoticCount", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Benign" - }, - { - "@id": "bts:LikelyBenign" - }, - { - "@id": "bts:LikelyPathogenic" - }, - { - "@id": "bts:Pathogenic" - }, - { - "@id": "bts:UncertainSignificance" - } - ], - "sms:displayName": "Pathogenicity", + "sms:displayName": "Mitotic Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ploidy", + "@id": "bts:AJCCClinicalM", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", - "rdfs:label": "Ploidy", + "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalM", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27121,22 +27270,25 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aneuploid" + "@id": "bts:M0" }, { - "@id": "bts:Diploid" + "@id": "bts:M1" }, { - "@id": "bts:Hyperdiploid" + "@id": "bts:M1a" }, { - "@id": "bts:Hypodiploid" + "@id": "bts:M1b" }, { - "@id": "bts:NearDiploid" + "@id": "bts:M1c" }, { - "@id": "bts:Tetraploid" + "@id": "bts:MX" + }, + { + "@id": "bts:CM0(i+)" }, { "@id": "bts:Unknown" @@ -27145,188 +27297,115 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Ploidy", + "sms:displayName": "AJCC Clinical M", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SecondExon", + "@id": "bts:AJCCClinicalN", "@type": "rdfs:Class", - "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", - "rdfs:label": "SecondExon", + "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalN", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Second Exon", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondGeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SecondGeneSymbol", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second Gene Symbol", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SpecializedMolecularTest", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SpecializedMolecularTest", - "rdfs:subClassOf": [ + "@id": "bts:N0" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Specialized Molecular Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestAnalyteType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestAnalyteType", - "rdfs:subClassOf": [ + "@id": "bts:N0(i+)" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:N0(i-)" + }, { - "@id": "bts:DNA" + "@id": "bts:N0(mol+)" }, { - "@id": "bts:MRNA" + "@id": "bts:N0(mol-)" }, { - "@id": "bts:MiRNA" + "@id": "bts:N1" }, { - "@id": "bts:ProteinAnalyte" + "@id": "bts:N1a" }, { - "@id": "bts:TotalRNA" + "@id": "bts:N1b" }, { - "@id": "bts:Unknown" + "@id": "bts:N1bI" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Test Analyte Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestUnits", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestUnits", - "rdfs:subClassOf": [ + "@id": "bts:N1bII" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Test Units", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestValue", - "@type": "rdfs:Class", - "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", - "rdfs:label": "TestValue", - "rdfs:subClassOf": [ + "@id": "bts:N1bIII" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Test Value", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Transcript", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Transcript", - "rdfs:subClassOf": [ + "@id": "bts:N1bIV" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VariantOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "VariantOrigin", - "rdfs:subClassOf": [ + "@id": "bts:N1c" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:N1mi" + }, { - "@id": "bts:Germline" + "@id": "bts:N2" }, { - "@id": "bts:Somatic" + "@id": "bts:N2a" + }, + { + "@id": "bts:N2b" + }, + { + "@id": "bts:N2c" + }, + { + "@id": "bts:N3" + }, + { + "@id": "bts:N3a" + }, + { + "@id": "bts:N3b" + }, + { + "@id": "bts:N3c" + }, + { + "@id": "bts:N4" + }, + { + "@id": "bts:NX" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Variant Origin", + "sms:displayName": "AJCC Clinical N", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VariantType", + "@id": "bts:AJCCClinicalStage", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of genetic variation.", - "rdfs:label": "VariantType", + "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", + "rdfs:label": "AJCCClinicalStage", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27334,70 +27413,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Alleles" + "@id": "bts:Stage0" }, { - "@id": "bts:Amplification" + "@id": "bts:Stage0a" }, { - "@id": "bts:Chrimerism" + "@id": "bts:Stage0is" }, { - "@id": "bts:Conversion" + "@id": "bts:StageI" }, { - "@id": "bts:Deletion" + "@id": "bts:StageIA" }, { - "@id": "bts:Deletion-Insertion" + "@id": "bts:StageIA1" }, { - "@id": "bts:Duplication" + "@id": "bts:StageIA2" }, { - "@id": "bts:Extension" + "@id": "bts:StageIB" }, { - "@id": "bts:Gain" + "@id": "bts:StageIB1" }, { - "@id": "bts:Hypermethylation" + "@id": "bts:StageIB2" }, { - "@id": "bts:Insertion" + "@id": "bts:StageIC" }, { - "@id": "bts:Inversion" + "@id": "bts:StageII" }, { - "@id": "bts:Loss" + "@id": "bts:StageIIA" }, { - "@id": "bts:Methylation" + "@id": "bts:StageIIA1" }, { - "@id": "bts:Mosaicism" + "@id": "bts:StageIIA2" }, { - "@id": "bts:Other" + "@id": "bts:StageIIB" }, { - "@id": "bts:PartialMethylation" + "@id": "bts:StageIIC" }, { - "@id": "bts:Rearrangement" + "@id": "bts:StageIIC1" }, { - "@id": "bts:RepeatedSequences" + "@id": "bts:StageIII" }, { - "@id": "bts:Splice" + "@id": "bts:StageIIIA" }, { - "@id": "bts:Substitution" + "@id": "bts:StageIIIB" }, { - "@id": "bts:Translocation" + "@id": "bts:StageIIIC" + }, + { + "@id": "bts:StageIIIC1" + }, + { + "@id": "bts:StageIIIC2" + }, + { + "@id": "bts:StageIS" + }, + { + "@id": "bts:StageIV" + }, + { + "@id": "bts:StageIVA" + }, + { + "@id": "bts:StageIVB" + }, + { + "@id": "bts:StageIVC" + }, + { + "@id": "bts:StageTis" + }, + { + "@id": "bts:StageX" }, { "@id": "bts:Unknown" @@ -27406,18 +27512,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Variant Type", + "sms:displayName": "AJCC Clinical Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zygosity", + "@id": "bts:AJCCClinicalT", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", - "rdfs:label": "Zygosity", + "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalT", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27425,223 +27531,172 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Heterozygous" + "@id": "bts:T0" }, { - "@id": "bts:Hemizygous" + "@id": "bts:T1" }, { - "@id": "bts:Homozygous" + "@id": "bts:T1a" }, { - "@id": "bts:Nullizygous" + "@id": "bts:T1a1" }, { - "@id": "bts:Unknown" + "@id": "bts:T1a2" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Zygosity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SourceHTANBiospecimenID", - "@type": "rdfs:Class", - "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", - "rdfs:label": "SourceHTANBiospecimenID", - "rdfs:subClassOf": [ + "@id": "bts:T1b" + }, { - "@id": "bts:Biosample" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Source HTAN Biospecimen ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", - "rdfs:label": "CollectionDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:T1b1" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:AdjacentBiospecimenIDs", - "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenIDs", - "rdfs:subClassOf": [ + "@id": "bts:T1b2" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adjacent Biospecimen IDs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Biospecimen Type", - "rdfs:label": "BiospecimenType", - "rdfs:subClassOf": [ + "@id": "bts:T1c" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:T1mi" + }, { - "@id": "bts:TissueBiospecimenType" + "@id": "bts:T2" }, { - "@id": "bts:BloodBiospecimenType" + "@id": "bts:T2a" }, { - "@id": "bts:AnalyteBiospecimenType" + "@id": "bts:T2a1" }, { - "@id": "bts:MouthRinseBiospecimenType" + "@id": "bts:T2a2" }, { - "@id": "bts:StoolBiospecimenType" + "@id": "bts:T2b" }, { - "@id": "bts:UrineBiospecimenType" + "@id": "bts:T2c" }, { - "@id": "bts:AscitesBiospecimenType" + "@id": "bts:T2d" }, { - "@id": "bts:SputumBiospecimenType" + "@id": "bts:T3" }, { - "@id": "bts:FluidsBiospecimenType" + "@id": "bts:T3a" }, { - "@id": "bts:BoneMarrowBiospecimenType" + "@id": "bts:T3b" }, { - "@id": "bts:CellsBiospecimenType" - } - ], - "sms:displayName": "Biospecimen Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", - "rdfs:subClassOf": [ + "@id": "bts:T3c" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:T3d" + }, { - "@id": "bts:Autopsy" + "@id": "bts:T4" }, { - "@id": "bts:Biopsy" + "@id": "bts:T4a" }, { - "@id": "bts:FineNeedleAspirate" + "@id": "bts:T4b" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:T4c" }, { - "@id": "bts:PunchBiopsy" + "@id": "bts:T4d" }, { - "@id": "bts:ShaveBiopsy" + "@id": "bts:T4e" }, { - "@id": "bts:Excision" + "@id": "bts:TX" }, { - "@id": "bts:Re-excision" + "@id": "bts:Ta" }, { - "@id": "bts:SentinelNodeBiopsy" + "@id": "bts:Tis" }, { - "@id": "bts:Lymphadenectomy-RegionalNodes" + "@id": "bts:Tis(DCIS)" }, { - "@id": "bts:OtherAcquisitionMethod" + "@id": "bts:Tis(LCIS)" }, { - "@id": "bts:Noninducedsputum" + "@id": "bts:Tis(Paget's)" }, { - "@id": "bts:Inducedsputum" + "@id": "bts:Unknown" }, { - "@id": "bts:BAL(bronchialalveolarlavage)" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Clinical T", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCPathologicM", + "@type": "rdfs:Class", + "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", + "rdfs:label": "AJCCPathologicM", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:M0" }, { - "@id": "bts:Cytobrush" + "@id": "bts:M1" }, { - "@id": "bts:Blooddraw" + "@id": "bts:M1a" }, { - "@id": "bts:Fluidcollection" + "@id": "bts:M1b" }, { - "@id": "bts:Forcepsbiopsy" + "@id": "bts:M1c" }, { - "@id": "bts:Coreneedlebiopsy" + "@id": "bts:MX" }, { - "@id": "bts:Endoscopicbiopsy" + "@id": "bts:CM0(i+)" }, { - "@id": "bts:Notspecified" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Acquisition Method Type", - "sms:required": "sms:true", + "sms:displayName": "AJCC Pathologic M", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FixativeType", + "@id": "bts:AJCCPathologicN", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", + "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", + "rdfs:label": "AJCCPathologicN", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27649,87 +27704,96 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Acetone" + "@id": "bts:N0" }, { - "@id": "bts:Alcohol" + "@id": "bts:N0(i+)" }, { - "@id": "bts:Formalin" + "@id": "bts:N0(i-)" }, { - "@id": "bts:Glutaraldehyde" + "@id": "bts:N0(mol+)" }, { - "@id": "bts:OCTmedia" + "@id": "bts:N0(mol-)" }, { - "@id": "bts:RNAlater" + "@id": "bts:N1" }, { - "@id": "bts:Saline" + "@id": "bts:N1a" }, { - "@id": "bts:95%Ethanol" + "@id": "bts:N1b" }, { - "@id": "bts:Dimidoester" + "@id": "bts:N1bI" }, { - "@id": "bts:Carbodiimide" + "@id": "bts:N1bII" }, { - "@id": "bts:Dimethylacetamide" + "@id": "bts:N1bIII" }, { - "@id": "bts:Para-benzoquinone" + "@id": "bts:N1bIV" }, { - "@id": "bts:PAXgenetissue" + "@id": "bts:N1c" }, { - "@id": "bts:TCLlysisbuffer" + "@id": "bts:N1mi" }, { - "@id": "bts:NP40lysisbuffer" + "@id": "bts:N2" }, { - "@id": "bts:Methacarn" + "@id": "bts:N2a" }, { - "@id": "bts:Cryo-store" + "@id": "bts:N2b" }, { - "@id": "bts:Carnoy'sFixative" + "@id": "bts:N2c" }, { - "@id": "bts:Polaxamer" + "@id": "bts:N3" }, { - "@id": "bts:Other" + "@id": "bts:N3a" }, { - "@id": "bts:None" + "@id": "bts:N3b" + }, + { + "@id": "bts:N3c" + }, + { + "@id": "bts:N4" + }, + { + "@id": "bts:NX" }, { "@id": "bts:Unknown" }, { - "@id": "bts:Unfixed" + "@id": "bts:NotReported" } ], - "sms:displayName": "Fixative Type", - "sms:required": "sms:true", + "sms:displayName": "AJCC Pathologic N", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StorageMethod", + "@id": "bts:AJCCPathologicStage", "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", + "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", + "rdfs:label": "AJCCPathologicStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27737,168 +27801,117 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Ambienttemperature" + "@id": "bts:Stage0" }, { - "@id": "bts:Cutslide" + "@id": "bts:Stage0a" }, { - "@id": "bts:Fresh" + "@id": "bts:Stage0is" }, { - "@id": "bts:Frozenat-20C" + "@id": "bts:StageI" }, { - "@id": "bts:Frozenat-70C" + "@id": "bts:StageIA" }, { - "@id": "bts:Frozenat-80C" + "@id": "bts:StageIA1" }, { - "@id": "bts:Frozenat-150C" + "@id": "bts:StageIA2" }, { - "@id": "bts:Frozeninliquidnitrogen" + "@id": "bts:StageIB" }, { - "@id": "bts:Frozeninvaporphase" + "@id": "bts:StageIB1" }, { - "@id": "bts:Paraffinblock" + "@id": "bts:StageIB2" }, { - "@id": "bts:RNAlaterat4C" + "@id": "bts:StageIC" }, { - "@id": "bts:RNAlaterat25C" + "@id": "bts:StageII" }, { - "@id": "bts:RNAlaterat-20C" + "@id": "bts:StageIIA" }, { - "@id": "bts:Refrigeratedat4degrees" + "@id": "bts:StageIIA1" }, { - "@id": "bts:Refrigeratedvacuumchamber" + "@id": "bts:StageIIA2" }, { - "@id": "bts:4Cinvacuumchamber" + "@id": "bts:StageIIB" }, { - "@id": "bts:Desiccantat4C" + "@id": "bts:StageIIC" }, { - "@id": "bts:NotApplicable" + "@id": "bts:StageIIC1" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", - "rdfs:label": "ProcessingDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:StageIII" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:ProtocolLink", - "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label": "ProtocolLink", - "rdfs:subClassOf": [ + "@id": "bts:StageIIIA" + }, { - "@id": "bts:InformationContentEntity" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Protocol Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteDataSource", - "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", - "rdfs:subClassOf": [ + "@id": "bts:StageIIIB" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Site Data Source", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionMedia", - "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", - "rdfs:subClassOf": [ + "@id": "bts:StageIIIC" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StageIIIC1" + }, { - "@id": "bts:DMEM" + "@id": "bts:StageIIIC2" }, { - "@id": "bts:DMEM+Serum" + "@id": "bts:StageIS" }, { - "@id": "bts:RPMI" + "@id": "bts:StageIV" }, { - "@id": "bts:RPMI+Serum" + "@id": "bts:StageIVA" }, { - "@id": "bts:PBS" + "@id": "bts:StageIVB" }, { - "@id": "bts:PBS+Serum" + "@id": "bts:StageIVC" }, { - "@id": "bts:None" + "@id": "bts:StageTis" + }, + { + "@id": "bts:StageX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Collection Media", + "sms:displayName": "AJCC Pathologic Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MountingMedium", + "@id": "bts:AJCCPathologicT", "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", + "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", + "rdfs:label": "AJCCPathologicT", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27906,253 +27919,209 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aqueouswaterbased" + "@id": "bts:T0" }, { - "@id": "bts:Non-AqueousSolventbased" + "@id": "bts:T1" }, { - "@id": "bts:Xylene" + "@id": "bts:T1a" }, { - "@id": "bts:Toluene" + "@id": "bts:T1a1" }, { - "@id": "bts:AntifadewithDAPI" + "@id": "bts:T1a2" }, { - "@id": "bts:AntifadewithoutDAPI" + "@id": "bts:T1b" }, { - "@id": "bts:PBS" + "@id": "bts:T1b1" }, { - "@id": "bts:Unknown" + "@id": "bts:T1b2" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mounting Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingLocation", - "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentBy", - "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pathologist" + "@id": "bts:T1c" }, { - "@id": "bts:ResearchScientist" + "@id": "bts:T1mi" }, { - "@id": "bts:Other" + "@id": "bts:T2" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment By", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Digital" + "@id": "bts:T2a" }, { - "@id": "bts:Microscopy" + "@id": "bts:T2a1" }, { - "@id": "bts:Other" + "@id": "bts:T2a2" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PreinvasiveMorphology", - "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", - "rdfs:label": "PreinvasiveMorphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Melanocytichyperplasia" + "@id": "bts:T2b" }, { - "@id": "bts:Atypicalmelanocyticproliferation" + "@id": "bts:T2c" }, { - "@id": "bts:Melanomainsitu-superficialspreading" + "@id": "bts:T2d" }, { - "@id": "bts:Melanomainsitu-lentigomalignatype" + "@id": "bts:T3" }, { - "@id": "bts:Melanomainsitu-acral-lentiginous" + "@id": "bts:T3a" }, { - "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" + "@id": "bts:T3b" }, { - "@id": "bts:Persistentmelanomainsitu" + "@id": "bts:T3c" }, { - "@id": "bts:Melanomainsitu-nototherwiseclassified" + "@id": "bts:T3d" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:T4" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:T4a" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:T4b" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:T4c" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:T4d" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:T4e" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:TX" }, { - "@id": "bts:Invasivemelanoma-other" + "@id": "bts:Ta" }, { - "@id": "bts:NormalWDA" + "@id": "bts:Tis" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:Tis(DCIS)" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:Tis(LCIS)" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:Tis(Paget's)" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:Unknown" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Pathologic T", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCStagingSystemEdition", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", + "rdfs:label": "AJCCStagingSystemEdition", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:1st" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:2nd" }, { - "@id": "bts:SquamousCarcinomainsitu" + "@id": "bts:3rd" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:4th" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:5th" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:6th" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:7th" }, { - "@id": "bts:Hamartoma" + "@id": "bts:8th" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:NotReported" } ], - "sms:displayName": "Preinvasive Morphology", + "sms:displayName": "AJCC Staging System Edition", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorInfiltratingLymphocytes", + "@id": "bts:CogNeuroblastomaRiskGroup", "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:comment": "Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.", + "rdfs:label": "CogNeuroblastomaRiskGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", + "schema:rangeIncludes": [ + { + "@id": "bts:HighRisk" + }, + { + "@id": "bts:IntermediateRisk" + }, + { + "@id": "bts:LowRisk" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cog Neuroblastoma Risk Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DegreeofDysplasia", + "@id": "bts:CogRhabdomyosarcomaRiskGroup", "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", + "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).", + "rdfs:label": "CogRhabdomyosarcomaRiskGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28160,257 +28129,336 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" - }, - { - "@id": "bts:Milddysplasia" + "@id": "bts:HighRisk" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:IntermediateRisk" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:LowRisk" }, { - "@id": "bts:CarcinomainSitu" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" } ], - "sms:displayName": "Degree of Dysplasia", + "sms:displayName": "Cog Rhabdomyosarcoma Risk Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DysplasiaFraction", + "@id": "bts:GleasonGradeGroup", "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", + "rdfs:comment": "The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "GleasonGradeGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dysplasia Fraction", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NumberProliferatingCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Group1" + }, + { + "@id": "bts:Group2" + }, + { + "@id": "bts:Group3" + }, + { + "@id": "bts:Group4" + }, + { + "@id": "bts:Group5" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number Proliferating Cells", + "sms:displayName": "Gleason Grade Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentEosinophilInfiltration", + "@id": "bts:GleasonGradeTertiary", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", + "rdfs:label": "GleasonGradeTertiary", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Eosinophil Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentGranulocyteInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Granulocyte Infiltration", + "sms:displayName": "Gleason Grade Tertiary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentInflamInfiltration", + "@id": "bts:GleasonPatternsPercent", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", + "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", + "rdfs:label": "GleasonPatternsPercent", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Inflam Infiltration", + "sms:displayName": "Gleason Patterns Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentLymphocyteInfiltration", + "@id": "bts:GreatestTumorDimension", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", + "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", + "rdfs:label": "GreatestTumorDimension", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Lymphocyte Infiltration", + "sms:displayName": "Greatest Tumor Dimension", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentMonocyteInfiltration", + "@id": "bts:IGCCCGStage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", + "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", + "rdfs:label": "IGCCCGStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Monocyte Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentNecrosis", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:GoodPrognosis" + }, + { + "@id": "bts:IntermediatePrognosis" + }, + { + "@id": "bts:PoorPrognosis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Necrosis", + "sms:displayName": "IGCCCG Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNeutrophilInfiltration", + "@id": "bts:INPCGrade", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", + "rdfs:label": "INPCGrade", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Neutrophil Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Differentiating" + }, + { + "@id": "bts:PoorlyDifferentiated" + }, + { + "@id": "bts:Undifferentiated" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNormalCells", + "@id": "bts:INPCHistologicGroup", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", + "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", + "rdfs:label": "INPCHistologicGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Normal Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:Favorable" + }, + { + "@id": "bts:Unfavorable" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Histologic Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentStromalCells", + "@id": "bts:INRGStage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", + "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", + "rdfs:label": "INRGStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Stromal Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:L1" + }, + { + "@id": "bts:L2" + }, + { + "@id": "bts:M" + }, + { + "@id": "bts:Ms" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INRG Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorCells", + "@id": "bts:INSSStage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", + "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", + "rdfs:label": "INSSStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:Stage1" + }, + { + "@id": "bts:Stage2A" + }, + { + "@id": "bts:Stage2B" + }, + { + "@id": "bts:Stage3" + }, + { + "@id": "bts:Stage4" + }, + { + "@id": "bts:Stage4S" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INSS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorNuclei", + "@id": "bts:InternationalPrognosticIndex", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", + "rdfs:comment": "The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.", + "rdfs:label": "InternationalPrognosticIndex", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Nuclei", + "schema:rangeIncludes": [ + { + "@id": "bts:LowRisk" + }, + { + "@id": "bts:Low-IntermediateRisk" + }, + { + "@id": "bts:High-IntermediateRisk" + }, + { + "@id": "bts:HighRisk" + } + ], + "sms:displayName": "International Prognostic Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FiducialMarker", + "@id": "bts:IRSGroup", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", + "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28418,19 +28466,34 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NuclearStain-DAPI" + "@id": "bts:GroupI" }, { - "@id": "bts:FluorescentBeads" + "@id": "bts:GroupIa" }, { - "@id": "bts:GridSlides-Hemocytometer" + "@id": "bts:GroupIb" }, { - "@id": "bts:AdhesiveMarkers" + "@id": "bts:GroupII" }, { - "@id": "bts:Other" + "@id": "bts:GroupIIa" + }, + { + "@id": "bts:GroupIIc" + }, + { + "@id": "bts:GroupIII" + }, + { + "@id": "bts:GroupIIIa" + }, + { + "@id": "bts:GroupIIIb" + }, + { + "@id": "bts:GroupIV" }, { "@id": "bts:Unknown" @@ -28439,18 +28502,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Fiducial Marker", + "sms:displayName": "IRS Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlicingMethod", + "@id": "bts:IRSStage", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", + "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28458,22 +28521,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Vibratome" - }, - { - "@id": "bts:Cryosectioning" - }, - { - "@id": "bts:Tissuemolds" + "@id": "bts:1" }, { - "@id": "bts:Slidingmicrotome" + "@id": "bts:2" }, { - "@id": "bts:Sectioning" + "@id": "bts:3" }, { - "@id": "bts:Other" + "@id": "bts:4" }, { "@id": "bts:Unknown" @@ -28482,173 +28539,157 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Slicing Method", + "sms:displayName": "IRS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LysisBuffer", + "@id": "bts:ISSStage", "@type": "rdfs:Class", - "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", - "rdfs:label": "LysisBuffer", + "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", + "rdfs:label": "ISSStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lysis Buffer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MethodofNucleicAcidIsolation", - "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", - "rdfs:label": "MethodofNucleicAcidIsolation", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Method of Nucleic Acid Isolation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Biosample", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Biosample", - "rdfs:subClassOf": [ + "@id": "bts:I" + }, { - "@id": "bts:Thing" + "@id": "bts:II" + }, + { + "@id": "bts:III" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Biosample", + "sms:displayName": "ISS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SRRSBiospecimen", + "@id": "bts:LymphNodeInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", - "rdfs:label": "SRRSBiospecimen", + "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", + "rdfs:label": "LymphNodeInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Biospecimen", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "schema:rangeIncludes": [ { - "@id": "bts:Patient" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Axillary" + }, { - "@id": "bts:Component" + "@id": "bts:Cervical" }, { - "@id": "bts:HTANBiospecimenID" + "@id": "bts:Epitrochlear" }, { - "@id": "bts:SourceHTANBiospecimenID" + "@id": "bts:Femoral" }, { - "@id": "bts:HTANParentID" + "@id": "bts:Hilar" }, { - "@id": "bts:AdjacentBiospecimenIDs" + "@id": "bts:Iliac-common" }, { - "@id": "bts:BiospecimenType" + "@id": "bts:Iliac-external" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Iliac" }, { - "@id": "bts:CollectionDaysfromIndex" + "@id": "bts:NOS" }, { - "@id": "bts:AcquisitionMethodType" + "@id": "bts:Inguinal" }, { - "@id": "bts:IschemicTime" + "@id": "bts:Mediastinal" }, { - "@id": "bts:IschemicTemperature" + "@id": "bts:Mesenteric" }, { - "@id": "bts:CollectionMedia" + "@id": "bts:None" }, { - "@id": "bts:TopographyCode" + "@id": "bts:Occipital" }, { - "@id": "bts:AdditionalTopography" + "@id": "bts:Paraaortic" }, { - "@id": "bts:FixativeType" + "@id": "bts:Parotid" }, { - "@id": "bts:StorageMethod" + "@id": "bts:Popliteal" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:Retroperitoneal" }, { - "@id": "bts:HistologicMorphologyCode" + "@id": "bts:Splenic" }, { - "@id": "bts:PreservationMethod" + "@id": "bts:Submandibular" }, { - "@id": "bts:ProcessingDaysfromIndex" + "@id": "bts:Supraclavicular" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], + "sms:displayName": "Lymph Node Involved Site", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IschemicTime", + "@id": "bts:MarginDistance", "@type": "rdfs:Class", - "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", - "rdfs:label": "IschemicTime", + "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", + "rdfs:label": "MarginDistance", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ischemic Time", + "sms:displayName": "Margin Distance", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IschemicTemperature", + "@id": "bts:MarginsInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", - "rdfs:label": "IschemicTemperature", + "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", + "rdfs:label": "MarginsInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28656,39 +28697,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:WarmIschemia" + "@id": "bts:GerotaFascia" }, { - "@id": "bts:ColdIschemia" + "@id": "bts:Parenchyma" }, { - "@id": "bts:Ambientair" + "@id": "bts:PerinephricFat" }, { - "@id": "bts:4Cwetice" + "@id": "bts:Renal" }, { - "@id": "bts:Negative-20C" + "@id": "bts:RenalCapsule" }, { - "@id": "bts:DryIce" + "@id": "bts:RenalSinus" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:RenalVein" }, { - "@id": "bts:Unknown" + "@id": "bts:Ureter" } ], - "sms:displayName": "Ischemic Temperature", + "sms:displayName": "Margins Involved Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TopographyCode", + "@id": "bts:MedulloblastomaMolecularClassification", "@type": "rdfs:Class", - "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", - "rdfs:label": "TopographyCode", + "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", + "rdfs:label": "MedulloblastomaMolecularClassification", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -28699,973 +28740,1467 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:C00.0" - }, - { - "@id": "bts:C00.1" - }, - { - "@id": "bts:C00.2" - }, - { - "@id": "bts:C00.3" + "@id": "bts:NotDetermined" }, { - "@id": "bts:C00.4" + "@id": "bts:Non-WNT/non-SHHActivated" }, { - "@id": "bts:C00.5" + "@id": "bts:SHH-Activated" }, { - "@id": "bts:C00.6" + "@id": "bts:WNT-Activated" }, { - "@id": "bts:C00.8" + "@id": "bts:Unknown" }, { - "@id": "bts:C01.9" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Medulloblastoma Molecular Classification", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MicropapillaryFeatures", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", + "rdfs:label": "MicropapillaryFeatures", + "rdfs:subClassOf": [ { - "@id": "bts:C02.0" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C02.1" + "@id": "bts:Absent" }, { - "@id": "bts:C02.2" + "@id": "bts:Present" }, { - "@id": "bts:C02.3" + "@id": "bts:Unknown" }, { - "@id": "bts:C02.4" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Micropapillary Features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MitosisKaryorrhexisIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", + "rdfs:label": "MitosisKaryorrhexisIndex", + "rdfs:subClassOf": [ { - "@id": "bts:C02.8" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C02.9" + "@id": "bts:High" }, { - "@id": "bts:C03.0" + "@id": "bts:Intermediate" }, { - "@id": "bts:C03.1" + "@id": "bts:Low" }, { - "@id": "bts:C03.9" + "@id": "bts:Unknown" }, { - "@id": "bts:C04.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mitosis Karyorrhexis Index", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NonNodalRegionalDisease", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", + "rdfs:label": "NonNodalRegionalDisease", + "rdfs:subClassOf": [ { - "@id": "bts:C04.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C04.8" + "@id": "bts:Absent" }, { - "@id": "bts:C04.9" + "@id": "bts:Indeterminate" }, { - "@id": "bts:C05.0" + "@id": "bts:Present" }, { - "@id": "bts:C05.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C05.2" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Regional Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NonNodalTumorDeposits", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", + "rdfs:label": "NonNodalTumorDeposits", + "rdfs:subClassOf": [ { - "@id": "bts:C05.8" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C05.9" + "@id": "bts:Yes" }, { - "@id": "bts:C06.0" + "@id": "bts:No" }, { - "@id": "bts:C06.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C06.2" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Tumor Deposits", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianSpecimenStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", + "rdfs:label": "OvarianSpecimenStatus", + "rdfs:subClassOf": [ { - "@id": "bts:C06.8" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C06.9" + "@id": "bts:OvarianCapsuleIntact" }, { - "@id": "bts:C07.9" + "@id": "bts:OvarianCapsuleRuptured" }, { - "@id": "bts:C08.0" + "@id": "bts:OvarianCapsuleFragmented" }, { - "@id": "bts:C08.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C08.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ovarian Specimen Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianSurfaceInvolvement", + "@type": "rdfs:Class", + "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", + "rdfs:label": "OvarianSurfaceInvolvement", + "rdfs:subClassOf": [ { - "@id": "bts:C08.9" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C09.0" + "@id": "bts:Absent" }, { - "@id": "bts:C09.1" + "@id": "bts:Present" }, { - "@id": "bts:C09.8" + "@id": "bts:Indeterminate" }, { - "@id": "bts:C09.9" + "@id": "bts:Unknown" }, { - "@id": "bts:C10.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ovarian Surface Involvement", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnantatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", + "rdfs:label": "PregnantatDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:C10.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C10.2" + "@id": "bts:Yes" }, { - "@id": "bts:C10.3" + "@id": "bts:No" }, { - "@id": "bts:C10.4" + "@id": "bts:Unknown" }, { - "@id": "bts:C10.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pregnant at Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryGleasonGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "PrimaryGleasonGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C10.9" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C11.0" + "@id": "bts:Pattern1" }, { - "@id": "bts:C11.1" + "@id": "bts:Pattern2" }, { - "@id": "bts:C11.2" + "@id": "bts:Pattern3" }, { - "@id": "bts:C11.3" + "@id": "bts:Pattern4" }, { - "@id": "bts:C11.8" - }, + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Primary Gleason Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondaryGleasonGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "SecondaryGleasonGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C11.9" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C12.9" + "@id": "bts:Pattern1" }, { - "@id": "bts:C13.0" + "@id": "bts:Pattern2" }, { - "@id": "bts:C13.1" + "@id": "bts:Pattern3" }, { - "@id": "bts:C13.2" + "@id": "bts:Pattern4" }, { - "@id": "bts:C13.8" - }, - { - "@id": "bts:C13.9" - }, - { - "@id": "bts:C14.0" - }, - { - "@id": "bts:C14.2" - }, - { - "@id": "bts:C14.8" - }, - { - "@id": "bts:C15.0" - }, - { - "@id": "bts:C15.1" - }, - { - "@id": "bts:C15.2" - }, - { - "@id": "bts:C15.3" - }, - { - "@id": "bts:C15.4" - }, - { - "@id": "bts:C15.5" - }, - { - "@id": "bts:C15.8" - }, + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Secondary Gleason Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SupratentorialLocalization", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", + "rdfs:label": "SupratentorialLocalization", + "rdfs:subClassOf": [ { - "@id": "bts:C15.9" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C16.0" + "@id": "bts:CerebralCortex" }, { - "@id": "bts:C16.1" + "@id": "bts:DeepGray" }, { - "@id": "bts:C16.2" + "@id": "bts:SpinalCord" }, { - "@id": "bts:C16.3" + "@id": "bts:WhiteMatter" }, { - "@id": "bts:C16.4" + "@id": "bts:Unknown" }, { - "@id": "bts:C16.5" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Supratentorial Localization", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorDepth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", + "rdfs:label": "TumorDepth", + "rdfs:subClassOf": [ { - "@id": "bts:C16.6" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tumor Depth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHOCNSGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO CNS Grade", + "rdfs:label": "WHOCNSGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C16.8" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C16.9" + "@id": "bts:GradeI" }, { - "@id": "bts:C17.0" + "@id": "bts:GradeII" }, { - "@id": "bts:C17.1" + "@id": "bts:GradeIII" }, { - "@id": "bts:C17.2" + "@id": "bts:GradeIV" }, { - "@id": "bts:C17.3" + "@id": "bts:GradeNotAssigned" }, { - "@id": "bts:C17.8" + "@id": "bts:Unknown" }, { - "@id": "bts:C17.9" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO CNS Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHONTEGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO NTE Grade", + "rdfs:label": "WHONTEGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C18.0" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C18.1" + "@id": "bts:G1" }, { - "@id": "bts:C18.2" + "@id": "bts:G2" }, { - "@id": "bts:C18.3" + "@id": "bts:G3" }, { - "@id": "bts:C18.4" + "@id": "bts:GX" }, { - "@id": "bts:C18.5" + "@id": "bts:Unknown" }, { - "@id": "bts:C18.6" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO NTE Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AAChange", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "AAChange", + "rdfs:subClassOf": [ { - "@id": "bts:C18.7" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "AA Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Antigen", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Antigen", + "rdfs:subClassOf": [ { - "@id": "bts:C18.8" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C18.9" + "@id": "bts:BCL6" }, { - "@id": "bts:C19.9" + "@id": "bts:CA-125" }, { - "@id": "bts:C20.9" + "@id": "bts:CA19-9" }, { - "@id": "bts:C21.0" + "@id": "bts:CCND1" }, { - "@id": "bts:C21.1" + "@id": "bts:CD10" }, { - "@id": "bts:C21.2" + "@id": "bts:CD117" }, { - "@id": "bts:C21.8" + "@id": "bts:CD138" }, { - "@id": "bts:C22.0" + "@id": "bts:CD14" }, { - "@id": "bts:C22.1" + "@id": "bts:CD15" }, { - "@id": "bts:C23.9" + "@id": "bts:CD19" }, { - "@id": "bts:C24.0" + "@id": "bts:CD20" }, { - "@id": "bts:C24.1" + "@id": "bts:CD22" }, { - "@id": "bts:C24.8" + "@id": "bts:CD23" }, { - "@id": "bts:C24.9" + "@id": "bts:CD25" }, { - "@id": "bts:C25.0" + "@id": "bts:CD3" }, { - "@id": "bts:C25.1" + "@id": "bts:CD30" }, { - "@id": "bts:C25.2" + "@id": "bts:CD33" }, { - "@id": "bts:C25.3" + "@id": "bts:CD34" }, { - "@id": "bts:C25.4" + "@id": "bts:CD45" }, { - "@id": "bts:C25.7" + "@id": "bts:CD5" }, { - "@id": "bts:C25.8" + "@id": "bts:CD56" }, { - "@id": "bts:C25.9" + "@id": "bts:CD7" }, { - "@id": "bts:C26.0" + "@id": "bts:CD79A" }, { - "@id": "bts:C26.8" + "@id": "bts:CEA" }, { - "@id": "bts:C26.9" + "@id": "bts:HLA-DR" }, { - "@id": "bts:C30.0" + "@id": "bts:Mesothelin" }, { - "@id": "bts:C30.1" + "@id": "bts:NSE" }, { - "@id": "bts:C31.0" + "@id": "bts:SquamousCellCarcinomaAntigen" }, { - "@id": "bts:C31.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C31.2" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Antigen", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalBiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "ClinicalBiospecimenType", + "rdfs:subClassOf": [ { - "@id": "bts:C31.3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C31.8" + "@id": "bts:Blood" }, { - "@id": "bts:C31.9" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:C32.0" + "@id": "bts:BuccalMucosa" }, { - "@id": "bts:C32.1" + "@id": "bts:BuffyCoat" }, { - "@id": "bts:C32.2" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:C32.3" + "@id": "bts:ConnectiveTissue" }, { - "@id": "bts:C32.8" + "@id": "bts:EmbryonicFluid" }, { - "@id": "bts:C32.9" + "@id": "bts:EmbryonicTissue" }, { - "@id": "bts:C33.9" + "@id": "bts:Feces" }, { - "@id": "bts:C34.0" + "@id": "bts:Granulocyte" }, { - "@id": "bts:C34.1" + "@id": "bts:MuscleTissue" }, { - "@id": "bts:C34.2" + "@id": "bts:NerveTissue" }, { - "@id": "bts:C34.3" + "@id": "bts:PeritonealFluid" }, { - "@id": "bts:C34.8" + "@id": "bts:Plasma" }, { - "@id": "bts:C34.9" + "@id": "bts:PleuralFluid" }, { - "@id": "bts:C37.9" + "@id": "bts:Saliva" }, { - "@id": "bts:C38.0" + "@id": "bts:Serum" }, { - "@id": "bts:C38.1" + "@id": "bts:Skin" }, { - "@id": "bts:C38.2" + "@id": "bts:SoftTissue" }, { - "@id": "bts:C38.3" + "@id": "bts:TissueNOS" }, { - "@id": "bts:C38.4" + "@id": "bts:UninvolvedTissueNOS" }, { - "@id": "bts:C38.8" + "@id": "bts:Urine" }, { - "@id": "bts:C39.0" + "@id": "bts:Unknown" }, { - "@id": "bts:C39.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Clinical Biospecimen Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeUpper", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeUpper", + "rdfs:subClassOf": [ { - "@id": "bts:C39.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Upper", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeLower", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:subClassOf": [ { - "@id": "bts:C40.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Lower", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CellCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CellCount", + "rdfs:subClassOf": [ { - "@id": "bts:C40.1" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Chromosome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Chromosome", + "rdfs:subClassOf": [ { - "@id": "bts:C40.3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C40.8" + "@id": "bts:Chr1" }, { - "@id": "bts:C40.9" + "@id": "bts:Chr2" }, { - "@id": "bts:C41.0" + "@id": "bts:Chr3" }, { - "@id": "bts:C41.1" + "@id": "bts:Chr4" }, { - "@id": "bts:C41.2" + "@id": "bts:Chr5" }, { - "@id": "bts:C41.3" + "@id": "bts:Chr6" }, { - "@id": "bts:C41.4" + "@id": "bts:Chr7" }, { - "@id": "bts:C41.8" + "@id": "bts:Chr8" }, { - "@id": "bts:C41.9" + "@id": "bts:Chr9" }, { - "@id": "bts:C42.0" + "@id": "bts:Chr10" }, { - "@id": "bts:C42.1" + "@id": "bts:Chr11" }, { - "@id": "bts:C42.2" + "@id": "bts:Chr12" }, { - "@id": "bts:C42.3" + "@id": "bts:Chr13" }, { - "@id": "bts:C42.4" + "@id": "bts:Chr14" }, { - "@id": "bts:C44.0" + "@id": "bts:Chr15" }, { - "@id": "bts:C44.1" + "@id": "bts:Chr16" }, { - "@id": "bts:C44.2" + "@id": "bts:Chr17" }, { - "@id": "bts:C44.3" + "@id": "bts:Chr18" }, { - "@id": "bts:C44.4" + "@id": "bts:Chr19" }, { - "@id": "bts:C44.5" + "@id": "bts:Chr20" }, { - "@id": "bts:C44.6" + "@id": "bts:Chr21" }, { - "@id": "bts:C44.7" + "@id": "bts:Chr22" }, { - "@id": "bts:C47.0" + "@id": "bts:Chr23" }, { - "@id": "bts:C47.1" + "@id": "bts:ChrM" }, { - "@id": "bts:C47.2" + "@id": "bts:ChrX" }, { - "@id": "bts:C47.3" + "@id": "bts:ChrY" }, { - "@id": "bts:C47.4" + "@id": "bts:Unknown" }, { - "@id": "bts:C47.5" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Chromosome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Clonality", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Clonality", + "rdfs:subClassOf": [ { - "@id": "bts:C47.6" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C47.8" + "@id": "bts:Clonal" }, { - "@id": "bts:C47.9" - }, + "@id": "bts:Non-clonal" + } + ], + "sms:displayName": "Clonality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CopyNumber", + "rdfs:subClassOf": [ { - "@id": "bts:C48.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Copy Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cytoband", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Cytoband", + "rdfs:subClassOf": [ { - "@id": "bts:C48.1" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cytoband", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Exon", + "@type": "rdfs:Class", + "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Exon", + "rdfs:subClassOf": [ { - "@id": "bts:C48.2" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneFamily", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "rdfs:label": "HistoneFamily", + "rdfs:subClassOf": [ { - "@id": "bts:C48.8" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C49.0" + "@id": "bts:H1" }, { - "@id": "bts:C49.1" + "@id": "bts:H2A" }, { - "@id": "bts:C49.2" + "@id": "bts:H2B" }, { - "@id": "bts:C49.3" + "@id": "bts:H3" }, { - "@id": "bts:C49.4" + "@id": "bts:H4" }, { - "@id": "bts:C49.5" + "@id": "bts:Unknown" }, { - "@id": "bts:C49.6" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Family", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneVariant", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "HistoneVariant", + "rdfs:subClassOf": [ { - "@id": "bts:C49.8" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C49.9" + "@id": "bts:CENP-A" }, { - "@id": "bts:C50.0" + "@id": "bts:H2A-Bbd" }, { - "@id": "bts:C50.1" + "@id": "bts:H2A.X" }, { - "@id": "bts:C50.2" + "@id": "bts:H2A.Z" }, { - "@id": "bts:C50.3" + "@id": "bts:H2A.Z.1" }, { - "@id": "bts:C50.4" + "@id": "bts:H2A.Z.2" }, { - "@id": "bts:C50.5" + "@id": "bts:H2A.Z.2.2" }, { - "@id": "bts:C50.6" + "@id": "bts:H3.1" }, { - "@id": "bts:C50.8" + "@id": "bts:H3.2" }, { - "@id": "bts:C50.9" + "@id": "bts:H3.3" }, { - "@id": "bts:C51.0" + "@id": "bts:H3.5" }, { - "@id": "bts:C51.1" + "@id": "bts:H3.X" }, { - "@id": "bts:C51.2" + "@id": "bts:H3.Y" }, { - "@id": "bts:C51.8" + "@id": "bts:H3t(H3.4)" }, { - "@id": "bts:C51.9" + "@id": "bts:MH2A" }, { - "@id": "bts:C52.9" + "@id": "bts:MH2A.1" }, { - "@id": "bts:C53.0" + "@id": "bts:MH2A.2" }, { - "@id": "bts:C53.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C53.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Variant", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Intron", + "@type": "rdfs:Class", + "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", + "rdfs:label": "Intron", + "rdfs:subClassOf": [ { - "@id": "bts:C53.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Intron", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LaboratoryTest", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", + "rdfs:label": "LaboratoryTest", + "rdfs:subClassOf": [ { - "@id": "bts:C54.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C54.1" + "@id": "bts:AbsoluteNeutrophil" }, { - "@id": "bts:C54.2" + "@id": "bts:Albumin" }, { - "@id": "bts:C54.3" + "@id": "bts:AlphaFetoprotein" }, { - "@id": "bts:C54.8" + "@id": "bts:B-cellgenotyping" }, { - "@id": "bts:C54.9" + "@id": "bts:Basophil" }, { - "@id": "bts:C55.9" + "@id": "bts:Beta2Microglobulin" }, { - "@id": "bts:C56.9" + "@id": "bts:BloodUreaNitrogen" }, { - "@id": "bts:C57.0" + "@id": "bts:C-ReactiveProtein" }, { - "@id": "bts:C57.1" + "@id": "bts:Calcium" }, { - "@id": "bts:C57.2" + "@id": "bts:Cellularity" }, { - "@id": "bts:C57.3" + "@id": "bts:CirculatingTumorCells" }, { - "@id": "bts:C57.4" + "@id": "bts:Creatinine" }, { - "@id": "bts:C57.7" + "@id": "bts:Eosinophil" }, { - "@id": "bts:C57.8" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:C57.9" + "@id": "bts:Glucose" }, { - "@id": "bts:C60.0" + "@id": "bts:Hematocrit" }, { - "@id": "bts:C60.1" + "@id": "bts:Hemoglobin" }, { - "@id": "bts:C60.2" + "@id": "bts:HPV-E6/E7" }, { - "@id": "bts:C60.8" + "@id": "bts:HumanChorionicGonadotropin" }, { - "@id": "bts:C60.9" + "@id": "bts:HumanPapillomavirus" }, { - "@id": "bts:C61.9" + "@id": "bts:ImmunoglobulinA" }, { - "@id": "bts:C62.0" + "@id": "bts:ImmunoglobulinG" }, { - "@id": "bts:C62.1" + "@id": "bts:ImmunoglobulinM" }, { - "@id": "bts:C62.9" + "@id": "bts:LactateDehydrogenase" }, { - "@id": "bts:C63.0" + "@id": "bts:Leukocytes" }, { - "@id": "bts:C63.1" + "@id": "bts:LuteinizingHormone" }, { - "@id": "bts:C63.2" + "@id": "bts:Lymphoblasts" }, { - "@id": "bts:C63.7" + "@id": "bts:Lymphocytes" }, { - "@id": "bts:C63.8" + "@id": "bts:MProtein" }, { - "@id": "bts:C63.9" + "@id": "bts:Metamyelocytes" }, { - "@id": "bts:C64.9" + "@id": "bts:Myeloblasts" }, { - "@id": "bts:C65.9" + "@id": "bts:Myelocytes" }, { - "@id": "bts:C66.9" + "@id": "bts:NeutrophilBands" }, { - "@id": "bts:C67.0" + "@id": "bts:Platelets" }, { - "@id": "bts:C67.1" + "@id": "bts:Prolymphocytes" }, { - "@id": "bts:C67.2" + "@id": "bts:Promonocytes" }, { - "@id": "bts:C67.4" + "@id": "bts:Promyelocytes" }, { - "@id": "bts:C67.6" + "@id": "bts:SegmentedNeutrophil" }, { - "@id": "bts:C67.7" + "@id": "bts:SerumFreeImmunoglobulinLightChain" }, { - "@id": "bts:C67.8" + "@id": "bts:Kappa" }, { - "@id": "bts:C67.9" + "@id": "bts:Lambda" }, { - "@id": "bts:C68.0" + "@id": "bts:NOS" }, { - "@id": "bts:C68.1" + "@id": "bts:Testosterone" }, { - "@id": "bts:C68.8" + "@id": "bts:TotalBilirubin" }, { - "@id": "bts:C68.9" + "@id": "bts:TotalProtein" }, { - "@id": "bts:C69.0" + "@id": "bts:Unknown" }, { - "@id": "bts:C69.1" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laboratory Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociAbnormalCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", + "rdfs:label": "LociAbnormalCount", + "rdfs:subClassOf": [ { - "@id": "bts:C69.2" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Abnormal Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci tested.", + "rdfs:label": "LociCount", + "rdfs:subClassOf": [ { - "@id": "bts:C69.3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Locus", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label": "Locus", + "rdfs:subClassOf": [ { - "@id": "bts:C69.4" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Locus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MismatchRepairMutation", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MismatchRepairMutation", + "rdfs:subClassOf": [ { - "@id": "bts:C69.5" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C69.6" + "@id": "bts:Yes" }, { - "@id": "bts:C69.8" + "@id": "bts:No" }, { - "@id": "bts:C69.9" + "@id": "bts:Unknown" }, { - "@id": "bts:C70.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mismatch Repair Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularConsequence", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularConsequence", + "rdfs:subClassOf": [ { - "@id": "bts:C70.1" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C70.9" + "@id": "bts:3PrimeUTRVariant" }, { - "@id": "bts:C71.0" + "@id": "bts:5PrimeUTRVariant" }, { - "@id": "bts:C71.1" + "@id": "bts:CodingSequenceVariant" }, { - "@id": "bts:C71.2" + "@id": "bts:DownstreamGeneVariant" }, { - "@id": "bts:C71.3" + "@id": "bts:FeatureElongation" }, { - "@id": "bts:C71.4" + "@id": "bts:FeatureTruncation" }, { - "@id": "bts:C71.5" + "@id": "bts:FrameshiftVariant" }, { - "@id": "bts:C71.6" + "@id": "bts:IncompleteTerminalCodonVariant" }, { - "@id": "bts:C71.7" + "@id": "bts:InframeDeletion" }, { - "@id": "bts:C71.8" + "@id": "bts:InframeInsertion" }, { - "@id": "bts:C71.9" + "@id": "bts:IntergenicVariant" }, { - "@id": "bts:C72.0" + "@id": "bts:IntronVariant" }, { - "@id": "bts:C72.1" + "@id": "bts:MaturemiRNAVariant" }, { - "@id": "bts:C72.2" + "@id": "bts:MissenseVariant" }, { - "@id": "bts:C72.3" + "@id": "bts:NMDTranscriptVariant" }, { - "@id": "bts:C72.4" + "@id": "bts:Non-codingTranscriptExonVariant" }, { - "@id": "bts:C72.5" + "@id": "bts:Non-codingTranscriptVariant" }, { - "@id": "bts:C72.8" + "@id": "bts:ProteinAlteringVariant" }, { - "@id": "bts:C72.9" + "@id": "bts:RegulatoryRegionAblation" }, { - "@id": "bts:C73.9" + "@id": "bts:RegulatoryRegionAmplification" }, { - "@id": "bts:C74.0" + "@id": "bts:RegulatoryRegionVariant" }, { - "@id": "bts:C74.1" + "@id": "bts:SpliceAcceptorVariant" }, { - "@id": "bts:C74.9" + "@id": "bts:SpliceDonorVariant" }, { - "@id": "bts:C75.0" + "@id": "bts:SpliceRegionVariant" }, { - "@id": "bts:C75.1" + "@id": "bts:StartLost" }, { - "@id": "bts:C75.2" + "@id": "bts:StopGain" }, { - "@id": "bts:C75.3" + "@id": "bts:StopLost" }, { - "@id": "bts:C75.4" + "@id": "bts:StopRetainedVariant" }, { - "@id": "bts:C75.5" + "@id": "bts:SynonymousVariant" }, { - "@id": "bts:C75.8" + "@id": "bts:TFBindingSiteVariant" }, { - "@id": "bts:C75.9" + "@id": "bts:TFBSAblation" }, { - "@id": "bts:C76.0" + "@id": "bts:TFBSAmplification" }, { - "@id": "bts:C76.1" + "@id": "bts:TranscriptAblation" }, { - "@id": "bts:C76.2" + "@id": "bts:TranscriptAmplification" }, { - "@id": "bts:C76.3" - }, + "@id": "bts:UpstreamGeneVariant" + } + ], + "sms:displayName": "Molecular Consequence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pathogenicity", + "@type": "rdfs:Class", + "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "rdfs:label": "Pathogenicity", + "rdfs:subClassOf": [ { - "@id": "bts:C76.4" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C76.5" + "@id": "bts:Benign" }, { - "@id": "bts:C76.7" + "@id": "bts:LikelyBenign" }, { - "@id": "bts:C76.8" + "@id": "bts:LikelyPathogenic" }, { - "@id": "bts:C77.0" + "@id": "bts:Pathogenic" }, { - "@id": "bts:C77.1" - }, + "@id": "bts:UncertainSignificance" + } + ], + "sms:displayName": "Pathogenicity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ploidy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", + "rdfs:label": "Ploidy", + "rdfs:subClassOf": [ { - "@id": "bts:C77.2" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C77.3" + "@id": "bts:Aneuploid" }, { - "@id": "bts:C77.4" + "@id": "bts:Diploid" }, { - "@id": "bts:C77.5" + "@id": "bts:Hyperdiploid" }, { - "@id": "bts:C77.8" + "@id": "bts:Hypodiploid" }, { - "@id": "bts:C77.9" + "@id": "bts:NearDiploid" }, { - "@id": "bts:C80.9" + "@id": "bts:Tetraploid" }, { "@id": "bts:Unknown" @@ -29674,123 +30209,188 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Topography Code", + "sms:displayName": "Ploidy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdditionalTopography", + "@id": "bts:SecondExon", "@type": "rdfs:Class", - "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", - "rdfs:label": "AdditionalTopography", + "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label": "SecondExon", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Skinofscalp" - }, - { - "@id": "bts:Skinofeyelid" - }, - { - "@id": "bts:Skinofnose" - }, - { - "@id": "bts:Skinoflip" - }, - { - "@id": "bts:Skinofear" - }, - { - "@id": "bts:Skinofneck" - }, - { - "@id": "bts:Skinofotherpartsofface" - }, - { - "@id": "bts:Skinofchest" - }, - { - "@id": "bts:Skinofback" - }, - { - "@id": "bts:Skinofabdomen" - }, + "sms:displayName": "Second Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondGeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SecondGeneSymbol", + "rdfs:subClassOf": [ { - "@id": "bts:Skinoftrunk" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Gene Symbol", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpecializedMolecularTest", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SpecializedMolecularTest", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofbreast" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Specialized Molecular Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestAnalyteType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestAnalyteType", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofupperlimbandshoulder" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofpalm" + "@id": "bts:DNA" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:MRNA" }, { - "@id": "bts:Skinofsole" + "@id": "bts:MiRNA" }, { - "@id": "bts:Skinofpenis" + "@id": "bts:ProteinAnalyte" }, { - "@id": "bts:Skinofscrotum" + "@id": "bts:TotalRNA" }, { - "@id": "bts:Skinofvulva" + "@id": "bts:Unknown" }, { - "@id": "bts:SkinNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Test Analyte Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestUnits", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestUnits", + "rdfs:subClassOf": [ { - "@id": "bts:HilarAirway" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Units", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestValue", + "@type": "rdfs:Class", + "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", + "rdfs:label": "TestValue", + "rdfs:subClassOf": [ { - "@id": "bts:Peri-tumoralAirway" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Transcript", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Transcript", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:MolecularTest" } ], - "sms:displayName": "Additional Topography", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Transcript", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologicMorphologyCode", + "@id": "bts:VariantOrigin", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", - "rdfs:label": "HistologicMorphologyCode", + "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "VariantOrigin", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Histologic Morphology Code", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Germline" + }, + { + "@id": "bts:Somatic" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Variant Origin", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PreservationMethod", + "@id": "bts:VariantType", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the method used to preserve the sample.", - "rdfs:label": "PreservationMethod", + "rdfs:comment": "The text term used to describe the type of genetic variation.", + "rdfs:label": "VariantType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -29798,58 +30398,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Cryopreserved" + "@id": "bts:Alleles" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" + "@id": "bts:Amplification" }, { - "@id": "bts:Cryopreservationindryice-deadtissue" + "@id": "bts:Chrimerism" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-livecells" + "@id": "bts:Conversion" }, { - "@id": "bts:Formalinfixedparaffinembedded-FFPE" + "@id": "bts:Deletion" }, { - "@id": "bts:Formalinfixed-unbuffered" + "@id": "bts:Deletion-Insertion" }, { - "@id": "bts:Formalinfixed-buffered" + "@id": "bts:Duplication" }, { - "@id": "bts:Fresh" + "@id": "bts:Extension" }, { - "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + "@id": "bts:Gain" }, { - "@id": "bts:OCT" + "@id": "bts:Hypermethylation" }, { - "@id": "bts:SnapFrozen" + "@id": "bts:Insertion" }, { - "@id": "bts:Frozen" + "@id": "bts:Inversion" }, { - "@id": "bts:Negative80DegC" + "@id": "bts:Loss" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:Methylation" }, { - "@id": "bts:Freshdissociated" + "@id": "bts:Mosaicism" }, { - "@id": "bts:Freshdissociatedandsinglecellsorted" + "@id": "bts:Other" }, { - "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + "@id": "bts:PartialMethylation" }, { - "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + "@id": "bts:Rearrangement" + }, + { + "@id": "bts:RepeatedSequences" + }, + { + "@id": "bts:Splice" + }, + { + "@id": "bts:Substitution" + }, + { + "@id": "bts:Translocation" }, { "@id": "bts:Unknown" @@ -29858,221 +30470,242 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Preservation Method", - "sms:required": "sms:true", + "sms:displayName": "Variant Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OtherAssay", + "@id": "bts:Zygosity", "@type": "rdfs:Class", - "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", - "rdfs:label": "OtherAssay", + "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", + "rdfs:label": "Zygosity", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - }, - { - "@id": "bts:DataType" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Assay", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Heterozygous" }, { - "@id": "bts:Filename" + "@id": "bts:Hemizygous" }, { - "@id": "bts:FileFormat" + "@id": "bts:Homozygous" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Nullizygous" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Unknown" }, { - "@id": "bts:AssayType" + "@id": "bts:NotReported" } ], + "sms:displayName": "Zygosity", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AssayType", + "@id": "bts:SourceHTANBiospecimenID", "@type": "rdfs:Class", - "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", - "rdfs:label": "AssayType", + "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", + "rdfs:label": "SourceHTANBiospecimenID", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Assay Type", - "sms:required": "sms:true", + "sms:displayName": "Source HTAN Biospecimen ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExSeqMinimal", + "@id": "bts:CollectionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Minimal metadata for the ExSeq assay", - "rdfs:label": "ExSeqMinimal", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", + "rdfs:label": "CollectionDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq Minimal", + "sms:displayName": "Collection Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:AdjacentBiospecimenIDs", + "@type": "rdfs:Class", + "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", + "rdfs:label": "AdjacentBiospecimenIDs", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adjacent Biospecimen IDs", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:BiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "Biospecimen Type", + "rdfs:label": "BiospecimenType", + "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" } ], - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:TissueBiospecimenType" }, { - "@id": "bts:Filename" + "@id": "bts:BloodBiospecimenType" }, { - "@id": "bts:FileFormat" + "@id": "bts:AnalyteBiospecimenType" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:MouthRinseBiospecimenType" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:StoolBiospecimenType" }, { - "@id": "bts:AssayType" + "@id": "bts:UrineBiospecimenType" + }, + { + "@id": "bts:AscitesBiospecimenType" + }, + { + "@id": "bts:SputumBiospecimenType" + }, + { + "@id": "bts:FluidsBiospecimenType" + }, + { + "@id": "bts:BoneMarrowBiospecimenType" + }, + { + "@id": "bts:CellsBiospecimenType" } ], + "sms:displayName": "Biospecimen Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel1", + "@id": "bts:AcquisitionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", - "rdfs:label": "ScRNA-seqLevel1", + "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", + "rdfs:label": "AcquisitionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANDataFileID" + "@id": "bts:Autopsy" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:Biopsy" }, { - "@id": "bts:CryopreservedCellsinSample" + "@id": "bts:FineNeedleAspirate" }, { - "@id": "bts:SingleCellIsolationMethod" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:PunchBiopsy" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:ShaveBiopsy" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:Excision" }, { - "@id": "bts:Read1" + "@id": "bts:Re-excision" }, { - "@id": "bts:Read2" + "@id": "bts:SentinelNodeBiopsy" }, { - "@id": "bts:EndBias" + "@id": "bts:Lymphadenectomy-RegionalNodes" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:OtherAcquisitionMethod" }, { - "@id": "bts:SpikeIn" + "@id": "bts:Noninducedsputum" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:Inducedsputum" }, { - "@id": "bts:TotalNumberofInputCells" + "@id": "bts:BAL(bronchialalveolarlavage)" }, { - "@id": "bts:InputCellsandNuclei" + "@id": "bts:Cytobrush" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:Blooddraw" }, { - "@id": "bts:SingleCellDissociationDaysfromIndex" + "@id": "bts:Fluidcollection" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:Forcepsbiopsy" }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex" + "@id": "bts:Coreneedlebiopsy" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Endoscopicbiopsy" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:Notspecified" } ], + "sms:displayName": "Acquisition Method Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidSource", + "@id": "bts:FixativeType", "@type": "rdfs:Class", - "rdfs:comment": "The source of the input nucleic molecule", - "rdfs:label": "NucleicAcidSource", + "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", + "rdfs:label": "FixativeType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30080,126 +30713,87 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:SingleCell" + "@id": "bts:Acetone" }, { - "@id": "bts:BulkWholeCell" + "@id": "bts:Alcohol" }, { - "@id": "bts:SingleNucleus" + "@id": "bts:Formalin" }, { - "@id": "bts:BulkNuclei" + "@id": "bts:Glutaraldehyde" }, { - "@id": "bts:Micro-region" - } - ], - "sms:displayName": "Nucleic Acid Source", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CryopreservedCellsinSample", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", - "rdfs:label": "CryopreservedCellsinSample", - "rdfs:subClassOf": [ + "@id": "bts:OCTmedia" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RNAlater" + }, { - "@id": "bts:Yes" + "@id": "bts:Saline" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Cryopreserved Cells in Sample", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SingleCellIsolationMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", - "rdfs:label": "SingleCellIsolationMethod", - "rdfs:subClassOf": [ + "@id": "bts:95%Ethanol" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Dimidoester" + }, { - "@id": "bts:MicrofluidicsChip" + "@id": "bts:Carbodiimide" }, { - "@id": "bts:Droplets" + "@id": "bts:Dimethylacetamide" }, { - "@id": "bts:FACS" + "@id": "bts:Para-benzoquinone" }, { - "@id": "bts:Plates" + "@id": "bts:PAXgenetissue" }, { - "@id": "bts:10x" + "@id": "bts:TCLlysisbuffer" }, { - "@id": "bts:NucleiIsolation" - } - ], - "sms:displayName": "Single Cell Isolation Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DissociationMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", - "rdfs:label": "DissociationMethod", - "rdfs:subClassOf": [ + "@id": "bts:NP40lysisbuffer" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Methacarn" + }, { - "@id": "bts:GentleMACS" + "@id": "bts:Cryo-store" }, { - "@id": "bts:Dounce" + "@id": "bts:Carnoy'sFixative" }, { - "@id": "bts:EnzymaticDigestion" + "@id": "bts:Polaxamer" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Other" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unfixed" } ], - "sms:displayName": "Dissociation Method", + "sms:displayName": "Fixative Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryConstructionMethod", + "@id": "bts:StorageMethod", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "LibraryConstructionMethod", + "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", + "rdfs:label": "StorageMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30207,131 +30801,128 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" + "@id": "bts:Ambienttemperature" }, { - "@id": "bts:Smart-SeqV4" + "@id": "bts:Cutslide" }, { - "@id": "bts:10xV1.0" + "@id": "bts:Fresh" }, { - "@id": "bts:10xV1.1" + "@id": "bts:Frozenat-20C" }, { - "@id": "bts:10xV2" + "@id": "bts:Frozenat-70C" }, { - "@id": "bts:10xV3" + "@id": "bts:Frozenat-80C" }, { - "@id": "bts:10xV3.1" + "@id": "bts:Frozenat-150C" }, { - "@id": "bts:CEL-seq2" + "@id": "bts:Frozeninliquidnitrogen" }, { - "@id": "bts:Drop-seq" + "@id": "bts:Frozeninvaporphase" }, { - "@id": "bts:InDropsV2" + "@id": "bts:Paraffinblock" }, { - "@id": "bts:InDropsV3" + "@id": "bts:RNAlaterat4C" }, { - "@id": "bts:TruDrop" + "@id": "bts:RNAlaterat25C" }, { - "@id": "bts:Sci-ATAC-seq" + "@id": "bts:RNAlaterat-20C" }, { - "@id": "bts:NexteraXT" + "@id": "bts:Refrigeratedat4degrees" }, { - "@id": "bts:10xMultiome" + "@id": "bts:Refrigeratedvacuumchamber" }, { - "@id": "bts:10xFLEX" + "@id": "bts:4Cinvacuumchamber" }, { - "@id": "bts:10xGEM3'" + "@id": "bts:Desiccantat4C" }, { - "@id": "bts:10xGEM5'" + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Library Construction Method", + "sms:displayName": "Storage Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ReadIndicator", + "@id": "bts:ProcessingDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", - "rdfs:label": "ReadIndicator", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", + "rdfs:label": "ProcessingDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:R1" - }, - { - "@id": "bts:R2" - }, - { - "@id": "bts:R1&R2" - }, - { - "@id": "bts:I1" - }, + "sms:displayName": "Processing Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:ProtocolLink", + "@type": "rdfs:Class", + "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label": "ProtocolLink", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:InformationContentEntity" } ], - "sms:displayName": "Read Indicator", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Protocol Link", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Read1", + "@id": "bts:SiteDataSource", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "Read1", + "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", + "rdfs:label": "SiteDataSource", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" - }, - { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "Read1", - "sms:required": "sms:true", + "sms:displayName": "Site Data Source", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Read2", + "@id": "bts:CollectionMedia", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "Read2", + "rdfs:comment": "Material Specimen is collected into post procedure", + "rdfs:label": "CollectionMedia", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30339,24 +30930,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:DMEM" }, { - "@id": "bts:CDNA" + "@id": "bts:DMEM+Serum" + }, + { + "@id": "bts:RPMI" + }, + { + "@id": "bts:RPMI+Serum" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:PBS+Serum" + }, + { + "@id": "bts:None" } ], - "sms:displayName": "Read2", - "sms:required": "sms:true", + "sms:displayName": "Collection Media", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EndBias", + "@id": "bts:MountingMedium", "@type": "rdfs:Class", - "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "rdfs:label": "EndBias", + "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", + "rdfs:label": "MountingMedium", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30364,27 +30970,62 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:3Prime" + "@id": "bts:Aqueouswaterbased" }, { - "@id": "bts:5Prime" + "@id": "bts:Non-AqueousSolventbased" }, { - "@id": "bts:FullLengthTranscript" + "@id": "bts:Xylene" + }, + { + "@id": "bts:Toluene" + }, + { + "@id": "bts:AntifadewithDAPI" + }, + { + "@id": "bts:AntifadewithoutDAPI" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "End Bias", - "sms:required": "sms:true", + "sms:displayName": "Mounting Medium", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReverseTranscriptionPrimer", + "@id": "bts:ProcessingLocation", "@type": "rdfs:Class", - "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", - "rdfs:label": "ReverseTranscriptionPrimer", + "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", + "rdfs:label": "ProcessingLocation", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistologyAssessmentBy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", + "rdfs:label": "HistologyAssessmentBy", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30392,30 +31033,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Oligo-dT" + "@id": "bts:Pathologist" }, { - "@id": "bts:Poly-dT" + "@id": "bts:ResearchScientist" }, { - "@id": "bts:Featurebarcoding" + "@id": "bts:Other" }, { - "@id": "bts:Random" + "@id": "bts:Unknown" } ], - "sms:displayName": "Reverse Transcription Primer", - "sms:required": "sms:true", + "sms:displayName": "Histology Assessment By", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpikeIn", + "@id": "bts:HistologyAssessmentMedium", "@type": "rdfs:Class", - "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", - "rdfs:label": "SpikeIn", + "rdfs:comment": "The method of assessment used to characterize histology", + "rdfs:label": "HistologyAssessmentMedium", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30423,30 +31064,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ERCC" + "@id": "bts:Digital" }, { - "@id": "bts:OtherSpikeIn" + "@id": "bts:Microscopy" }, { - "@id": "bts:NoSpikeIn" + "@id": "bts:Other" }, { - "@id": "bts:PhiX" + "@id": "bts:Unknown" } ], - "sms:displayName": "Spike In", - "sms:required": "sms:true", + "sms:displayName": "Histology Assessment Medium", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SequencingPlatform", + "@id": "bts:PreinvasiveMorphology", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "SequencingPlatform", + "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", + "rdfs:label": "PreinvasiveMorphology", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30454,565 +31095,530 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:IlluminaNextSeq500" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:IlluminaNextSeq550" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:IlluminaNextSeq2500" + "@id": "bts:Melanomainsitu-superficialspreading" }, { - "@id": "bts:IlluminaNovaSeq6000" + "@id": "bts:Melanomainsitu-lentigomalignatype" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:Melanomainsitu-acral-lentiginous" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:Melanomainsitu-nototherwiseclassified" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:IlluminaGenomeAnalyzerII" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:IlluminaGenomeAnalyzerIIx" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:IlluminaHiSeq2000" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:IlluminaHiSeq2500" + "@id": "bts:Invasivemelanoma-other" }, { - "@id": "bts:IlluminaHiSeq4000" + "@id": "bts:NormalWDA" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:IonTorrentPGM" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:IonTorrentProton" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:IonTorrentS5" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:PacBioRS" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:SquamousCarcinomainsitu" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:Atypicaladenomatoushyperplasia" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:Adenocarcinomainsitu-nonmucinous" }, { - "@id": "bts:GridION" + "@id": "bts:Adenocarcinomainsitu-mucinous" }, { - "@id": "bts:PromethION" + "@id": "bts:BenigntumorNOS" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:Hamartoma" }, { - "@id": "bts:Revio" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:IlluminaNextSeq1000" + "@id": "bts:Nodiagnosispossible" + } + ], + "sms:displayName": "Preinvasive Morphology", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorInfiltratingLymphocytes", + "@type": "rdfs:Class", + "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", + "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tumor Infiltrating Lymphocytes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DegreeofDysplasia", + "@type": "rdfs:Class", + "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", + "rdfs:label": "DegreeofDysplasia", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" }, { - "@id": "bts:IlluminaNextSeq2000" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:Other" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:Unknown" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:NotReported" + "@id": "bts:CarcinomainSitu" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Sequencing Platform", - "sms:required": "sms:true", + "sms:displayName": "Degree of Dysplasia", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofInputCells", + "@id": "bts:DysplasiaFraction", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells loaded/placed on plates", - "rdfs:label": "TotalNumberofInputCells", + "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", + "rdfs:label": "DysplasiaFraction", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Input Cells", - "sms:required": "sms:true", + "sms:displayName": "Dysplasia Fraction", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InputCellsandNuclei", + "@id": "bts:NumberProliferatingCells", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", - "rdfs:label": "InputCellsandNuclei", + "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", + "rdfs:label": "NumberProliferatingCells", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Input Cells and Nuclei", - "sms:required": "sms:true", + "sms:displayName": "Number Proliferating Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationDaysfromIndex", + "@id": "bts:PercentEosinophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "LibraryPreparationDaysfromIndex", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", + "rdfs:label": "PercentEosinophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Days from Index", + "sms:displayName": "Percent Eosinophil Infiltration", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:SingleCellDissociationDaysfromIndex", + "@id": "bts:PercentGranulocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SingleCellDissociationDaysfromIndex", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", + "rdfs:label": "PercentGranulocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell Dissociation Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Percent Granulocyte Infiltration", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex", + "@id": "bts:PercentInflamInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", + "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", + "rdfs:label": "PercentInflamInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Library Construction Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Percent Inflam Infiltration", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex", + "@id": "bts:PercentLymphocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "NucleicAcidCaptureDaysfromIndex", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", + "rdfs:label": "PercentLymphocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleic Acid Capture Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Percent Lymphocyte Infiltration", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:TechnicalReplicateGroup", + "@id": "bts:PercentMonocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", - "rdfs:label": "TechnicalReplicateGroup", + "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", + "rdfs:label": "PercentMonocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Technical Replicate Group", + "sms:displayName": "Percent Monocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel2", + "@id": "bts:PercentNecrosis", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", - "rdfs:label": "ScRNA-seqLevel2", + "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNecrosis", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 2", + "sms:displayName": "Percent Necrosis", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:PercentNeutrophilInfiltration", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", + "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:GenomeAnnotationURL" - }, - { - "@id": "bts:Checksum" - }, - { - "@id": "bts:WhitelistCellBarcodeFileLink" - }, - { - "@id": "bts:CellBarcodeTag" - }, - { - "@id": "bts:UMITag" - }, - { - "@id": "bts:AppliedHardTrimming" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScRNAseqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScRNAseqWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellRanger" - }, - { - "@id": "bts:STARsolo" - }, - { - "@id": "bts:HCAOptimus" - }, - { - "@id": "bts:DropEST" - }, - { - "@id": "bts:SEQC" - }, - { - "@id": "bts:Cufflinks" - }, - { - "@id": "bts:DEXSeq" - }, - { - "@id": "bts:HTSeq-FPKM" - }, - { - "@id": "bts:Cellannotation" - }, - { - "@id": "bts:Differentiationtrajectoryanalysis" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "scRNAseq Workflow Type", - "sms:required": "sms:true", + "sms:displayName": "Percent Neutrophil Infiltration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowVersion", + "@id": "bts:PercentNormalCells", "@type": "rdfs:Class", - "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", - "rdfs:label": "WorkflowVersion", + "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNormalCells", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Version", - "sms:required": "sms:true", + "sms:displayName": "Percent Normal Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription", + "@id": "bts:PercentStromalCells", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", - "rdfs:label": "ScRNAseqWorkflowParametersDescription", + "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", + "rdfs:label": "PercentStromalCells", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNAseq Workflow Parameters Description", - "sms:required": "sms:true", + "sms:displayName": "Percent Stromal Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowLink", + "@id": "bts:PercentTumorCells", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "WorkflowLink", + "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", + "rdfs:label": "PercentTumorCells", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Link", - "sms:required": "sms:true", + "sms:displayName": "Percent Tumor Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReference", + "@id": "bts:PercentTumorNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", - "rdfs:label": "GenomicReference", + "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", + "rdfs:label": "PercentTumorNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference", - "sms:required": "sms:true", + "sms:displayName": "Percent Tumor Nuclei", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:FiducialMarker", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", + "rdfs:label": "FiducialMarker", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:GenomeAnnotationURL", - "@type": "rdfs:Class", - "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", - "rdfs:label": "GenomeAnnotationURL", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:NuclearStain-DAPI" + }, + { + "@id": "bts:FluorescentBeads" + }, + { + "@id": "bts:GridSlides-Hemocytometer" + }, + { + "@id": "bts:AdhesiveMarkers" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Genome Annotation URL", - "sms:required": "sms:true", + "sms:displayName": "Fiducial Marker", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WhitelistCellBarcodeFileLink", + "@id": "bts:SlicingMethod", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible cell barcodes. URL", - "rdfs:label": "WhitelistCellBarcodeFileLink", + "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", + "rdfs:label": "SlicingMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whitelist Cell Barcode File Link", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Vibratome" + }, + { + "@id": "bts:Cryosectioning" + }, + { + "@id": "bts:Tissuemolds" + }, + { + "@id": "bts:Slidingmicrotome" + }, + { + "@id": "bts:Sectioning" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Slicing Method", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeTag", + "@id": "bts:LysisBuffer", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", - "rdfs:label": "CellBarcodeTag", + "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", + "rdfs:label": "LysisBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Tag", - "sms:required": "sms:true", + "sms:displayName": "Lysis Buffer", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UMITag", + "@id": "bts:MethodofNucleicAcidIsolation", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", - "rdfs:label": "UMITag", + "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", + "rdfs:label": "MethodofNucleicAcidIsolation", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Tag", - "sms:required": "sms:true", + "sms:displayName": "Method of Nucleic Acid Isolation", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AppliedHardTrimming", + "@id": "bts:Biosample", "@type": "rdfs:Class", - "rdfs:comment": "Was Hard Trimming applied", - "rdfs:label": "AppliedHardTrimming", + "rdfs:comment": "TBD", + "rdfs:label": "Biosample", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-AppliedHardTrimming" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Applied Hard Trimming", - "sms:required": "sms:true", + "sms:displayName": "Biosample", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel3", + "@id": "bts:SRRSBiospecimen", "@type": "rdfs:Class", - "rdfs:comment": "Gene and Isoform expression files", - "rdfs:label": "ScRNA-seqLevel3", + "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", + "rdfs:label": "SRRSBiospecimen", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 3", + "sms:displayName": "SRRS Biospecimen", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScRNA-seqLevel2" + "@id": "bts:Patient" } ], "sms:requiresDependency": [ @@ -31020,1360 +31626,1130 @@ "@id": "bts:Component" }, { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:DataCategory" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:MatrixType" + "@id": "bts:HTANParentID" }, { - "@id": "bts:LinkedMatrices" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:CellMedianNumberReads" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:CellMedianNumberGenes" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:CellTotal" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:ScRNAseqWorkflowType" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription" + "@id": "bts:IschemicTime" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:IschemicTemperature" }, { - "@id": "bts:WorkflowVersion" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:DataCategory", - "@type": "rdfs:Class", - "rdfs:comment": "Specific content type of the data file.", - "rdfs:label": "DataCategory", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:GeneExpression" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:TranscriptExpression" + "@id": "bts:TopographyCode" }, { - "@id": "bts:ExonExpressionQuantification" + "@id": "bts:AdditionalTopography" }, { - "@id": "bts:GeneExpressionQuantification" + "@id": "bts:FixativeType" }, { - "@id": "bts:IsoformExpressionQuantification" + "@id": "bts:StorageMethod" }, { - "@id": "bts:SpliceJunctionQuantification" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Data Category", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MatrixType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of data stored in matrix.", - "rdfs:label": "MatrixType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:RawCounts" + "@id": "bts:HistologicMorphologyCode" }, { - "@id": "bts:NormalizedCounts" + "@id": "bts:PreservationMethod" }, { - "@id": "bts:ScaledCounts" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:BatchCorrectedCounts" + "@id": "bts:ProtocolLink" } ], - "sms:displayName": "Matrix Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LinkedMatrices", + "@id": "bts:IschemicTime", "@type": "rdfs:Class", - "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", - "rdfs:label": "LinkedMatrices", + "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", + "rdfs:label": "IschemicTime", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Linked Matrices", + "sms:displayName": "Ischemic Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberReads", - "@type": "rdfs:Class", - "rdfs:comment": "Median number of reads per cell. Number", - "rdfs:label": "CellMedianNumberReads", - "rdfs:subClassOf": [ - { - "@id": "bts:ScRNA-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Median Number Reads", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CellMedianNumberGenes", - "@type": "rdfs:Class", - "rdfs:comment": "Median number of genes detected per cell. Number", - "rdfs:label": "CellMedianNumberGenes", - "rdfs:subClassOf": [ - { - "@id": "bts:ScRNA-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Median Number Genes", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CellTotal", - "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", - "rdfs:label": "CellTotal", - "rdfs:subClassOf": [ - { - "@id": "bts:ScRNA-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Total", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScRNA-seqLevel4", + "@id": "bts:IschemicTemperature", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScRNA-seqLevel4", + "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", + "rdfs:label": "IschemicTemperature", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScRNA-seqLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, + "schema:rangeIncludes": [ { - "@id": "bts:Filename" + "@id": "bts:WarmIschemia" }, { - "@id": "bts:FileFormat" + "@id": "bts:ColdIschemia" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:Ambientair" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:4Cwetice" }, { - "@id": "bts:ScRNAseqWorkflowType" + "@id": "bts:Negative-20C" }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription" + "@id": "bts:DryIce" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:LiquidNitrogen" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:Unknown" } ], + "sms:displayName": "Ischemic Temperature", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqLevel1", + "@id": "bts:TopographyCode", "@type": "rdfs:Class", - "rdfs:comment": "Raw sequencing files for the Slide-seq assay.", - "rdfs:label": "Slide-seqLevel1", + "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", + "rdfs:label": "TopographyCode", "rdfs:subClassOf": [ { - 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}, - "sms:displayName": "Not Applicable", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkRNA-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", - "rdfs:label": "BulkRNA-seqLevel1", - "rdfs:subClassOf": [ + "@id": "bts:C40.0" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk RNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:C40.1" + }, { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:C40.3" + }, { - "@id": "bts:Component" + "@id": "bts:C40.8" }, { - "@id": "bts:Filename" + "@id": "bts:C40.9" }, { - "@id": "bts:FileFormat" + "@id": "bts:C41.0" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:C41.1" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:C41.2" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:C41.3" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:C41.4" }, { - 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"@id": "bts:FragmentMaximumLength" + "@id": "bts:C47.2" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:C47.3" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:C47.4" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:C47.5" }, { - "@id": "bts:LaneNumber" + "@id": "bts:C47.6" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:C47.8" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:C47.9" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:C48.0" }, { - "@id": "bts:TargetDepth" + "@id": "bts:C48.1" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:C48.2" }, { - "@id": "bts:TranscriptIntegrityNumber" + "@id": "bts:C48.8" }, { - "@id": "bts:RIN" + "@id": "bts:C49.0" }, { - "@id": "bts:DV200" + "@id": "bts:C49.1" }, { - "@id": "bts:AdapterContent" + "@id": "bts:C49.2" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:C49.3" }, { - "@id": "bts:Encoding" + "@id": "bts:C49.4" }, { - "@id": "bts:KmerContent" + "@id": "bts:C49.5" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:C49.6" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:C49.8" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:C49.9" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:C50.0" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:C50.1" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:C50.2" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:C50.3" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:C50.4" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:C50.5" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:C50.6" }, { - "@id": "bts:TotalReads" + "@id": "bts:C50.8" }, { - "@id": "bts:QCWorkflowType" + "@id": "bts:C50.9" }, { - "@id": "bts:QCWorkflowVersion" + "@id": "bts:C51.0" }, { - "@id": "bts:QCWorkflowLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryLayout", - "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "LibraryLayout", - "rdfs:subClassOf": [ + "@id": "bts:C51.1" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C51.2" + }, { - "@id": "bts:PairedEnd" + "@id": "bts:C51.8" }, { - "@id": "bts:SingleRead" + "@id": "bts:C51.9" }, { - "@id": "bts:Mid-length" + "@id": "bts:C52.9" }, { - "@id": "bts:LongRead" + "@id": "bts:C53.0" + }, + { + "@id": "bts:C53.1" + }, + { + "@id": "bts:C53.8" + }, + { + "@id": "bts:C53.9" + }, + { + "@id": "bts:C54.0" + }, + { + "@id": "bts:C54.1" + }, + { + "@id": "bts:C54.2" + }, + { + "@id": "bts:C54.3" + }, + { + "@id": "bts:C54.8" + }, + { + "@id": "bts:C54.9" + }, + { + "@id": "bts:C55.9" + }, + { + "@id": "bts:C56.9" + }, + { + "@id": "bts:C57.0" + }, + { + "@id": "bts:C57.1" + }, + { + "@id": "bts:C57.2" + }, + { + "@id": "bts:C57.3" + }, + { + "@id": "bts:C57.4" + }, + { + "@id": "bts:C57.7" + }, + { + "@id": "bts:C57.8" + }, + { + "@id": "bts:C57.9" + }, + { + "@id": "bts:C60.0" + }, + { + "@id": "bts:C60.1" + }, + { + "@id": "bts:C60.2" + }, + { + "@id": "bts:C60.8" + }, + { + "@id": "bts:C60.9" + }, + { + "@id": "bts:C61.9" + }, + { + "@id": "bts:C62.0" + }, + { + "@id": "bts:C62.1" + }, + { + "@id": "bts:C62.9" + }, + { + "@id": "bts:C63.0" + }, + { + "@id": "bts:C63.1" + }, + { + "@id": "bts:C63.2" + }, + { + "@id": "bts:C63.7" + }, + { + "@id": "bts:C63.8" + }, + { + "@id": "bts:C63.9" + }, + { + "@id": "bts:C64.9" + }, + { + "@id": "bts:C65.9" + }, + { + "@id": "bts:C66.9" + }, + { + "@id": "bts:C67.0" + }, + { + "@id": "bts:C67.1" + }, + { + "@id": "bts:C67.2" + }, + { + "@id": "bts:C67.4" + }, + { + "@id": "bts:C67.6" + }, + { + "@id": "bts:C67.7" + }, + { + "@id": "bts:C67.8" + }, + { + "@id": "bts:C67.9" + }, + { + "@id": "bts:C68.0" + }, + { + "@id": "bts:C68.1" + }, + { + "@id": "bts:C68.8" + }, + { + "@id": "bts:C68.9" + }, + { + "@id": "bts:C69.0" + }, + { + "@id": "bts:C69.1" + }, + { + "@id": "bts:C69.2" + }, + { + "@id": "bts:C69.3" + }, + { + "@id": "bts:C69.4" + }, + { + "@id": "bts:C69.5" + }, + { + "@id": "bts:C69.6" + }, + { + "@id": "bts:C69.8" + }, + { + "@id": "bts:C69.9" + }, + { + "@id": "bts:C70.0" + }, + { + "@id": "bts:C70.1" + }, + { + "@id": "bts:C70.9" + }, + { + "@id": "bts:C71.0" + }, + { + "@id": "bts:C71.1" + }, + { + "@id": "bts:C71.2" + }, + { + "@id": "bts:C71.3" + }, + { + "@id": "bts:C71.4" + }, + { + "@id": "bts:C71.5" + }, + { + "@id": "bts:C71.6" + }, + { + "@id": "bts:C71.7" + }, + { + "@id": "bts:C71.8" + }, + { + "@id": "bts:C71.9" + }, + { + "@id": "bts:C72.0" + }, + { + "@id": "bts:C72.1" + }, + { + "@id": "bts:C72.2" + }, + { + "@id": "bts:C72.3" + }, + { + "@id": "bts:C72.4" + }, + { + "@id": "bts:C72.5" + }, + { + "@id": "bts:C72.8" + }, + { + "@id": "bts:C72.9" + }, + { + "@id": "bts:C73.9" + }, + { + "@id": "bts:C74.0" + }, + { + "@id": "bts:C74.1" + }, + { + "@id": "bts:C74.9" + }, + { + "@id": "bts:C75.0" + }, + { + "@id": "bts:C75.1" + }, + { + "@id": "bts:C75.2" + }, + { + "@id": "bts:C75.3" + }, + { + "@id": "bts:C75.4" + }, + { + "@id": "bts:C75.5" + }, + { + "@id": "bts:C75.8" + }, + { + "@id": "bts:C75.9" + }, + { + "@id": "bts:C76.0" + }, + { + "@id": "bts:C76.1" + }, + { + "@id": "bts:C76.2" + }, + { + "@id": "bts:C76.3" + }, + { + "@id": "bts:C76.4" + }, + { + "@id": "bts:C76.5" + }, + { + "@id": "bts:C76.7" + }, + { + "@id": "bts:C76.8" + }, + { + "@id": "bts:C77.0" + }, + { + "@id": "bts:C77.1" + }, + { + "@id": "bts:C77.2" + }, + { + "@id": "bts:C77.3" + }, + { + "@id": "bts:C77.4" + }, + { + "@id": "bts:C77.5" + }, + { + "@id": "bts:C77.8" + }, + { + "@id": "bts:C77.9" + }, + { + "@id": "bts:C80.9" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Topography Code", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Micro-regionSeqPlatform", + "@id": "bts:AdditionalTopography", "@type": "rdfs:Class", - "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", - "rdfs:label": "Micro-regionSeqPlatform", + "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", + "rdfs:label": "AdditionalTopography", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -32381,58 +32757,104 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RarecytePick-Seq" + "@id": "bts:Skinofscalp" }, { - "@id": "bts:LaserCaptureMicrodissection" - } - ], - "sms:displayName": "Micro-region Seq Platform", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ROITag", - "@type": "rdfs:Class", - "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", - "rdfs:label": "ROITag", - "rdfs:subClassOf": [ + "@id": "bts:Skinofeyelid" + }, { - "@id": "bts:Sequencing" + "@id": "bts:Skinofnose" + }, + { + "@id": "bts:Skinoflip" + }, + { + "@id": "bts:Skinofear" + }, + { + "@id": "bts:Skinofneck" + }, + { + "@id": "bts:Skinofotherpartsofface" + }, + { + "@id": "bts:Skinofchest" + }, + { + "@id": "bts:Skinofback" + }, + { + "@id": "bts:Skinofabdomen" + }, + { + "@id": "bts:Skinoftrunk" + }, + { + "@id": "bts:Skinofbreast" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:Skinofpalm" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:HilarAirway" + }, + { + "@id": "bts:Peri-tumoralAirway" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI Tag", + "sms:displayName": "Additional Topography", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReadLength", + "@id": "bts:HistologicMorphologyCode", "@type": "rdfs:Class", - "rdfs:comment": "The length of the sequencing reads. Can be integer, null", - "rdfs:label": "ReadLength", + "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:label": "HistologicMorphologyCode", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Read Length", + "sms:displayName": "Histologic Morphology Code", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibrarySelectionMethod", + "@id": "bts:PreservationMethod", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "LibrarySelectionMethod", + "rdfs:comment": "Text term that represents the method used to preserve the sample.", + "rdfs:label": "PreservationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -32440,141 +32862,134 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HybridSelection" + "@id": "bts:Cryopreserved" }, { - "@id": "bts:PCR" + "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" }, { - "@id": "bts:AffinityEnrichment" + "@id": "bts:Cryopreservationindryice-deadtissue" }, { - "@id": "bts:Poly-TEnrichment" + "@id": "bts:Cryopreservationinliquidnitrogen-livecells" }, { - "@id": "bts:Random" + "@id": "bts:Formalinfixedparaffinembedded-FFPE" }, { - "@id": "bts:RRNADepletion" + "@id": "bts:Formalinfixed-unbuffered" }, { - "@id": "bts:MiRNASizeFractionation" + "@id": "bts:Formalinfixed-buffered" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Library Selection Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitName", - "rdfs:subClassOf": [ + "@id": "bts:Fresh" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitVendor", - "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVendor", - "rdfs:subClassOf": [ + "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + }, { - "@id": "bts:Sequencing" + "@id": "bts:OCT" + }, + { + "@id": "bts:SnapFrozen" + }, + { + "@id": "bts:Frozen" + }, + { + "@id": "bts:Negative80DegC" + }, + { + "@id": "bts:LiquidNitrogen" + }, + { + "@id": "bts:Freshdissociated" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsorted" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + }, + { + "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Vendor", + "sms:displayName": "Preservation Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitVersion", + "@id": "bts:AssayType", "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVersion", + "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", + "rdfs:label": "AssayType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Version", + "sms:displayName": "Assay Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterName", + "@id": "bts:ExSeqMinimal", "@type": "rdfs:Class", - "rdfs:comment": "Name of the sequencing adapter. String", - "rdfs:label": "AdapterName", + "rdfs:comment": "Minimal metadata for the ExSeq assay", + "rdfs:label": "ExSeqMinimal", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Name", + "sms:displayName": "ExSeq Minimal", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterSequence", - "@type": "rdfs:Class", - "rdfs:comment": "Base sequence of the sequencing adapter. String", - "rdfs:label": "AdapterSequence", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BaseCallerName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the base caller. String", - "rdfs:label": "BaseCallerName", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Base Caller Name", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerVersion", + "@id": "bts:ScRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Version of the base caller. String", - "rdfs:label": "BaseCallerVersion", + "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", + "rdfs:label": "ScRNA-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32583,117 +32998,97 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Version", + "sms:displayName": "scRNA-seq Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FlowCellBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", - "rdfs:label": "FlowCellBarcode", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Flow Cell Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMaximumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMaximumLength", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Maximum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMeanLength", - "@type": "rdfs:Class", - "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentMeanLength", - "rdfs:subClassOf": [ + "@id": "bts:Component" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Mean Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMinimumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMinimumLength", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Minimum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentStandardDeviationLength", - "@type": "rdfs:Class", - "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentStandardDeviationLength", - "rdfs:subClassOf": [ + "@id": "bts:FileFormat" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Standard Deviation Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LaneNumber", - "@type": "rdfs:Class", - "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", - "rdfs:label": "LaneNumber", - "rdfs:subClassOf": [ + "@id": "bts:HTANParentBiospecimenID" + }, { - "@id": "bts:Sequencing" + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:NucleicAcidSource" + }, + { + "@id": "bts:CryopreservedCellsinSample" + }, + { + "@id": "bts:SingleCellIsolationMethod" + }, + { + "@id": "bts:DissociationMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" + }, + { + "@id": "bts:ReadIndicator" + }, + { + "@id": "bts:Read1" + }, + { + "@id": "bts:Read2" + }, + { + "@id": "bts:EndBias" + }, + { + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:SpikeIn" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:TotalNumberofInputCells" + }, + { + "@id": "bts:InputCellsandNuclei" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SingleCellDissociationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:TechnicalReplicateGroup" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lane Number", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryStrand", + "@id": "bts:NucleicAcidSource", "@type": "rdfs:Class", - "rdfs:comment": "Library stranded-ness.", - "rdfs:label": "LibraryStrand", + "rdfs:comment": "The source of the input nucleic molecule", + "rdfs:label": "NucleicAcidSource", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32704,81 +33099,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Unstranded" + "@id": "bts:SingleCell" }, { - "@id": "bts:FirstStranded" + "@id": "bts:BulkWholeCell" }, { - "@id": "bts:SecondStranded" + "@id": "bts:SingleNucleus" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Library Strand", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MultiplexBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", - "rdfs:label": "MultiplexBarcode", - "rdfs:subClassOf": [ + "@id": "bts:BulkNuclei" + }, { - "@id": "bts:Sequencing" + "@id": "bts:Micro-region" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Multiplex Barcode", - "sms:required": "sms:false", + "sms:displayName": "Nucleic Acid Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SizeSelectionRange", + "@id": "bts:CryopreservedCellsinSample", "@type": "rdfs:Class", - "rdfs:comment": "Range of size selection. String", - "rdfs:label": "SizeSelectionRange", + "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", + "rdfs:label": "CryopreservedCellsinSample", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Size Selection Range", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TargetDepth", - "@type": "rdfs:Class", - "rdfs:comment": "The targeted read depth prior to sequencing. Integer", - "rdfs:label": "TargetDepth", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Yes" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Target Depth", - "sms:required": "sms:false", + "sms:displayName": "Cryopreserved Cells in Sample", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ToTrimAdapterSequence", + "@id": "bts:SingleCellIsolationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Does the user suggest adapter trimming?", - "rdfs:label": "ToTrimAdapterSequence", + "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", + "rdfs:label": "SingleCellIsolationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32786,72 +33158,64 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-TrimAdapterSequence" + "@id": "bts:MicrofluidicsChip" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "To Trim Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TranscriptIntegrityNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", - "rdfs:label": "TranscriptIntegrityNumber", - "rdfs:subClassOf": [ + "@id": "bts:Droplets" + }, { - "@id": "bts:Sequencing" + "@id": "bts:FACS" + }, + { + "@id": "bts:Plates" + }, + { + "@id": "bts:10x" + }, + { + "@id": "bts:NucleiIsolation" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript Integrity Number", - "sms:required": "sms:false", + "sms:displayName": "Single Cell Isolation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RIN", + "@id": "bts:DissociationMethod", "@type": "rdfs:Class", - "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", - "rdfs:label": "RIN", + "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", + "rdfs:label": "DissociationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RIN", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DV200", - "@type": "rdfs:Class", - "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", - "rdfs:label": "DV200", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:GentleMACS" + }, + { + "@id": "bts:Dounce" + }, + { + "@id": "bts:EnzymaticDigestion" + }, + { + "@id": "bts:NotApplicable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DV200", - "sms:required": "sms:false", + "sms:displayName": "Dissociation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterContent", + "@id": "bts:LibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "AdapterContent", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "LibraryConstructionMethod", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32862,30 +33226,69 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:Smart-seq2" }, { - "@id": "bts:PASS" + "@id": "bts:Smart-SeqV4" }, { - "@id": "bts:WARN" + "@id": "bts:10xV1.0" }, { - "@id": "bts:Unknown" + "@id": "bts:10xV1.1" }, { - "@id": "bts:NotReported" + "@id": "bts:10xV2" + }, + { + "@id": "bts:10xV3" + }, + { + "@id": "bts:10xV3.1" + }, + { + "@id": "bts:CEL-seq2" + }, + { + "@id": "bts:Drop-seq" + }, + { + "@id": "bts:InDropsV2" + }, + { + "@id": "bts:InDropsV3" + }, + { + "@id": "bts:TruDrop" + }, + { + "@id": "bts:Sci-ATAC-seq" + }, + { + "@id": "bts:NexteraXT" + }, + { + "@id": "bts:10xMultiome" + }, + { + "@id": "bts:10xFLEX" + }, + { + "@id": "bts:10xGEM3'" + }, + { + "@id": "bts:10xGEM5'" } ], - "sms:displayName": "Adapter Content", - "sms:required": "sms:false", + "sms:displayName": "Library Construction Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BasicStatistics", + "@id": "bts:ReadIndicator", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "BasicStatistics", + "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", + "rdfs:label": "ReadIndicator", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32896,50 +33299,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:R1" }, { - "@id": "bts:PASS" + "@id": "bts:R2" }, { - "@id": "bts:WARN" + "@id": "bts:R1&R2" }, { - "@id": "bts:Unknown" + "@id": "bts:I1" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" } ], - "sms:displayName": "Basic Statistics", - "sms:required": "sms:false", + "sms:displayName": "Read Indicator", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Encoding", + "@id": "bts:Read1", "@type": "rdfs:Class", - "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", - "rdfs:label": "Encoding", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "Read1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Encoding", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:KmerContent", + "@id": "bts:Read2", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "KmerContent", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "Read2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32947,33 +33358,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:NotReported" + "@id": "bts:CDNA" } ], - "sms:displayName": "Kmer Content", - "sms:required": "sms:false", + "sms:displayName": "Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OverrepresentedSequences", + "@id": "bts:EndBias", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "OverrepresentedSequences", + "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", + "rdfs:label": "EndBias", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32981,33 +33383,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" + "@id": "bts:3Prime" }, { - "@id": "bts:Unknown" + "@id": "bts:5Prime" }, { - "@id": "bts:NotReported" + "@id": "bts:FullLengthTranscript" } ], - "sms:displayName": "Overrepresented Sequences", - "sms:required": "sms:false", + "sms:displayName": "End Bias", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseNContent", + "@id": "bts:ReverseTranscriptionPrimer", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseNContent", + "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", + "rdfs:label": "ReverseTranscriptionPrimer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -33015,33 +33411,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:Oligo-dT" }, { - "@id": "bts:WARN" + "@id": "bts:Poly-dT" }, { - "@id": "bts:Unknown" + "@id": "bts:Featurebarcoding" }, { - "@id": "bts:NotReported" + "@id": "bts:Random" } ], - "sms:displayName": "Per Base N Content", - "sms:required": "sms:false", + "sms:displayName": "Reverse Transcription Primer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceContent", + "@id": "bts:SpikeIn", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceContent", + "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", + "rdfs:label": "SpikeIn", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -33049,33 +33442,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:ERCC" }, { - "@id": "bts:WARN" + "@id": "bts:OtherSpikeIn" }, { - "@id": "bts:Unknown" + "@id": "bts:NoSpikeIn" }, { - "@id": "bts:NotReported" + "@id": "bts:PhiX" } ], - "sms:displayName": "Per Base Sequence Content", - "sms:required": "sms:false", + "sms:displayName": "Spike In", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceQuality", + "@id": "bts:SequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceQuality", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "SequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Device" } ], "schema:isPartOf": { @@ -33083,115 +33473,103 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:IlluminaNextSeq500" }, { - "@id": "bts:PASS" + "@id": "bts:IlluminaNextSeq550" }, { - "@id": "bts:WARN" + "@id": "bts:IlluminaNextSeq2500" }, { - "@id": "bts:Unknown" + "@id": "bts:IlluminaNovaSeq6000" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Quality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceGCContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceGCContent", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaMiSeq" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:454GSFLXTitanium" + }, { - "@id": "bts:FAIL" + "@id": "bts:ABSOLiD4" }, { - "@id": "bts:PASS" + "@id": "bts:ABSOLiD2" }, { - "@id": "bts:WARN" + "@id": "bts:ABSOLiD3" }, { - "@id": "bts:Unknown" + "@id": "bts:CompleteGenomics" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence GC Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceQualityScore", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceQualityScore", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaHiSeqXTen" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IlluminaHiSeqXFive" + }, { - "@id": "bts:FAIL" + "@id": "bts:IlluminaGenomeAnalyzerII" }, { - "@id": "bts:PASS" + "@id": "bts:IlluminaGenomeAnalyzerIIx" }, { - "@id": "bts:WARN" + "@id": "bts:IlluminaHiSeq2000" }, { - "@id": "bts:Unknown" + "@id": "bts:IlluminaHiSeq2500" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence Quality Score", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerTileSequenceQuality", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerTileSequenceQuality", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaHiSeq4000" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IlluminaNextSeq" + }, { - "@id": "bts:FAIL" + "@id": "bts:IonTorrentPGM" }, { - "@id": "bts:PASS" + "@id": "bts:IonTorrentProton" }, { - "@id": "bts:WARN" + "@id": "bts:IonTorrentS5" + }, + { + "@id": "bts:PacBioRS" + }, + { + "@id": "bts:NovaSeq6000" + }, + { + "@id": "bts:NovaSeqS4" + }, + { + "@id": "bts:UltimaGenomicsUG100" + }, + { + "@id": "bts:OxfordNanoporeminION" + }, + { + "@id": "bts:GridION" + }, + { + "@id": "bts:PromethION" + }, + { + "@id": "bts:PacBioSequel2" + }, + { + "@id": "bts:Revio" + }, + { + "@id": "bts:IlluminaNextSeq1000" + }, + { + "@id": "bts:IlluminaNextSeq2000" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -33200,15 +33578,15 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Per Tile Sequence Quality", - "sms:required": "sms:false", + "sms:displayName": "Sequencing Platform", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentGCContent", + "@id": "bts:TotalNumberofInputCells", "@type": "rdfs:Class", - "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", - "rdfs:label": "PercentGCContent", + "rdfs:comment": "Number of cells loaded/placed on plates", + "rdfs:label": "TotalNumberofInputCells", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33217,49 +33595,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent GC Content", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Input Cells", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceDuplicationLevels", + "@id": "bts:InputCellsandNuclei", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceDuplicationLevels", + "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label": "InputCellsandNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Duplication Levels", - "sms:required": "sms:false", + "sms:displayName": "Input Cells and Nuclei", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceLengthDistribution", + "@id": "bts:LibraryPreparationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceLengthDistribution", + "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "LibraryPreparationDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33268,49 +33629,36 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Length Distribution", + "sms:displayName": "Library Preparation Days from Index", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:TotalReads", + "@id": "bts:SingleCellDissociationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Total number of reads per sample. Integer", - "rdfs:label": "TotalReads", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SingleCellDissociationDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Reads", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Single Cell Dissociation Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:QCWorkflowType", + "@id": "bts:SequencingLibraryConstructionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", - "rdfs:label": "QCWorkflowType", + "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33319,15 +33667,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Sequencing Library Construction Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:QCWorkflowVersion", + "@id": "bts:NucleicAcidCaptureDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Major version for a workflow. String", - "rdfs:label": "QCWorkflowVersion", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "NucleicAcidCaptureDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33336,15 +33686,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Version", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Nucleic Acid Capture Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:QCWorkflowLink", + "@id": "bts:TechnicalReplicateGroup", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used. String", - "rdfs:label": "QCWorkflowLink", + "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", + "rdfs:label": "TechnicalReplicateGroup", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33353,15 +33705,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Link", + "sms:displayName": "Technical Replicate Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel2", + "@id": "bts:ScRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq alignment protocol description", - "rdfs:label": "BulkRNA-seqLevel2", + "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", + "rdfs:label": "ScRNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33370,11 +33722,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 2", + "sms:displayName": "scRNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel1" + "@id": "bts:ScRNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -33394,102 +33746,49 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:MSIWorkflowLink" - }, - { - "@id": "bts:MSIScore" + "@id": "bts:ScRNAseqWorkflowType" }, { - "@id": "bts:MSIStatus" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ScRNAseqWorkflowParametersDescription" }, { - "@id": "bts:TotalReads" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:GenomicReference" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Checksum" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:WhitelistCellBarcodeFileLink" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:CellBarcodeTag" }, { - "@id": "bts:ShortReads" + "@id": "bts:UMITag" }, { - "@id": "bts:Islowestlevel" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AlignmentWorkflowUrl", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", - "rdfs:label": "AlignmentWorkflowUrl", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:AppliedHardTrimming" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Alignment Workflow Url", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AlignmentWorkflowType", + "@id": "bts:ScRNAseqWorkflowType", "@type": "rdfs:Class", "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "AlignmentWorkflowType", + "rdfs:label": "ScRNAseqWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33500,105 +33799,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BWA" - }, - { - "@id": "bts:BWAwithBQSR" - }, - { - "@id": "bts:BWA-aln" - }, - { - "@id": "bts:BWA-mem" - }, - { - "@id": "bts:BWAwithMarkDuplicatesandBQSR" - }, - { - "@id": "bts:STAR2-Pass" - }, - { - "@id": "bts:STAR2-PassChimeric" - }, - { - "@id": "bts:STAR2-PassGenome" - }, - { - "@id": "bts:STAR2-PassTranscriptome" - }, - { - "@id": "bts:Bowtie" - }, - { - "@id": "bts:Bismark" - }, - { - "@id": "bts:GSNAP" - }, - { - "@id": "bts:BSMAP" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BS-Seeker2" - }, - { - "@id": "bts:BS-Seeker" - }, - { - "@id": "bts:RMAP" - }, - { - "@id": "bts:MethylCoder" - }, - { - "@id": "bts:BRAT-BW" - }, - { - "@id": "bts:Pash" + "@id": "bts:CellRanger" }, { - "@id": "bts:Segemehl" + "@id": "bts:STARsolo" }, { - "@id": "bts:Bisulfighter" + "@id": "bts:HCAOptimus" }, { - "@id": "bts:BatMeth" + "@id": "bts:DropEST" }, { - "@id": "bts:LAST" + "@id": "bts:SEQC" }, { - "@id": "bts:ERNE-BS5" + "@id": "bts:Cufflinks" }, { - "@id": "bts:B-SOLANA" + "@id": "bts:DEXSeq" }, { - "@id": "bts:SOCS-B" + "@id": "bts:HTSeq-FPKM" }, { - "@id": "bts:BWA-meth" + "@id": "bts:Cellannotation" }, { - "@id": "bts:OtherAlignmentWorkflow" + "@id": "bts:Differentiationtrajectoryanalysis" }, { - "@id": "bts:None" + "@id": "bts:Other" } ], - "sms:displayName": "Alignment Workflow Type", + "sms:displayName": "scRNAseq Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IndexFileName", + "@id": "bts:WorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "The name (or part of a name) of a file (of any type). String", - "rdfs:label": "IndexFileName", + "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", + "rdfs:label": "WorkflowVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33607,15 +33849,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Index File Name", + "sms:displayName": "Workflow Version", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageBaseQuality", + "@id": "bts:ScRNAseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Average base quality collected from samtools. Number", - "rdfs:label": "AverageBaseQuality", + "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", + "rdfs:label": "ScRNAseqWorkflowParametersDescription", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33624,15 +33866,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Base Quality", - "sms:required": "sms:false", + "sms:displayName": "scRNAseq Workflow Parameters Description", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageInsertSize", + "@id": "bts:WorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Average insert size collected from samtools. Integer", - "rdfs:label": "AverageInsertSize", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "WorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33641,15 +33883,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Insert Size", - "sms:required": "sms:false", + "sms:displayName": "Workflow Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageReadLength", + "@id": "bts:GenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "Average read length collected from samtools. Integer", - "rdfs:label": "AverageReadLength", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", + "rdfs:label": "GenomicReference", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33658,15 +33900,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Read Length", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Contamination", + "@id": "bts:GenomicReferenceURL", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", - "rdfs:label": "Contamination", + "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", + "rdfs:label": "GenomicReferenceURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33675,15 +33917,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ContaminationError", + "@id": "bts:GenomeAnnotationURL", "@type": "rdfs:Class", - "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", - "rdfs:label": "ContaminationError", + "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", + "rdfs:label": "GenomeAnnotationURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33692,15 +33934,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination Error", - "sms:required": "sms:false", + "sms:displayName": "Genome Annotation URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MeanCoverage", + "@id": "bts:WhitelistCellBarcodeFileLink", "@type": "rdfs:Class", - "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", - "rdfs:label": "MeanCoverage", + "rdfs:comment": "Link to file listing all possible cell barcodes. URL", + "rdfs:label": "WhitelistCellBarcodeFileLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33709,15 +33951,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Coverage", - "sms:required": "sms:false", + "sms:displayName": "Whitelist Cell Barcode File Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIWorkflowLink", + "@id": "bts:CellBarcodeTag", "@type": "rdfs:Class", - "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", - "rdfs:label": "MSIWorkflowLink", + "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", + "rdfs:label": "CellBarcodeTag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33726,15 +33968,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Workflow Link", - "sms:required": "sms:false", + "sms:displayName": "Cell Barcode Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIScore", + "@id": "bts:UMITag", "@type": "rdfs:Class", - "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", - "rdfs:label": "MSIScore", + "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", + "rdfs:label": "UMITag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33743,15 +33985,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Score", - "sms:required": "sms:false", + "sms:displayName": "UMI Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIStatus", + "@id": "bts:AppliedHardTrimming", "@type": "rdfs:Class", - "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", - "rdfs:label": "MSIStatus", + "rdfs:comment": "Was Hard Trimming applied", + "rdfs:label": "AppliedHardTrimming", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33762,27 +34004,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MSI" - }, - { - "@id": "bts:MSI-low" - }, - { - "@id": "bts:MSI-high" + "@id": "bts:Yes-AppliedHardTrimming" }, { - "@id": "bts:MSS" + "@id": "bts:No" } ], - "sms:displayName": "MSI Status", - "sms:required": "sms:false", + "sms:displayName": "Applied Hard Trimming", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PairsOnDiffCHR", + "@id": "bts:ScRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", - "rdfs:label": "PairsOnDiffCHR", + "rdfs:comment": "Gene and Isoform expression files", + "rdfs:label": "ScRNA-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33791,15 +34027,67 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pairs On Diff CHR", + "sms:displayName": "scRNA-seq Level 3", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScRNA-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:LinkedMatrices" + }, + { + "@id": "bts:CellMedianNumberReads" + }, + { + "@id": "bts:CellMedianNumberGenes" + }, + { + "@id": "bts:CellTotal" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:WorkflowVersion" + } + ], "sms:validationRules": [] }, { - "@id": "bts:TotalUniquelyMapped", + "@id": "bts:DataCategory", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that map to genome. Integer", - "rdfs:label": "TotalUniquelyMapped", + "rdfs:comment": "Specific content type of the data file.", + "rdfs:label": "DataCategory", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33808,15 +34096,38 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Uniquely Mapped", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:GeneExpression" + }, + { + "@id": "bts:TranscriptExpression" + }, + { + "@id": "bts:ExonExpressionQuantification" + }, + { + "@id": "bts:GeneExpressionQuantification" + }, + { + "@id": "bts:IsoformExpressionQuantification" + }, + { + "@id": "bts:SpliceJunctionQuantification" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Data Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalUnmappedreads", + "@id": "bts:MatrixType", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that did not map to genome. Integer", - "rdfs:label": "TotalUnmappedreads", + "rdfs:comment": "Type of data stored in matrix.", + "rdfs:label": "MatrixType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33825,15 +34136,29 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Unmapped reads", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:RawCounts" + }, + { + "@id": "bts:NormalizedCounts" + }, + { + "@id": "bts:ScaledCounts" + }, + { + "@id": "bts:BatchCorrectedCounts" + } + ], + "sms:displayName": "Matrix Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsDuplicated", + "@id": "bts:LinkedMatrices", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", - "rdfs:label": "ProportionReadsDuplicated", + "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", + "rdfs:label": "LinkedMatrices", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33842,66 +34167,66 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Duplicated", + "sms:displayName": "Linked Matrices", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMapped", + "@id": "bts:CellMedianNumberReads", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", - "rdfs:label": "ProportionReadsMapped", + "rdfs:comment": "Median number of reads per cell. Number", + "rdfs:label": "CellMedianNumberReads", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped", - "sms:required": "sms:false", + "sms:displayName": "Cell Median Number Reads", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionTargetsNoCoverage", + "@id": "bts:CellMedianNumberGenes", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", - "rdfs:label": "ProportionTargetsNoCoverage", + "rdfs:comment": "Median number of genes detected per cell. Number", + "rdfs:label": "CellMedianNumberGenes", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Targets No Coverage", - "sms:required": "sms:false", + "sms:displayName": "Cell Median Number Genes", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionBaseMismatch", + "@id": "bts:CellTotal", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", - "rdfs:label": "ProportionBaseMismatch", + "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", + "rdfs:label": "CellTotal", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Base Mismatch", - "sms:required": "sms:false", + "sms:displayName": "Cell Total", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ShortReads", + "@id": "bts:ScRNA-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that were too short. Integer", - "rdfs:label": "ShortReads", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScRNA-seqLevel4", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33910,53 +34235,62 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Short Reads", + "sms:displayName": "scRNA-seq Level 4", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Islowestlevel", - "@type": "rdfs:Class", - "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", - "rdfs:label": "Islowestlevel", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ScRNA-seqLevel2" + "@id": "bts:ScRNA-seqLevel3" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Yes-Islowestlevel" + "@id": "bts:Component" }, { - "@id": "bts:No" + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" } ], - "sms:displayName": "Is lowest level", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel3", + "@id": "bts:Slide-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq gene expression matrices", - "rdfs:label": "BulkRNA-seqLevel3", + "rdfs:comment": "Raw sequencing files for the Slide-seq assay.", + "rdfs:label": "Slide-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 3", + "sms:displayName": "Slide-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -33970,40 +34304,70 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:PseudoAlignmentUsed" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:DataCategory" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:ExpressionUnits" + "@id": "bts:SpatialRead1" }, { - "@id": "bts:MatrixType" + "@id": "bts:SpatialRead2" }, { - "@id": "bts:FusionGeneDetected" + "@id": "bts:EndBias" }, { - "@id": "bts:FusionGeneIdentity" + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:SpatialBarcodeOffset" + }, + { + "@id": "bts:SpatialBarcodeandUMI" + }, + { + "@id": "bts:SpikeIn" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex" } ], "sms:validationRules": [] }, { - "@id": "bts:PseudoAlignmentUsed", + "@id": "bts:SpatialRead1", "@type": "rdfs:Class", - "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", - "rdfs:label": "PseudoAlignmentUsed", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "SpatialRead1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -34011,24 +34375,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-PseudoAlignmentUsed" + "@id": "bts:CDNA" }, { - "@id": "bts:No" + "@id": "bts:SpatialBarcodeandUMI" } ], - "sms:displayName": "Pseudo Alignment Used", + "sms:displayName": "Spatial Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExpressionUnits", + "@id": "bts:SpatialRead2", "@type": "rdfs:Class", - "rdfs:comment": "How quantities are corrected for gene length", - "rdfs:label": "ExpressionUnits", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "SpatialRead2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -34036,64 +34400,80 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TPM" - }, - { - "@id": "bts:RPKM" - }, - { - "@id": "bts:FPKM" - }, - { - "@id": "bts:Counts" + "@id": "bts:CDNA" }, { - "@id": "bts:Other" - }, + "@id": "bts:SpatialBarcodeandUMI" + } + ], + "sms:displayName": "Spatial Read2", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialBarcodeOffset", + "@type": "rdfs:Class", + "rdfs:comment": "Offset in sequence for spot barcode read (in bp): number", + "rdfs:label": "SpatialBarcodeOffset", + "rdfs:subClassOf": [ { - "@id": "bts:NA" + "@id": "bts:SpatialTranscriptomics" } ], - "sms:displayName": "Expression Units", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Barcode Offset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneDetected", + "@id": "bts:SpatialBarcodeandUMI", "@type": "rdfs:Class", - "rdfs:comment": "Was a fusion gene identified?", - "rdfs:label": "FusionGeneDetected", + "rdfs:comment": "Spot and transcript identifiers", + "rdfs:label": "SpatialBarcodeandUMI", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" + }, + { + "@id": "bts:SpatialRead1" + }, + { + "@id": "bts:SpatialRead2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Spatial Barcode and UMI", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:Yes-FusionGeneDetected" + "@id": "bts:SpatialBarcodeOffset" }, { - "@id": "bts:No" + "@id": "bts:SpatialBarcodeLength" }, { - "@id": "bts:Unknown" + "@id": "bts:UMIBarcodeOffset" + }, + { + "@id": "bts:UMIBarcodeLength" } ], - "sms:displayName": "Fusion Gene Detected", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:FusionGeneIdentity", + "@id": "bts:SpatialLibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "The gene symbols of fused genes.", - "rdfs:label": "FusionGeneIdentity", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "SpatialLibraryConstructionMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -34101,48 +34481,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EWS-FLI" + "@id": "bts:Smart-seq2" }, { - "@id": "bts:EWS-ERG" + "@id": "bts:Smart-SeqV4" }, { - "@id": "bts:SYT-SSX1" + "@id": "bts:10xV1.0" }, { - "@id": "bts:SYT-SSX2" + "@id": "bts:10xV1.1" }, { - "@id": "bts:EWS-WT1" + "@id": "bts:10xV2" }, { - "@id": "bts:OtherFusionGene" + "@id": "bts:10xV3" + }, + { + "@id": "bts:10xV3.1" + }, + { + "@id": "bts:Drop-seq" + }, + { + "@id": "bts:InDropsV2" + }, + { + "@id": "bts:InDropsV3" + }, + { + "@id": "bts:TruDrop" + }, + { + "@id": "bts:NexteraXT" } ], - "sms:displayName": "Fusion Gene Identity", + "sms:displayName": "Spatial Library Construction Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SpatialTranscriptomics", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Transcriptomics", "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] + "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel1", + "@id": "bts:Slide-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing raw files", - "rdfs:label": "BulkWESLevel1", + "rdfs:comment": "Aligned sequencing files and QC for the Slide-seq assay.", + "rdfs:label": "Slide-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 1", + "sms:displayName": "Slide-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Slide-seqLevel1" } ], "sms:requiresDependency": [ @@ -34156,94 +34569,218 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:Slide-seqWorkflowType" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:Slide-seqWorkflowParameterDescription" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:ReadLength" + "@id": "bts:GenomicReference" }, { - "@id": "bts:TargetCaptureKit" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:Checksum" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:MatchedSpatialBarcodeTag" }, { - "@id": "bts:AdapterName" + "@id": "bts:UMITag" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:AppliedHardTrimming" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze the Slide-seq data set. String", + "rdfs:label": "Slide-seqWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Workflow Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqWorkflowParameterDescription", + "@type": "rdfs:Class", + "rdfs:comment": "Parameters used to run the Slide-seq workflow. String", + "rdfs:label": "Slide-seqWorkflowParameterDescription", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Workflow Parameter Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialBarcodeTag", + "@type": "rdfs:Class", + "rdfs:comment": "SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)", + "rdfs:label": "SpatialBarcodeTag", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Barcode Tag", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MatchedSpatialBarcodeTag", + "@type": "rdfs:Class", + "rdfs:comment": "SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)", + "rdfs:label": "MatchedSpatialBarcodeTag", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matched Spatial Barcode Tag", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).", + "rdfs:label": "Slide-seqLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Slide-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:Filename" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:FileFormat" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:RunID" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:DataCategory" }, { - "@id": "bts:LaneNumber" + "@id": "bts:MatrixType" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:Slide-seqWorkflowType" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:Slide-seqWorkflowParameterDescription" }, { - "@id": "bts:TargetDepth" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:BeadsTotal" + }, + { + "@id": "bts:MedianUMICountsperSpot" + }, + { + "@id": "bts:MedianNumberGenesperSpatialSpot" + }, + { + "@id": "bts:Slide-seqBeadFileType" + }, + { + "@id": "bts:Slide-seqFragmentSize" } ], "sms:validationRules": [] }, { - "@id": "bts:TargetCaptureKit", + "@id": "bts:RunID", "@type": "rdfs:Class", - "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", - "rdfs:label": "TargetCaptureKit", + "rdfs:comment": "A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.", + "rdfs:label": "RunID", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Run ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SequencingBatchID", + "@type": "rdfs:Class", + "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", + "rdfs:label": "SequencingBatchID", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34252,167 +34789,387 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, + "sms:displayName": "Sequencing Batch ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BeadsTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Number of sequenced beads. Applies to raw counts matrix only. Integer", + "rdfs:label": "BeadsTotal", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Beads Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedianUMICountsperSpot", + "@type": "rdfs:Class", + "rdfs:comment": "The median number of UMI counts per tissue covered spot.", + "rdfs:label": "MedianUMICountsperSpot", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median UMI Counts per Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:MedianNumberGenesperSpatialSpot", + "@type": "rdfs:Class", + "rdfs:comment": "The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.", + "rdfs:label": "MedianNumberGenesperSpatialSpot", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median Number Genes per Spatial Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:Slide-seqBeadFileType", + "@type": "rdfs:Class", + "rdfs:comment": "The type of Level 3 file submitted as part of the Slide-seq workflow.", + "rdfs:label": "Slide-seqBeadFileType", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, "schema:rangeIncludes": [ { - "@id": "bts:NotApplicable" + "@id": "bts:MatrixFeatures" }, { - "@id": "bts:CustomTargetsFileProvided" + "@id": "bts:MatrixBarcodes" }, { - "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" + "@id": "bts:AllBeadLocations" }, { - "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" + "@id": "bts:AllBeadBarcodes" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" + "@id": "bts:MatchedBeadBarcodes" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" + "@id": "bts:MatchedBeadLocations" }, { - "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Slide-seq Bead File Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqFragmentSize", + "@type": "rdfs:Class", + "rdfs:comment": "Average cDNA length associated with the experiemtn. Integer", + "rdfs:label": "Slide-seqFragmentSize", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Fragment Size", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatrixFeatures", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatrixFeatures", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matrix Features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatrixBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatrixBarcodes", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matrix Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AllBeadLocations", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AllBeadLocations", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "All Bead Locations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AllBeadBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AllBeadBarcodes", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "All Bead Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatchedBeadBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatchedBeadBarcodes", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matched Bead Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatchedBeadLocations", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatchedBeadLocations", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matched Bead Locations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NotApplicable", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NotApplicable", + "rdfs:subClassOf": [ + { + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" + "@id": "bts:SomaticVariantsSampleType" }, { - "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:CustomMSKIMPACTPanel-341Genes" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:CustomMSKIMPACTPanel-410Genes" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:CustomMSKIMPACTPanel-468Genes" + "@id": "bts:PatientColonoscopyPerformedIndicator" }, { - "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + "@id": "bts:ReplicateType" }, { - "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" }, { - "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" + "@id": "bts:ColorectalCancerKRASIndicator" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" + "@id": "bts:ColonPolypOccurenceIndicator" }, { - "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" + "@id": "bts:FamilyHistoryColorectalPolyp" }, { - "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" + "@id": "bts:ColorectalPolypNewIndicator" }, { - "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:FoundationMedicineT5aPanel-322Genes" + "@id": "bts:RefluxTreatmentType" }, { - "@id": "bts:FoundationMedicineT7Panel-429Genes" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" + "@id": "bts:ColorectalCancerTumorBorderConfiguration" }, { - "@id": "bts:NexteraDNAExome" + "@id": "bts:ColorectalPolypShape" }, { - "@id": "bts:NexteraRapidCaptureExomev1.2" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:SeqCapEZHGSCVCRomev2.1" + "@id": "bts:SpecimenLaterality" }, { - "@id": "bts:SeqCapEZHumanExomev2.0" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:SeqCapEZHumanExomev3.0" + "@id": "bts:Slide-seqBeadFileType" }, { - "@id": "bts:SureSelectHumanAllExonv3" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:SureSelectHumanAllExonv4" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:SureSelectHumanAllExonv5" + "@id": "bts:ColorectalPolypAdenomaType" }, { - "@id": "bts:SureSelectHumanAllExonv5+UTR" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:TruSeqAmpliconCancerPanel" + "@id": "bts:CutaneousMelanomaAdditionalFindings" }, { - "@id": "bts:TruSeqExomeEnrichment-62Mb" + "@id": "bts:CauseofDeath" }, { - "@id": "bts:TruSeqRNAExome" + "@id": "bts:TumorGrade" }, { - "@id": "bts:TruSightMyeloidSequencingPanel" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:XGenExomeResearchPanelv1.0" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" + "@id": "bts:TestResult" }, { - "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" + "@id": "bts:StorageMethod" }, { - "@id": "bts:SureSelectHumanAllExonv6" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Unknown" + "@id": "bts:ConcomitantMedicationReceivedType" + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome" + }, + { + "@id": "bts:CancerAssociatedGeneMutations" + }, + { + "@id": "bts:MutationalSignatures" + }, + { + "@id": "bts:PrecancerousConditionType" } ], - "sms:displayName": "Target Capture Kit", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Not Applicable", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel2", + "@id": "bts:BulkRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", - "rdfs:label": "BulkWESLevel2", + "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", + "rdfs:label": "BulkRNA-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34421,11 +35178,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 2", + "sms:displayName": "Bulk RNA-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkWESLevel1" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -34439,142 +35196,169 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:GenomicReference" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:IndexFileName" + "@id": "bts:Micro-regionSeqPlatform" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:ROITag" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:Contamination" + "@id": "bts:ReadLength" }, { - "@id": "bts:ContaminationError" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:AdapterContent" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:Encoding" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:SpikeIn" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:AdapterName" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:QCWorkflowType" + "@id": "bts:LaneNumber" }, { - "@id": "bts:QCWorkflowVersion" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:QCWorkflowLink" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:MSIWorkflowLink" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:MSIScore" + "@id": "bts:TargetDepth" }, { - "@id": "bts:MSIStatus" + "@id": "bts:ToTrimAdapterSequence" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:TranscriptIntegrityNumber" }, { - "@id": "bts:TotalReads" + "@id": "bts:RIN" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:DV200" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:AdapterContent" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Encoding" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:KmerContent" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:ShortReads" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:Islowestlevel" + "@id": "bts:PerSequenceGCContent" + }, + { + "@id": "bts:PerSequenceQualityScore" + }, + { + "@id": "bts:PerTileSequenceQuality" + }, + { + "@id": "bts:PercentGCContent" + }, + { + "@id": "bts:SequenceDuplicationLevels" + }, + { + "@id": "bts:SequenceLengthDistribution" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:QCWorkflowType" + }, + { + "@id": "bts:QCWorkflowVersion" + }, + { + "@id": "bts:QCWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage10x", + "@id": "bts:LibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage10x", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "LibraryLayout", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34583,15 +35367,29 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 10x", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:PairedEnd" + }, + { + "@id": "bts:SingleRead" + }, + { + "@id": "bts:Mid-length" + }, + { + "@id": "bts:LongRead" + } + ], + "sms:displayName": "Library Layout", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage30X", + "@id": "bts:Micro-regionSeqPlatform", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage30X", + "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", + "rdfs:label": "Micro-regionSeqPlatform", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34600,15 +35398,23 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 30X", + "schema:rangeIncludes": [ + { + "@id": "bts:RarecytePick-Seq" + }, + { + "@id": "bts:LaserCaptureMicrodissection" + } + ], + "sms:displayName": "Micro-region Seq Platform", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel3", + "@id": "bts:ROITag", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing called variants", - "rdfs:label": "BulkWESLevel3", + "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", + "rdfs:label": "ROITag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34617,64 +35423,75 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 3", + "sms:displayName": "ROI Tag", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:ReadLength", + "@type": "rdfs:Class", + "rdfs:comment": "The length of the sequencing reads. Can be integer, null", + "rdfs:label": "ReadLength", + "rdfs:subClassOf": [ { - "@id": "bts:BulkWESLevel2" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Read Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LibrarySelectionMethod", + "@type": "rdfs:Class", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "LibrarySelectionMethod", + "rdfs:subClassOf": [ { - "@id": "bts:GenomicReference" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:HybridSelection" }, { - "@id": "bts:GermlineVariantsWorkflowURL" + "@id": "bts:PCR" }, { - "@id": "bts:GermlineVariantsWorkflowType" + "@id": "bts:AffinityEnrichment" }, { - "@id": "bts:SomaticVariantsWorkflowURL" + "@id": "bts:Poly-TEnrichment" }, { - "@id": "bts:SomaticVariantsWorkflowType" + "@id": "bts:Random" }, { - "@id": "bts:SomaticVariantsSampleType" + "@id": "bts:RRNADepletion" }, { - "@id": "bts:StructuralVariantWorkflowURL" + "@id": "bts:MiRNASizeFractionation" }, { - "@id": "bts:StructuralVariantWorkflowType" + "@id": "bts:Other" } ], + "sms:displayName": "Library Selection Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowURL", + "@id": "bts:LibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", - "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34683,15 +35500,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Germline Variants Workflow URL", + "sms:displayName": "Library Preparation Kit Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowType", + "@id": "bts:LibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVendor", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34700,26 +35517,49 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GATK4" - }, + "sms:displayName": "Library Preparation Kit Vendor", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LibraryPreparationKitVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVersion", + "rdfs:subClassOf": [ { - "@id": "bts:OtherGermlineVariantsWorkflowType" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Library Preparation Kit Version", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AdapterName", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the sequencing adapter. String", + "rdfs:label": "AdapterName", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Germline Variants Workflow Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adapter Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowURL", + "@id": "bts:AdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:comment": "Base sequence of the sequencing adapter. String", + "rdfs:label": "AdapterSequence", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34728,15 +35568,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Somatic Variants Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowType", + "@id": "bts:BaseCallerName", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:comment": "Name of the base caller. String", + "rdfs:label": "BaseCallerName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34745,44 +35585,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaVEMan" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:MuTect2" - }, - { - "@id": "bts:MuSE" - }, - { - "@id": "bts:Pindel" - }, - { - "@id": "bts:SomaticSniper" - }, - { - "@id": "bts:VarScan2" - }, - { - "@id": "bts:OtherSomaticVariantsWorkflowType" - }, + "sms:displayName": "Base Caller Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BaseCallerVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Version of the base caller. String", + "rdfs:label": "BaseCallerVersion", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Somatic Variants Workflow Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Base Caller Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsSampleType", + "@id": "bts:FlowCellBarcode", "@type": "rdfs:Class", - "rdfs:comment": "Is the sample case or control in somatic variant analysis", - "rdfs:label": "SomaticVariantsSampleType", + "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", + "rdfs:label": "FlowCellBarcode", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34791,26 +35619,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaseSample" - }, - { - "@id": "bts:ControlSample" - }, + "sms:displayName": "Flow Cell Barcode", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentMaximumLength", + "@type": "rdfs:Class", + "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMaximumLength", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Somatic Variants Sample Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Maximum Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowURL", + "@id": "bts:FragmentMeanLength", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", - "rdfs:label": "StructuralVariantWorkflowURL", + "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentMeanLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34819,15 +35653,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Structural Variant Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Fragment Mean Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowType", + "@id": "bts:FragmentMinimumLength", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "StructuralVariantWorkflowType", + "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMinimumLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34836,117 +35670,134 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BRASS" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:CNV" - }, - { - "@id": "bts:CNVkit" - }, - { - "@id": "bts:OtherStructuralVariantWorkflowType" - }, + "sms:displayName": "Fragment Minimum Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentStandardDeviationLength", + "@type": "rdfs:Class", + "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentStandardDeviationLength", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Structural Variant Workflow Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Standard Deviation Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLevel1", + "@id": "bts:LaneNumber", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", - "rdfs:label": "MicroarrayLevel1", + "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label": "LaneNumber", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 1", + "sms:displayName": "Lane Number", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:LibraryStrand", + "@type": "rdfs:Class", + "rdfs:comment": "Library stranded-ness.", + "rdfs:label": "LibraryStrand", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NucleicAcidSource" + "@id": "bts:Unstranded" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:FirstStranded" }, { - "@id": "bts:MicroarrayMolecule" + "@id": "bts:SecondStranded" }, { - "@id": "bts:MicroarrayLabel" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Library Strand", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MultiplexBarcode", + "@type": "rdfs:Class", + "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", + "rdfs:label": "MultiplexBarcode", + "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayValueDefinition" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Multiplex Barcode", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SizeSelectionRange", + "@type": "rdfs:Class", + "rdfs:comment": "Range of size selection. String", + "rdfs:label": "SizeSelectionRange", + "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayProtocolAuxiliaryFile" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Size Selection Range", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayPlatformID", + "@id": "bts:TargetDepth", "@type": "rdfs:Class", - "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", - "rdfs:label": "MicroarrayPlatformID", + "rdfs:comment": "The targeted read depth prior to sequencing. Integer", + "rdfs:label": "TargetDepth", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Platform ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match GPL\\d+" - ] + "sms:displayName": "Target Depth", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:MicroarrayMolecule", + "@id": "bts:ToTrimAdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "Microarray is measuring this kind of molecule", - "rdfs:label": "MicroarrayMolecule", + "rdfs:comment": "Does the user suggest adapter trimming?", + "rdfs:label": "ToTrimAdapterSequence", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -34954,142 +35805,157 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DNA" + "@id": "bts:Yes-TrimAdapterSequence" }, { - "@id": "bts:RNA" + "@id": "bts:No" } ], - "sms:displayName": "Microarray Molecule", - "sms:required": "sms:true", + "sms:displayName": "To Trim Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLabel", + "@id": "bts:TranscriptIntegrityNumber", "@type": "rdfs:Class", - "rdfs:comment": "Microarray used this kind of label", - "rdfs:label": "MicroarrayLabel", + "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", + "rdfs:label": "TranscriptIntegrityNumber", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Label", - "sms:required": "sms:true", + "sms:displayName": "Transcript Integrity Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayValueDefinition", + "@id": "bts:RIN", "@type": "rdfs:Class", - "rdfs:comment": "What the provided value signifies", - "rdfs:label": "MicroarrayValueDefinition", + "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", + "rdfs:label": "RIN", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Value Definition", - "sms:required": "sms:true", + "sms:displayName": "RIN", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayProtocolAuxiliaryFile", + "@id": "bts:DV200", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", - "rdfs:label": "MicroarrayProtocolAuxiliaryFile", + "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", + "rdfs:label": "DV200", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Protocol Auxiliary File", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match syn\\d+" - ] + "sms:displayName": "DV200", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLevel2", + "@id": "bts:AdapterContent", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", - "rdfs:label": "MicroarrayLevel2", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "AdapterContent", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:MicroarrayLevel1" - } - ], - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:FAIL" }, { - "@id": "bts:Filename" + "@id": "bts:PASS" }, { - "@id": "bts:FileFormat" + "@id": "bts:WARN" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Unknown" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Adapter Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BasicStatistics", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "BasicStatistics", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:PASS" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:WARN" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:Unknown" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:NotReported" } ], + "sms:displayName": "Basic Statistics", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NormalizationMethod", + "@id": "bts:Encoding", "@type": "rdfs:Class", - "rdfs:comment": "Description of Normalization Process", - "rdfs:label": "NormalizationMethod", + "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", + "rdfs:label": "Encoding", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Normalization Method", + "sms:displayName": "Encoding", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel1", + "@id": "bts:KmerContent", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", - "rdfs:label": "ScATAC-seqLevel1", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "KmerContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35098,109 +35964,35 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:DissociationMethod" - }, - { - "@id": "bts:SingleNucleusBuffer" - }, - { - "@id": "bts:SingleCellIsolationMethod" - }, - { - "@id": "bts:TranspositionReaction" - }, - { - "@id": "bts:ScATACseqLibraryLayout" - }, - { - "@id": "bts:NucleusIdentifier" - }, - { - "@id": "bts:NucleiBarcodeLength" - }, - { - "@id": "bts:NucleiBarcodeRead" - }, - { - "@id": "bts:ScATACseqRead1" - }, - { - "@id": "bts:ScATACseqRead2" - }, - { - "@id": "bts:ScATACseqRead3" - }, - { - "@id": "bts:LibraryConstructionMethod" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:ThresholdforMinimumPassingReads" - }, - { - "@id": "bts:TotalNumberofPassingNuclei" - }, - { - "@id": "bts:MedianFractionofReadsinPeaks" - }, - { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" - }, + "schema:rangeIncludes": [ { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:FAIL" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:PASS" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:WARN" }, { - "@id": "bts:TotalReads" + "@id": "bts:Unknown" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:NotReported" } ], + "sms:displayName": "Kmer Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SingleNucleusBuffer", + "@id": "bts:OverrepresentedSequences", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation buffer", - "rdfs:label": "SingleNucleusBuffer", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "OverrepresentedSequences", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35208,30 +36000,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NIB" + "@id": "bts:FAIL" }, { - "@id": "bts:10x" + "@id": "bts:PASS" }, { - "@id": "bts:Omni" + "@id": "bts:WARN" }, { - "@id": "bts:TST" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Single Nucleus Buffer", - "sms:required": "sms:true", + "sms:displayName": "Overrepresented Sequences", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TranspositionReaction", + "@id": "bts:PerBaseNContent", "@type": "rdfs:Class", - "rdfs:comment": "Name of the transposase, transposon sequences", - "rdfs:label": "TranspositionReaction", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseNContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35239,39 +36034,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Tn5" - }, - { - "@id": "bts:EZ-Tn5" - }, - { - "@id": "bts:Tn5-059" + "@id": "bts:FAIL" }, { - "@id": "bts:NexteraTn5" + "@id": "bts:PASS" }, { - "@id": "bts:Diagenode-unloadedApex-Bio" + "@id": "bts:WARN" }, { - "@id": "bts:Diagenode-loadedApex-Bio" + "@id": "bts:Unknown" }, { - "@id": "bts:In-House" + "@id": "bts:NotReported" } ], - "sms:displayName": "Transposition Reaction", - "sms:required": "sms:true", + "sms:displayName": "Per Base N Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqLibraryLayout", + "@id": "bts:PerBaseSequenceContent", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "ScATACseqLibraryLayout", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35279,21 +36068,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Per Base Sequence Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleusIdentifier", + "@id": "bts:PerBaseSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", - "rdfs:label": "NucleusIdentifier", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceQuality", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35301,64 +36102,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NucleiBarcode" - } - ], - "sms:displayName": "Nucleus Identifier", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiBarcodeLength", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Length", - "rdfs:label": "NucleiBarcodeLength", - "rdfs:subClassOf": [ + "@id": "bts:FAIL" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:PASS" }, { - "@id": "bts:NucleiBarcode" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Barcode Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiBarcodeRead", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Read", - "rdfs:label": "NucleiBarcodeRead", - "rdfs:subClassOf": [ + "@id": "bts:WARN" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Unknown" }, { - "@id": "bts:NucleiBarcode" + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Barcode Read", - "sms:required": "sms:true", + "sms:displayName": "Per Base Sequence Quality", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead1", + "@id": "bts:PerSequenceGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScATACseqRead1", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceGCContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35366,36 +36136,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:FAIL" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:PASS" }, { - "@id": "bts:DNAInsert" + "@id": "bts:WARN" }, { - "@id": "bts:SampleIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:CellBarcode" + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Read1", - "sms:required": "sms:true", + "sms:displayName": "Per Sequence GC Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead2", + "@id": "bts:PerSequenceQualityScore", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScATACseqRead2", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceQualityScore", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35403,33 +36170,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:FAIL" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:PASS" }, { - "@id": "bts:DNAInsert" + "@id": "bts:WARN" }, { - "@id": "bts:SampleIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:CellBarcode" + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Read2", - "sms:required": "sms:true", + "sms:displayName": "Per Sequence Quality Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead3", + "@id": "bts:PerTileSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScATACseqRead3", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerTileSequenceQuality", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35437,142 +36204,183 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:FAIL" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:PASS" }, { - "@id": "bts:DNAInsert" + "@id": "bts:WARN" }, { - "@id": "bts:SampleIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:CellBarcode" + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Read3", + "sms:displayName": "Per Tile Sequence Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ThresholdforMinimumPassingReads", + "@id": "bts:PercentGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Threshold for calling cells", - "rdfs:label": "ThresholdforMinimumPassingReads", + "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", + "rdfs:label": "PercentGCContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Threshold for Minimum Passing Reads", - "sms:required": "sms:true", + "sms:displayName": "Percent GC Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofPassingNuclei", + "@id": "bts:SequenceDuplicationLevels", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei sequenced", - "rdfs:label": "TotalNumberofPassingNuclei", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceDuplicationLevels", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Passing Nuclei", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Duplication Levels", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinPeaks", + "@id": "bts:SequenceLengthDistribution", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in peaks (FRIP)", - "rdfs:label": "MedianFractionofReadsinPeaks", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceLengthDistribution", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Peaks", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], + "sms:displayName": "Sequence Length Distribution", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", + "@id": "bts:TotalReads", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", - "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", + "rdfs:comment": "Total number of reads per sample. Integer", + "rdfs:label": "TotalReads", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "sms:displayName": "Total Reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", + "rdfs:label": "QCWorkflowType", + "rdfs:subClassOf": [ { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianPassingReadPercentage", + "@id": "bts:QCWorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", - "rdfs:label": "MedianPassingReadPercentage", + "rdfs:comment": "Major version for a workflow. String", + "rdfs:label": "QCWorkflowVersion", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Passing Read Percentage", - "sms:required": "sms:true", + "sms:displayName": "QC Workflow Version", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@id": "bts:QCWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Contamination from mitochondrial sequences", - "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:comment": "Link to workflow used. String", + "rdfs:label": "QCWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", - "sms:required": "sms:true", + "sms:displayName": "QC Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel2", + "@id": "bts:BulkRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", - "rdfs:label": "ScATAC-seqLevel2", + "rdfs:comment": "Bulk RNA-seq alignment protocol description", + "rdfs:label": "BulkRNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35581,11 +36389,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 2", + "sms:displayName": "Bulk RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:BulkRNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -35629,81 +36437,78 @@ "@id": "bts:AverageReadLength" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:Contamination" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ContaminationError" }, { - "@id": "bts:TotalReads" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:MapQ30" + "@id": "bts:MSIScore" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:MSIStatus" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:TotalReads" }, { - "@id": "bts:ShortReads" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:Contamination" + "@id": "bts:ShortReads" }, { - "@id": "bts:ContaminationError" + "@id": "bts:Islowestlevel" } ], "sms:validationRules": [] }, { - "@id": "bts:MapQ30", + "@id": "bts:AlignmentWorkflowUrl", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads with Quality >= 30.", - "rdfs:label": "MapQ30", + "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", + "rdfs:label": "AlignmentWorkflowUrl", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MapQ30", - "sms:required": "sms:false", + "sms:displayName": "Alignment Workflow Url", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel3", + "@id": "bts:AlignmentWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files containing peak information for cells", - "rdfs:label": "ScATAC-seqLevel3", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "AlignmentWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35712,797 +36517,638 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScATAC-seqObjectID" - }, - { - "@id": "bts:NCountPeaks" - }, - { - "@id": "bts:NFeaturePeaks" - }, - { - "@id": "bts:TotalRead-Pairs" - }, - { - "@id": "bts:DuplicateRead-Pairs" - }, - { - "@id": "bts:ChimericRead-Pairs" - }, - { - "@id": "bts:UnmappedRead-Pairs" - }, - { - "@id": "bts:LowMapQ" - }, + "schema:rangeIncludes": [ { - "@id": "bts:MitochondrialRead-Pairs" + "@id": "bts:BWA" }, { - "@id": "bts:PassedFilters" + "@id": "bts:BWAwithBQSR" }, { - "@id": "bts:TSSFragments" + "@id": "bts:BWA-aln" }, { - "@id": "bts:DNaseSensitiveRegionFragments" + "@id": "bts:BWA-mem" }, { - "@id": "bts:EnhancerRegionFragments" + "@id": "bts:BWAwithMarkDuplicatesandBQSR" }, { - "@id": "bts:PromoterRegionFragments" + "@id": "bts:STAR2-Pass" }, { - "@id": "bts:OnTargetFragments" + "@id": "bts:STAR2-PassChimeric" }, { - "@id": "bts:BlacklistRegionFragments" + "@id": "bts:STAR2-PassGenome" }, { - "@id": "bts:PeakRegionFragments" + "@id": "bts:STAR2-PassTranscriptome" }, { - "@id": "bts:PeakRegionCutsites" + "@id": "bts:Bowtie" }, { - "@id": "bts:NucleosomeSignal" + "@id": "bts:Bismark" }, { - "@id": "bts:NucleosomePercentile" + "@id": "bts:GSNAP" }, { - "@id": "bts:TSSEnrichment" + "@id": "bts:BSMAP" }, { - "@id": "bts:TSSPercentile" + "@id": "bts:BSmooth" }, { - "@id": "bts:PctReadsinPeaks" + "@id": "bts:BS-Seeker2" }, { - "@id": "bts:BlacklistRatio" + "@id": "bts:BS-Seeker" }, { - "@id": "bts:SeuratClusters" + "@id": "bts:RMAP" }, { - "@id": "bts:NCountRNA" + "@id": "bts:MethylCoder" }, { - "@id": "bts:NFeatureRNA" + "@id": "bts:BRAT-BW" }, { - "@id": "bts:MACS2Seqnames" + "@id": "bts:Pash" }, { - "@id": "bts:MACS2Start" + "@id": "bts:Segemehl" }, { - "@id": "bts:MACS2End" + "@id": "bts:Bisulfighter" }, { - "@id": "bts:MACS2Width" + "@id": "bts:BatMeth" }, { - "@id": "bts:MACS2Strand" + "@id": "bts:LAST" }, { - "@id": "bts:MACS2Name" + "@id": "bts:ERNE-BS5" }, { - "@id": "bts:MACS2Score" + "@id": "bts:B-SOLANA" }, { - "@id": "bts:MACS2FoldChange" + "@id": "bts:SOCS-B" }, { - "@id": "bts:MACS2NegLog10pvalueSummit" + "@id": "bts:BWA-meth" }, { - "@id": "bts:MACS2NegLog10qvalueSummit" + "@id": "bts:OtherAlignmentWorkflow" }, { - "@id": "bts:MACS2RelativeSummitPosition" + "@id": "bts:None" } ], + "sms:displayName": "Alignment Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqObjectID", + "@id": "bts:IndexFileName", "@type": "rdfs:Class", - "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", - "rdfs:label": "ScATAC-seqObjectID", + "rdfs:comment": "The name (or part of a name) of a file (of any type). String", + "rdfs:label": "IndexFileName", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Object ID", - "sms:required": "sms:false", + "sms:displayName": "Index File Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NCountPeaks", + "@id": "bts:AverageBaseQuality", "@type": "rdfs:Class", - "rdfs:comment": "Total number of fragments in peaks", - "rdfs:label": "NCountPeaks", + "rdfs:comment": "Average base quality collected from samtools. Number", + "rdfs:label": "AverageBaseQuality", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nCount Peaks", + "sms:displayName": "Average Base Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NFeaturePeaks", + "@id": "bts:AverageInsertSize", "@type": "rdfs:Class", - "rdfs:comment": "Number of peaks with at least one read", - "rdfs:label": "NFeaturePeaks", + "rdfs:comment": "Average insert size collected from samtools. Integer", + "rdfs:label": "AverageInsertSize", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nFeature Peaks", + "sms:displayName": "Average Insert Size", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalRead-Pairs", + "@id": "bts:AverageReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Total read-pairs", - "rdfs:label": "TotalRead-Pairs", + "rdfs:comment": "Average read length collected from samtools. Integer", + "rdfs:label": "AverageReadLength", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Read-Pairs", + "sms:displayName": "Average Read Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DuplicateRead-Pairs", + "@id": "bts:Contamination", "@type": "rdfs:Class", - "rdfs:comment": "Number of duplicate read-pairs", - "rdfs:label": "DuplicateRead-Pairs", + "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", + "rdfs:label": "Contamination", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Duplicate Read-Pairs", + "sms:displayName": "Contamination", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChimericRead-Pairs", + "@id": "bts:ContaminationError", "@type": "rdfs:Class", - "rdfs:comment": "Number of chimerically mapped read-pairs", - "rdfs:label": "ChimericRead-Pairs", + "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", + "rdfs:label": "ContaminationError", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Chimeric Read-Pairs", + "sms:displayName": "Contamination Error", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UnmappedRead-Pairs", + "@id": "bts:MeanCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs with at least one end not mapped", - "rdfs:label": "UnmappedRead-Pairs", + "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", + "rdfs:label": "MeanCoverage", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Unmapped Read-Pairs", + "sms:displayName": "Mean Coverage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LowMapQ", + "@id": "bts:MSIWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", - "rdfs:label": "LowMapQ", + "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", + "rdfs:label": "MSIWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LowMapQ", + "sms:displayName": "MSI Workflow Link", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitochondrialRead-Pairs", + "@id": "bts:MSIScore", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", - "rdfs:label": "MitochondrialRead-Pairs", + "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", + "rdfs:label": "MSIScore", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mitochondrial Read-Pairs", + "sms:displayName": "MSI Score", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PassedFilters", + "@id": "bts:MSIStatus", "@type": "rdfs:Class", - "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", - "rdfs:label": "PassedFilters", + "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", + "rdfs:label": "MSIStatus", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Passed Filters", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TSSFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping with TSS regions", - "rdfs:label": "TSSFragments", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "TSS Fragments", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DNaseSensitiveRegionFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", - "rdfs:label": "DNaseSensitiveRegionFragments", - "rdfs:subClassOf": [ + "@id": "bts:MSI" + }, { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DNase Sensitive Region Fragments", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EnhancerRegionFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping enhancer regions", - "rdfs:label": "EnhancerRegionFragments", - "rdfs:subClassOf": [ + "@id": "bts:MSI-low" + }, { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Enhancer Region Fragments", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PromoterRegionFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping promoter regions", - "rdfs:label": "PromoterRegionFragments", - "rdfs:subClassOf": [ + "@id": "bts:MSI-high" + }, { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:MSS" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Promoter Region Fragments", + "sms:displayName": "MSI Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OnTargetFragments", + "@id": "bts:PairsOnDiffCHR", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", - "rdfs:label": "OnTargetFragments", + "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", + "rdfs:label": "PairsOnDiffCHR", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "On Target Fragments", + "sms:displayName": "Pairs On Diff CHR", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BlacklistRegionFragments", + "@id": "bts:TotalUniquelyMapped", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping blacklisted regions", - "rdfs:label": "BlacklistRegionFragments", + "rdfs:comment": "Number of reads that map to genome. Integer", + "rdfs:label": "TotalUniquelyMapped", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blacklist Region Fragments", + "sms:displayName": "Total Uniquely Mapped", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeakRegionFragments", + "@id": "bts:TotalUnmappedreads", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping peaks", - "rdfs:label": "PeakRegionFragments", + "rdfs:comment": "Number of reads that did not map to genome. Integer", + "rdfs:label": "TotalUnmappedreads", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peak Region Fragments", + "sms:displayName": "Total Unmapped reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeakRegionCutsites", + "@id": "bts:ProportionReadsDuplicated", "@type": "rdfs:Class", - "rdfs:comment": "Number of ends of fragments in peak regions", - "rdfs:label": "PeakRegionCutsites", + "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", + "rdfs:label": "ProportionReadsDuplicated", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peak Region Cutsites", + "sms:displayName": "Proportion Reads Duplicated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleosomeSignal", + "@id": "bts:ProportionReadsMapped", "@type": "rdfs:Class", - "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", - "rdfs:label": "NucleosomeSignal", + "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", + "rdfs:label": "ProportionReadsMapped", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleosome Signal", + "sms:displayName": "Proportion Reads Mapped", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleosomePercentile", + "@id": "bts:ProportionTargetsNoCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Percentile rank of nucleosome score", - "rdfs:label": "NucleosomePercentile", + "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", + "rdfs:label": "ProportionTargetsNoCoverage", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleosome Percentile", + "sms:displayName": "Proportion Targets No Coverage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TSSEnrichment", + "@id": "bts:ProportionBaseMismatch", "@type": "rdfs:Class", - "rdfs:comment": "Transcription start site (TSS) enrichment score", - "rdfs:label": "TSSEnrichment", + "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", + "rdfs:label": "ProportionBaseMismatch", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Enrichment", + "sms:displayName": "Proportion Base Mismatch", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TSSPercentile", + "@id": "bts:ShortReads", "@type": "rdfs:Class", - "rdfs:comment": "Percentile rank of TSS score", - "rdfs:label": "TSSPercentile", + "rdfs:comment": "Number of reads that were too short. Integer", + "rdfs:label": "ShortReads", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Percentile", + "sms:displayName": "Short Reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PctReadsinPeaks", + "@id": "bts:Islowestlevel", "@type": "rdfs:Class", - "rdfs:comment": "Percentage of reads in peaks", - "rdfs:label": "PctReadsinPeaks", + "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", + "rdfs:label": "Islowestlevel", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:ScRNA-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pct Reads in Peaks", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BlacklistRatio", - "@type": "rdfs:Class", - "rdfs:comment": "Ratio of reads in blacklist regions", - "rdfs:label": "BlacklistRatio", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blacklist Ratio", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SeuratClusters", - "@type": "rdfs:Class", - "rdfs:comment": "Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm", - "rdfs:label": "SeuratClusters", - "rdfs:subClassOf": [ + "@id": "bts:Yes-Islowestlevel" + }, { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Seurat Clusters", + "sms:displayName": "Is lowest level", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NCountRNA", + "@id": "bts:BulkRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Total number of fragments in genes", - "rdfs:label": "NCountRNA", + "rdfs:comment": "Bulk RNA-seq gene expression matrices", + "rdfs:label": "BulkRNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nCount RNA", + "sms:displayName": "Bulk RNA-seq Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NFeatureRNA", - "@type": "rdfs:Class", - "rdfs:comment": "Number of genes detected in cell", - "rdfs:label": "NFeatureRNA", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:BulkRNA-seqLevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "nFeature RNA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Seqnames", - "@type": "rdfs:Class", - "rdfs:comment": "Chromosome id", - "rdfs:label": "MACS2Seqnames", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Seqnames", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Start", - "@type": "rdfs:Class", - "rdfs:comment": "Genomic starting position in MACS2", - "rdfs:label": "MACS2Start", - "rdfs:subClassOf": [ + "@id": "bts:Component" + }, { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Start", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2End", - "@type": "rdfs:Class", - "rdfs:comment": "Genomic ending position in MACS2", - "rdfs:label": "MACS2End", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:PseudoAlignmentUsed" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:ExpressionUnits" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:FusionGeneDetected" + }, + { + "@id": "bts:FusionGeneIdentity" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 End", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MACS2Width", + "@id": "bts:PseudoAlignmentUsed", "@type": "rdfs:Class", - "rdfs:comment": "Width of the peak in bases in MACS2", - "rdfs:label": "MACS2Width", + "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", + "rdfs:label": "PseudoAlignmentUsed", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Width", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Strand", - "@type": "rdfs:Class", - "rdfs:comment": "DNA stand aligned with in MACS2", - "rdfs:label": "MACS2Strand", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Yes-PseudoAlignmentUsed" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Strand", - "sms:required": "sms:false", + "sms:displayName": "Pseudo Alignment Used", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2Name", + "@id": "bts:ExpressionUnits", "@type": "rdfs:Class", - "rdfs:comment": "Name of the peak in MACS2", - "rdfs:label": "MACS2Name", + "rdfs:comment": "How quantities are corrected for gene length", + "rdfs:label": "ExpressionUnits", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Score", - "@type": "rdfs:Class", - "rdfs:comment": "Peak score (proportional to q-value) in MACS2", - "rdfs:label": "MACS2Score", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:TPM" + }, + { + "@id": "bts:RPKM" + }, + { + "@id": "bts:FPKM" + }, + { + "@id": "bts:Counts" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:NA" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Score", - "sms:required": "sms:false", + "sms:displayName": "Expression Units", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2FoldChange", + "@id": "bts:FusionGeneDetected", "@type": "rdfs:Class", - "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", - "rdfs:label": "MACS2FoldChange", + "rdfs:comment": "Was a fusion gene identified?", + "rdfs:label": "FusionGeneDetected", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Fold Change", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2NegLog10pvalueSummit", - "@type": "rdfs:Class", - "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", - "rdfs:label": "MACS2NegLog10pvalueSummit", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Yes-FusionGeneDetected" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Neg Log10 pvalue Summit", + "sms:displayName": "Fusion Gene Detected", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MACS2NegLog10qvalueSummit", + "@id": "bts:FusionGeneIdentity", "@type": "rdfs:Class", - "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", - "rdfs:label": "MACS2NegLog10qvalueSummit", + "rdfs:comment": "The gene symbols of fused genes.", + "rdfs:label": "FusionGeneIdentity", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Neg Log10 qvalue Summit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2RelativeSummitPosition", - "@type": "rdfs:Class", - "rdfs:comment": "Position of the peak summit related to the start position in MACS2", - "rdfs:label": "MACS2RelativeSummitPosition", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:EWS-FLI" + }, + { + "@id": "bts:EWS-ERG" + }, + { + "@id": "bts:SYT-SSX1" + }, + { + "@id": "bts:SYT-SSX2" + }, + { + "@id": "bts:EWS-WT1" + }, + { + "@id": "bts:OtherFusionGene" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Relative Summit Position", + "sms:displayName": "Fusion Gene Identity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:ScmC-seqLevel1", + "@id": "bts:BulkWESLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw scmC-seq data.", - "rdfs:label": "ScmC-seqLevel1", + "rdfs:comment": "Bulk Whole Exome Sequencing raw files", + "rdfs:label": "BulkWESLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36511,7 +37157,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scmC-seq Level 1", + "sms:displayName": "Bulk WES Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -36535,123 +37181,91 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:ScmCseqRead1" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:ScmCseqRead2" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:ScmCseqRead3" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:SingleCellIsolationMethod" + "@id": "bts:ReadLength" }, { - "@id": "bts:SingleNucleusBuffer" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:SingleNucleusCapture" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:BisulfiteConversion" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:NucleusIdentifier" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:AdapterName" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:MedianFractionofReadsinPeaks" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:ThresholdforMinimumPassingReads" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:TotalNumberofPassingNuclei" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:TotalReads" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScmCseqRead1", - "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScmCseqRead1", - "rdfs:subClassOf": [ + "@id": "bts:FragmentStandardDeviationLength" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LaneNumber" + }, { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "scmCseq Read1", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScmCseqRead2", - "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScmCseqRead2", - "rdfs:subClassOf": [ + "@id": "bts:LibraryPreparationDaysfromIndex" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SizeSelectionRange" + }, { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:TargetDepth" }, { - "@id": "bts:CDNA" + "@id": "bts:ToTrimAdapterSequence" } ], - "sms:displayName": "scmCseq Read2", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScmCseqRead3", + "@id": "bts:TargetCaptureKit", "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScmCseqRead3", + "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", + "rdfs:label": "TargetCaptureKit", "rdfs:subClassOf": [ { - "@id": "bts:ScmC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -36659,199 +37273,165 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:NotApplicable" }, { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "scmCseq Read3", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SingleNucleusCapture", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation method", - "rdfs:label": "SingleNucleusCapture", - "rdfs:subClassOf": [ + "@id": "bts:CustomTargetsFileProvided" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" + }, { - "@id": "bts:Plates" + "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" }, { - "@id": "bts:10x" + "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" }, { - "@id": "bts:Droplet" - } - ], - "sms:displayName": "Single Nucleus Capture", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BisulfiteConversion", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the kit used in bisulfite conversion.", - "rdfs:label": "BisulfiteConversion", - "rdfs:subClassOf": [ + "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" + }, { - "@id": "bts:BulkMethylation-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" + }, { - "@id": "bts:ZimoEZDNAMethylationKit" + "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" }, { - "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" + "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" }, { - "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" + "@id": "bts:CustomMSKIMPACTPanel-341Genes" }, { - "@id": "bts:NEBNextEnzymaticMethyl-seqKit" + "@id": "bts:CustomMSKIMPACTPanel-410Genes" }, { - "@id": "bts:AgilentSureSelectXTMethyl-Seq" - } - ], - "sms:displayName": "Bisulfite Conversion", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PeaksCallingSoftware", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name of peaks calling tool", - "rdfs:label": "PeaksCallingSoftware", - "rdfs:subClassOf": [ + "@id": "bts:CustomMSKIMPACTPanel-468Genes" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Peaks Calling Software", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScmC-seqLevel2", - "@type": "rdfs:Class", - "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", - "rdfs:label": "ScmC-seqLevel2", - "rdfs:subClassOf": [ + "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scmC-seq Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "sms:requiresDependency": [ + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + }, { - "@id": "bts:Component" + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" }, { - "@id": "bts:Filename" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" }, { - "@id": "bts:FileFormat" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" }, { - "@id": "bts:AlignmentWorkflowUrl" + "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" }, { - "@id": "bts:GenomicReference" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" }, { - "@id": "bts:IndexFileName" + "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" }, { - "@id": "bts:Contamination" + "@id": "bts:FoundationMedicineT5aPanel-322Genes" }, { - "@id": "bts:ContaminationError" + "@id": "bts:FoundationMedicineT7Panel-429Genes" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" }, { - "@id": "bts:TotalReads" + "@id": "bts:NexteraDNAExome" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:NexteraRapidCaptureExomev1.2" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:SeqCapEZHGSCVCRomev2.1" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:SeqCapEZHumanExomev2.0" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:SeqCapEZHumanExomev3.0" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:SureSelectHumanAllExonv3" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:SureSelectHumanAllExonv4" }, { - "@id": "bts:ShortReads" + "@id": "bts:SureSelectHumanAllExonv5" + }, + { + "@id": "bts:SureSelectHumanAllExonv5+UTR" + }, + { + "@id": "bts:TruSeqAmpliconCancerPanel" + }, + { + "@id": "bts:TruSeqExomeEnrichment-62Mb" + }, + { + "@id": "bts:TruSeqRNAExome" + }, + { + "@id": "bts:TruSightMyeloidSequencingPanel" + }, + { + "@id": "bts:XGenExomeResearchPanelv1.0" + }, + { + "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" + }, + { + "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" + }, + { + "@id": "bts:SureSelectHumanAllExonv6" + }, + { + "@id": "bts:Unknown" } ], + "sms:displayName": "Target Capture Kit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel4", + "@id": "bts:BulkWESLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScATAC-seqLevel4", + "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", + "rdfs:label": "BulkWESLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36860,11 +37440,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 4", + "sms:displayName": "Bulk WES Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel3" + "@id": "bts:BulkWESLevel1" } ], "sms:requiresDependency": [ @@ -36884,221 +37464,170 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ScATACseqWorkflowType" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:ScATACseqWorkflowParametersDescription" + "@id": "bts:GenomicReference" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:WorkflowLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScATACseqWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowParametersDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", - "rdfs:label": "ScATACseqWorkflowParametersDescription", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Parameters Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScDNA-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Single-cell DNA-seq", - "rdfs:label": "ScDNA-seqLevel1", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scDNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:SequencingBatchID" - }, - { - "@id": "bts:LibraryLayout" + "@id": "bts:IndexFileName" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:ReadLength" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:Contamination" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:ContaminationError" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:AdapterName" + "@id": "bts:AdapterContent" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:Encoding" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:PerSequenceGCContent" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:PerSequenceQualityScore" }, { - "@id": "bts:LaneNumber" + "@id": "bts:PerTileSequenceQuality" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:PercentGCContent" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:SequenceDuplicationLevels" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:SequenceLengthDistribution" }, { - "@id": "bts:TargetDepth" + "@id": "bts:QCWorkflowType" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:QCWorkflowVersion" }, { - "@id": "bts:AdapterContent" + "@id": "bts:QCWorkflowLink" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:Encoding" + "@id": "bts:MSIScore" }, { - "@id": "bts:KmerContent" + "@id": "bts:MSIStatus" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:TotalReads" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:ShortReads" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:TotalReads" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:QCWorkflowType" - }, + "@id": "bts:Islowestlevel" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionCoverage10x", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage10x", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowVersion" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion Coverage 10x", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionCoverage30X", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage30X", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowLink" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion Coverage 30X", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScDNA-seqLevel2", + "@id": "bts:BulkWESLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", - "rdfs:label": "ScDNA-seqLevel2", + "rdfs:comment": "Bulk Whole Exome Sequencing called variants", + "rdfs:label": "BulkWESLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37107,11 +37636,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scDNA-seq Level 2", + "sms:displayName": "Bulk WES Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScDNA-seqLevel1" + "@id": "bts:BulkWESLevel2" } ], "sms:requiresDependency": [ @@ -37130,12 +37659,6 @@ { "@id": "bts:HTANDataFileID" }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, { "@id": "bts:GenomicReference" }, @@ -37143,73 +37666,170 @@ "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:IndexFileName" + "@id": "bts:GermlineVariantsWorkflowURL" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:GermlineVariantsWorkflowType" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:SomaticVariantsWorkflowURL" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:SomaticVariantsWorkflowType" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:SomaticVariantsSampleType" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:StructuralVariantWorkflowURL" }, { - "@id": "bts:TotalReads" - }, + "@id": "bts:StructuralVariantWorkflowType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:GermlineVariantsWorkflowURL", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", + "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:subClassOf": [ { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Germline Variants Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:GermlineVariantsWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GATK4" }, { - "@id": "bts:MapQ30" + "@id": "bts:OtherGermlineVariantsWorkflowType" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:None" + } + ], + "sms:displayName": "Germline Variants Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsWorkflowURL", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Somatic Variants Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CaVEMan" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:GATK4" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:MuTect2" }, { - "@id": "bts:ShortReads" + "@id": "bts:MuSE" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:Pindel" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:SomaticSniper" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:VarScan2" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:OtherSomaticVariantsWorkflowType" }, { - "@id": "bts:ProportionMitochondrialReads" + "@id": "bts:None" + } + ], + "sms:displayName": "Somatic Variants Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsSampleType", + "@type": "rdfs:Class", + "rdfs:comment": "Is the sample case or control in somatic variant analysis", + "rdfs:label": "SomaticVariantsSampleType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CaseSample" }, { - "@id": "bts:Contamination" + "@id": "bts:ControlSample" }, { - "@id": "bts:ContaminationError" + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Somatic Variants Sample Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionMitochondrialReads", + "@id": "bts:StructuralVariantWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of reads mapping to mitochondria.", - "rdfs:label": "ProportionMitochondrialReads", + "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", + "rdfs:label": "StructuralVariantWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37218,15 +37838,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Mitochondrial Reads", - "sms:required": "sms:false", + "sms:displayName": "Structural Variant Workflow URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel1", + "@id": "bts:StructuralVariantWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", - "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "StructuralVariantWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37235,7 +37855,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 1", + "schema:rangeIncludes": [ + { + "@id": "bts:BRASS" + }, + { + "@id": "bts:GATK4" + }, + { + "@id": "bts:CNV" + }, + { + "@id": "bts:CNVkit" + }, + { + "@id": "bts:OtherStructuralVariantWorkflowType" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Structural Variant Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", + "rdfs:label": "MicroarrayLevel1", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -37253,40 +37910,62 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:BisulfiteConversion" + "@id": "bts:MicroarrayPlatformID" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:MicroarrayMolecule" }, { - "@id": "bts:ReplicateType" + "@id": "bts:MicroarrayLabel" }, { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:MicroarrayValueDefinition" }, { - "@id": "bts:TotalDNAInput" + "@id": "bts:MicroarrayProtocolAuxiliaryFile" } ], "sms:validationRules": [] }, { - "@id": "bts:ReplicateType", + "@id": "bts:MicroarrayPlatformID", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", - "rdfs:label": "ReplicateType", + "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", + "rdfs:label": "MicroarrayPlatformID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Platform ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match GPL\\d+" + ] + }, + { + "@id": "bts:MicroarrayMolecule", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray is measuring this kind of molecule", + "rdfs:label": "MicroarrayMolecule", + "rdfs:subClassOf": [ + { + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { @@ -37294,77 +37973,142 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Technicalreplicate" + "@id": "bts:DNA" }, { - "@id": "bts:Biologicalreplicate" - }, + "@id": "bts:RNA" + } + ], + "sms:displayName": "Microarray Molecule", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayLabel", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray used this kind of label", + "rdfs:label": "MicroarrayLabel", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:MicroarrayLevel1" } ], - "sms:displayName": "Replicate Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Label", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationAssayType", + "@id": "bts:MicroarrayValueDefinition", "@type": "rdfs:Class", - "rdfs:comment": "Assay types normally determine genomic coverage", - "rdfs:label": "BulkMethylationAssayType", + "rdfs:comment": "What the provided value signifies", + "rdfs:label": "MicroarrayValueDefinition", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Microarray Value Definition", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayProtocolAuxiliaryFile", + "@type": "rdfs:Class", + "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", + "rdfs:label": "MicroarrayProtocolAuxiliaryFile", + "rdfs:subClassOf": [ { - "@id": "bts:Wholegenome" - }, + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Protocol Auxiliary File", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match syn\\d+" + ] + }, + { + "@id": "bts:MicroarrayLevel2", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", + "rdfs:label": "MicroarrayLevel2", + "rdfs:subClassOf": [ { - "@id": "bts:TargetedGenome" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:BeadchipArray" + "@id": "bts:MicroarrayLevel1" } ], - "sms:displayName": "Bulk Methylation Assay Type", - "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:TargetedGenome" + "@id": "bts:Component" }, { - "@id": "bts:BeadchipArray" + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:MicroarrayPlatformID" + }, + { + "@id": "bts:NormalizationMethod" } ], "sms:validationRules": [] }, { - "@id": "bts:TotalDNAInput", + "@id": "bts:NormalizationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", - "rdfs:label": "TotalDNAInput", + "rdfs:comment": "Description of Normalization Process", + "rdfs:label": "NormalizationMethod", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:RPPALevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total DNA Input", + "sms:displayName": "Normalization Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel2", + "@id": "bts:ScATAC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", - "rdfs:label": "BulkMethylation-seqLevel2", + "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", + "rdfs:label": "ScATAC-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37373,12 +38117,9 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 2", + "sms:displayName": "scATAC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ - { - "@id": "bts:BulkMethylation-seqLevel1" - }, { "@id": "bts:Biospecimen" } @@ -37394,97 +38135,91 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:Trimmer" - }, - { - "@id": "bts:BulkMethylationGenomicReference" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:IndexFileName" + "@id": "bts:SingleNucleusBuffer" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:DuplicateRemovalSoftware" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:ScATACseqLibraryLayout" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:NucleusIdentifier" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:NucleiBarcodeLength" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:NucleiBarcodeRead" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:ScATACseqRead1" }, { - "@id": "bts:Contamination" + "@id": "bts:ScATACseqRead2" }, { - "@id": "bts:ContaminationError" + "@id": "bts:ScATACseqRead3" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:LibraryConstructionMethod" }, { - "@id": "bts:TotalReads" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:ThresholdforMinimumPassingReads" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:TotalNumberofPassingNuclei" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:MedianFractionofReadsinPeaks" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:MedianPassingReadPercentage" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" }, { - "@id": "bts:ShortReads" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X" + "@id": "bts:TotalReads" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:ProtocolLink" } ], "sms:validationRules": [] }, { - "@id": "bts:Trimmer", + "@id": "bts:SingleNucleusBuffer", "@type": "rdfs:Class", - "rdfs:comment": "Software used for trimming", - "rdfs:label": "Trimmer", + "rdfs:comment": "Nuclei isolation buffer", + "rdfs:label": "SingleNucleusBuffer", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37492,51 +38227,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FASTXtoolkit" + "@id": "bts:NIB" }, { - "@id": "bts:SolexaQA" + "@id": "bts:10x" }, { - "@id": "bts:Btrim" + "@id": "bts:Omni" }, { - "@id": "bts:Cutadapt" - }, + "@id": "bts:TST" + } + ], + "sms:displayName": "Single Nucleus Buffer", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TranspositionReaction", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the transposase, transposon sequences", + "rdfs:label": "TranspositionReaction", + "rdfs:subClassOf": [ { - "@id": "bts:Kraken" + "@id": "bts:ScATAC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Tn5" }, { - "@id": "bts:PRINSEQ" + "@id": "bts:EZ-Tn5" }, { - "@id": "bts:Adapterremoval" + "@id": "bts:Tn5-059" }, { - "@id": "bts:TrimGalore!" + "@id": "bts:NexteraTn5" }, { - "@id": "bts:ConDeTri" + "@id": "bts:Diagenode-unloadedApex-Bio" }, { - "@id": "bts:ERNE-FILTER" + "@id": "bts:Diagenode-loadedApex-Bio" }, { - "@id": "bts:Trimmo-matic" + "@id": "bts:In-House" } ], - "sms:displayName": "Trimmer", + "sms:displayName": "Transposition Reaction", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationGenomicReference", + "@id": "bts:ScATACseqLibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "The human genome reference used in the alignment of reads", - "rdfs:label": "BulkMethylationGenomicReference", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "ScATACseqLibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37544,27 +38298,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HG19" - }, - { - "@id": "bts:HG38" - }, - { - "@id": "bts:T2TCHM13" + "@id": "bts:ScATACseqPairedEnd" } ], - "sms:displayName": "Bulk Methylation Genomic Reference", + "sms:displayName": "scATACseq Library Layout", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DuplicateRemovalSoftware", + "@id": "bts:NucleusIdentifier", "@type": "rdfs:Class", - "rdfs:comment": "Software used for remove duplicate reads", - "rdfs:label": "DuplicateRemovalSoftware", + "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", + "rdfs:label": "NucleusIdentifier", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37572,107 +38320,101 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Samtoolssort" - }, - { - "@id": "bts:PicardMarkDuplicates" + "@id": "bts:NucleiBarcode" } ], - "sms:displayName": "Duplicate Removal Software", + "sms:displayName": "Nucleus Identifier", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X", + "@id": "bts:NucleiBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", - "rdfs:label": "ProportionofMinimumCpGCoverage10X", + "rdfs:comment": "Nuclei Barcode Length", + "rdfs:label": "NucleiBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NucleiBarcode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion of Minimum CpG Coverage 10X", - "sms:required": "sms:false", + "sms:displayName": "Nuclei Barcode Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel3", + "@id": "bts:NucleiBarcodeRead", "@type": "rdfs:Class", - "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", - "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:comment": "Nuclei Barcode Read", + "rdfs:label": "NucleiBarcodeRead", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NucleiBarcode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "Nuclei Barcode Read", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATACseqRead1", + "@type": "rdfs:Class", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScATACseqRead1", + "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:Biospecimen" + "@id": "bts:ScATACseqPairedEnd" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:DMCCallingTool" - }, - { - "@id": "bts:DMCCallingWorkflowURL" - }, - { - "@id": "bts:DMRCallingTool" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DMRCallingWorkflowURL" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:PUC19methylationratio" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Lambdamethylationratio" + "@id": "bts:DNAInsert" }, { - "@id": "bts:DMCdatafileformat" + "@id": "bts:SampleIndex" }, { - "@id": "bts:DMRdatafileFormat" + "@id": "bts:CellBarcode" } ], + "sms:displayName": "scATACseq Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMCCallingTool", + "@id": "bts:ScATACseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMCCallingTool", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScATACseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:ScATACseqPairedEnd" } ], "schema:isPartOf": { @@ -37680,67 +38422,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" - }, - { - "@id": "bts:MethylSig" - }, - { - "@id": "bts:DSS" - }, - { - "@id": "bts:MOABS" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:DSS-single" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Metilene" + "@id": "bts:DNAInsert" }, { - "@id": "bts:MACAU" + "@id": "bts:SampleIndex" }, { - "@id": "bts:MethylDackel" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "DMC Calling Tool", + "sms:displayName": "scATACseq Read2", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMCCallingWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMCCallingWorkflowURL", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DMC Calling Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] - }, - { - "@id": "bts:DMRCallingTool", + "@id": "bts:ScATACseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMRCallingTool", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScATACseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37748,158 +38456,155 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" - }, - { - "@id": "bts:MethylSig" - }, - { - "@id": "bts:DSS" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:MOABS" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:DSS-single" + "@id": "bts:DNAInsert" }, { - "@id": "bts:Metilene" + "@id": "bts:SampleIndex" }, { - "@id": "bts:MACAU" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "DMR Calling Tool", - "sms:required": "sms:true", + "sms:displayName": "scATACseq Read3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMRCallingWorkflowURL", + "@id": "bts:ThresholdforMinimumPassingReads", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMRCallingWorkflowURL", + "rdfs:comment": "Threshold for calling cells", + "rdfs:label": "ThresholdforMinimumPassingReads", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DMR Calling Workflow URL", + "sms:displayName": "Threshold for Minimum Passing Reads", "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] + "sms:validationRules": [] }, { - "@id": "bts:PUC19methylationratio", + "@id": "bts:TotalNumberofPassingNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", - "rdfs:label": "PUC19methylationratio", + "rdfs:comment": "Number of nuclei sequenced", + "rdfs:label": "TotalNumberofPassingNuclei", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "pUC19 methylation ratio", + "sms:displayName": "Total Number of Passing Nuclei", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Lambdamethylationratio", + "@id": "bts:MedianFractionofReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", - "rdfs:label": "Lambdamethylationratio", + "rdfs:comment": "Median fraction of reads in peaks (FRIP)", + "rdfs:label": "MedianFractionofReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lambda methylation ratio", + "sms:displayName": "Median Fraction of Reads in Peaks", "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PeaksCallingSoftware" + } + ], "sms:validationRules": [] }, { - "@id": "bts:DMCdatafileformat", + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files", - "rdfs:label": "DMCdatafileformat", + "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, + "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:BedGraph" + "@id": "bts:PeaksCallingSoftware" } ], - "sms:displayName": "DMC data file format", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMRdatafileFormat", + "@id": "bts:MedianPassingReadPercentage", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files.", - "rdfs:label": "DMRdatafileFormat", + "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", + "rdfs:label": "MedianPassingReadPercentage", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, + "sms:displayName": "Median Passing Read Percentage", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@type": "rdfs:Class", + "rdfs:comment": "Contamination from mitochondrial sequences", + "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:subClassOf": [ { - "@id": "bts:BedGraph" + "@id": "bts:ScATAC-seqLevel1" } ], - "sms:displayName": "DMR data file Format", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel1", + "@id": "bts:ScATAC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Raw imaging data", - "rdfs:label": "ImagingLevel1", + "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", + "rdfs:label": "ScATAC-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 1", + "sms:displayName": "scATAC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScATAC-seqLevel1" } ], "sms:requiresDependency": [ @@ -37913,242 +38618,124 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:GenomicReference" }, { - "@id": "bts:CommitSHA" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:Pre-processingCompleted" + "@id": "bts:IndexFileName" }, { - "@id": "bts:Pre-processingRequired" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:Comment" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingAssayType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of imaging assay", - "rdfs:label": "ImagingAssayType", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AverageInsertSize" + }, { - "@id": "bts:H&E" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:CyCIF" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:T-CyCIF" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:IHC" + "@id": "bts:TotalReads" }, { - "@id": "bts:MIHC" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:MxIF" - }, - { - "@id": "bts:SABER" - }, - { - "@id": "bts:IMC" - }, - { - "@id": "bts:CODEX" + "@id": "bts:MapQ30" }, { - "@id": "bts:GeoMX-DSP" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:MIBI" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:MERFISH" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:ExSeq" + "@id": "bts:ShortReads" }, { - "@id": "bts:RareCyteOrion" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Imaging Assay Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SoftwareandVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Name of software used to generate expression values. String", - "rdfs:label": "SoftwareandVersion", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Software and Version", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CommitSHA", - "@type": "rdfs:Class", - "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", - "rdfs:label": "CommitSHA", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Commit SHA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pre-processingCompleted", - "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingCompleted", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:TileStitching" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:Channel/CycleRegistration" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:TMAde-arraying" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" }, { - "@id": "bts:None" + "@id": "bts:Contamination" }, { - "@id": "bts:Other" + "@id": "bts:ContaminationError" } ], - "sms:displayName": "Pre-processing Completed", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingRequired", + "@id": "bts:MapQ30", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingRequired", + "rdfs:comment": "Number of reads with Quality >= 30.", + "rdfs:label": "MapQ30", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Pre-processing Required", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Comment", - "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Comment", + "sms:displayName": "MapQ30", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel2", + "@id": "bts:ScATAC-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Raw and pre-processed image data", - "rdfs:label": "ImagingLevel2", + "rdfs:comment": "Processed data files containing peak information for cells", + "rdfs:label": "ScATAC-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 2", + "sms:displayName": "scATAC-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel1" + "@id": "bts:ScATAC-seqLevel2" } ], "sms:requiresDependency": [ @@ -38162,1022 +38749,792 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" + "@id": "bts:ScATAC-seqObjectID" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:NCountPeaks" }, { - "@id": "bts:Microscope" + "@id": "bts:NFeaturePeaks" }, { - "@id": "bts:Objective" + "@id": "bts:TotalRead-Pairs" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:DuplicateRead-Pairs" }, { - "@id": "bts:LensNA" + "@id": "bts:ChimericRead-Pairs" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:UnmappedRead-Pairs" }, { - "@id": "bts:WorkingDistanceUnit" + "@id": "bts:LowMapQ" }, { - "@id": "bts:Immersion" + "@id": "bts:MitochondrialRead-Pairs" }, { - "@id": "bts:Pyramid" + "@id": "bts:PassedFilters" }, { - "@id": "bts:Zstack" + "@id": "bts:TSSFragments" }, { - "@id": "bts:Tseries" + "@id": "bts:DNaseSensitiveRegionFragments" }, { - "@id": "bts:PassedQC" + "@id": "bts:EnhancerRegionFragments" }, { - "@id": "bts:Comment" + "@id": "bts:PromoterRegionFragments" }, { - "@id": "bts:FOVnumber" + "@id": "bts:OnTargetFragments" }, { - "@id": "bts:FOVX" + "@id": "bts:BlacklistRegionFragments" }, { - "@id": "bts:FOVXUnit" + "@id": "bts:PeakRegionFragments" }, { - "@id": "bts:FOVY" + "@id": "bts:PeakRegionCutsites" }, { - "@id": "bts:FOVYUnit" + "@id": "bts:NucleosomeSignal" }, { - "@id": "bts:FrameAveraging" + "@id": "bts:NucleosomePercentile" }, { - "@id": "bts:ImageID" + "@id": "bts:TSSEnrichment" }, { - "@id": "bts:DimensionOrder" + "@id": "bts:TSSPercentile" }, { - "@id": "bts:PhysicalSizeX" + "@id": "bts:PctReadsinPeaks" }, { - "@id": "bts:PhysicalSizeXUnit" + "@id": "bts:BlacklistRatio" }, { - "@id": "bts:PhysicalSizeY" + "@id": "bts:SeuratClusters" }, { - "@id": "bts:PhysicalSizeYUnit" + "@id": "bts:NCountRNA" }, { - "@id": "bts:PhysicalSizeZ" + "@id": "bts:NFeatureRNA" }, { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:MACS2Seqnames" }, { - "@id": "bts:PixelsBigEndian" + "@id": "bts:MACS2Start" }, { - "@id": "bts:PlaneCount" + "@id": "bts:MACS2End" }, { - "@id": "bts:SizeC" + "@id": "bts:MACS2Width" }, { - "@id": "bts:SizeT" + "@id": "bts:MACS2Strand" }, { - "@id": "bts:SizeX" + "@id": "bts:MACS2Name" }, { - "@id": "bts:SizeY" + "@id": "bts:MACS2Score" }, { - "@id": "bts:SizeZ" + "@id": "bts:MACS2FoldChange" }, { - "@id": "bts:PixelType" + "@id": "bts:MACS2NegLog10pvalueSummit" }, { - "@id": "bts:MERFISHPositionsFile" + "@id": "bts:MACS2NegLog10qvalueSummit" }, { - "@id": "bts:MERFISHCodebookFile" + "@id": "bts:MACS2RelativeSummitPosition" } ], "sms:validationRules": [] }, { - "@id": "bts:ChannelMetadataFilename", + "@id": "bts:ScATAC-seqObjectID", "@type": "rdfs:Class", - "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label": "ChannelMetadataFilename", + "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", + "rdfs:label": "ScATAC-seqObjectID", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ScATAC-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Metadata Filename", - "sms:required": "sms:true", + "sms:displayName": "scATAC-seq Object ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Microscope", + "@id": "bts:NCountPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", + "rdfs:comment": "Total number of fragments in peaks", + "rdfs:label": "NCountPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", + "sms:displayName": "nCount Peaks", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Objective", + "@id": "bts:NFeaturePeaks", "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", + "rdfs:comment": "Number of peaks with at least one read", + "rdfs:label": "NFeaturePeaks", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Objective", + "sms:displayName": "nFeature Peaks", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NominalMagnification", + "@id": "bts:TotalRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", + "rdfs:comment": "Total read-pairs", + "rdfs:label": "TotalRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "Total Read-Pairs", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:LensNA", + "@id": "bts:DuplicateRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", - "rdfs:label": "LensNA", + "rdfs:comment": "Number of duplicate read-pairs", + "rdfs:label": "DuplicateRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LensNA", + "sms:displayName": "Duplicate Read-Pairs", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:WorkingDistance", + "@id": "bts:ChimericRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", + "rdfs:comment": "Number of chimerically mapped read-pairs", + "rdfs:label": "ChimericRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "WorkingDistance", + "sms:displayName": "Chimeric Read-Pairs", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:WorkingDistanceUnit" - } - ], "sms:validationRules": [] }, { - "@id": "bts:WorkingDistanceUnit", + "@id": "bts:UnmappedRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", + "rdfs:comment": "Number of read-pairs with at least one end not mapped", + "rdfs:label": "UnmappedRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", + "sms:displayName": "Unmapped Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Immersion", + "@id": "bts:LowMapQ", "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", + "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", + "rdfs:label": "LowMapQ", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Air" - }, - { - "@id": "bts:Oil" - }, - { - "@id": "bts:Water" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", + "sms:displayName": "LowMapQ", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pyramid", + "@id": "bts:MitochondrialRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", + "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", + "rdfs:label": "MitochondrialRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", + "sms:displayName": "Mitochondrial Read-Pairs", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zstack", + "@id": "bts:PassedFilters", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", + "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", + "rdfs:label": "PassedFilters", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Zstack", - "sms:required": "sms:true", + "sms:displayName": "Passed Filters", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tseries", + "@id": "bts:TSSFragments", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", + "rdfs:comment": "Number of fragments overlapping with TSS regions", + "rdfs:label": "TSSFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Tseries", - "sms:required": "sms:true", + "sms:displayName": "TSS Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PassedQC", + "@id": "bts:DNaseSensitiveRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", + "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", + "rdfs:label": "DNaseSensitiveRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", + "sms:displayName": "DNase Sensitive Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVnumber", + "@id": "bts:EnhancerRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", + "rdfs:comment": "Number of fragments overlapping enhancer regions", + "rdfs:label": "EnhancerRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOV number", + "sms:displayName": "Enhancer Region Fragments", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVX", + "@id": "bts:PromoterRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", + "rdfs:comment": "Number of fragments overlapping promoter regions", + "rdfs:label": "PromoterRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVX", + "sms:displayName": "Promoter Region Fragments", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVXUnit", + "@id": "bts:OnTargetFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", + "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", + "rdfs:label": "OnTargetFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", + "sms:displayName": "On Target Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVY", + "@id": "bts:BlacklistRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", + "rdfs:comment": "Number of fragments overlapping blacklisted regions", + "rdfs:label": "BlacklistRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVY", + "sms:displayName": "Blacklist Region Fragments", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVYUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVYUnit", + "@id": "bts:PeakRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", + "rdfs:comment": "Number of fragments overlapping peaks", + "rdfs:label": "PeakRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVYUnit", + "sms:displayName": "Peak Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FrameAveraging", + "@id": "bts:PeakRegionCutsites", "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label": "FrameAveraging", + "rdfs:comment": "Number of ends of fragments in peak regions", + "rdfs:label": "PeakRegionCutsites", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Frame Averaging", + "sms:displayName": "Peak Region Cutsites", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageID", + "@id": "bts:NucleosomeSignal", "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", + "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", + "rdfs:label": "NucleosomeSignal", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", + "sms:displayName": "Nucleosome Signal", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DimensionOrder", + "@id": "bts:NucleosomePercentile", "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", + "rdfs:comment": "Percentile rank of nucleosome score", + "rdfs:label": "NucleosomePercentile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:XYZCT" - }, - { - "@id": "bts:XYZTC" - }, - { - "@id": "bts:XYCTZ" - }, - { - "@id": "bts:XYCZT" - }, - { - "@id": "bts:XYTZC" - }, - { - "@id": "bts:ZYX" - } - ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", + "sms:displayName": "Nucleosome Percentile", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeX", + "@id": "bts:TSSEnrichment", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeX", + "rdfs:comment": "Transcription start site (TSS) enrichment score", + "rdfs:label": "TSSEnrichment", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeXUnit" - } - ], + "sms:displayName": "TSS Enrichment", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeXUnit", + "@id": "bts:TSSPercentile", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", + "rdfs:comment": "Percentile rank of TSS score", + "rdfs:label": "TSSPercentile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", + "sms:displayName": "TSS Percentile", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeY", + "@id": "bts:PctReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeY", + "rdfs:comment": "Percentage of reads in peaks", + "rdfs:label": "PctReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeYUnit" - } - ], + "sms:displayName": "Pct Reads in Peaks", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:BlacklistRatio", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "Ratio of reads in blacklist regions", + "rdfs:label": "BlacklistRatio", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", + "sms:displayName": "Blacklist Ratio", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZ", + "@id": "bts:SeuratClusters", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeZ", + "rdfs:comment": "Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm", + "rdfs:label": "SeuratClusters", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeZ", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeZUnit" - } - ], + "sms:displayName": "Seurat Clusters", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZUnit", + "@id": "bts:NCountRNA", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeZUnit", + "rdfs:comment": "Total number of fragments in genes", + "rdfs:label": "NCountRNA", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeZUnit", - "sms:required": "sms:true", + "sms:displayName": "nCount RNA", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PixelsBigEndian", + "@id": "bts:NFeatureRNA", "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", + "rdfs:comment": "Number of genes detected in cell", + "rdfs:label": "NFeatureRNA", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, + "sms:displayName": "nFeature RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Seqnames", + "@type": "rdfs:Class", + "rdfs:comment": "Chromosome id", + "rdfs:label": "MACS2Seqnames", + "rdfs:subClassOf": [ { - "@id": "bts:False" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "Pixels BigEndian", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Seqnames", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PlaneCount", + "@id": "bts:MACS2Start", "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", - "rdfs:label": "PlaneCount", + "rdfs:comment": "Genomic starting position in MACS2", + "rdfs:label": "MACS2Start", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PlaneCount", - "sms:required": "sms:true", + "sms:displayName": "MACS2 Start", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeC", + "@id": "bts:MACS2End", "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", + "rdfs:comment": "Genomic ending position in MACS2", + "rdfs:label": "MACS2End", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeC", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 End", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeT", + "@id": "bts:MACS2Width", "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", + "rdfs:comment": "Width of the peak in bases in MACS2", + "rdfs:label": "MACS2Width", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeT", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Width", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeX", + "@id": "bts:MACS2Strand", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", + "rdfs:comment": "DNA stand aligned with in MACS2", + "rdfs:label": "MACS2Strand", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeX", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Strand", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeY", + "@id": "bts:MACS2Name", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeY", + "rdfs:comment": "Name of the peak in MACS2", + "rdfs:label": "MACS2Name", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeY", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Name", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeZ", + "@id": "bts:MACS2Score", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeZ", + "rdfs:comment": "Peak score (proportional to q-value) in MACS2", + "rdfs:label": "MACS2Score", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeZ", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Score", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:PixelType", + "@id": "bts:MACS2FoldChange", "@type": "rdfs:Class", - "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", - "rdfs:label": "PixelType", + "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", + "rdfs:label": "MACS2FoldChange", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Int8" - }, - { - "@id": "bts:Int16" - }, - { - "@id": "bts:Int32" - }, - { - "@id": "bts:Uint8" - }, - { - "@id": "bts:Uint16" - }, - { - "@id": "bts:Uint32" - }, - { - "@id": "bts:Float" - }, - { - "@id": "bts:Double" - }, + "sms:displayName": "MACS2 Fold Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2NegLog10pvalueSummit", + "@type": "rdfs:Class", + "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10pvalueSummit", + "rdfs:subClassOf": [ { - "@id": "bts:Bit" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "PixelType", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Neg Log10 pvalue Summit", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHPositionsFile", + "@id": "bts:MACS2NegLog10qvalueSummit", "@type": "rdfs:Class", - "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", - "rdfs:label": "MERFISHPositionsFile", + "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10qvalueSummit", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Positions File", + "sms:displayName": "MACS2 Neg Log10 qvalue Summit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHCodebookFile", + "@id": "bts:MACS2RelativeSummitPosition", "@type": "rdfs:Class", - "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", - "rdfs:label": "MERFISHCodebookFile", + "rdfs:comment": "Position of the peak summit related to the start position in MACS2", + "rdfs:label": "MACS2RelativeSummitPosition", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Codebook File", + "sms:displayName": "MACS2 Relative Summit Position", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Segmentation", + "@id": "bts:ScmC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Object segmentations", - "rdfs:label": "ImagingLevel3Segmentation", + "rdfs:comment": "Files contain raw scmC-seq data.", + "rdfs:label": "ScmC-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Segmentation", + "sms:displayName": "scmC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -39191,91 +39548,104 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:Parameterfile" + "@id": "bts:ScmCseqRead1" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:ScmCseqRead2" }, { - "@id": "bts:CommitSHA" + "@id": "bts:ScmCseqRead3" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:NumberofObjects" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingSegmentationDataType", - "@type": "rdfs:Class", - "rdfs:comment": "Specifies how the segmentation is stored", - "rdfs:label": "ImagingSegmentationDataType", - "rdfs:subClassOf": [ + "@id": "bts:SingleNucleusBuffer" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SingleNucleusCapture" + }, { - "@id": "bts:Mask" + "@id": "bts:BisulfiteConversion" }, { - "@id": "bts:Outline" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:Polygon" + "@id": "bts:NucleusIdentifier" }, { - "@id": "bts:ProbabilityMap" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:Point" + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:MedianFractionofReadsinPeaks" + }, + { + "@id": "bts:MedianPassingReadPercentage" + }, + { + "@id": "bts:PeaksCallingSoftware" + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:ThresholdforMinimumPassingReads" + }, + { + "@id": "bts:TotalNumberofPassingNuclei" + }, + { + "@id": "bts:TotalReads" } ], - "sms:displayName": "Imaging Segmentation Data Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Parameterfile", + "@id": "bts:ScmCseqRead1", "@type": "rdfs:Class", - "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", - "rdfs:label": "Parameterfile", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScmCseqRead1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Parameter file", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingObjectClass", + "@id": "bts:ScmCseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "Defines the structure that the mask delineates", - "rdfs:label": "ImagingObjectClass", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScmCseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -39283,70 +39653,138 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Nucleus" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:Cytoplasm" + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read2", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScmCseqRead3", + "@type": "rdfs:Class", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScmCseqRead3", + "rdfs:subClassOf": [ + { + "@id": "bts:ScmC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:Plasmamembrane" + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read3", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SingleNucleusCapture", + "@type": "rdfs:Class", + "rdfs:comment": "Nuclei isolation method", + "rdfs:label": "SingleNucleusCapture", + "rdfs:subClassOf": [ + { + "@id": "bts:ScmC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Plates" }, { - "@id": "bts:Wholecell" + "@id": "bts:10x" }, { - "@id": "bts:Spot" + "@id": "bts:Droplet" + } + ], + "sms:displayName": "Single Nucleus Capture", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BisulfiteConversion", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the kit used in bisulfite conversion.", + "rdfs:label": "BisulfiteConversion", + "rdfs:subClassOf": [ + { + "@id": "bts:BulkMethylation-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ZimoEZDNAMethylationKit" }, { - "@id": "bts:ImagingObjectClassOther" + "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" + }, + { + "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" + }, + { + "@id": "bts:NEBNextEnzymaticMethyl-seqKit" + }, + { + "@id": "bts:AgilentSureSelectXTMethyl-Seq" } ], - "sms:displayName": "Imaging Object Class", + "sms:displayName": "Bisulfite Conversion", "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] + "sms:validationRules": [] }, { - "@id": "bts:NumberofObjects", + "@id": "bts:PeaksCallingSoftware", "@type": "rdfs:Class", - "rdfs:comment": "The number of objects (eg cells) described", - "rdfs:label": "NumberofObjects", + "rdfs:comment": "Generic name of peaks calling tool", + "rdfs:label": "PeaksCallingSoftware", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Objects", + "sms:displayName": "Peaks Calling Software", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Image", + "@id": "bts:ScmC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Quality controlled imaging data", - "rdfs:label": "ImagingLevel3Image", + "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", + "rdfs:label": "ScmC-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Image", + "sms:displayName": "scmC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ImagingLevel2" + "@id": "bts:ScmC-seqLevel1" } ], "sms:requiresDependency": [ @@ -39360,203 +39798,339 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANParentChannelMetadataID" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:GenomicReference" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:IndexFileName" }, { - "@id": "bts:Microscope" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:Objective" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:LensNA" + "@id": "bts:Contamination" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:ContaminationError" }, { - "@id": "bts:Immersion" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:Pyramid" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:Zstack" + "@id": "bts:TotalReads" }, { - "@id": "bts:Tseries" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PassedQC" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:Comment" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:FOVnumber" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:FOVX" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:FOVY" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:FrameAveraging" + "@id": "bts:ShortReads" } ], "sms:validationRules": [] }, { - "@id": "bts:HTANParentChannelMetadataID", + "@id": "bts:ScATAC-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID for a level 3 channels table.", - "rdfs:label": "HTANParentChannelMetadataID", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScATAC-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel4" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent Channel Metadata ID", + "sms:displayName": "scATAC-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScATAC-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScATACseqWorkflowType" + }, + { + "@id": "bts:ScATACseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ScATACseqWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScATACseqWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATACseq Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Channels", + "@id": "bts:ScATACseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Channel-level Metadata Attributes", - "rdfs:label": "ImagingLevel3Channels", + "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", + "rdfs:label": "ScATACseqWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Channels", + "sms:displayName": "scATACseq Workflow Parameters Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScDNA-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Single-cell DNA-seq", + "rdfs:label": "ScDNA-seqLevel1", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scDNA-seq Level 1", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], "sms:requiresDependency": [ { - "@id": "bts:HTANChannelMetadataID" + "@id": "bts:Component" }, { - "@id": "bts:ChannelID" + "@id": "bts:Filename" }, { - "@id": "bts:ChannelName" + "@id": "bts:FileFormat" }, { - "@id": "bts:ChannelPassedQC" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CycleNumber" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SubCycleNumber" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:AntibodyRole" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:TargetName" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:AntibodyName" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:RRIDidentifier" + "@id": "bts:ReadLength" }, { - "@id": "bts:Fluorophore" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:Clone" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:Lot" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:Vendor" + "@id": "bts:AdapterName" }, { - "@id": "bts:CatalogNumber" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:ExcitationWavelength" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:EmissionWavelength" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:ExcitationBandwidth" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:EmissionBandwidth" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:MetalIsotopeMass" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:OligoBarcodeUpperStrand" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:OligoBarcodeLowerStrand" + "@id": "bts:LaneNumber" }, { - "@id": "bts:Dilution" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:Concentration" + "@id": "bts:MultiplexBarcode" + }, + { + "@id": "bts:SizeSelectionRange" + }, + { + "@id": "bts:TargetDepth" + }, + { + "@id": "bts:ToTrimAdapterSequence" + }, + { + "@id": "bts:AdapterContent" + }, + { + "@id": "bts:BasicStatistics" + }, + { + "@id": "bts:Encoding" + }, + { + "@id": "bts:KmerContent" + }, + { + "@id": "bts:OverrepresentedSequences" + }, + { + "@id": "bts:PerBaseNContent" + }, + { + "@id": "bts:PerBaseSequenceContent" + }, + { + "@id": "bts:PerBaseSequenceQuality" + }, + { + "@id": "bts:PerSequenceGCContent" + }, + { + "@id": "bts:PerSequenceQualityScore" + }, + { + "@id": "bts:PerTileSequenceQuality" + }, + { + "@id": "bts:PercentGCContent" + }, + { + "@id": "bts:SequenceDuplicationLevels" + }, + { + "@id": "bts:SequenceLengthDistribution" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:QCWorkflowType" + }, + { + "@id": "bts:QCWorkflowVersion" + }, + { + "@id": "bts:QCWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", + "@id": "bts:ScDNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", + "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", + "rdfs:label": "ScDNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", + "sms:displayName": "scDNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScDNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -39566,123 +40140,172 @@ { "@id": "bts:Filename" }, - { - "@id": "bts:RunID" - }, { "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:GenomicReference" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:IndexFileName" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:EndBias" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:CaptureArea" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:TotalReads" }, { - "@id": "bts:SlideVersion" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:SlideID" + "@id": "bts:MapQ30" }, { - "@id": "bts:ImageRe-orientation" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PermeabilizationTime" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:RIN" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:DV200" + "@id": "bts:ShortReads" + }, + { + "@id": "bts:ProportionCoverage10x" + }, + { + "@id": "bts:ProportionCoverage30X" + }, + { + "@id": "bts:ProportionTargetsNoCoverage" + }, + { + "@id": "bts:ProportionBaseMismatch" + }, + { + "@id": "bts:ProportionMitochondrialReads" + }, + { + "@id": "bts:Contamination" + }, + { + "@id": "bts:ContaminationError" } ], "sms:validationRules": [] }, { - "@id": "bts:CaptureArea", + "@id": "bts:ProportionMitochondrialReads", "@type": "rdfs:Class", - "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", - "rdfs:label": "CaptureArea", + "rdfs:comment": "Proportion of reads mapping to mitochondria.", + "rdfs:label": "ProportionMitochondrialReads", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Proportion Mitochondrial Reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", + "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:A" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:B" + "@id": "bts:Filename" }, { - "@id": "bts:C" + "@id": "bts:FileFormat" }, { - "@id": "bts:D" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:A1" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:B1" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:C1" + "@id": "bts:BisulfiteConversion" }, { - "@id": "bts:D1" + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:ReplicateType" + }, + { + "@id": "bts:BulkMethylationAssayType" + }, + { + "@id": "bts:TotalDNAInput" } ], - "sms:displayName": "Capture Area", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlideVersion", + "@id": "bts:ReplicateType", "@type": "rdfs:Class", - "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "rdfs:label": "SlideVersion", + "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", + "rdfs:label": "ReplicateType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -39690,99 +40313,93 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:V1" - }, - { - "@id": "bts:V2" + "@id": "bts:Technicalreplicate" }, { - "@id": "bts:V3" + "@id": "bts:Biologicalreplicate" }, { - "@id": "bts:V4" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Slide Version", - "sms:required": "sms:false", + "sms:displayName": "Replicate Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SlideID", + "@id": "bts:BulkMethylationAssayType", "@type": "rdfs:Class", - "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", - "rdfs:label": "SlideID", + "rdfs:comment": "Assay types normally determine genomic coverage", + "rdfs:label": "BulkMethylationAssayType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImageRe-orientation", - "@type": "rdfs:Class", - "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", - "rdfs:label": "ImageRe-orientation", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Wholegenome" + }, + { + "@id": "bts:TargetedGenome" + }, + { + "@id": "bts:BeadchipArray" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:displayName": "Bulk Methylation Assay Type", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:TRUE" + "@id": "bts:TargetedGenome" }, { - "@id": "bts:FALSE" + "@id": "bts:BeadchipArray" } ], - "sms:displayName": "Image Re-orientation", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PermeabilizationTime", + "@id": "bts:TotalDNAInput", "@type": "rdfs:Class", - "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", - "rdfs:label": "PermeabilizationTime", + "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", + "rdfs:label": "TotalDNAInput", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylationAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Permeabilization Time", + "sms:displayName": "Total DNA Input", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "@id": "bts:BulkMethylation-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", + "rdfs:label": "BulkMethylation-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", + "sms:displayName": "Bulk Methylation-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:BulkMethylation-seqLevel1" + }, + { + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -39795,9 +40412,6 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:Checksum" - }, { "@id": "bts:HTANParentDataFileID" }, @@ -39805,132 +40419,91 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:UMITag" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:WhitelistSpatialBarcodeFileLink" + "@id": "bts:Trimmer" }, { - "@id": "bts:SpatialBarcodeTag" + "@id": "bts:BulkMethylationGenomicReference" }, { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:IndexFileName" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:GenomicReference" + "@id": "bts:DuplicateRemovalSoftware" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:RunID" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:CaptureArea" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:WhitelistSpatialBarcodeFileLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", - "rdfs:label": "WhitelistSpatialBarcodeFileLink", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Whitelist Spatial Barcode File Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", - "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Contamination" + }, { - "@id": "bts:Component" + "@id": "bts:ContaminationError" }, { - "@id": "bts:Filename" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:FileFormat" + "@id": "bts:TotalReads" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:RunID" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:VisiumFileType" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:SlideID" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:CaptureArea" + "@id": "bts:ShortReads" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:ProportionofMinimumCpGCoverage10X" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:ProportionCoverage30X" } ], "sms:validationRules": [] }, { - "@id": "bts:VisiumFileType", + "@id": "bts:Trimmer", "@type": "rdfs:Class", - "rdfs:comment": "The file type generated for the visium experiment.", - "rdfs:label": "VisiumFileType", + "rdfs:comment": "Software used for trimming", + "rdfs:label": "Trimmer", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { @@ -39938,79 +40511,134 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Referencepng" + "@id": "bts:FASTXtoolkit" }, { - "@id": "bts:Referencejpg" + "@id": "bts:SolexaQA" }, { - "@id": "bts:Jsonscalefactors" + "@id": "bts:Btrim" }, { - "@id": "bts:Probedatasetcsv" + "@id": "bts:Cutadapt" }, { - "@id": "bts:Qcresulthtml" + "@id": "bts:Kraken" }, { - "@id": "bts:Filteredmex" + "@id": "bts:PRINSEQ" }, { - "@id": "bts:Unfilteredmex" + "@id": "bts:Adapterremoval" }, { - "@id": "bts:TissuePositions" + "@id": "bts:TrimGalore!" }, { - "@id": "bts:Barcodes" + "@id": "bts:ConDeTri" }, { - "@id": "bts:Features" + "@id": "bts:ERNE-FILTER" }, { - "@id": "bts:Fiducialimagepng" - }, + "@id": "bts:Trimmo-matic" + } + ], + "sms:displayName": "Trimmer", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylationGenomicReference", + "@type": "rdfs:Class", + "rdfs:comment": "The human genome reference used in the alignment of reads", + "rdfs:label": "BulkMethylationGenomicReference", + "rdfs:subClassOf": [ { - "@id": "bts:Fiducialimagejpg" - }, + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Detectedimagepng" + "@id": "bts:HG19" }, { - "@id": "bts:Detectedjpg" + "@id": "bts:HG38" }, { - "@id": "bts:Highresimage" + "@id": "bts:T2TCHM13" + } + ], + "sms:displayName": "Bulk Methylation Genomic Reference", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DuplicateRemovalSoftware", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for remove duplicate reads", + "rdfs:label": "DuplicateRemovalSoftware", + "rdfs:subClassOf": [ + { + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Samtoolssort" }, { - "@id": "bts:Lowresimage" + "@id": "bts:PicardMarkDuplicates" } ], - "sms:displayName": "Visium File Type", + "sms:displayName": "Duplicate Removal Software", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "@id": "bts:ProportionofMinimumCpGCoverage10X", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", + "rdfs:label": "ProportionofMinimumCpGCoverage10X", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", + "sms:displayName": "Proportion of Minimum CpG Coverage 10X", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", + "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + "@id": "bts:BulkMethylation-seqLevel2" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -40023,9 +40651,6 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:HTANParentBiospecimenID" - }, { "@id": "bts:HTANParentDataFileID" }, @@ -40033,1259 +40658,1698 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:RunID" - }, - { - "@id": "bts:VisiumFileType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:CaptureArea" + "@id": "bts:DMCCallingTool" }, { - "@id": "bts:Spotsundertissue" + "@id": "bts:DMCCallingWorkflowURL" }, { - "@id": "bts:MeanReadsperSpatialSpot" + "@id": "bts:DMRCallingTool" }, { - "@id": "bts:MedianNumberGenesperSpatialSpot" + "@id": "bts:DMRCallingWorkflowURL" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:PUC19methylationratio" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Lambdamethylationratio" }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome" + "@id": "bts:DMCdatafileformat" }, { - "@id": "bts:MedianUMICountsperSpot" + "@id": "bts:DMRdatafileFormat" } ], "sms:validationRules": [] }, { - "@id": "bts:Spotsundertissue", + "@id": "bts:DMCCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "The number of barcodes associated with a spot under tissue.", - "rdfs:label": "Spotsundertissue", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMCCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spots under tissue", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MeanReadsperSpatialSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", - "rdfs:label": "MeanReadsperSpatialSpot", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mean Reads per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:SequencingSaturation", - "@type": "rdfs:Class", - "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", - "rdfs:label": "SequencingSaturation", - "rdfs:subClassOf": [ + "@id": "bts:MethylKit" + }, { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BSmooth" + }, + { + "@id": "bts:BiSeq" + }, + { + "@id": "bts:MethylSig" + }, + { + "@id": "bts:DSS" + }, + { + "@id": "bts:MOABS" + }, + { + "@id": "bts:DSS-single" + }, + { + "@id": "bts:Metilene" + }, + { + "@id": "bts:MACAU" + }, + { + "@id": "bts:MethylDackel" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Saturation", + "sms:displayName": "DMC Calling Tool", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome", + "@id": "bts:DMCCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", - "rdfs:label": "ProportionReadsMappedtoTranscriptome", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMCCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped to Transcriptome", + "sms:displayName": "DMC Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "@id": "bts:DMRCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMRCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, + "schema:rangeIncludes": [ { - "@id": "bts:FileFormat" + "@id": "bts:MethylKit" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:BSmooth" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:BiSeq" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:MethylSig" }, { - "@id": "bts:RunID" + "@id": "bts:DSS" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:MOABS" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:DSS-single" }, { - "@id": "bts:VisiumWorkflowType" + "@id": "bts:Metilene" }, { - "@id": "bts:VisiumWorkflowParametersDescription" + "@id": "bts:MACAU" } ], + "sms:displayName": "DMR Calling Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:VisiumWorkflowType", + "@id": "bts:DMRCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", - "rdfs:label": "VisiumWorkflowType", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMRCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Visium Workflow Type", + "sms:displayName": "DMR Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:VisiumWorkflowParametersDescription", + "@id": "bts:PUC19methylationratio", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow..", - "rdfs:label": "VisiumWorkflowParametersDescription", + "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", + "rdfs:label": "PUC19methylationratio", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Visium Workflow Parameters Description", + "sms:displayName": "pUC19 methylation ratio", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Referencepng", + "@id": "bts:Lambdamethylationratio", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencepng", + "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", + "rdfs:label": "Lambdamethylationratio", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "reference png", - "sms:required": "sms:false", + "sms:displayName": "Lambda methylation ratio", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Referencejpg", + "@id": "bts:DMCdatafileformat", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencejpg", + "rdfs:comment": "Format of the data files", + "rdfs:label": "DMCdatafileformat", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "reference jpg", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:BED" + }, + { + "@id": "bts:BedGraph" + } + ], + "sms:displayName": "DMC data file format", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Jsonscalefactors", + "@id": "bts:DMRdatafileFormat", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Jsonscalefactors", + "rdfs:comment": "Format of the data files.", + "rdfs:label": "DMRdatafileFormat", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "json scale factors", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:BED" + }, + { + "@id": "bts:BedGraph" + } + ], + "sms:displayName": "DMR data file Format", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Probedatasetcsv", + "@id": "bts:ImagingLevel1", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Probedatasetcsv", + "rdfs:comment": "Raw imaging data", + "rdfs:label": "ImagingLevel1", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "probe dataset csv", + "sms:displayName": "Imaging Level 1", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:Pre-processingCompleted" + }, + { + "@id": "bts:Pre-processingRequired" + }, + { + "@id": "bts:Comment" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Qcresulthtml", + "@id": "bts:ImagingAssayType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Qcresulthtml", + "rdfs:comment": "Type of imaging assay", + "rdfs:label": "ImagingAssayType", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "qc result html", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:H&E" + }, + { + "@id": "bts:CyCIF" + }, + { + "@id": "bts:T-CyCIF" + }, + { + "@id": "bts:IHC" + }, + { + "@id": "bts:MIHC" + }, + { + "@id": "bts:MxIF" + }, + { + "@id": "bts:SABER" + }, + { + "@id": "bts:IMC" + }, + { + "@id": "bts:CODEX" + }, + { + "@id": "bts:GeoMX-DSP" + }, + { + "@id": "bts:MIBI" + }, + { + "@id": "bts:MERFISH" + }, + { + "@id": "bts:ExSeq" + }, + { + "@id": "bts:RareCyteOrion" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Imaging Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Filteredmex", + "@id": "bts:SoftwareandVersion", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Filteredmex", + "rdfs:comment": "Name of software used to generate expression values. String", + "rdfs:label": "SoftwareandVersion", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "filtered mex", - "sms:required": "sms:false", + "sms:displayName": "Software and Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Unfilteredmex", + "@id": "bts:CommitSHA", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Unfilteredmex", + "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", + "rdfs:label": "CommitSHA", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "unfiltered mex", + "sms:displayName": "Commit SHA", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TissuePositions", + "@id": "bts:Pre-processingCompleted", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TissuePositions", + "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingCompleted", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tissue_positions", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Illuminationcorrection" + }, + { + "@id": "bts:TileStitching" + }, + { + "@id": "bts:Channel/CycleRegistration" + }, + { + "@id": "bts:TMAde-arraying" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Pre-processing Completed", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Barcodes", + "@id": "bts:Pre-processingRequired", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Barcodes", + "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingRequired", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "barcodes", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Illuminationcorrection" + }, + { + "@id": "bts:TileStitching" + }, + { + "@id": "bts:Channel/CycleRegistration" + }, + { + "@id": "bts:TMAde-arraying" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Pre-processing Required", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Features", + "@id": "bts:Comment", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Features", + "rdfs:comment": "Free text field (generally for QC comment)", + "rdfs:label": "Comment", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "features", + "sms:displayName": "Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fiducialimagepng", + "@id": "bts:ImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fiducialimagepng", + "rdfs:comment": "Raw and pre-processed image data", + "rdfs:label": "ImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "fiducial image png", + "sms:displayName": "Imaging Level 2", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ChannelMetadataFilename" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:Microscope" + }, + { + "@id": "bts:Objective" + }, + { + "@id": "bts:NominalMagnification" + }, + { + "@id": "bts:LensNA" + }, + { + "@id": "bts:WorkingDistance" + }, + { + "@id": "bts:WorkingDistanceUnit" + }, + { + "@id": "bts:Immersion" + }, + { + "@id": "bts:Pyramid" + }, + { + "@id": "bts:Zstack" + }, + { + "@id": "bts:Tseries" + }, + { + "@id": "bts:PassedQC" + }, + { + "@id": "bts:Comment" + }, + { + "@id": "bts:FOVnumber" + }, + { + "@id": "bts:FOVX" + }, + { + "@id": "bts:FOVXUnit" + }, + { + "@id": "bts:FOVY" + }, + { + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:FrameAveraging" + }, + { + "@id": "bts:ImageID" + }, + { + "@id": "bts:DimensionOrder" + }, + { + "@id": "bts:PhysicalSizeX" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeY" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZ" + }, + { + "@id": "bts:PhysicalSizeZUnit" + }, + { + "@id": "bts:PixelsBigEndian" + }, + { + "@id": "bts:PlaneCount" + }, + { + "@id": "bts:SizeC" + }, + { + "@id": "bts:SizeT" + }, + { + "@id": "bts:SizeX" + }, + { + "@id": "bts:SizeY" + }, + { + "@id": "bts:SizeZ" + }, + { + "@id": "bts:PixelType" + }, + { + "@id": "bts:MERFISHPositionsFile" + }, + { + "@id": "bts:MERFISHCodebookFile" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Fiducialimagejpg", + "@id": "bts:ChannelMetadataFilename", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fiducialimagejpg", + "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label": "ChannelMetadataFilename", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "fiducial image jpg", - "sms:required": "sms:false", + "sms:displayName": "Channel Metadata Filename", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Detectedimagepng", + "@id": "bts:Microscope", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Detectedimagepng", + "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", + "rdfs:label": "Microscope", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "detected image png", - "sms:required": "sms:false", + "sms:displayName": "Microscope", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Detectedjpg", + "@id": "bts:Objective", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Detectedjpg", + "rdfs:comment": "Objective", + "rdfs:label": "Objective", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "detected jpg", + "sms:displayName": "Objective", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Highresimage", + "@id": "bts:NominalMagnification", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Highresimage", + "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", + "rdfs:label": "NominalMagnification", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "high res image", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "NominalMagnification", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Lowresimage", + "@id": "bts:LensNA", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Lowresimage", + "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label": "LensNA", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "low res image", + "sms:displayName": "LensNA", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:A", + "@id": "bts:WorkingDistance", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "A", + "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", + "rdfs:label": "WorkingDistance", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "A", + "sms:displayName": "WorkingDistance", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:WorkingDistanceUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:B", + "@id": "bts:WorkingDistanceUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "B", + "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" - }, - { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "B", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:C", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "C", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Cm" }, { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "C", + "sms:displayName": "WorkingDistanceUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:D", + "@id": "bts:Immersion", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "D", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "D", + "schema:rangeIncludes": [ + { + "@id": "bts:Air" + }, + { + "@id": "bts:Oil" + }, + { + "@id": "bts:Water" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Immersion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:A1", + "@id": "bts:Pyramid", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "A1", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "A1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Pyramid", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:B1", + "@id": "bts:Zstack", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "B1", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "B1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Zstack", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:C1", + "@id": "bts:Tseries", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "C1", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "C1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Tseries", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:D1", + "@id": "bts:PassedQC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "D1", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "D1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelsQC" + } + ], + "sms:displayName": "Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:V1", + "@id": "bts:FOVnumber", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V1", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V1", + "sms:displayName": "FOV number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:V2", + "@id": "bts:FOVX", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V2", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V2", + "sms:displayName": "FOVX", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:requiresDependency": [ + { + "@id": "bts:FOVXUnit" + } + ], + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:V3", + "@id": "bts:FOVXUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V3", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V3", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVXUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:V4", + "@id": "bts:FOVY", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V4", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V4", + "sms:displayName": "FOVY", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:requiresDependency": [ + { + "@id": "bts:FOVYUnit" + } + ], + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:TRUE", + "@id": "bts:FOVYUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TRUE", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", "rdfs:subClassOf": [ { - "@id": "bts:ImageRe-orientation" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TRUE", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVYUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FALSE", + "@id": "bts:FrameAveraging", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "FALSE", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", "rdfs:subClassOf": [ { - "@id": "bts:ImageRe-orientation" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FALSE", + "sms:displayName": "Frame Averaging", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeLength", + "@id": "bts:ImageID", "@type": "rdfs:Class", - "rdfs:comment": "Length of spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeLength", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode Length", + "sms:displayName": "Image ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CDNA", + "@id": "bts:DimensionOrder", "@type": "rdfs:Class", - "rdfs:comment": "Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase", - "rdfs:label": "CDNA", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SpatialRead1" + "@id": "bts:XYZCT" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:XYZTC" }, { - "@id": "bts:ScmCseqRead1" + "@id": "bts:XYCTZ" }, { - "@id": "bts:ScmCseqRead2" + "@id": "bts:XYCZT" }, { - "@id": "bts:ScmCseqRead3" + "@id": "bts:XYTZC" }, { - "@id": "bts:Read1" - }, + "@id": "bts:ZYX" + } + ], + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeX", + "rdfs:subClassOf": [ { - "@id": "bts:Read2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cDNA", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:CDNAOffset" - }, - { - "@id": "bts:CDNALength" + "@id": "bts:PhysicalSizeXUnit" } ], "sms:validationRules": [] }, { - "@id": "bts:Smart-seq2", + "@id": "bts:PhysicalSizeXUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Smart-seq2", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Smart-seq2", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Smart-SeqV4", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Smart-SeqV4", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Cm" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Smart-SeqV4", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeXUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xV1.0", + "@id": "bts:PhysicalSizeY", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV1.0", + "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeY", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV1.0", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeYUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:10xV1.1", + "@id": "bts:PhysicalSizeYUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV1.1", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV1.1", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV2", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV2", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Cm" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV2", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xV3", + "@id": "bts:PhysicalSizeZ", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeZ", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV3", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeZ", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeZUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:10xV3.1", + "@id": "bts:PhysicalSizeZUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3.1", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeZUnit", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV3.1", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Drop-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Drop-seq", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Cm" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Drop-seq", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeZUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InDropsV2", + "@id": "bts:PixelsBigEndian", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV2", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "inDropsV2", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InDropsV3", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV3", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:True" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:False" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "inDropsV3", - "sms:required": "sms:false", + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TruDrop", + "@id": "bts:PlaneCount", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TruDrop", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TruDrop", - "sms:required": "sms:false", + "sms:displayName": "PlaneCount", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NexteraXT", + "@id": "bts:SizeC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NexteraXT", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nextera XT", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeC", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:UMIBarcodeOffset", + "@id": "bts:SizeT", "@type": "rdfs:Class", - "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", - "rdfs:label": "UMIBarcodeOffset", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Offset", + "sms:displayName": "SizeT", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:UMIBarcodeLength", + "@id": "bts:SizeX", "@type": "rdfs:Class", - "rdfs:comment": "Length of UMI barcode read (in bp): number", - "rdfs:label": "UMIBarcodeLength", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Length", + "sms:displayName": "SizeX", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "@id": "bts:SizeY", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, + "sms:displayName": "SizeY", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeZ", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", + "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Imaging" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeZ", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:PixelType", + "@type": "rdfs:Class", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", + "rdfs:subClassOf": [ { - "@id": "bts:HTANParentBiospecimenID" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANDataFileID" + "@id": "bts:Int8" }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile" + "@id": "bts:Int16" }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform" + "@id": "bts:Int32" }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod" + "@id": "bts:Uint8" }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName" + "@id": "bts:Uint16" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor" + "@id": "bts:Uint32" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion" + "@id": "bts:Float" }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile" + "@id": "bts:Double" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Bit" } ], + "sms:displayName": "PixelType", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile", + "@id": "bts:MERFISHPositionsFile", "@type": "rdfs:Class", - "rdfs:comment": "The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxDSPPKCFile", + "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", + "rdfs:label": "MERFISHPositionsFile", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP PKC File", - "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] + "sms:displayName": "MERFISH Positions File", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform", + "@id": "bts:MERFISHCodebookFile", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "GeoMxDSPNGSSequencingPlatform", + "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", + "rdfs:label": "MERFISHCodebookFile", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Sequencing Platform", + "sms:displayName": "MERFISH Codebook File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", + "@id": "bts:ImagingLevel3Segmentation", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "GeoMxDSPNGSLibrarySelectionMethod", + "rdfs:comment": "Object segmentations", + "rdfs:label": "ImagingLevel3Segmentation", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Selection Method", + "sms:displayName": "Imaging Level 3 Segmentation", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingSegmentationDataType" + }, + { + "@id": "bts:Parameterfile" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:ImagingObjectClass" + }, + { + "@id": "bts:NumberofObjects" + } + ], "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName", + "@id": "bts:ImagingSegmentationDataType", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPNGSLibraryPreparationKitName", + "rdfs:comment": "Specifies how the segmentation is stored", + "rdfs:label": "ImagingSegmentationDataType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Preparation Kit Name", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Mask" + }, + { + "@id": "bts:Outline" + }, + { + "@id": "bts:Polygon" + }, + { + "@id": "bts:ProbabilityMap" + }, + { + "@id": "bts:Point" + } + ], + "sms:displayName": "Imaging Segmentation Data Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor", + "@id": "bts:Parameterfile", "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPLibraryPreparationKitVendor", + "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", + "rdfs:label": "Parameterfile", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Library Preparation Kit Vendor", + "sms:displayName": "Parameter file", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion", + "@id": "bts:ImagingObjectClass", "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPLibraryPreparationKitVersion", + "rdfs:comment": "Defines the structure that the mask delineates", + "rdfs:label": "ImagingObjectClass", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Library Preparation Kit Version", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:Nucleus" + }, + { + "@id": "bts:Cytoplasm" + }, + { + "@id": "bts:Plasmamembrane" + }, + { + "@id": "bts:Wholecell" + }, + { + "@id": "bts:Spot" + }, + { + "@id": "bts:ImagingObjectClassOther" + } + ], + "sms:displayName": "Imaging Object Class", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile", + "@id": "bts:NumberofObjects", "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxLabWorksheetFile", + "rdfs:comment": "The number of objects (eg cells) described", + "rdfs:label": "NumberofObjects", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File", - "sms:required": "sms:false", + "sms:displayName": "Number of Objects", + "sms:required": "sms:true", "sms:validationRules": [ - "list", - "regex match syn\\d+" + "int" ] }, { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "@id": "bts:ImagingLevel3Image", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", - "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "rdfs:comment": "Quality controlled imaging data", + "rdfs:label": "ImagingLevel3Image", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -41294,68 +42358,117 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", + "sms:displayName": "Imaging Level 3 Image", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ImagingLevel2" + } + ], "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, { "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Scanname" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:ROIname" + "@id": "bts:HTANParentChannelMetadataID" }, { - "@id": "bts:Segmentname" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Tags" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:QCstatus" + "@id": "bts:Microscope" }, { - "@id": "bts:ScanHeight" + "@id": "bts:Objective" }, { - "@id": "bts:ScanWidth" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:LensNA" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:BindingDensity" + "@id": "bts:Immersion" }, { - "@id": "bts:Positivenormfactor" + "@id": "bts:Pyramid" }, { - "@id": "bts:Surfacearea" + "@id": "bts:Zstack" }, { - "@id": "bts:Nucleicount" + "@id": "bts:Tseries" }, { - "@id": "bts:TissueStain" + "@id": "bts:PassedQC" + }, + { + "@id": "bts:Comment" + }, + { + "@id": "bts:FOVnumber" + }, + { + "@id": "bts:FOVX" + }, + { + "@id": "bts:FOVY" + }, + { + "@id": "bts:FrameAveraging" } ], "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "@id": "bts:HTANParentChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", - "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "rdfs:comment": "HTAN ID for a level 3 channels table.", + "rdfs:label": "HTANParentChannelMetadataID", + "rdfs:subClassOf": [ + { + "@id": "bts:ImagingLevel4" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Channel Metadata ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingLevel3Channels", + "@type": "rdfs:Class", + "rdfs:comment": "Channel-level Metadata Attributes", + "rdfs:label": "ImagingLevel3Channels", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -41364,83 +42477,185 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", + "sms:displayName": "Imaging Level 3 Channels", "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANChannelMetadataID" }, { - "@id": "bts:Scanname" + "@id": "bts:ChannelID" }, { - "@id": "bts:Slidename" + "@id": "bts:ChannelName" }, { - "@id": "bts:ROIname" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:Segmentname" + "@id": "bts:CycleNumber" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:SubCycleNumber" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:AntibodyRole" }, { - "@id": "bts:Tags" + "@id": "bts:TargetName" }, { - "@id": "bts:ScanHeight" + "@id": "bts:AntibodyName" }, { - "@id": "bts:ScanWidth" + "@id": "bts:RRIDidentifier" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:Fluorophore" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:Clone" }, { - "@id": "bts:Surfacearea" + "@id": "bts:Lot" }, { - "@id": "bts:Nucleicount" + "@id": "bts:Vendor" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:MapQ30" + "@id": "bts:ExcitationWavelength" }, { - "@id": "bts:Rawreads" + "@id": "bts:EmissionWavelength" }, { - "@id": "bts:Stitchedreads" + "@id": "bts:ExcitationBandwidth" }, { - "@id": "bts:Alignedreads" + "@id": "bts:EmissionBandwidth" }, { - "@id": "bts:Deduplicatedreads" + "@id": "bts:MetalIsotopeElement" }, { - "@id": "bts:InSituNegativemedian" + "@id": "bts:MetalIsotopeMass" }, { - "@id": "bts:Biologicalprobemedian" + "@id": "bts:OligoBarcodeUpperStrand" + }, + { + "@id": "bts:OligoBarcodeLowerStrand" + }, + { + "@id": "bts:Dilution" + }, + { + "@id": "bts:Concentration" } ], "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPAssayType", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The assay type which was used for the GeoMx DSP pipeline.", - "rdfs:label": "GeoMxDSPAssayType", + "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ReadIndicator" + }, + { + "@id": "bts:SpatialRead1" + }, + { + "@id": "bts:SpatialRead2" + }, + { + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:EndBias" + }, + { + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SlideVersion" + }, + { + "@id": "bts:SlideID" + }, + { + "@id": "bts:ImageRe-orientation" + }, + { + "@id": "bts:PermeabilizationTime" + }, + { + "@id": "bts:RIN" + }, + { + "@id": "bts:DV200" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CaptureArea", + "@type": "rdfs:Class", + "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", + "rdfs:label": "CaptureArea", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41451,95 +42666,129 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RNAnCounter" + "@id": "bts:A" }, { - "@id": "bts:ProteinnCounter" + "@id": "bts:B" }, { - "@id": "bts:ProteinNGS" + "@id": "bts:C" }, { - "@id": "bts:RNANGS" + "@id": "bts:D" + }, + { + "@id": "bts:A1" + }, + { + "@id": "bts:B1" + }, + { + "@id": "bts:C1" + }, + { + "@id": "bts:D1" } ], - "sms:displayName": "GeoMx DSP Assay Type", - "sms:required": "sms:true", + "sms:displayName": "Capture Area", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RNAnCounter", + "@id": "bts:SlideVersion", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNAnCounter", + "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "rdfs:label": "SlideVersion", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RNA nCounter", + "schema:rangeIncludes": [ + { + "@id": "bts:V1" + }, + { + "@id": "bts:V2" + }, + { + "@id": "bts:V3" + }, + { + "@id": "bts:V4" + } + ], + "sms:displayName": "Slide Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProteinnCounter", + "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProteinnCounter", + "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", + "rdfs:label": "SlideID", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protein nCounter", + "sms:displayName": "Slide ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProteinNGS", + "@id": "bts:ImageRe-orientation", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProteinNGS", + "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", + "rdfs:label": "ImageRe-orientation", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protein NGS", + "schema:rangeIncludes": [ + { + "@id": "bts:TRUE" + }, + { + "@id": "bts:FALSE" + } + ], + "sms:displayName": "Image Re-orientation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RNANGS", + "@id": "bts:PermeabilizationTime", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNANGS", + "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", + "rdfs:label": "PermeabilizationTime", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RNA NGS", + "sms:displayName": "Permeabilization Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41548,20 +42797,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" - }, - { - "@id": "bts:ImagingLevel2" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -41575,46 +42815,58 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Checksum" + }, + { + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:UMITag" }, { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" + "@id": "bts:WhitelistSpatialBarcodeFileLink" }, { - "@id": "bts:GeoMxDSPUniqueProbeCount" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:GeoMxDSPUniqueTargetCount" + "@id": "bts:AppliedHardTrimming" }, { - "@id": "bts:GeoMxDSPGenomicReference" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:MatrixType" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:GeoMxDSPWorkflowType" + "@id": "bts:GenomicReference" }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:GeoMxDSPWorkflowLink" + "@id": "bts:GenomeAnnotationURL" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:CaptureArea" } ], "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "@id": "bts:WhitelistSpatialBarcodeFileLink", "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", - "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", + "rdfs:label": "WhitelistSpatialBarcodeFileLink", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41623,18 +42875,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", + "sms:displayName": "Whitelist Spatial Barcode File Link", "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPUniqueProbeCount", + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique probes reported.", - "rdfs:label": "GeoMxDSPUniqueProbeCount", + "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41643,17 +42892,61 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Unique Probe Count", + "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:VisiumFileType" + }, + { + "@id": "bts:SlideID" + }, + { + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPUniqueTargetCount", + "@id": "bts:VisiumFileType", "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique genes reported.", - "rdfs:label": "GeoMxDSPUniqueTargetCount", + "rdfs:comment": "The file type generated for the visium experiment.", + "rdfs:label": "VisiumFileType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41662,17 +42955,65 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Unique Target Count", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "schema:rangeIncludes": [ + { + "@id": "bts:Referencepng" + }, + { + "@id": "bts:Referencejpg" + }, + { + "@id": "bts:Jsonscalefactors" + }, + { + "@id": "bts:Probedatasetcsv" + }, + { + "@id": "bts:Qcresulthtml" + }, + { + "@id": "bts:Filteredmex" + }, + { + "@id": "bts:Unfilteredmex" + }, + { + "@id": "bts:TissuePositions" + }, + { + "@id": "bts:Barcodes" + }, + { + "@id": "bts:Features" + }, + { + "@id": "bts:Fiducialimagepng" + }, + { + "@id": "bts:Fiducialimagejpg" + }, + { + "@id": "bts:Detectedimagepng" + }, + { + "@id": "bts:Detectedjpg" + }, + { + "@id": "bts:Highresimage" + }, + { + "@id": "bts:Lowresimage" + } + ], + "sms:displayName": "Visium File Type", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPGenomicReference", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", - "rdfs:label": "GeoMxDSPGenomicReference", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41681,17 +43022,79 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Genomic Reference", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:VisiumFileType" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:Spotsundertissue" + }, + { + "@id": "bts:MeanReadsperSpatialSpot" + }, + { + "@id": "bts:MedianNumberGenesperSpatialSpot" + }, + { + "@id": "bts:SequencingSaturation" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:ProportionReadsMappedtoTranscriptome" + }, + { + "@id": "bts:MedianUMICountsperSpot" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowType", + "@id": "bts:Spotsundertissue", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", - "rdfs:label": "GeoMxDSPWorkflowType", + "rdfs:comment": "The number of barcodes associated with a spot under tissue.", + "rdfs:label": "Spotsundertissue", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41700,15 +43103,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Spots under tissue", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription", + "@id": "bts:MeanReadsperSpatialSpot", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", - "rdfs:label": "GeoMxDSPWorkflowParameterDescription", + "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", + "rdfs:label": "MeanReadsperSpatialSpot", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41717,15 +43122,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Parameter Description", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Mean Reads per Spatial Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:GeoMxDSPWorkflowLink", + "@id": "bts:SequencingSaturation", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "GeoMxDSPWorkflowLink", + "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", + "rdfs:label": "SequencingSaturation", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41734,746 +43141,995 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Link", - "sms:required": "sms:false", + "sms:displayName": "Sequencing Saturation", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Scanname", + "@id": "bts:ProportionReadsMappedtoTranscriptome", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", - "rdfs:label": "Scanname", + "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", + "rdfs:label": "ProportionReadsMappedtoTranscriptome", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan name", + "sms:displayName": "Proportion Reads Mapped to Transcriptome", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIname", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", - "rdfs:label": "ROIname", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI name", - "sms:required": "sms:true", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:VisiumWorkflowType" + }, + { + "@id": "bts:VisiumWorkflowParametersDescription" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Segmentname", + "@id": "bts:VisiumWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Name given to segment at time of generation", - "rdfs:label": "Segmentname", + "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", + "rdfs:label": "VisiumWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Segment name", + "sms:displayName": "Visium Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIXCoordinate", + "@id": "bts:VisiumWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "X location within the image", - "rdfs:label": "ROIXCoordinate", + "rdfs:comment": "Parameters used to run the workflow..", + "rdfs:label": "VisiumWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI X Coordinate", + "sms:displayName": "Visium Workflow Parameters Description", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIYCoordinate", + "@id": "bts:Referencepng", "@type": "rdfs:Class", - "rdfs:comment": "Y location within the image", - "rdfs:label": "ROIYCoordinate", + "rdfs:comment": "TBD", + "rdfs:label": "Referencepng", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI Y Coordinate", - "sms:required": "sms:true", + "sms:displayName": "reference png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tags", + "@id": "bts:Referencejpg", "@type": "rdfs:Class", - "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", - "rdfs:label": "Tags", + "rdfs:comment": "TBD", + "rdfs:label": "Referencejpg", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tags", - "sms:required": "sms:true", + "sms:displayName": "reference jpg", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:QCstatus", + "@id": "bts:Jsonscalefactors", "@type": "rdfs:Class", - "rdfs:comment": "ROI quality control flag as reported by the application", - "rdfs:label": "QCstatus", + "rdfs:comment": "TBD", + "rdfs:label": "Jsonscalefactors", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC status", + "sms:displayName": "json scale factors", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanHeight", + "@id": "bts:Probedatasetcsv", "@type": "rdfs:Class", - "rdfs:comment": "Height of the scan for GeoMx Analysis", - "rdfs:label": "ScanHeight", + "rdfs:comment": "TBD", + "rdfs:label": "Probedatasetcsv", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Height", - "sms:required": "sms:true", + "sms:displayName": "probe dataset csv", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanWidth", + "@id": "bts:Qcresulthtml", "@type": "rdfs:Class", - "rdfs:comment": "Width of the scan for GeoMx Analysis", - "rdfs:label": "ScanWidth", + "rdfs:comment": "TBD", + "rdfs:label": "Qcresulthtml", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Width", - "sms:required": "sms:true", + "sms:displayName": "qc result html", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetX", + "@id": "bts:Filteredmex", "@type": "rdfs:Class", - "rdfs:comment": "Offset X of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetX", + "rdfs:comment": "TBD", + "rdfs:label": "Filteredmex", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset X", - "sms:required": "sms:true", + "sms:displayName": "filtered mex", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetY", + "@id": "bts:Unfilteredmex", "@type": "rdfs:Class", - "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetY", + "rdfs:comment": "TBD", + "rdfs:label": "Unfilteredmex", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset Y", - "sms:required": "sms:true", + "sms:displayName": "unfiltered mex", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BindingDensity", + "@id": "bts:TissuePositions", "@type": "rdfs:Class", - "rdfs:comment": "The binding density as reported by the application", - "rdfs:label": "BindingDensity", + "rdfs:comment": "TBD", + "rdfs:label": "TissuePositions", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Binding Density", + "sms:displayName": "tissue_positions", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Positivenormfactor", + "@id": "bts:Barcodes", "@type": "rdfs:Class", - "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", - "rdfs:label": "Positivenormfactor", + "rdfs:comment": "TBD", + "rdfs:label": "Barcodes", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Positive norm factor", + "sms:displayName": "barcodes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Surfacearea", + "@id": "bts:Features", "@type": "rdfs:Class", - "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", - "rdfs:label": "Surfacearea", + "rdfs:comment": "TBD", + "rdfs:label": "Features", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, + "@id": "bts:VisiumFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Fiducialimagepng", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Fiducialimagepng", + "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Surface area", - "sms:required": "sms:true", + "sms:displayName": "fiducial image png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nucleicount", + "@id": "bts:Fiducialimagejpg", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", - "rdfs:label": "Nucleicount", + "rdfs:comment": "TBD", + "rdfs:label": "Fiducialimagejpg", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, + "@id": "bts:VisiumFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "fiducial image jpg", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Detectedimagepng", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Detectedimagepng", + "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei count", - "sms:required": "sms:true", + "sms:displayName": "detected image png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TissueStain", + "@id": "bts:Detectedjpg", "@type": "rdfs:Class", - "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", - "rdfs:label": "TissueStain", + "rdfs:comment": "TBD", + "rdfs:label": "Detectedjpg", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tissue Stain", + "sms:displayName": "detected jpg", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slidename", + "@id": "bts:Highresimage", "@type": "rdfs:Class", - "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", - "rdfs:label": "Slidename", + "rdfs:comment": "TBD", + "rdfs:label": "Highresimage", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide name", + "sms:displayName": "high res image", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rawreads", + "@id": "bts:Lowresimage", "@type": "rdfs:Class", - "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", - "rdfs:label": "Rawreads", + "rdfs:comment": "TBD", + "rdfs:label": "Lowresimage", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Raw reads", + "sms:displayName": "low res image", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Stitchedreads", + "@id": "bts:A", "@type": "rdfs:Class", - "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", - "rdfs:label": "Stitchedreads", + "rdfs:comment": "TBD", + "rdfs:label": "A", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stitched reads", + "sms:displayName": "A", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Alignedreads", + "@id": "bts:B", "@type": "rdfs:Class", - "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", - "rdfs:label": "Alignedreads", + "rdfs:comment": "TBD", + "rdfs:label": "B", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Aligned reads", + "sms:displayName": "B", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Deduplicatedreads", + "@id": "bts:C", "@type": "rdfs:Class", - "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", - "rdfs:label": "Deduplicatedreads", + "rdfs:comment": "TBD", + "rdfs:label": "C", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Deduplicated reads", + "sms:displayName": "C", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InSituNegativemedian", + "@id": "bts:D", "@type": "rdfs:Class", - "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", - "rdfs:label": "InSituNegativemedian", + "rdfs:comment": "TBD", + "rdfs:label": "D", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "In Situ Negative median", + "sms:displayName": "D", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Biologicalprobemedian", + "@id": "bts:A1", "@type": "rdfs:Class", - "rdfs:comment": "Is the median count from all probes except the negative control probes. 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Specific model of the sequencing instrument.", + "rdfs:label": "GeoMxDSPNGSSequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loop Window", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like ", - " regex search -?\\d+" - ] + "sms:displayName": "GeoMx DSP NGS Sequencing Platform", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:StripeWindow", + "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant architectural stripes. 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Multiple files are listed as comma separated values.", + "rdfs:label": "SynapseIDofGeoMxLabWorksheetFile", "rdfs:subClassOf": [ { - "@id": "bts:BiotinEnrichment" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File", + "sms:required": "sms:false", + "sms:validationRules": [ + "list", + "regex match syn\\d+" + ] + }, + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "@type": "rdfs:Class", + "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", + "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "rdfs:subClassOf": [ { - "@id": "bts:ChannelPassedQC" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Pyramid" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Zstack" + "@id": "bts:Scanname" }, { - "@id": "bts:Tseries" + "@id": "bts:ROIname" }, { - "@id": "bts:PassedQC" + "@id": "bts:Segmentname" }, { - "@id": "bts:WellIndex" + "@id": "bts:ROIXCoordinate" }, { - "@id": "bts:CryopreservedCellsinSample" + "@id": "bts:ROIYCoordinate" }, { - "@id": "bts:PrematureAtBirth" + "@id": "bts:Tags" }, { - "@id": "bts:AlcoholHistory" + "@id": "bts:QCstatus" }, { - "@id": "bts:AsbestosExposure" + "@id": "bts:ScanHeight" }, { - "@id": "bts:CoalDustExposure" + "@id": "bts:ScanWidth" }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" + "@id": "bts:ScanOffsetX" }, { - "@id": "bts:RadonExposure" + "@id": "bts:ScanOffsetY" }, { - "@id": "bts:RespirableCrystallineSilicaExposure" + "@id": "bts:BindingDensity" }, { - "@id": "bts:SecondhandSmokeasChild" + "@id": "bts:Positivenormfactor" }, { - "@id": "bts:HepatitisSustainedVirologicalResponse" + "@id": "bts:Surfacearea" }, { - "@id": "bts:HAARTTreatmentIndicator" + "@id": "bts:Nucleicount" }, { - "@id": "bts:RiskFactorTreatment" - }, + "@id": "bts:TissueStain" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "@type": "rdfs:Class", + "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", + "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "rdfs:subClassOf": [ { - "@id": "bts:ChemoConcurrenttoRadiation" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:TreatmentEffectIndicator" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:SatelliteMetastasisPresentIndicator" + "@id": "bts:Scanname" }, { - "@id": "bts:Immunosuppression" + "@id": "bts:Slidename" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:ROIname" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:Segmentname" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:ROIXCoordinate" }, { - "@id": "bts:KnownGeneticPredispositionMutation" + "@id": "bts:ROIYCoordinate" }, { - "@id": "bts:MismatchRepairMutation" + "@id": "bts:Tags" }, { - "@id": "bts:NonNodalTumorDeposits" + "@id": "bts:ScanHeight" }, { - "@id": "bts:PregnantatDiagnosis" + "@id": "bts:ScanWidth" }, { - "@id": "bts:PriorMalignancy" + "@id": "bts:ScanOffsetX" }, { - "@id": "bts:PriorTreatment" + "@id": "bts:ScanOffsetY" }, { - "@id": "bts:LymphaticInvasionPresent" + "@id": "bts:Surfacearea" }, { - "@id": "bts:PerineuralInvasionPresent" + "@id": "bts:Nucleicount" }, { - "@id": "bts:SynchronousMalignancy" + "@id": "bts:SequencingSaturation" }, { - "@id": "bts:TumorConfinedtoOrganofOrigin" + "@id": "bts:MapQ30" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:Rawreads" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:Stitchedreads" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:Alignedreads" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:Deduplicatedreads" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:InSituNegativemedian" }, { - "@id": "bts:ColonPolypOccurenceIndicator" - }, + "@id": "bts:Biologicalprobemedian" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:GeoMxDSPAssayType", + "@type": "rdfs:Class", + "rdfs:comment": "The assay type which was used for the GeoMx DSP pipeline.", + "rdfs:label": "GeoMxDSPAssayType", + "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistoryColorectalPolyp" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:RNAnCounter" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:ProteinnCounter" }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id": "bts:ProteinNGS" }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" - }, + "@id": "bts:RNANGS" + } + ], + "sms:displayName": "GeoMx DSP Assay Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:RNAnCounter", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RNAnCounter", + "rdfs:subClassOf": [ { - "@id": "bts:HistoryofBlisteringSunburn" - }, - { - "@id": "bts:Tool" - }, - { - "@id": "bts:PublicationcontainsHTANID" - }, - { - "@id": "bts:BarrettsEsophagusGobletCellsPresent" - }, - { - "@id": "bts:TreatmentorTherapy" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "yes", + "sms:displayName": "RNA nCounter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:No", + "@id": "bts:ProteinnCounter", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "No", + "rdfs:label": "ProteinnCounter", "rdfs:subClassOf": [ { - "@id": "bts:BiotinEnrichment" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:WellIndex" - }, - { - "@id": "bts:CryopreservedCellsinSample" - }, - { - "@id": "bts:ToTrimAdapterSequence" - }, - { - "@id": "bts:AppliedHardTrimming" - }, - { - "@id": "bts:PseudoAlignmentUsed" - }, - { - "@id": "bts:FusionGeneDetected" - }, - { - "@id": "bts:PrematureAtBirth" - }, - { - "@id": "bts:AlcoholHistory" - }, - { - "@id": "bts:AsbestosExposure" - }, - { - "@id": "bts:CoalDustExposure" - }, - { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" - }, - { - "@id": "bts:RadonExposure" - }, - { - "@id": "bts:RespirableCrystallineSilicaExposure" - }, - { - "@id": "bts:SecondhandSmokeasChild" - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse" - }, - { - "@id": "bts:HAARTTreatmentIndicator" - }, - { - "@id": "bts:ProgressionorRecurrence" - }, - { - "@id": "bts:RiskFactorTreatment" - }, - { - "@id": "bts:ChemoConcurrenttoRadiation" - }, - { - "@id": "bts:TreatmentEffectIndicator" - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:COVID19OccurrenceIndicator" - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator" - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup" - }, - { - "@id": "bts:KnownGeneticPredispositionMutation" - }, - { - "@id": "bts:MismatchRepairMutation" - }, - { - "@id": "bts:NonNodalTumorDeposits" - }, - { - "@id": "bts:PregnantatDiagnosis" - }, - { - "@id": "bts:PriorMalignancy" - }, - { - "@id": "bts:PriorTreatment" - }, - { - "@id": "bts:AnaplasiaPresent" - }, - { - "@id": "bts:LymphaticInvasionPresent" - }, - { - "@id": "bts:PerineuralInvasionPresent" - }, - { - "@id": "bts:SynchronousMalignancy" - }, - { - "@id": "bts:TumorConfinedtoOrganofOrigin" - }, - { - "@id": "bts:VascularInvasionPresent" - }, - { - "@id": "bts:HistoryofPriorColonPolyps" - }, - { - "@id": "bts:FamilyColonCancerHistoryIndicator" - }, - { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" - }, - { - "@id": "bts:PatientColonoscopyPerformedIndicator" - }, - { - "@id": "bts:ColorectalCancerKRASIndicator" - }, - { - "@id": "bts:ColonPolypOccurenceIndicator" - }, - { - "@id": "bts:FamilyHistoryColorectalPolyp" - }, - { - "@id": "bts:ColorectalPolypNewIndicator" - }, - { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" - }, - { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" - }, - { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" - }, - { - "@id": "bts:HistoryofBlisteringSunburn" - }, - { - "@id": "bts:Tool" - }, - { - "@id": "bts:Islowestlevel" - }, - { - "@id": "bts:PublicationcontainsHTANID" - }, - { - "@id": "bts:BarrettsEsophagusGobletCellsPresent" - }, - { - "@id": "bts:PrecancerCase" - }, - { - "@id": "bts:TreatmentorTherapy" - }, - { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" - }, - { - "@id": "bts:HistoryofAtypicalNevi" - }, - { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "no", + "sms:displayName": "Protein nCounter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MACS2", + "@id": "bts:ProteinNGS", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MACS2", + "rdfs:label": "ProteinNGS", "rdfs:subClassOf": [ { - "@id": "bts:StripeCalling" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2", + "sms:displayName": "Protein NGS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Other", + "@id": "bts:RNANGS", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Other", + "rdfs:label": "RNANGS", "rdfs:subClassOf": [ { - "@id": "bts:StripeCalling" - }, - { - "@id": "bts:LoopCalling" - }, - { - "@id": "bts:HistologyAssessmentBy" - }, - { - "@id": "bts:HistologyAssessmentMedium" - }, - { - "@id": "bts:AlcoholType" - }, - { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" - }, - { - "@id": "bts:BreastCancerGenomicTestPerformed" - }, - { - "@id": "bts:DataCollectionMode" - }, - { - "@id": "bts:Immersion" - }, - { - "@id": "bts:TypeofTobaccoUsed" - }, - { - "@id": "bts:PrecancerousConditionType" - }, - { - "@id": "bts:COVID19ComplicationsSeverity" - }, - { - "@id": "bts:ClassificationofTumor" - }, - { - "@id": "bts:BreastCarcinomaDetectionMethodType" - }, - { - "@id": "bts:PriorInvasiveBreastDisease" - }, - { - "@id": "bts:BreastCarcinomaSurgicalProcedureName" - }, - { - "@id": "bts:OvarianCancerSurgicalOutcome" - }, - { - "@id": "bts:MSScanMode" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:ExpressionUnits" - }, - { - "@id": "bts:SlideChargeType" - }, - { - "@id": "bts:FiducialMarker" - }, - { - "@id": "bts:ReasonTreatmentEnded" - }, - { - "@id": "bts:LabTestsforMMRStatus" - }, - { - "@id": "bts:BreastCarcinomaHistologyCategory" - }, - { - "@id": "bts:GliomaSpecificMetastasisSites" - }, - { - "@id": "bts:AdditonalFindingsUninvolvedProstate" - }, - { - "@id": "bts:SlicingMethod" - }, - { - "@id": "bts:ImmunosuppressiveTreatmentType" - }, - { - "@id": "bts:LungCancerDetectionMethodType" - }, - { - "@id": "bts:ColorectalCancerDetectionMethodType" - }, - { - "@id": "bts:BreastBiopsyProcedureFindingType" - }, - { - "@id": "bts:BreastCancerAssessmentTests" - }, - { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" - }, - { - "@id": "bts:SarcomaTumorExtensionType" - }, - { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" - }, - { - "@id": "bts:Pre-processingCompleted" - }, - { - "@id": "bts:Pre-processingRequired" - }, - { - "@id": "bts:MSSource" - }, - { - "@id": "bts:Race" - }, - { - "@id": "bts:DataCategory" - }, - { - "@id": "bts:ExtentofTumorResection" - }, - { - "@id": "bts:ColorectalPolypType" - }, - { - "@id": "bts:BreastCarcinomaERStainingIntensity" - }, - { - "@id": "bts:BreastCarcinomaPRStainingIntensity" - }, - { - "@id": "bts:SarcomaSubtype" - }, - { - "@id": "bts:LibrarySelectionMethod" - }, - { - "@id": "bts:CutaneousMelanomaAdditionalFindings" - }, - { - "@id": "bts:DiabetesTreatmentType" - }, - { - "@id": "bts:OvarianCancerHistologicSubtype" - }, - { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" - }, - { - "@id": "bts:ProstateCarcinomaHistologicType" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:MolecularAnalysisMethod" - }, - { - "@id": "bts:LungAdjacentHistologyType" - }, - { - "@id": "bts:VariantType" - }, - { - "@id": "bts:LungCancerParticipantProcedureHistory" - }, - { - "@id": "bts:MethodofDiagnosis" - }, - { - "@id": "bts:FixativeType" - }, - { - "@id": "bts:HPVPositiveType" - }, - { - "@id": "bts:ConcomitantMedicationReceivedType" - }, - { - "@id": "bts:TreatmentType" - }, - { - "@id": "bts:CurrentLungCancerSymptoms" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:MutationalSignatures" - }, - { - "@id": "bts:LungCancerHarboringGenomicAberrations" - }, - { - "@id": "bts:RelationshipType" - }, - { - "@id": "bts:LungTopography" - }, - { - "@id": "bts:Comorbidity" - }, - { - "@id": "bts:PriorSitesofRadiation" - }, - { - "@id": "bts:License" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "other", + "sms:displayName": "RNA NGS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HiCCUPS", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HiCCUPS", + "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "rdfs:subClassOf": [ { - "@id": "bts:LoopCalling" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiCCUPS", + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Cooltools", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cooltools", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:LoopCalling" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cooltools", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingLevel4", - "@type": "rdfs:Class", - "rdfs:comment": "Derived imaging data: Object-by-feature array", - "rdfs:label": "ImagingLevel4", - "rdfs:subClassOf": [ + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" + }, { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:ImagingLevel2" + }, { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "sms:requiresDependency": [ @@ -43285,210 +44594,104 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:HTANParentChannelMetadataID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:GeoMxDSPAssayType" }, { - "@id": "bts:Parameterfile" + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:GeoMxDSPUniqueProbeCount" }, { - "@id": "bts:CommitSHA" + "@id": "bts:GeoMxDSPUniqueTargetCount" }, { - "@id": "bts:NumberofObjects" + "@id": "bts:GeoMxDSPGenomicReference" }, { - "@id": "bts:NumberofFeatures" + "@id": "bts:MatrixType" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:GeoMxDSPWorkflowType" }, { - "@id": "bts:ImagingSummaryStatistic" + "@id": "bts:GeoMxDSPWorkflowParameterDescription" + }, + { + "@id": "bts:GeoMxDSPWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:NumberofFeatures", + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", "@type": "rdfs:Class", - "rdfs:comment": "The number of features (eg channels) described", - "rdfs:label": "NumberofFeatures", + "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", + "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Features", + "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", "sms:required": "sms:true", "sms:validationRules": [ - "int" + "list", + "regex match syn\\d+" ] }, { - "@id": "bts:ImagingSummaryStatistic", + "@id": "bts:GeoMxDSPUniqueProbeCount", "@type": "rdfs:Class", - "rdfs:comment": "Function used to summarize object/feature intensity", - "rdfs:label": "ImagingSummaryStatistic", + "rdfs:comment": "Total number of unique probes reported.", + "rdfs:label": "GeoMxDSPUniqueProbeCount", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Mean" - }, - { - "@id": "bts:Median" - }, - { - "@id": "bts:NotSpecified" - } - ], - "sms:displayName": "Imaging Summary Statistic", + "sms:displayName": "GeoMx DSP Unique Probe Count", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:SRRSImagingLevel2", + "@id": "bts:GeoMxDSPUniqueTargetCount", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN raw and pre-processed image data", - "rdfs:label": "SRRSImagingLevel2", + "rdfs:comment": "Total number of unique genes reported.", + "rdfs:label": "GeoMxDSPUniqueTargetCount", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Imaging Level 2", + "sms:displayName": "GeoMx DSP Unique Target Count", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:Microscope" - }, - { - "@id": "bts:Objective" - }, - { - "@id": "bts:NominalMagnification" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:FrameAveraging" - }, - { - "@id": "bts:ImageID" - }, - { - "@id": "bts:DimensionOrder" - }, - { - "@id": "bts:PhysicalSizeX" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeY" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PixelsBigEndian" - }, - { - "@id": "bts:PlaneCount" - }, - { - "@id": "bts:SizeC" - }, - { - "@id": "bts:SizeT" - }, - { - "@id": "bts:SizeX" - }, - { - "@id": "bts:SizeY" - }, - { - "@id": "bts:SizeZ" - }, - { - "@id": "bts:PixelType" - } - ], - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:10XGenomicsXeniumISSExperiment", + "@id": "bts:GeoMxDSPGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment", - "rdfs:label": "10XGenomicsXeniumISSExperiment", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", + "rdfs:label": "GeoMxDSPGenomicReference", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43497,82 +44700,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10X Genomics Xenium ISS Experiment", + "sms:displayName": "GeoMx DSP Genomic Reference", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:XeniumBundleContents" - }, - { - "@id": "bts:SlideID" - }, - { - "@id": "bts:ROIname" - }, - { - "@id": "bts:PanelName" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:TotalNumberofCells" - }, - { - "@id": "bts:TotalNumberofTargets" - }, - { - "@id": "bts:Surfacearea" - }, - { - "@id": "bts:ExperimentIFChannels" - }, - { - "@id": "bts:TranscriptsperCell" - }, - { - "@id": "bts:PercentofTranscriptswithinCells" - }, - { - "@id": "bts:DecodedTranscripts" - }, - { - "@id": "bts:XeniumIFimageHTANFileID" - }, - { - "@id": "bts:XeniumHEimageHTANFileID" - } - ], - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:XeniumBundleContents", + "@id": "bts:GeoMxDSPWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "A comma separated list of filenames within the Xenium bundle zip file", - "rdfs:label": "XeniumBundleContents", + "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", + "rdfs:label": "GeoMxDSPWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43581,15 +44719,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium Bundle Contents", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PanelName", + "@id": "bts:GeoMxDSPWorkflowParameterDescription", "@type": "rdfs:Class", - "rdfs:comment": "The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))", - "rdfs:label": "PanelName", + "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", + "rdfs:label": "GeoMxDSPWorkflowParameterDescription", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43598,15 +44736,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Panel Name", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Parameter Description", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofCells", + "@id": "bts:GeoMxDSPWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "The total number of cells analyzed on the flow cell", - "rdfs:label": "TotalNumberofCells", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "GeoMxDSPWorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43615,546 +44753,439 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Cells", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofTargets", + "@id": "bts:Scanname", "@type": "rdfs:Class", - "rdfs:comment": "Refers to the target of an assay. Can be genes/transcripts or probes", - "rdfs:label": "TotalNumberofTargets", + "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", + "rdfs:label": "Scanname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Targets", + "sms:displayName": "Scan name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExperimentIFChannels", + "@id": "bts:ROIname", "@type": "rdfs:Class", - "rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)", - "rdfs:label": "ExperimentIFChannels", + "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", + "rdfs:label": "ROIname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Experiment IF Channels", + "sms:displayName": "ROI name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TranscriptsperCell", + "@id": "bts:Segmentname", "@type": "rdfs:Class", - "rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide", - "rdfs:label": "TranscriptsperCell", + "rdfs:comment": "Name given to segment at time of generation", + "rdfs:label": "Segmentname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcripts per Cell", + "sms:displayName": "Segment name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentofTranscriptswithinCells", + "@id": "bts:ROIXCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of transcripts assigned to assayed cells", - "rdfs:label": "PercentofTranscriptswithinCells", + "rdfs:comment": "X location within the image", + "rdfs:label": "ROIXCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent of Transcripts within Cells", + "sms:displayName": "ROI X Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DecodedTranscripts", + "@id": "bts:ROIYCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).", - "rdfs:label": "DecodedTranscripts", + "rdfs:comment": "Y location within the image", + "rdfs:label": "ROIYCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Decoded Transcripts", + "sms:displayName": "ROI Y Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:XeniumIFimageHTANFileID", + "@id": "bts:Tags", "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumIFimageHTANFileID", + "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", + "rdfs:label": "Tags", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium IF image HTAN File ID", - "sms:required": "sms:false", + "sms:displayName": "Tags", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:XeniumHEimageHTANFileID", + "@id": "bts:QCstatus", "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumHEimageHTANFileID", + "rdfs:comment": "ROI quality control flag as reported by the application", + "rdfs:label": "QCstatus", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium HE image HTAN File ID", + "sms:displayName": "QC status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPALevel2", + "@id": "bts:ScanHeight", "@type": "rdfs:Class", - "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", - "rdfs:label": "RPPALevel2", + "rdfs:comment": "Height of the scan for GeoMx Analysis", + "rdfs:label": "ScanHeight", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANRPPAAntibodyTable" - }, - { - "@id": "bts:AssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - } - ], + "sms:displayName": "Scan Height", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HTANRPPAAntibodyTable", + "@id": "bts:ScanWidth", "@type": "rdfs:Class", - "rdfs:comment": "A table containing antibody level metadata for RPPA", - "rdfs:label": "HTANRPPAAntibodyTable", + "rdfs:comment": "Width of the scan for GeoMx Analysis", + "rdfs:label": "ScanWidth", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table", + "sms:displayName": "Scan Width", "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:HTANRPPAAntibodyTableID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:AbNameReportedonDataset" - }, - { - "@id": "bts:GENCODEGeneSymbolTarget" - }, - { - "@id": "bts:UNIPROTProteinIDTarget" - }, - { - "@id": "bts:PhosphoproteinFlag" - }, - { - "@id": "bts:Vendor" - }, - { - "@id": "bts:CatalogNumber" - }, - { - "@id": "bts:InternalAbID" - }, - { - "@id": "bts:Species" - }, - { - "@id": "bts:RPPADilution" - }, - { - "@id": "bts:PhosphoSite" - }, - { - "@id": "bts:RPPAValidationStatus" - }, - { - "@id": "bts:Clone" - }, - { - "@id": "bts:Clonality" - }, - { - "@id": "bts:AntibodyNotes" - } - ], "sms:validationRules": [] }, { - "@id": "bts:HTANRPPAAntibodyTableID", + "@id": "bts:ScanOffsetX", "@type": "rdfs:Class", - "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", - "rdfs:label": "HTANRPPAAntibodyTableID", + "rdfs:comment": "Offset X of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetX", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table ID", + "sms:displayName": "Scan Offset X", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AbNameReportedonDataset", + "@id": "bts:ScanOffsetY", "@type": "rdfs:Class", - "rdfs:comment": "The antibody name.", - "rdfs:label": "AbNameReportedonDataset", + "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetY", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ab Name Reported on Dataset", + "sms:displayName": "Scan Offset Y", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GENCODEGeneSymbolTarget", + "@id": "bts:BindingDensity", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", - "rdfs:label": "GENCODEGeneSymbolTarget", + "rdfs:comment": "The binding density as reported by the application", + "rdfs:label": "BindingDensity", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GENCODE Gene Symbol Target", - "sms:required": "sms:true", + "sms:displayName": "Binding Density", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UNIPROTProteinIDTarget", + "@id": "bts:Positivenormfactor", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", - "rdfs:label": "UNIPROTProteinIDTarget", + "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", + "rdfs:label": "Positivenormfactor", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UNIPROT Protein ID Target", - "sms:required": "sms:true", + "sms:displayName": "Positive norm factor", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhosphoproteinFlag", + "@id": "bts:Surfacearea", "@type": "rdfs:Class", - "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", - "rdfs:label": "PhosphoproteinFlag", + "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", + "rdfs:label": "Surfacearea", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Phosphoprotein Flag", + "sms:displayName": "Surface area", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Vendor", + "@id": "bts:Nucleicount", "@type": "rdfs:Class", - "rdfs:comment": "Vendor", - "rdfs:label": "Vendor", + "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", + "rdfs:label": "Nucleicount", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Vendor", - "sms:required": "sms:false", + "sms:displayName": "Nuclei count", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CatalogNumber", + "@id": "bts:TissueStain", "@type": "rdfs:Class", - "rdfs:comment": "Catalog Number", - "rdfs:label": "CatalogNumber", + "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", + "rdfs:label": "TissueStain", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Catalog Number", + "sms:displayName": "Tissue Stain", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InternalAbID", + "@id": "bts:Slidename", "@type": "rdfs:Class", - "rdfs:comment": "Internal lab ID for an antibody.", - "rdfs:label": "InternalAbID", + "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", + "rdfs:label": "Slidename", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Internal Ab ID", - "sms:required": "sms:true", + "sms:displayName": "Slide name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Species", + "@id": "bts:Rawreads", "@type": "rdfs:Class", - "rdfs:comment": "Host animal.", - "rdfs:label": "Species", + "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", + "rdfs:label": "Rawreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Mouse" - }, - { - "@id": "bts:Rabbit" - }, - { - "@id": "bts:Goat" - } - ], - "sms:displayName": "Species", - "sms:required": "sms:true", + "sms:displayName": "Raw reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPADilution", + "@id": "bts:Stitchedreads", "@type": "rdfs:Class", - "rdfs:comment": "The dilution ratio.", - "rdfs:label": "RPPADilution", + "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", + "rdfs:label": "Stitchedreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Dilution", + "sms:displayName": "Stitched reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhosphoSite", + "@id": "bts:Alignedreads", "@type": "rdfs:Class", - "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", - "rdfs:label": "PhosphoSite", + "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", + "rdfs:label": "Alignedreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Phospho Site", + "sms:displayName": "Aligned reads", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:PhosphoproteinFlag" - } - ], "sms:validationRules": [] }, { - "@id": "bts:RPPAValidationStatus", + "@id": "bts:Deduplicatedreads", "@type": "rdfs:Class", - "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", - "rdfs:label": "RPPAValidationStatus", + "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", + "rdfs:label": "Deduplicatedreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Valid" - }, - { - "@id": "bts:UsewithCaution" - }, - { - "@id": "bts:UnderEvaluation" - }, - { - "@id": "bts:UsedforQC" - } - ], - "sms:displayName": "RPPA Validation Status", + "sms:displayName": "Deduplicated reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clone", + "@id": "bts:InSituNegativemedian", "@type": "rdfs:Class", - "rdfs:comment": "Clone", - "rdfs:label": "Clone", + "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", + "rdfs:label": "InSituNegativemedian", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Clone", + "sms:displayName": "In Situ Negative median", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AntibodyNotes", + "@id": "bts:Biologicalprobemedian", "@type": "rdfs:Class", - "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", - "rdfs:label": "AntibodyNotes", + "rdfs:comment": "Is the median count from all probes except the negative control probes. A measure of signal to background for each segment", + "rdfs:label": "Biologicalprobemedian", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody Notes", + "sms:displayName": "Biological probe median", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPALevel3", + "@id": "bts:HI-C-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", - "rdfs:label": "RPPALevel3", + "rdfs:comment": "Unaligned sequence data", + "rdfs:label": "HI-C-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 3", + "sms:displayName": "HI-C-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -44165,6 +45196,12 @@ { "@id": "bts:Component" }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, { "@id": "bts:Filename" }, @@ -44172,209 +45209,238 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:GenomicReference" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:AssayType" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:CrosslinkingCondtion" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:DNADigestionCondition" + }, + { + "@id": "bts:NucleiPermeabilizationMethod" + }, + { + "@id": "bts:LigationCondition" + }, + { + "@id": "bts:BiotinEnrichment" + }, + { + "@id": "bts:DNAInputAmount" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:ProtocolLink" } ], "sms:validationRules": [] }, { - "@id": "bts:RPPALevel4", + "@id": "bts:CrosslinkingCondtion", "@type": "rdfs:Class", - "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", - "rdfs:label": "RPPALevel4", + "rdfs:comment": "Detailed condition for DNA crosslinking", + "rdfs:label": "CrosslinkingCondtion", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "Crosslinking Condtion", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DNADigestionCondition", + "@type": "rdfs:Class", + "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", + "rdfs:label": "DNADigestionCondition", + "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DNA Digestion Condition", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleiPermeabilizationMethod", + "@type": "rdfs:Class", + "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", + "rdfs:label": "NucleiPermeabilizationMethod", + "rdfs:subClassOf": [ { - "@id": "bts:HTANParentBiospecimenID" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei Permeabilization Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LigationCondition", + "@type": "rdfs:Class", + "rdfs:comment": "Name of ligase and condition for proximity ligation", + "rdfs:label": "LigationCondition", + "rdfs:subClassOf": [ { - "@id": "bts:HTANParentDataFileID" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ligation Condition", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BiotinEnrichment", + "@type": "rdfs:Class", + "rdfs:comment": "Whether biotin is used for enriching ligation product", + "rdfs:label": "BiotinEnrichment", + "rdfs:subClassOf": [ { - "@id": "bts:HTANDataFileID" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:AssayType" + "@id": "bts:Yes" }, { - "@id": "bts:BatchCorrectionMethod" + "@id": "bts:No" } ], + "sms:displayName": "Biotin Enrichment", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BatchCorrectionMethod", + "@id": "bts:DNAInputAmount", "@type": "rdfs:Class", - "rdfs:comment": "Method that was used to batch correct Level 3 data", - "rdfs:label": "BatchCorrectionMethod", + "rdfs:comment": "Amount of DNA for library construction, in nanograms.", + "rdfs:label": "DNAInputAmount", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Batch Correction Method", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "DNA Input Amount", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:NanostringCosMxSMIExperiment", + "@id": "bts:HI-C-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)", - "rdfs:label": "NanostringCosMxSMIExperiment", + "rdfs:comment": "Aligned read pairs, contact matrix", + "rdfs:label": "HI-C-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nanostring CosMx SMI Experiment", + "sms:displayName": "HI-C-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:HI-C-seqLevel1" } ], "sms:requiresDependency": [ { "@id": "bts:Component" }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:CosMxBundleContents" - }, - { - "@id": "bts:SlideID" - }, - { - "@id": "bts:CosMxAssayType" - }, - { - "@id": "bts:PanelName" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:TotalNumberofCells" - }, - { - "@id": "bts:TotalNumberofTargets" - }, - { - "@id": "bts:NumberofFOVs" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Surfacearea" + "@id": "bts:Filename" }, { - "@id": "bts:ExperimentIFChannels" + "@id": "bts:FileFormat" }, { - "@id": "bts:TranscriptsperCell" + "@id": "bts:GenomicReference" }, { - "@id": "bts:PercentofTranscriptswithinCells" + "@id": "bts:AlignedReadLength" }, { - "@id": "bts:MeanTotalTranscriptsperArea" + "@id": "bts:Tool" }, { - "@id": "bts:UniqueGenes" + "@id": "bts:Resolution" }, { - "@id": "bts:TotalNegativeProbeCounts" + "@id": "bts:NormalizationMethod" } ], "sms:validationRules": [] }, { - "@id": "bts:CosMxBundleContents", + "@id": "bts:AlignedReadLength", "@type": "rdfs:Class", - "rdfs:comment": "A comma separated list of filenames within the CosMx bundle zip file", - "rdfs:label": "CosMxBundleContents", + "rdfs:comment": "Read length used for alignment if hard trimming was applied", + "rdfs:label": "AlignedReadLength", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CosMx Bundle Contents", + "sms:displayName": "Aligned Read Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CosMxAssayType", + "@id": "bts:Tool", "@type": "rdfs:Class", - "rdfs:comment": "The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay", - "rdfs:label": "CosMxAssayType", + "rdfs:comment": "Were any software or computational tools generated for this content", + "rdfs:label": "Tool", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Publication" } ], "schema:isPartOf": { @@ -44382,753 +45448,1093 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RNA" + "@id": "bts:Yes" }, { - "@id": "bts:Protein" + "@id": "bts:No" } ], - "sms:displayName": "CosMx Assay Type", + "sms:displayName": "Tool", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NumberofFOVs", + "@id": "bts:Resolution", "@type": "rdfs:Class", - "rdfs:comment": "The total number of FOVs recorded for the sample on a single flow cell", - "rdfs:label": "NumberofFOVs", + "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", + "rdfs:label": "Resolution", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of FOVs", + "sms:displayName": "Resolution", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MeanTotalTranscriptsperArea", + "@id": "bts:HI-C-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "The mean total transcripts per um3", - "rdfs:label": "MeanTotalTranscriptsperArea", + "rdfs:comment": "Summary data for the HI-C-seq assay.", + "rdfs:label": "HI-C-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Total Transcripts per Area", - "sms:required": "sms:true", + "sms:displayName": "HI-C-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:HI-C-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:StripeCalling" + }, + { + "@id": "bts:LoopWindow" + }, + { + "@id": "bts:StripeWindow" + }, + { + "@id": "bts:LoopCalling" + } + ], "sms:validationRules": [] }, { - "@id": "bts:UniqueGenes", + "@id": "bts:StripeCalling", "@type": "rdfs:Class", - "rdfs:comment": "The total unique genes detected above background", - "rdfs:label": "UniqueGenes", + "rdfs:comment": "Tool used for identifying architectural stripe-forming, interaction hotspots.", + "rdfs:label": "StripeCalling", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Unique Genes", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:MACS2" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Stripe Calling", + "sms:required": "sms:true", + "sms:validationRules": [ + "list", + "-?\\d+" + ] }, { - "@id": "bts:TotalNegativeProbeCounts", + "@id": "bts:LoopWindow", "@type": "rdfs:Class", - "rdfs:comment": "Mean Total Negative probe counts/cell", - "rdfs:label": "TotalNegativeProbeCounts", + "rdfs:comment": "Binning size used for calling significant dot interactions (loops)", + "rdfs:label": "LoopWindow", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Negative Probe Counts", + "sms:displayName": "Loop Window", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like ", + " regex search -?\\d+" + ] }, { - "@id": "bts:RNA", + "@id": "bts:StripeWindow", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNA", + "rdfs:comment": "Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.", + "rdfs:label": "StripeWindow", "rdfs:subClassOf": [ { - "@id": "bts:CosMxAssayType" - }, - { - "@id": "bts:MicroarrayMolecule" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RNA", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Stripe Window", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like ", + " regex search -?\\d+" + ] }, { - "@id": "bts:Protein", + "@id": "bts:LoopCalling", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Protein", + "rdfs:comment": "Tool used for identifying loop interactions", + "rdfs:label": "LoopCalling", "rdfs:subClassOf": [ { - "@id": "bts:CosMxAssayType" - }, - { - "@id": "bts:AnalyteType" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "protein", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:HiCCUPS" + }, + { + "@id": "bts:Cooltools" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Loop Calling", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryLevel1", + "@id": "bts:Yes", "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1", - "rdfs:label": "MassSpectrometryLevel1", + "rdfs:comment": "TBD", + "rdfs:label": "Yes", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Spectrometry Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:BiotinEnrichment" + }, { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:ChannelPassedQC" + }, { - "@id": "bts:Component" + "@id": "bts:Pyramid" }, { - "@id": "bts:Filename" + "@id": "bts:Zstack" }, { - "@id": "bts:FileFormat" + "@id": "bts:Tseries" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:PassedQC" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:WellIndex" }, { - "@id": "bts:MSBatchID" + "@id": "bts:CryopreservedCellsinSample" }, { - "@id": "bts:MS-basedAssayType" + "@id": "bts:PrematureAtBirth" }, { - "@id": "bts:AnalyteType" + "@id": "bts:AlcoholHistory" }, { - "@id": "bts:MS-basedTargeted" + "@id": "bts:AsbestosExposure" }, { - "@id": "bts:MSInstrumentVendorandModel" + "@id": "bts:CoalDustExposure" }, { - "@id": "bts:MSSource" + "@id": "bts:EnvironmentalTobaccoSmokeExposure" }, { - "@id": "bts:Polarity" + "@id": "bts:RadonExposure" }, { - "@id": "bts:MassRangeLowValue" + "@id": "bts:RespirableCrystallineSilicaExposure" }, { - "@id": "bts:MassRangeHighValue" + "@id": "bts:SecondhandSmokeasChild" }, { - "@id": "bts:DataCollectionMode" + "@id": "bts:HepatitisSustainedVirologicalResponse" }, { - "@id": "bts:MSScanMode" + "@id": "bts:HAARTTreatmentIndicator" }, { - "@id": "bts:MSLabeling" + "@id": "bts:RiskFactorTreatment" }, { - 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This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))", + "rdfs:label": "PanelName", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Resin", + "sms:displayName": "Panel Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCLengthValue", + "@id": "bts:TotalNumberofCells", "@type": "rdfs:Class", - "rdfs:comment": "LC column length in cm.", - "rdfs:label": "LCLengthValue", + "rdfs:comment": "The total number of cells analyzed on the flow cell", + "rdfs:label": "TotalNumberofCells", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Length Value", + "sms:displayName": "Total Number of Cells", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCTempValue", + "@id": "bts:TotalNumberofTargets", "@type": "rdfs:Class", - "rdfs:comment": "LC temperature in C.", - "rdfs:label": "LCTempValue", + "rdfs:comment": "Refers to the target of an assay. Can be genes/transcripts or probes", + "rdfs:label": "TotalNumberofTargets", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Temp Value", + "sms:displayName": "Total Number of Targets", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCIDValue", + "@id": "bts:ExperimentIFChannels", "@type": "rdfs:Class", - "rdfs:comment": "LC column inner diameter in microns.", - "rdfs:label": "LCIDValue", + "rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)", + "rdfs:label": "ExperimentIFChannels", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC ID Value", + "sms:displayName": "Experiment IF Channels", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCFlowRate", + "@id": "bts:TranscriptsperCell", "@type": "rdfs:Class", - "rdfs:comment": "LC flow rate in nL/min.", - "rdfs:label": "LCFlowRate", + "rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide", + "rdfs:label": "TranscriptsperCell", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Flow Rate", + "sms:displayName": "Transcripts per Cell", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCGradient", + "@id": "bts:PercentofTranscriptswithinCells", "@type": "rdfs:Class", - "rdfs:comment": "The program dictates the mobile phase solvent composition over the course of the chromatographic run.", - "rdfs:label": "LCGradient", + "rdfs:comment": "The percentage of transcripts assigned to assayed cells", + "rdfs:label": "PercentofTranscriptswithinCells", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Gradient", + "sms:displayName": "Percent of Transcripts within Cells", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCMobilePhaseA", + "@id": "bts:DecodedTranscripts", "@type": "rdfs:Class", - "rdfs:comment": "Composition of mobile phase A", - "rdfs:label": "LCMobilePhaseA", + "rdfs:comment": "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).", + "rdfs:label": "DecodedTranscripts", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Mobile Phase A", + "sms:displayName": "Decoded Transcripts", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LCMobilePhaseB", + "@id": "bts:XeniumIFimageHTANFileID", "@type": "rdfs:Class", - "rdfs:comment": "Composition of mobile phase B", - "rdfs:label": "LCMobilePhaseB", + "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", + "rdfs:label": "XeniumIFimageHTANFileID", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Mobile Phase B", - "sms:required": "sms:true", + "sms:displayName": "Xenium IF image HTAN File ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSInstrumentMetadataFile", + "@id": "bts:XeniumHEimageHTANFileID", "@type": "rdfs:Class", - "rdfs:comment": "Additional file containing instrument metadata details. Use either synapse_path or entity_Id", - "rdfs:label": "MSInstrumentMetadataFile", + "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", + "rdfs:label": "XeniumHEimageHTANFileID", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MS Instrument Metadata File", + "sms:displayName": "Xenium HE image HTAN File ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryLevel2", + "@id": "bts:RPPALevel2", "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2", - "rdfs:label": "MassSpectrometryLevel2", + "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", + "rdfs:label": "RPPALevel2", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -45137,11 +46543,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Level 2", + "sms:displayName": "RPPA Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -45155,7 +46561,7 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:HTANParticipantID" }, { "@id": "bts:HTANParentBiospecimenID" @@ -45164,52 +46570,41 @@ "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:MSAssayCategory" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:HTANRPPAAntibodyTable" }, { - "@id": "bts:MassSpectrometryAuxiliaryFile" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MSAssayCategory", - "@type": "rdfs:Class", - "rdfs:comment": "Type of Mass Spectrometry performed.", - "rdfs:label": "MSAssayCategory", - "rdfs:subClassOf": [ + "@id": "bts:AssayType" + }, { - "@id": "bts:MassSpectrometryLevel2" + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MS Assay Category", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryAuxiliaryFile", + "@id": "bts:HTANRPPAAntibodyTable", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).", - "rdfs:label": "MassSpectrometryAuxiliaryFile", + "rdfs:comment": "A table containing antibody level metadata for RPPA", + "rdfs:label": "HTANRPPAAntibodyTable", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:RPPALevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Auxiliary File", - "sms:required": "sms:false", + "sms:displayName": "HTAN RPPA Antibody Table", + "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:Component" + "@id": "bts:HTANRPPAAntibodyTableID" }, { "@id": "bts:Filename" @@ -45218,175 +46613,126 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:AbNameReportedonDataset" }, { - "@id": "bts:HTANDataFileID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MassSpectrometryLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3", - "rdfs:label": "MassSpectrometryLevel3", - "rdfs:subClassOf": [ + "@id": "bts:GENCODEGeneSymbolTarget" + }, { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Spectrometry Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:UNIPROTProteinIDTarget" + }, { - "@id": "bts:MassSpectrometryLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:PhosphoproteinFlag" + }, { - "@id": "bts:Component" + "@id": "bts:Vendor" }, { - "@id": "bts:Filename" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:FileFormat" + "@id": "bts:InternalAbID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Species" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:RPPADilution" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:PhosphoSite" }, { - "@id": "bts:MSAssayCategory" + "@id": "bts:RPPAValidationStatus" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Clone" }, { - "@id": "bts:MassSpectrometryAuxiliaryFile" + "@id": "bts:Clonality" + }, + { + "@id": "bts:AntibodyNotes" } ], "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryLevel4", + "@id": "bts:HTANRPPAAntibodyTableID", "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4", - "rdfs:label": "MassSpectrometryLevel4", + "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", + "rdfs:label": "HTANRPPAAntibodyTableID", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:MassSpectrometryLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:MSAssayCategory" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:MassSpectrometryAuxiliaryFile" - } - ], + "sms:displayName": "HTAN RPPA Antibody Table ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HTANChannelMetadataID", + "@id": "bts:AbNameReportedonDataset", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID for this channel metadata table (same for all rows)", - "rdfs:label": "HTANChannelMetadataID", + "rdfs:comment": "The antibody name.", + "rdfs:label": "AbNameReportedonDataset", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Channel Metadata ID", + "sms:displayName": "Ab Name Reported on Dataset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelID", + "@id": "bts:GENCODEGeneSymbolTarget", "@type": "rdfs:Class", - "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')", - "rdfs:label": "ChannelID", + "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", + "rdfs:label": "GENCODEGeneSymbolTarget", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel ID", + "sms:displayName": "GENCODE Gene Symbol Target", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelName", + "@id": "bts:UNIPROTProteinIDTarget", "@type": "rdfs:Class", - "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", - "rdfs:label": "ChannelName", + "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", + "rdfs:label": "UNIPROTProteinIDTarget", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Name", + "sms:displayName": "UNIPROT Protein ID Target", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelPassedQC", + "@id": "bts:PhosphoproteinFlag", "@type": "rdfs:Class", - "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", - "rdfs:label": "ChannelPassedQC", + "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", + "rdfs:label": "PhosphoproteinFlag", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -45394,21 +46740,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:True" }, { - "@id": "bts:No-ChannelFailedQC" + "@id": "bts:False" } ], - "sms:displayName": "Channel Passed QC", + "sms:displayName": "Phosphoprotein Flag", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CycleNumber", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", - "rdfs:label": "CycleNumber", + "rdfs:comment": "Vendor", + "rdfs:label": "Vendor", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel3Channels" @@ -45417,17 +46763,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cycle Number", + "sms:displayName": "Vendor", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SubCycleNumber", + "@id": "bts:CatalogNumber", "@type": "rdfs:Class", - "rdfs:comment": "Sub cycle number", - "rdfs:label": "SubCycleNumber", + "rdfs:comment": "Catalog Number", + "rdfs:label": "CatalogNumber", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel3Channels" @@ -45436,167 +46780,130 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sub Cycle Number", + "sms:displayName": "Catalog Number", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:AntibodyRole", + "@id": "bts:InternalAbID", "@type": "rdfs:Class", - "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", - "rdfs:label": "AntibodyRole", + "rdfs:comment": "Internal lab ID for an antibody.", + "rdfs:label": "InternalAbID", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Primary" - }, - { - "@id": "bts:Secondary" - } - ], - "sms:displayName": "Antibody Role", + "sms:displayName": "Internal Ab ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TargetName", + "@id": "bts:Species", "@type": "rdfs:Class", - "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", - "rdfs:label": "TargetName", + "rdfs:comment": "Host animal.", + "rdfs:label": "Species", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Target Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AntibodyName", - "@type": "rdfs:Class", - "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", - "rdfs:label": "AntibodyName", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:Mouse" + }, + { + "@id": "bts:Rabbit" + }, + { + "@id": "bts:Goat" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Antibody Name", + "sms:displayName": "Species", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RRIDidentifier", + "@id": "bts:RPPADilution", "@type": "rdfs:Class", - "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", - "rdfs:label": "RRIDidentifier", + "rdfs:comment": "The dilution ratio.", + "rdfs:label": "RPPADilution", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RRID identifier", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match AB_\\d+" - ] + "sms:displayName": "RPPA Dilution", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:Fluorophore", + "@id": "bts:PhosphoSite", "@type": "rdfs:Class", - "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", - "rdfs:label": "Fluorophore", + "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", + "rdfs:label": "PhosphoSite", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fluorophore", + "sms:displayName": "Phospho Site", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Lot", - "@type": "rdfs:Class", - "rdfs:comment": "Lot number from vendor", - "rdfs:label": "Lot", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:PhosphoproteinFlag" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lot", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExcitationWavelength", + "@id": "bts:RPPAValidationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Center/peak of the excitation spectrum (nm)", - "rdfs:label": "ExcitationWavelength", + "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", + "rdfs:label": "RPPAValidationStatus", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Excitation Wavelength", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:EmissionWavelength", - "@type": "rdfs:Class", - "rdfs:comment": "Center/peak of the emission spectrum (nm)", - "rdfs:label": "EmissionWavelength", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:Valid" + }, + { + "@id": "bts:UsewithCaution" + }, + { + "@id": "bts:UnderEvaluation" + }, + { + "@id": "bts:UsedforQC" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Emission Wavelength", + "sms:displayName": "RPPA Validation Status", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:ExcitationBandwidth", + "@id": "bts:Clone", "@type": "rdfs:Class", - "rdfs:comment": "Nominal width of excitation spectrum (nm)", - "rdfs:label": "ExcitationBandwidth", + "rdfs:comment": "Clone", + "rdfs:label": "Clone", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel3Channels" @@ -45605,523 +46912,783 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Excitation Bandwidth", + "sms:displayName": "Clone", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:EmissionBandwidth", + "@id": "bts:AntibodyNotes", "@type": "rdfs:Class", - "rdfs:comment": "Nominal width of emission spectrum (nm)", - "rdfs:label": "EmissionBandwidth", + "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", + "rdfs:label": "AntibodyNotes", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Emission Bandwidth", + "sms:displayName": "Antibody Notes", "sms:required": "sms:false", - "sms:validationRules": [ - 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Example: The MALDI Imaging analyte is lipids.", + "rdfs:label": "MS-basedTargeted", + "rdfs:subClassOf": [ { - "@id": "bts:Lv" - }, + "@id": "bts:MassSpectrometryLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Ts" + "@id": "bts:Targeted" }, { - "@id": "bts:Og" + "@id": "bts:Untargeted" } ], - "sms:displayName": "Metal Isotope Element", - "sms:required": "sms:false", - "sms:validationRules": [ - "str" - ] + "sms:displayName": "MS-based Targeted", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:MetalIsotopeMass", + "@id": "bts:MSInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "Element mass number", - "rdfs:label": "MetalIsotopeMass", + "rdfs:comment": "An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.", + "rdfs:label": "MSInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Metal Isotope Mass", - "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MS Instrument Vendor and Model", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:OligoBarcodeUpperStrand", + "@id": "bts:MSSource", "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Upper Strand", - "rdfs:label": "OligoBarcodeUpperStrand", + "rdfs:comment": "The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)", + "rdfs:label": "MSSource", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oligo Barcode Upper Strand", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:MALDI" + }, + { + "@id": "bts:MALDI-2" + }, + { + "@id": "bts:DESI" + }, + { + "@id": "bts:SIMS" + }, + { + "@id": "bts:NESI" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "MS Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OligoBarcodeLowerStrand", + "@id": "bts:Polarity", "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Lower Strand", - "rdfs:label": "OligoBarcodeLowerStrand", + "rdfs:comment": "The polarity of the mass analysis (positive or negative ion modes)", + "rdfs:label": "Polarity", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oligo Barcode Lower Strand", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Negative" + } + ], + "sms:displayName": "Polarity", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Dilution", + "@id": "bts:MassRangeLowValue", "@type": "rdfs:Class", - "rdfs:comment": "Dilution (eg 1:1000)", - "rdfs:label": "Dilution", + "rdfs:comment": "The low value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeLowValue", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dilution", - "sms:required": "sms:false", + "sms:displayName": "Mass Range Low Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Concentration", + "@id": "bts:MassRangeHighValue", "@type": "rdfs:Class", - "rdfs:comment": "Concentration (eg 10ug/mL)", - "rdfs:label": "Concentration", + "rdfs:comment": "The high value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeHighValue", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Concentration", - "sms:required": "sms:false", + "sms:displayName": "Mass Range High Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:No-ChannelFailedQC", + "@id": "bts:DataCollectionMode", "@type": "rdfs:Class", - "rdfs:comment": "Channel failed QC", - "rdfs:label": "No-ChannelFailedQC", + "rdfs:comment": "Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", + "rdfs:label": "DataCollectionMode", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ChannelPassedQC" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "No - Channel Failed QC", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:DDA" + }, + { + "@id": "bts:DIA" + }, + { + "@id": "bts:Other" } ], + "sms:displayName": "Data Collection Mode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelQCFailureType", + "@id": "bts:MSScanMode", "@type": "rdfs:Class", - "rdfs:comment": "Reason the channel failed QC", - "rdfs:label": "ChannelQCFailureType", + "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", + "rdfs:label": "MSScanMode", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -46129,951 +47696,1405 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Off-targetstaining" - }, - { - "@id": "bts:Auto-fluoresence" + "@id": "bts:MS" }, { - "@id": "bts:Stainingartefacet" + "@id": "bts:MS/MS" }, { - "@id": "bts:Imagingartefact" + "@id": "bts:MS3" }, { - "@id": "bts:Other/multiplechannelQCfaliuretypes" + "@id": "bts:Other" } ], - "sms:displayName": "Channel QC Failure Type", - "sms:required": "sms:false", + "sms:displayName": "MS Scan Mode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Off-targetstaining", + "@id": "bts:MSLabeling", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Off-targetstaining", + "rdfs:comment": "Indicates whether samples were labeled prior to MS analysis (e.g., TMT)", + "rdfs:label": "MSLabeling", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Off-target staining", - "sms:required": "sms:false", + "sms:displayName": "MS Labeling", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Auto-fluoresence", + "@id": "bts:LCInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Auto-fluoresence", + "rdfs:comment": "The manufacturer of the instrument used for LC.", + "rdfs:label": "LCInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Auto-fluoresence", - "sms:required": "sms:false", + "sms:displayName": "LC Instrument Vendor and Model", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Stainingartefacet", + "@id": "bts:LCColumnVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Stainingartefacet", + "rdfs:comment": "The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'", + "rdfs:label": "LCColumnVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Staining artefacet", - "sms:required": "sms:false", + "sms:displayName": "LC Column Vendor and Model", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Imagingartefact", + "@id": "bts:LCResin", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Imagingartefact", + "rdfs:comment": "Details of the resin used for lc, including vendor, particle size, pore size", + "rdfs:label": "LCResin", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging artefact", - "sms:required": "sms:false", + "sms:displayName": "LC Resin", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Other/multiplechannelQCfaliuretypes", + "@id": "bts:LCLengthValue", "@type": "rdfs:Class", - "rdfs:comment": "QC failure type not speficied", - "rdfs:label": "Other/multiplechannelQCfaliuretypes", + "rdfs:comment": "LC column length in cm.", + "rdfs:label": "LCLengthValue", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other/multiple channel QC faliure types", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:ChannelQCFailureComment" - } - ], + "sms:displayName": "LC Length Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelQCFailureComment", + "@id": "bts:LCTempValue", "@type": "rdfs:Class", - "rdfs:comment": "Custom comment on channel QC faliure", - "rdfs:label": "ChannelQCFailureComment", + "rdfs:comment": "LC temperature in C.", + "rdfs:label": "LCTempValue", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel QC Failure Comment", - "sms:required": "sms:false", + "sms:displayName": "LC Temp Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Primary", + "@id": "bts:LCIDValue", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Primary", + "rdfs:comment": "LC column inner diameter in microns.", + "rdfs:label": "LCIDValue", "rdfs:subClassOf": [ { - "@id": "bts:AntibodyRole" - }, - { - "@id": "bts:ClassificationofTumor" - }, - { - "@id": "bts:TumorTissueType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Primary", - "sms:required": "sms:false", + "sms:displayName": "LC ID Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Secondary", + "@id": "bts:LCFlowRate", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Secondary", + "rdfs:comment": "LC flow rate in nL/min.", + "rdfs:label": "LCFlowRate", "rdfs:subClassOf": [ { - "@id": "bts:AntibodyRole" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Secondary", - "sms:required": "sms:false", + "sms:displayName": "LC Flow Rate", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:H", + "@id": "bts:LCGradient", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "H", + "rdfs:comment": "The program dictates the mobile phase solvent composition over the course of the chromatographic run.", + "rdfs:label": "LCGradient", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "H", - "sms:required": "sms:false", + "sms:displayName": "LC Gradient", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:He", + "@id": "bts:LCMobilePhaseA", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "He", + "rdfs:comment": "Composition of mobile phase A", + "rdfs:label": "LCMobilePhaseA", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "He", - "sms:required": "sms:false", + "sms:displayName": "LC Mobile Phase A", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Li", + "@id": "bts:LCMobilePhaseB", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Li", + "rdfs:comment": "Composition of mobile phase B", + "rdfs:label": "LCMobilePhaseB", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Li", - "sms:required": "sms:false", + "sms:displayName": "LC Mobile Phase B", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Be", + "@id": "bts:MSInstrumentMetadataFile", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Be", + "rdfs:comment": "Additional file containing instrument metadata details. Use either synapse_path or entity_Id", + "rdfs:label": "MSInstrumentMetadataFile", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Be", + "sms:displayName": "MS Instrument Metadata File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:N", + "@id": "bts:MassSpectrometryLevel2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "N", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2", + "rdfs:label": "MassSpectrometryLevel2", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "N", + "sms:displayName": "Mass Spectrometry Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:O", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "O", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:MassSpectrometryLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "O", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:F", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "F", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:MSAssayCategory" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:MassSpectrometryAuxiliaryFile" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "F", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ne", + "@id": "bts:MSAssayCategory", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ne", + "rdfs:comment": "Type of Mass Spectrometry performed.", + "rdfs:label": "MSAssayCategory", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:MassSpectrometryLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ne", - "sms:required": "sms:false", + "sms:displayName": "MS Assay Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Na", + "@id": "bts:MassSpectrometryAuxiliaryFile", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Na", + "rdfs:comment": "Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).", + "rdfs:label": "MassSpectrometryAuxiliaryFile", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Na", + "sms:displayName": "Mass Spectrometry Auxiliary File", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Mg", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Mg", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mg", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Al", + "@id": "bts:MassSpectrometryLevel3", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Al", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3", + "rdfs:label": "MassSpectrometryLevel3", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Al", + "sms:displayName": "Mass Spectrometry Level 3", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:MassSpectrometryLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:MSAssayCategory" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:MassSpectrometryAuxiliaryFile" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Si", + "@id": "bts:MassSpectrometryLevel4", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Si", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4", + "rdfs:label": "MassSpectrometryLevel4", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Si", + "sms:displayName": "Mass Spectrometry Level 4", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:MassSpectrometryLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:MSAssayCategory" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:MassSpectrometryAuxiliaryFile" + } + ], "sms:validationRules": [] }, { - "@id": "bts:P", + "@id": "bts:HTANChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "P", + "rdfs:comment": "HTAN ID for this channel metadata table (same for all rows)", + "rdfs:label": "HTANChannelMetadataID", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "P", - "sms:required": "sms:false", + "sms:displayName": "HTAN Channel Metadata ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:S", + "@id": "bts:ChannelID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "S", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')", + "rdfs:label": "ChannelID", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "S", - "sms:required": "sms:false", + "sms:displayName": "Channel ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Cl", + "@id": "bts:ChannelName", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cl", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", + "rdfs:label": "ChannelName", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cl", - "sms:required": "sms:false", + "sms:displayName": "Channel Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Ar", + "@id": "bts:ChannelPassedQC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ar", + "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", + "rdfs:label": "ChannelPassedQC", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ar", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelFailedQC" + } + ], + "sms:displayName": "Channel Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:K", + "@id": "bts:CycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "K", + "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", + "rdfs:label": "CycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "K", + "sms:displayName": "Cycle Number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:Ca", + "@id": "bts:SubCycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ca", + "rdfs:comment": "Sub cycle number", + "rdfs:label": "SubCycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ca", + "sms:displayName": "Sub Cycle Number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:Sc", + "@id": "bts:AntibodyRole", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Sc", + "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", + "rdfs:label": "AntibodyRole", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sc", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Primary" + }, + { + "@id": "bts:Secondary" + } + ], + "sms:displayName": "Antibody Role", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Ti", + "@id": "bts:TargetName", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ti", + "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", + "rdfs:label": "TargetName", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ti", - "sms:required": "sms:false", + "sms:displayName": "Target Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:V", + "@id": "bts:AntibodyName", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V", + "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", + "rdfs:label": "AntibodyName", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaSpecimenClarkLevelValue" - }, - { - "@id": "bts:FitzpatrickSkinTone" - }, - { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V", - "sms:required": "sms:false", + "sms:displayName": "Antibody Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Cr", + "@id": "bts:RRIDidentifier", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cr", + "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", + "rdfs:label": "RRIDidentifier", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cr", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "RRID identifier", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match AB_\\d+" + ] }, { - "@id": "bts:Mn", + "@id": "bts:Fluorophore", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Mn", + "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", + "rdfs:label": "Fluorophore", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mn", + "sms:displayName": "Fluorophore", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fe", + "@id": "bts:Lot", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fe", + "rdfs:comment": "Lot number from vendor", + "rdfs:label": "Lot", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fe", + "sms:displayName": "Lot", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Co", + "@id": "bts:ExcitationWavelength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Co", + "rdfs:comment": "Center/peak of the excitation spectrum (nm)", + "rdfs:label": "ExcitationWavelength", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Co", + "sms:displayName": "Excitation Wavelength", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Ni", + "@id": "bts:EmissionWavelength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ni", + "rdfs:comment": "Center/peak of the emission spectrum (nm)", + "rdfs:label": "EmissionWavelength", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ni", + "sms:displayName": "Emission Wavelength", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Cu", + "@id": "bts:ExcitationBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cu", + "rdfs:comment": "Nominal width of excitation spectrum (nm)", + "rdfs:label": "ExcitationBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cu", + "sms:displayName": "Excitation Bandwidth", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Zn", + "@id": "bts:EmissionBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Zn", + "rdfs:comment": "Nominal width of emission spectrum (nm)", + "rdfs:label": "EmissionBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Zn", + "sms:displayName": "Emission Bandwidth", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Ga", + "@id": "bts:MetalIsotopeElement", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ga", + "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", + "rdfs:label": "MetalIsotopeElement", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ga", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ge", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ge", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:H" + }, + { + "@id": "bts:He" + }, + { + "@id": "bts:Li" + }, + { + "@id": "bts:Be" + }, + { + "@id": "bts:B" + }, + { + "@id": "bts:C" + }, + { + "@id": "bts:N" + }, + { + "@id": "bts:O" + }, + { + "@id": "bts:F" + }, + { + "@id": "bts:Ne" + }, + { + "@id": "bts:Na" + }, + { + "@id": "bts:Mg" + }, + { + "@id": "bts:Al" + }, + { + "@id": "bts:Si" + }, + { + "@id": "bts:P" + }, + { + "@id": "bts:S" + }, + { + "@id": "bts:Cl" + }, + { + "@id": "bts:Ar" + }, + { + "@id": "bts:K" + }, + { + "@id": "bts:Ca" + }, + { + "@id": "bts:Sc" + }, + { + "@id": "bts:Ti" + }, + { + "@id": "bts:V" + }, + { + "@id": "bts:Cr" + }, + { + "@id": "bts:Mn" + }, + { + "@id": "bts:Fe" + }, + { + "@id": "bts:Co" + }, + { + "@id": "bts:Ni" + }, + { + "@id": "bts:Cu" + }, + { + "@id": "bts:Zn" + }, + { + "@id": "bts:Ga" + }, + { + "@id": "bts:Ge" + }, + { + "@id": "bts:As" + }, + { + "@id": "bts:Se" + }, + { + "@id": "bts:Br" + }, + { + "@id": "bts:Kr" + }, + { + "@id": "bts:Rb" + }, + { + "@id": "bts:Sr" + }, + { + "@id": "bts:Y" + }, + { + "@id": "bts:Zr" + }, + { + "@id": "bts:Nb" + }, + { + "@id": "bts:Mo" + }, + { + "@id": "bts:Tc" + }, + { + "@id": "bts:Ru" + }, + { + "@id": "bts:Rh" + }, + { + "@id": "bts:Pd" + }, + { + "@id": "bts:Ag" + }, + { + "@id": "bts:Cd" + }, + { + "@id": "bts:In" + }, + { + "@id": "bts:Sn" + }, + { + "@id": "bts:Sb" + }, + { + "@id": "bts:Te" + }, + { + "@id": "bts:I" + }, + { + "@id": "bts:Xe" + }, + { + "@id": "bts:Cs" + }, + { + "@id": "bts:Ba" + }, + { + "@id": "bts:La" + }, + { + "@id": "bts:Ce" + }, + { + "@id": "bts:Pr" + }, + { + "@id": "bts:Nd" + }, + { + "@id": "bts:Pm" + }, + { + "@id": "bts:Sm" + }, + { + "@id": "bts:Eu" + }, + { + "@id": "bts:Gd" + }, + { + "@id": "bts:Tb" + }, + { + "@id": "bts:Dy" + }, + { + "@id": "bts:Ho" + }, + { + "@id": "bts:Er" + }, + { + "@id": "bts:Tm" + }, + { + "@id": "bts:Yb" + }, + { + "@id": "bts:Lu" + }, + { + "@id": "bts:Hf" + }, + { + "@id": "bts:Ta" + }, + { + "@id": "bts:W" + }, + { + "@id": "bts:Re" + }, + { + "@id": "bts:Os" + }, + { + "@id": "bts:Ir" + }, + { + "@id": "bts:Pt" + }, + { + "@id": "bts:Au" + }, + { + "@id": "bts:Hg" + }, + { + "@id": "bts:Tl" + }, + { + "@id": "bts:Pb" + }, + { + "@id": "bts:Bi" + }, + { + "@id": "bts:Po" + }, + { + "@id": "bts:At" + }, + { + "@id": "bts:Rn" + }, + { + "@id": "bts:Fr" + }, + { + "@id": "bts:Ra" + }, + { + "@id": "bts:Ac" + }, + { + "@id": "bts:Th" + }, + { + "@id": "bts:Pa" + }, + { + "@id": "bts:U" + }, + { + "@id": "bts:Np" + }, + { + "@id": "bts:Pu" + }, + { + "@id": "bts:Am" + }, + { + "@id": "bts:Bk" + }, + { + "@id": "bts:Cf" + }, + { + "@id": "bts:Es" + }, + { + "@id": "bts:Fm" + }, + { + "@id": "bts:Md" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Lr" + }, + { + "@id": "bts:Rf" + }, + { + "@id": "bts:Db" + }, + { + "@id": "bts:Sg" + }, + { + "@id": "bts:Bh" + }, + { + "@id": "bts:Hs" + }, + { + "@id": "bts:Mt" + }, + { + "@id": "bts:Ds" + }, + { + "@id": "bts:Rg" + }, + { + "@id": "bts:Cn" + }, + { + "@id": "bts:Nh" + }, + { + "@id": "bts:Fl" + }, + { + "@id": "bts:Mc" + }, + { + "@id": "bts:Lv" + }, + { + "@id": "bts:Ts" + }, + { + "@id": "bts:Og" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ge", + "sms:displayName": "Metal Isotope Element", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "str" + ] }, { - "@id": "bts:As", + "@id": "bts:MetalIsotopeMass", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "As", + "rdfs:comment": "Element mass number", + "rdfs:label": "MetalIsotopeMass", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "As", + "sms:displayName": "Metal Isotope Mass", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:Se", + "@id": "bts:OligoBarcodeUpperStrand", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Se", + "rdfs:comment": "Oligo Barcode - Upper Strand", + "rdfs:label": "OligoBarcodeUpperStrand", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Se", + "sms:displayName": "Oligo Barcode Upper Strand", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Br", + "@id": "bts:OligoBarcodeLowerStrand", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Br", + "rdfs:comment": "Oligo Barcode - Lower Strand", + "rdfs:label": "OligoBarcodeLowerStrand", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Br", + "sms:displayName": "Oligo Barcode Lower Strand", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Kr", + "@id": "bts:Dilution", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Kr", + "rdfs:comment": "Dilution (eg 1:1000)", + "rdfs:label": "Dilution", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Kr", + "sms:displayName": "Dilution", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rb", + "@id": "bts:Concentration", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Rb", + "rdfs:comment": "Concentration (eg 10ug/mL)", + "rdfs:label": "Concentration", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rb", + "sms:displayName": "Concentration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sr", + "@id": "bts:No-ChannelFailedQC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Sr", + "rdfs:comment": "Channel failed QC", + "rdfs:label": "No-ChannelFailedQC", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ChannelPassedQC" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sr", + "sms:displayName": "No - Channel Failed QC", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ChannelQCFailureType" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Y", + "@id": "bts:ChannelQCFailureType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Y", + "rdfs:comment": "Reason the channel failed QC", + "rdfs:label": "ChannelQCFailureType", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Y", + "schema:rangeIncludes": [ + { + "@id": "bts:Off-targetstaining" + }, + { + "@id": "bts:Auto-fluoresence" + }, + { + "@id": "bts:Stainingartefacet" + }, + { + "@id": "bts:Imagingartefact" + }, + { + "@id": "bts:Other/multiplechannelQCfaliuretypes" + } + ], + "sms:displayName": "Channel QC Failure Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zr", + "@id": "bts:Off-targetstaining", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Zr", + "rdfs:label": "Off-targetstaining", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Zr", + "sms:displayName": "Off-target staining", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nb", + "@id": "bts:Auto-fluoresence", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nb", + "rdfs:label": "Auto-fluoresence", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nb", + "sms:displayName": "Auto-fluoresence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mo", + "@id": "bts:Stainingartefacet", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mo", + "rdfs:label": "Stainingartefacet", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mo", + "sms:displayName": "Staining artefacet", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tc", + "@id": "bts:Imagingartefact", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tc", + "rdfs:label": "Imagingartefact", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tc", + "sms:displayName": "Imaging artefact", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ru", + "@id": "bts:Other/multiplechannelQCfaliuretypes", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ru", + "rdfs:comment": "QC failure type not speficied", + "rdfs:label": "Other/multiplechannelQCfaliuretypes", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ru", + "sms:displayName": "Other/multiple channel QC faliure types", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ChannelQCFailureComment" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Rh", + "@id": "bts:ChannelQCFailureComment", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Rh", + "rdfs:comment": "Custom comment on channel QC faliure", + "rdfs:label": "ChannelQCFailureComment", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rh", + "sms:displayName": "Channel QC Failure Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pd", + "@id": "bts:Primary", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pd", + "rdfs:label": "Primary", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AntibodyRole" + }, + { + "@id": "bts:ClassificationofTumor" + }, + { + "@id": "bts:TumorTissueType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pd", + "sms:displayName": "Primary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ag", + "@id": "bts:Secondary", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ag", + "rdfs:label": "Secondary", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AntibodyRole" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ag", + "sms:displayName": "Secondary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cd", + "@id": "bts:H", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cd", + "rdfs:label": "H", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47082,15 +49103,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cd", + "sms:displayName": "H", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:In", + "@id": "bts:He", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "In", + "rdfs:label": "He", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47099,15 +49120,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "In", + "sms:displayName": "He", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sn", + "@id": "bts:Li", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sn", + "rdfs:label": "Li", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47116,15 +49137,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sn", + "sms:displayName": "Li", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sb", + "@id": "bts:Be", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sb", + "rdfs:label": "Be", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47133,15 +49154,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sb", + "sms:displayName": "Be", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Te", + "@id": "bts:N", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Te", + "rdfs:label": "N", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47150,25 +49171,16 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Te", + "sms:displayName": "N", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:I", + "@id": "bts:O", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "I", + "rdfs:label": "O", "rdfs:subClassOf": [ - { - "@id": "bts:ISSStage" - }, - { - "@id": "bts:MelanomaSpecimenClarkLevelValue" - }, - { - "@id": "bts:FitzpatrickSkinTone" - }, { "@id": "bts:MetalIsotopeElement" } @@ -47176,15 +49188,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "I", + "sms:displayName": "O", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Xe", + "@id": "bts:F", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Xe", + "rdfs:label": "F", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47193,15 +49205,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xe", + "sms:displayName": "F", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cs", + "@id": "bts:Ne", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cs", + "rdfs:label": "Ne", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47210,15 +49222,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cs", + "sms:displayName": "Ne", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ba", + "@id": "bts:Na", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ba", + "rdfs:label": "Na", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47227,15 +49239,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ba", + "sms:displayName": "Na", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:La", + "@id": "bts:Mg", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "La", + "rdfs:label": "Mg", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47244,15 +49256,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "La", + "sms:displayName": "Mg", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ce", + "@id": "bts:Al", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ce", + "rdfs:label": "Al", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47261,15 +49273,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ce", + "sms:displayName": "Al", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pr", + "@id": "bts:Si", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pr", + "rdfs:label": "Si", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47278,15 +49290,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pr", + "sms:displayName": "Si", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nd", + "@id": "bts:P", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nd", + "rdfs:label": "P", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47295,15 +49307,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nd", + "sms:displayName": "P", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pm", + "@id": "bts:S", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pm", + "rdfs:label": "S", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47312,15 +49324,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pm", + "sms:displayName": "S", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sm", + "@id": "bts:Cl", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sm", + "rdfs:label": "Cl", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47329,15 +49341,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sm", + "sms:displayName": "Cl", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Eu", + "@id": "bts:Ar", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Eu", + "rdfs:label": "Ar", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47346,15 +49358,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Eu", + "sms:displayName": "Ar", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Gd", + "@id": "bts:K", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Gd", + "rdfs:label": "K", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47363,15 +49375,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gd", + "sms:displayName": "K", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tb", + "@id": "bts:Ca", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tb", + "rdfs:label": "Ca", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47380,15 +49392,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tb", + "sms:displayName": "Ca", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Dy", + "@id": "bts:Sc", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Dy", + "rdfs:label": "Sc", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47397,15 +49409,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dy", + "sms:displayName": "Sc", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ho", + "@id": "bts:Ti", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ho", + "rdfs:label": "Ti", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47414,16 +49426,22 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ho", + "sms:displayName": "Ti", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Er", + "@id": "bts:V", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Er", + "rdfs:label": "V", "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaSpecimenClarkLevelValue" + }, + { + "@id": "bts:FitzpatrickSkinTone" + }, { "@id": "bts:MetalIsotopeElement" } @@ -47431,15 +49449,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Er", + "sms:displayName": "V", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tm", + "@id": "bts:Cr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tm", + "rdfs:label": "Cr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47448,15 +49466,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tm", + "sms:displayName": "Cr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yb", + "@id": "bts:Mn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Yb", + "rdfs:label": "Mn", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47465,15 +49483,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yb", + "sms:displayName": "Mn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lu", + "@id": "bts:Fe", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lu", + "rdfs:label": "Fe", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47482,15 +49500,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lu", + "sms:displayName": "Fe", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hf", + "@id": "bts:Co", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hf", + "rdfs:label": "Co", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47499,22 +49517,16 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hf", + "sms:displayName": "Co", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ta", + "@id": "bts:Ni", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ta", + "rdfs:label": "Ni", "rdfs:subClassOf": [ - { - "@id": "bts:AJCCClinicalT" - }, - { - "@id": "bts:AJCCPathologicT" - }, { "@id": "bts:MetalIsotopeElement" } @@ -47522,15 +49534,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ta", + "sms:displayName": "Ni", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:W", + "@id": "bts:Cu", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "W", + "rdfs:label": "Cu", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47539,15 +49551,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "W", + "sms:displayName": "Cu", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Re", + "@id": "bts:Zn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Re", + "rdfs:label": "Zn", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47556,15 +49568,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Re", + "sms:displayName": "Zn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Os", + "@id": "bts:Ga", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Os", + "rdfs:label": "Ga", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47573,15 +49585,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Os", + "sms:displayName": "Ga", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ir", + "@id": "bts:Ge", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ir", + "rdfs:label": "Ge", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47590,15 +49602,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ir", + "sms:displayName": "Ge", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pt", + "@id": "bts:As", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pt", + "rdfs:label": "As", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47607,15 +49619,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pt", + "sms:displayName": "As", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Au", + "@id": "bts:Se", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Au", + "rdfs:label": "Se", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47624,15 +49636,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Au", + "sms:displayName": "Se", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hg", + "@id": "bts:Br", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hg", + "rdfs:label": "Br", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47641,15 +49653,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hg", + "sms:displayName": "Br", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tl", + "@id": "bts:Kr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tl", + "rdfs:label": "Kr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47658,15 +49670,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tl", + "sms:displayName": "Kr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pb", + "@id": "bts:Rb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pb", + "rdfs:label": "Rb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47675,15 +49687,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pb", + "sms:displayName": "Rb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bi", + "@id": "bts:Sr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bi", + "rdfs:label": "Sr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47692,15 +49704,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bi", + "sms:displayName": "Sr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Po", + "@id": "bts:Y", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Po", + "rdfs:label": "Y", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47709,15 +49721,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Po", + "sms:displayName": "Y", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:At", + "@id": "bts:Zr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "At", + "rdfs:label": "Zr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47726,15 +49738,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "At", + "sms:displayName": "Zr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rn", + "@id": "bts:Nb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rn", + "rdfs:label": "Nb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47743,15 +49755,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rn", + "sms:displayName": "Nb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fr", + "@id": "bts:Mo", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Fr", + "rdfs:label": "Mo", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47760,15 +49772,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fr", + "sms:displayName": "Mo", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ra", + "@id": "bts:Tc", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ra", + "rdfs:label": "Tc", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47777,15 +49789,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ra", + "sms:displayName": "Tc", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ac", + "@id": "bts:Ru", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ac", + "rdfs:label": "Ru", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47794,15 +49806,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ac", + "sms:displayName": "Ru", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Th", + "@id": "bts:Rh", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Th", + "rdfs:label": "Rh", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47811,15 +49823,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Th", + "sms:displayName": "Rh", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pa", + "@id": "bts:Pd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pa", + "rdfs:label": "Pd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47828,15 +49840,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pa", + "sms:displayName": "Pd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:U", + "@id": "bts:Ag", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "U", + "rdfs:label": "Ag", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47845,15 +49857,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "U", + "sms:displayName": "Ag", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Np", + "@id": "bts:Cd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Np", + "rdfs:label": "Cd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47862,15 +49874,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Np", + "sms:displayName": "Cd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pu", + "@id": "bts:In", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pu", + "rdfs:label": "In", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47879,15 +49891,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pu", + "sms:displayName": "In", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bk", + "@id": "bts:Sn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bk", + "rdfs:label": "Sn", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47896,15 +49908,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bk", + "sms:displayName": "Sn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cf", + "@id": "bts:Sb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cf", + "rdfs:label": "Sb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47913,15 +49925,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cf", + "sms:displayName": "Sb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Es", + "@id": "bts:Te", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Es", + "rdfs:label": "Te", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47930,16 +49942,25 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Es", + "sms:displayName": "Te", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fm", + "@id": "bts:I", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Fm", + "rdfs:label": "I", "rdfs:subClassOf": [ + { + "@id": "bts:ISSStage" + }, + { + "@id": "bts:MelanomaSpecimenClarkLevelValue" + }, + { + "@id": "bts:FitzpatrickSkinTone" + }, { "@id": "bts:MetalIsotopeElement" } @@ -47947,15 +49968,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fm", + "sms:displayName": "I", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lr", + "@id": "bts:Xe", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lr", + "rdfs:label": "Xe", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47964,15 +49985,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lr", + "sms:displayName": "Xe", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rf", + "@id": "bts:Cs", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rf", + "rdfs:label": "Cs", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47981,15 +50002,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rf", + "sms:displayName": "Cs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Db", + "@id": "bts:Ba", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Db", + "rdfs:label": "Ba", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47998,15 +50019,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Db", + "sms:displayName": "Ba", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sg", + "@id": "bts:La", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sg", + "rdfs:label": "La", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48015,15 +50036,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sg", + "sms:displayName": "La", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bh", + "@id": "bts:Ce", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bh", + "rdfs:label": "Ce", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48032,15 +50053,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bh", + "sms:displayName": "Ce", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hs", + "@id": "bts:Pr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hs", + "rdfs:label": "Pr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48049,15 +50070,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hs", + "sms:displayName": "Pr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mt", + "@id": "bts:Nd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mt", + "rdfs:label": "Nd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48066,15 +50087,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mt", + "sms:displayName": "Nd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ds", + "@id": "bts:Pm", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ds", + "rdfs:label": "Pm", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48083,15 +50104,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ds", + "sms:displayName": "Pm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rg", + "@id": "bts:Sm", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rg", + "rdfs:label": "Sm", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48100,15 +50121,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rg", + "sms:displayName": "Sm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cn", + "@id": "bts:Eu", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cn", + "rdfs:label": "Eu", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48117,15 +50138,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cn", + "sms:displayName": "Eu", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nh", + "@id": "bts:Gd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nh", + "rdfs:label": "Gd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48134,15 +50155,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nh", + "sms:displayName": "Gd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fl", + "@id": "bts:Tb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Fl", + "rdfs:label": "Tb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48151,15 +50172,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fl", + "sms:displayName": "Tb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mc", + "@id": "bts:Dy", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mc", + "rdfs:label": "Dy", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48168,15 +50189,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mc", + "sms:displayName": "Dy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lv", + "@id": "bts:Ho", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lv", + "rdfs:label": "Ho", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48185,15 +50206,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lv", + "sms:displayName": "Ho", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ts", + "@id": "bts:Er", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ts", + "rdfs:label": "Er", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48202,15 +50223,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ts", + "sms:displayName": "Er", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Og", + "@id": "bts:Tm", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Og", + "rdfs:label": "Tm", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48219,4070 +50240,2900 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Og", + "sms:displayName": "Tm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:H&E", + "@id": "bts:Yb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "H&E", + "rdfs:label": "Yb", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "H&E", + "sms:displayName": "Yb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CyCIF", + "@id": "bts:Lu", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CyCIF", + "rdfs:label": "Lu", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CyCIF", + "sms:displayName": "Lu", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:T-CyCIF", + "@id": "bts:Hf", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "T-CyCIF", + "rdfs:label": "Hf", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "t-CyCIF", + "sms:displayName": "Hf", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IHC", + "@id": "bts:Ta", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "IHC", + "rdfs:label": "Ta", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:AJCCClinicalT" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:AJCCPathologicT" + }, + { + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IHC", + "sms:displayName": "Ta", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MIHC", + "@id": "bts:W", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MIHC", + "rdfs:label": "W", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mIHC", + "sms:displayName": "W", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MxIF", + "@id": "bts:Re", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MxIF", + "rdfs:label": "Re", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MxIF", + "sms:displayName": "Re", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SABER", + "@id": "bts:Os", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "SABER", + "rdfs:label": "Os", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SABER", + "sms:displayName": "Os", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IMC", + "@id": "bts:Ir", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "IMC", + "rdfs:label": "Ir", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IMC", + "sms:displayName": "Ir", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CODEX", + "@id": "bts:Pt", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CODEX", + "rdfs:label": "Pt", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CODEX", + "sms:displayName": "Pt", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMX-DSP", + "@id": "bts:Au", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "GeoMX-DSP", + "rdfs:label": "Au", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMX-DSP", + "sms:displayName": "Au", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MIBI", + "@id": "bts:Hg", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MIBI", + "rdfs:label": "Hg", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MIBI", + "sms:displayName": "Hg", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISH", + "@id": "bts:Tl", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MERFISH", + "rdfs:label": "Tl", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH", + "sms:displayName": "Tl", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExSeq", + "@id": "bts:Pb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ExSeq", + "rdfs:label": "Pb", "rdfs:subClassOf": [ { - "@id": "bts:DataType" - }, - { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq", + "sms:displayName": "Pb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RareCyteOrion", + "@id": "bts:Bi", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "RareCyteOrion", + "rdfs:label": "Bi", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - 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"@id": "bts:PrimaryDiagnosis" + "@id": "bts:SpikeIn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Not Reported", + "sms:displayName": "PhiX", "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:SpikeInConcentration", + "@type": "rdfs:Class", + "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", + "rdfs:label": "SpikeInConcentration", + "rdfs:subClassOf": [ + { + "@id": "bts:ERCC" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spike In Concentration", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:NIB", "@type": "rdfs:Class", @@ -53337,23 +54188,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:RRNADepletion", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RRNADepletion", - "rdfs:subClassOf": [ - { - "@id": "bts:LibrarySelectionMethod" - 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"rdfs:label": "BulkWES", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk WES", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ElectronMicroscopy", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ElectronMicroscopy", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Electron Microscopy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HI-C-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HI-C-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HI-C-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RPPA", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RPPA", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RPPA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MassSpectrometry", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MassSpectrometry", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Spectrometry", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomics", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSImaging", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SRRSImaging", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Imaging", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Slide-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATAC-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScATAC-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATAC-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScDNA-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScDNA-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scDNA-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScRNA-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScRNA-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scRNA-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AccessoryManifest", - "@type": "rdfs:Class", - "rdfs:comment": "Accessory specific attributes", - "rdfs:label": "AccessoryManifest", - "rdfs:subClassOf": [ - { - "@id": "bts:Accessory" - }, - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Accessory Manifest", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:DatasetName" - }, - { - "@id": "bts:AccessorySynapseID" - }, - { - "@id": "bts:AccessoryDescription" - }, - { - "@id": "bts:DataType" - }, - { - "@id": "bts:HTANCenterID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:Accessory-associatedHTANParentDataFileID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:OtherDataTypeSpecified", - "@type": "rdfs:Class", - "rdfs:comment": "Other types of data associated with the content.", - "rdfs:label": "OtherDataTypeSpecified", - "rdfs:subClassOf": [ - { - "@id": "bts:Publication" - }, - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Data Type Specified", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] - }, { "@id": "bts:Accessory", "@type": "rdfs:Class", From a313b1dc0f11e3f9278aab307030231bc635a9b9 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 12:07:40 -0400 Subject: [PATCH 06/14] Changes: CDS template --- HTAN.model.csv | 13 +++++++------ cds-template.csv | 1 - dca-template-config.json | 5 +++++ 3 files changed, 12 insertions(+), 7 deletions(-) delete mode 100644 cds-template.csv diff --git a/HTAN.model.csv b/HTAN.model.csv index a260a913..d7545331 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -7,11 +7,12 @@ Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organis File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, -CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,"hg19, hg38_long_polya, Release 31 (GRCh38.p12)",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, -CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,, -CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like -CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,,,TRUE,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS Genomic Reference, CDS Library Layout, CDS Data Type, CDS Sequencing Platform, CDS Library Selection Method",, +CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, +CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,https://dataservice.datacommons.cancer.gov/#/resources,list like +CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://dataservice.datacommons.cancer.gov/#/resources, +CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning @@ -922,7 +923,7 @@ Publication Abstract,The abstract or short description of the content presented/ License,The type of license applicable to the content.,"0BSD, AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement, Proprietary, Other, Not licensed, Freeware",,,FALSE,Publication,,,list like PMID,The PubMed identifier associated with the publication (applicable to published manuscripts). Provide as a URL of the form https://pubmed.ncbi.nlm.nih.gov/{pmid},,,,FALSE,Publication,,,url Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like -Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,,,list like +Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,CDS Data Type,,list like Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url warning Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,, diff --git a/cds-template.csv b/cds-template.csv deleted file mode 100644 index 932a2e3e..00000000 --- a/cds-template.csv +++ /dev/null @@ -1 +0,0 @@ -Genomic Reference,Library layout,Data Type,Sequencing Platform,Library Selection Method,HTAN Data File ID,HTAN Parent Biospecimen ID,Filename,File Format \ No newline at end of file diff --git a/dca-template-config.json b/dca-template-config.json index bd4dd061..3b5efd4f 100644 --- a/dca-template-config.json +++ b/dca-template-config.json @@ -70,6 +70,11 @@ "schema_name": "BulkWESLevel2", "type": "file" }, + { + "display_name": "CDS Sequencing Template", + "schema_name": "CDSSequencingTemplate", + "type": "file" + }, { "display_name": "Bulk WES Level 3", "schema_name": "BulkWESLevel3", From 785b750c39bfd6d35ee9084c9931e3ab3d1d1a78 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 12:10:32 -0400 Subject: [PATCH 07/14] Revert "Merge branch 'cds-template' of https://github.com/ncihtan/data-models into cds-template" This reverts commit 61d71bea23bf6ffc018434e3b1ba3737e5b91182, reversing changes made to a313b1dc0f11e3f9278aab307030231bc635a9b9. --- HTAN.model.jsonld | 47005 ++++++++++++++++++++++---------------------- 1 file changed, 23247 insertions(+), 23758 deletions(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index c33b5b0e..f73558f7 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -2877,697 +2877,652 @@ "sms:validationRules": [] }, { - "@id": "bts:CDSGenomicReference", + "@id": "bts:Checksum", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "CDSGenomicReference", + "rdfs:comment": "MD5 checksum of the BAM file", + "rdfs:label": "Checksum", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:InformationContentEntity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Hg19" - }, - { - "@id": "bts:Hg38LongPolya" - }, - { - "@id": "bts:Release31(GRCh38.p12)" - } - ], - "sms:displayName": "CDS Genomic Reference", - "sms:required": "sms:false", + "sms:displayName": "Checksum", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Hg19", + "@id": "bts:HTANDataFileID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Hg19", + "rdfs:comment": "Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)", + "rdfs:label": "HTANDataFileID", "rdfs:subClassOf": [ { - "@id": "bts:CDSGenomicReference" + "@id": "bts:File" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "hg19", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "HTAN Data File ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" + ] }, { - "@id": "bts:Hg38LongPolya", + "@id": "bts:HTANBiospecimenID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Hg38LongPolya", + "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", + "rdfs:label": "HTANBiospecimenID", "rdfs:subClassOf": [ { - "@id": "bts:CDSGenomicReference" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "hg38_long_polya", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "HTAN Biospecimen ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" + ] }, { - "@id": "bts:Release31(GRCh38.p12)", + "@id": "bts:Biospecimen", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Release31(GRCh38.p12)", + "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", + "rdfs:label": "Biospecimen", "rdfs:subClassOf": [ { - "@id": "bts:CDSGenomicReference" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Release 31 (GRCh38.p12)", + "sms:displayName": "Biospecimen", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CDSLibraryLayout", - "@type": "rdfs:Class", - "rdfs:comment": "The read strategy or method that was used for sequencing and analysis of a nucleotide library.", - "rdfs:label": "CDSLibraryLayout", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Patient" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:PairedEnd" + "@id": "bts:Component" }, { - "@id": "bts:SingleRead" - } - ], - "sms:displayName": "CDS Library Layout", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PairedEnd", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "PairedEnd", - "rdfs:subClassOf": [ + "@id": "bts:HTANBiospecimenID" + }, { - "@id": "bts:CDSLibraryLayout" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:LibraryLayout" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Paired End", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SingleRead", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SingleRead", - "rdfs:subClassOf": [ + "@id": "bts:HTANParentID" + }, { - "@id": "bts:CDSLibraryLayout" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:LibraryLayout" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Single Read", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CDSDataType", - "@type": "rdfs:Class", - "rdfs:comment": "Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.", - "rdfs:label": "CDSDataType", - "rdfs:subClassOf": [ + "@id": "bts:CollectionDaysfromIndex" + }, { - "@id": "bts:Publication" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AdjacentBiospecimenIDs" + }, { - "@id": "bts:10xVisiumSpatialTranscriptomics" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:BulkMethylation-seq" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:BulkRNA-seq" + "@id": "bts:FixativeType" }, { - "@id": "bts:BulkWES" + "@id": "bts:StorageMethod" }, { - "@id": "bts:ElectronMicroscopy" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:ExSeq" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:HI-C-seq" + "@id": "bts:SiteDataSource" }, { - "@id": "bts:RPPA" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:Imaging" + "@id": "bts:MountingMedium" }, { - "@id": "bts:MassSpectrometry" + "@id": "bts:ProcessingLocation" }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics" + "@id": "bts:HistologyAssessmentBy" }, { - "@id": "bts:OtherAssay" + "@id": "bts:HistologyAssessmentMedium" }, { - "@id": "bts:SRRSImaging" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:Slide-seq" + "@id": "bts:TumorInfiltratingLymphocytes" }, { - "@id": "bts:ScATAC-seq" + "@id": "bts:DegreeofDysplasia" }, { - "@id": "bts:ScDNA-seq" + "@id": "bts:DysplasiaFraction" }, { - "@id": "bts:ScRNA-seq" + "@id": "bts:NumberProliferatingCells" }, { - "@id": "bts:AccessoryManifest" + "@id": "bts:PercentEosinophilInfiltration" }, { - "@id": "bts:OtherDataTypeSpecified" - } - ], - "sms:displayName": "CDS Data Type", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xVisiumSpatialTranscriptomics", - "rdfs:subClassOf": [ + "@id": "bts:PercentGranulocyteInfiltration" + }, { - "@id": "bts:CDSDataType" + "@id": "bts:PercentInflamInfiltration" }, { - "@id": "bts:DataType" + "@id": "bts:PercentLymphocyteInfiltration" + }, + { + "@id": "bts:PercentMonocyteInfiltration" + }, + { + "@id": "bts:PercentNecrosis" + }, + { + "@id": "bts:PercentNeutrophilInfiltration" + }, + { + "@id": "bts:PercentNormalCells" + }, + { + "@id": "bts:PercentStromalCells" + }, + { + "@id": "bts:PercentTumorCells" + }, + { + "@id": "bts:PercentTumorNuclei" + }, + { + "@id": "bts:FiducialMarker" + }, + { + "@id": "bts:SlicingMethod" + }, + { + "@id": "bts:LysisBuffer" + }, + { + "@id": "bts:MethodofNucleicAcidIsolation" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seq", + "@id": "bts:HTANParentID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkMethylation-seq", + "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", + "rdfs:label": "HTANParentID", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq", - "sms:required": "sms:false", + "sms:displayName": "HTAN Parent ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seq", + "@id": "bts:HTANParentBiospecimenID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkRNA-seq", + "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", + "rdfs:label": "HTANParentBiospecimenID", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq", - "sms:required": "sms:false", + "sms:displayName": "HTAN Parent Biospecimen ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkWES", + "@id": "bts:HTANParentDataFileID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkWES", + "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", + "rdfs:label": "HTANParentDataFileID", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:File" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES", - "sms:required": "sms:false", + "sms:displayName": "HTAN Parent Data File ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ElectronMicroscopy", + "@id": "bts:ClinicalDataTier2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ElectronMicroscopy", + "rdfs:comment": "Tier 2 Cancer Data", + "rdfs:label": "ClinicalDataTier2", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Electron Microscopy", + "sms:displayName": "Clinical Data Tier 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ExSeq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ExSeq", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:CDSDataType" + "@id": "bts:Component" }, { - "@id": "bts:DataType" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:SentinelLymphNodeCount" + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount" + }, + { + "@id": "bts:TumorExtranodalExtensionIndicator" + }, + { + "@id": "bts:SatelliteMetastasisPresentIndicator" + }, + { + "@id": "bts:OtherBiopsyResectionSite" + }, + { + "@id": "bts:ExtentofTumorResection" + }, + { + "@id": "bts:PriorSitesofRadiation" + }, + { + "@id": "bts:Immunosuppression" + }, + { + "@id": "bts:ConcomitantMedicationReceivedType" + }, + { + "@id": "bts:FamilyMemberVitalStatusIndicator" + }, + { + "@id": "bts:COVID19OccurrenceIndicator" + }, + { + "@id": "bts:COVID19CurrentStatus" + }, + { + "@id": "bts:COVID19PositiveLabTestIndicator" + }, + { + "@id": "bts:COVID19AntibodyTesting" + }, + { + "@id": "bts:COVID19ComplicationsSeverity" + }, + { + "@id": "bts:COVID19CancerTreatmentFollowup" + }, + { + "@id": "bts:Ecigvapeuse" + }, + { + "@id": "bts:Ecigvape30dayusenum" + }, + { + "@id": "bts:Ecigvapetimesperday" + }, + { + "@id": "bts:Typeofsmokeexposurecumulativeyears" + }, + { + "@id": "bts:Chewingtobaccodailyusecount" + }, + { + "@id": "bts:Secondhandsmokeexposureyears" + }, + { + "@id": "bts:KnownGeneticPredispositionMutation" + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome" + }, + { + "@id": "bts:CancerAssociatedGeneMutations" + }, + { + "@id": "bts:MutationalSignatures" + }, + { + "@id": "bts:MismatchRepairSystemStatus" + }, + { + "@id": "bts:LabTestsforMMRStatus" + }, + { + "@id": "bts:ModeofCancerDetection" + }, + { + "@id": "bts:EducationLevel" + }, + { + "@id": "bts:CountryofBirth" + }, + { + "@id": "bts:MedicallyUnderservedArea" + }, + { + "@id": "bts:RuralvsUrban" + }, + { + "@id": "bts:CancerIncidence" + }, + { + "@id": "bts:CancerIncidenceLocation" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ExSeq", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HI-C-seq", + "@id": "bts:TimepointLabel", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HI-C-seq", + "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label": "TimepointLabel", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq", - "sms:required": "sms:false", + "sms:displayName": "Timepoint Label", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RPPA", + "@id": "bts:StartDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RPPA", + "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label": "StartDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:Imaging", + "@id": "bts:StopDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Imaging", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging", + "sms:displayName": "Stop Days from Index", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:MassSpectrometry", + "@id": "bts:SentinelLymphNodeCount", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MassSpectrometry", + "rdfs:comment": "Numeric count of sentinel lymph nodes.", + "rdfs:label": "SentinelLymphNodeCount", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry", + "sms:displayName": "Sentinel Lymph Node Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics", + "@id": "bts:SentinelNodePositiveAssessmentCount", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomics", + "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", + "rdfs:label": "SentinelNodePositiveAssessmentCount", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics", + "sms:displayName": "Sentinel Node Positive Assessment Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OtherAssay", + "@id": "bts:TumorExtranodalExtensionIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", - "rdfs:label": "OtherAssay", + "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", + "rdfs:label": "TumorExtranodalExtensionIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - }, - { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Assay", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Absent" + }, { - "@id": "bts:Component" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Filename" + "@id": "bts:NO" }, { - "@id": "bts:FileFormat" + "@id": "bts:YES" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Nosourcedocumentation" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Notapplicable" }, { - "@id": "bts:AssayType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSImaging", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SRRSImaging", - "rdfs:subClassOf": [ + "@id": "bts:Notsampledordissected" + }, { - "@id": "bts:CDSDataType" + "@id": "bts:Present" }, { - "@id": "bts:DataType" + "@id": "bts:Present-extensive" + }, + { + "@id": "bts:Present-minimal" + }, + { + "@id": "bts:UNKNOWN" + }, + { + "@id": "bts:Unspecified" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Imaging", + "sms:displayName": "Tumor Extranodal Extension Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slide-seq", + "@id": "bts:SatelliteMetastasisPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Slide-seq", + "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", + "rdfs:label": "SatelliteMetastasisPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATAC-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScATAC-seq", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:CDSDataType" + "@id": "bts:Yes" }, { - "@id": "bts:DataType" + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATAC-seq", + "sms:displayName": "Satellite Metastasis Present Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScDNA-seq", + "@id": "bts:OtherBiopsyResectionSite", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScDNA-seq", + "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", + "rdfs:label": "OtherBiopsyResectionSite", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scDNA-seq", + "sms:displayName": "Other Biopsy Resection Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seq", + "@id": "bts:ExtentofTumorResection", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScRNA-seq", + "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", + "rdfs:label": "ExtentofTumorResection", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AccessoryManifest", - "@type": "rdfs:Class", - "rdfs:comment": "Accessory specific attributes", - "rdfs:label": "AccessoryManifest", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Accessory" + "@id": "bts:GrossTotalResection" }, { - "@id": "bts:CDSDataType" + "@id": "bts:OpenBiopsy" }, { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Accessory Manifest", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:SubtotalResection" + }, { - "@id": "bts:Component" + "@id": "bts:ExtensiveSubtotal" }, { - "@id": "bts:DatasetName" + "@id": "bts:Minor" }, { - "@id": "bts:AccessorySynapseID" + "@id": "bts:Optimaldebulking" }, { - "@id": "bts:AccessoryDescription" + "@id": "bts:Other" }, { - "@id": "bts:DataType" + "@id": "bts:Partialdebulking" }, { - "@id": "bts:HTANCenterID" + "@id": "bts:Segmental" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Suboptimal" }, { - "@id": "bts:Accessory-associatedHTANParentDataFileID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:OtherDataTypeSpecified", - "@type": "rdfs:Class", - "rdfs:comment": "Other types of data associated with the content.", - "rdfs:label": "OtherDataTypeSpecified", - "rdfs:subClassOf": [ + "@id": "bts:Suboptimaldebulking" + }, { - "@id": "bts:Publication" + "@id": "bts:NTR" }, { - "@id": "bts:CDSDataType" + "@id": "bts:Unknown" }, { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Data Type Specified", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] - }, - { - "@id": "bts:Publication", - "@type": "rdfs:Class", - "rdfs:comment": "An empty parent attribute for publications", - "rdfs:label": "Publication", - "rdfs:subClassOf": [ + "@id": "bts:NotReported" + }, { - "@id": "bts:Thing" + "@id": "bts:NotApplicable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Publication", + "sms:displayName": "Extent of Tumor Resection", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CDSSequencingPlatform", + "@id": "bts:PriorSitesofRadiation", "@type": "rdfs:Class", - "rdfs:comment": "The words used to describe the instrument used to carry out a high-throughput sequencing experiment.", - "rdfs:label": "CDSSequencingPlatform", + "rdfs:comment": "The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.", + "rdfs:label": "PriorSitesofRadiation", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -3575,2308 +3530,2063 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:IlluminaNextSeq500" + "@id": "bts:Abdomentotal" }, { - "@id": "bts:IlluminaNextSeq550" + "@id": "bts:AbdominalWall" }, { - "@id": "bts:IlluminaNextSeq2500" + "@id": "bts:Acetabulum" }, { - "@id": "bts:IlluminaNovaSeq6000" + "@id": "bts:Adenoid" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:Adipose" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:Adrenal" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:AlveolarRidge" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:AmnioticFluid" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:AnalSphincter" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:Ankle" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:Anorectum" }, { - "@id": "bts:IlluminaGenomeAnalyzerII" + "@id": "bts:AntecubitalFossa" }, { - "@id": "bts:IlluminaGenomeAnalyzerIIx" + "@id": "bts:Antrum" }, { - "@id": "bts:IlluminaHiSeq2000" + "@id": "bts:Anus" }, { - "@id": "bts:IlluminaHiSeq2500" + "@id": "bts:Aorta" }, { - "@id": "bts:IlluminaHiSeq4000" + "@id": "bts:AorticBody" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:Appendix" }, { - "@id": "bts:IonTorrentPGM" + "@id": "bts:AqueousFluid" }, { - "@id": "bts:IonTorrentProton" + "@id": "bts:Arm" }, { - "@id": "bts:IonTorrentS5" + "@id": "bts:Artery" }, { - "@id": "bts:PacBioRS" + "@id": "bts:AscendingColon" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:AscendingColonHepaticFlexure" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:Ascites" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:AuditoryCanal" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:AutonomicNervousSystem" }, { - "@id": "bts:GridION" + "@id": "bts:Axilla" }, { - "@id": "bts:PromethION" + "@id": "bts:Back" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:BileDuct" }, { - "@id": "bts:Revio" + "@id": "bts:Bladder" }, { - "@id": "bts:IlluminaNextSeq1000" + "@id": "bts:Blood" }, { - "@id": "bts:IlluminaNextSeq2000" + "@id": "bts:BloodVessel" }, { - "@id": "bts:Other" + "@id": "bts:Bodytotal" }, { - "@id": "bts:Unknown" + "@id": "bts:Bone" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "CDS Sequencing Platform", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:IlluminaNextSeq500", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "IlluminaNextSeq500", - "rdfs:subClassOf": [ + "@id": "bts:BoneMarrow" + }, { - "@id": "bts:CDSSequencingPlatform" + "@id": "bts:Bonenon-spine" }, { - "@id": "bts:SequencingPlatform" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - 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"@id": "bts:CDSLibrarySelectionMethod" - }, - { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "rRNA Depletion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Checksum", - "@type": "rdfs:Class", - "rdfs:comment": "MD5 checksum of the BAM file", - "rdfs:label": "Checksum", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:InformationContentEntity" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Checksum", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANDataFileID", - "@type": "rdfs:Class", - "rdfs:comment": "Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANDataFileID", - "rdfs:subClassOf": [ + "@id": "bts:Bachelor'sdegree" + }, { - "@id": "bts:File" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Data File ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] - }, - { - "@id": "bts:HTANBiospecimenID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANBiospecimenID", - "rdfs:subClassOf": [ + "@id": "bts:Doctoraldegreeorprofessionaldegree" + }, { - "@id": "bts:Biospecimen" + "@id": "bts:Gradeschool" + }, + { + "@id": "bts:Graduateorprofessionaldegree" + }, + { + "@id": "bts:Highschoolgraduate(includingequivalency)" + }, + { + "@id": "bts:Master'sdegree" + }, + { + "@id": "bts:Noformaleducation" + }, + { + "@id": "bts:Nothighschoolgraduate" + }, + { + "@id": "bts:Somecollegeorassociatedegree" + }, + { + "@id": "bts:Datanotavailable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Biospecimen ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:displayName": "Education Level", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:Biospecimen", + "@id": "bts:CountryofBirth", "@type": "rdfs:Class", - "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", - "rdfs:label": "Biospecimen", + "rdfs:comment": "Country where the patient was born.", + "rdfs:label": "CountryofBirth", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Afghanistan" }, { - "@id": "bts:HTANBiospecimenID" + "@id": "bts:Albania" }, { - "@id": "bts:SourceHTANBiospecimenID" + "@id": "bts:Algeria" }, { - "@id": "bts:HTANParentID" + "@id": "bts:Andorra" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Angola" }, { - "@id": "bts:CollectionDaysfromIndex" + "@id": "bts:Anguilla" }, { - "@id": "bts:AdjacentBiospecimenIDs" + "@id": "bts:AntiguaandBarbuda" }, { - "@id": "bts:BiospecimenType" + "@id": "bts:Argentina" }, { - "@id": "bts:AcquisitionMethodType" + "@id": "bts:Armenia" }, { - "@id": "bts:FixativeType" + "@id": "bts:Aruba" }, { - "@id": "bts:StorageMethod" + "@id": "bts:Australia" }, { - "@id": "bts:ProcessingDaysfromIndex" + "@id": "bts:Austria" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Azerbaijan" }, { - "@id": "bts:SiteDataSource" + "@id": "bts:Bahamas" }, { - "@id": "bts:CollectionMedia" + "@id": "bts:Bahrain" }, { - "@id": "bts:MountingMedium" + "@id": "bts:Bangladesh" }, { - "@id": "bts:ProcessingLocation" + "@id": "bts:Barbados" }, { - "@id": "bts:HistologyAssessmentBy" + "@id": "bts:Belarus" }, { - "@id": "bts:HistologyAssessmentMedium" + "@id": "bts:Belgium" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:Belize" }, { - "@id": "bts:TumorInfiltratingLymphocytes" + "@id": "bts:Benin" }, { - "@id": "bts:DegreeofDysplasia" + "@id": "bts:Bermuda" }, { - "@id": "bts:DysplasiaFraction" + "@id": "bts:Bhutan" }, { - "@id": "bts:NumberProliferatingCells" + "@id": "bts:Bolivia" }, { - "@id": "bts:PercentEosinophilInfiltration" + "@id": "bts:BosniaandHerzegovina" }, { - "@id": "bts:PercentGranulocyteInfiltration" + "@id": "bts:Botswana" }, { - "@id": "bts:PercentInflamInfiltration" + "@id": "bts:Brazil" }, { - "@id": "bts:PercentLymphocyteInfiltration" + "@id": "bts:Brunei" }, { - "@id": "bts:PercentMonocyteInfiltration" + "@id": "bts:Bulgaria" }, { - "@id": "bts:PercentNecrosis" + "@id": "bts:BurkinaFaso" }, { - "@id": "bts:PercentNeutrophilInfiltration" + "@id": "bts:Burundi" }, { - "@id": "bts:PercentNormalCells" + "@id": "bts:Cambodia" }, { - "@id": "bts:PercentStromalCells" + "@id": "bts:Cameroon" }, { - "@id": "bts:PercentTumorCells" + "@id": "bts:Canada" }, { - "@id": "bts:PercentTumorNuclei" + "@id": "bts:CapeVerde" }, { - "@id": "bts:FiducialMarker" + "@id": "bts:CaymanIslands" }, { - "@id": "bts:SlicingMethod" + "@id": "bts:CentralAfricanRepublic" }, { - "@id": "bts:LysisBuffer" + "@id": "bts:Chad" }, { - "@id": "bts:MethodofNucleicAcidIsolation" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", - "rdfs:label": "HTANParentID", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentBiospecimenID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", - "rdfs:label": "HTANParentBiospecimenID", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Biospecimen ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentDataFileID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", - "rdfs:label": "HTANParentDataFileID", - "rdfs:subClassOf": [ - { - "@id": "bts:File" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Data File ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Tier 2 Cancer Data", - "rdfs:label": "ClinicalDataTier2", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Chile" + }, { - "@id": "bts:Component" + "@id": "bts:China" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Colombia" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Comoros" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Congo" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:CookIslands" }, { - "@id": "bts:SentinelLymphNodeCount" + "@id": "bts:CostaRica" }, { - "@id": "bts:SentinelNodePositiveAssessmentCount" + "@id": "bts:Coted'Ivoire" }, { - "@id": "bts:TumorExtranodalExtensionIndicator" + "@id": "bts:Croatia" }, { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:OtherBiopsyResectionSite" - }, - { - "@id": "bts:ExtentofTumorResection" - }, - { - "@id": "bts:PriorSitesofRadiation" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:ConcomitantMedicationReceivedType" - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator" + "@id": "bts:Cuba" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:Curacao" }, { - "@id": "bts:COVID19CurrentStatus" + "@id": "bts:Cyprus" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:CzechRepublic(Czechia)" }, { - "@id": "bts:COVID19AntibodyTesting" + "@id": "bts:DemocraticRepublicoftheCongo" }, { - "@id": "bts:COVID19ComplicationsSeverity" + "@id": "bts:Denmark" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:Djibouti" }, { - "@id": "bts:Ecigvapeuse" + "@id": "bts:Dominica" }, { - "@id": "bts:Ecigvape30dayusenum" + "@id": "bts:DominicanRepublic" }, { - "@id": "bts:Ecigvapetimesperday" + "@id": "bts:Ecuador" }, { - "@id": "bts:Typeofsmokeexposurecumulativeyears" + "@id": "bts:Egypt" }, { - "@id": "bts:Chewingtobaccodailyusecount" + "@id": "bts:ElSalvador" }, { - "@id": "bts:Secondhandsmokeexposureyears" + "@id": "bts:EquatorialGuinea" }, { - "@id": "bts:KnownGeneticPredispositionMutation" + "@id": "bts:Eritrea" }, { - "@id": "bts:HereditaryCancerPredispositionSyndrome" + "@id": "bts:Estonia" }, { - "@id": "bts:CancerAssociatedGeneMutations" + "@id": "bts:Eswatini" }, { - "@id": "bts:MutationalSignatures" + "@id": "bts:Ethiopia" }, { - "@id": "bts:MismatchRepairSystemStatus" + "@id": "bts:FalklandIslands(Malvinas)" }, { - "@id": "bts:LabTestsforMMRStatus" + "@id": "bts:FaroeIslands" }, { - "@id": "bts:ModeofCancerDetection" + "@id": "bts:FederatedStatesofMicronesia" }, { - "@id": "bts:EducationLevel" + "@id": "bts:Fiji" }, { - "@id": "bts:CountryofBirth" + "@id": "bts:Finland" }, { - "@id": "bts:MedicallyUnderservedArea" + "@id": "bts:France" }, { - "@id": "bts:RuralvsUrban" + "@id": "bts:FrenchGuiana" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:FrenchPolynesia" }, { - "@id": "bts:CancerIncidenceLocation" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TimepointLabel", - "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StartDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", - "rdfs:label": "StartDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Start Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:StopDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", - "rdfs:label": "StopDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Stop Days from Index", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:SentinelLymphNodeCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric count of sentinel lymph nodes.", - "rdfs:label": "SentinelLymphNodeCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sentinel Lymph Node Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SentinelNodePositiveAssessmentCount", - "@type": "rdfs:Class", - "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", - "rdfs:label": "SentinelNodePositiveAssessmentCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sentinel Node Positive Assessment Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorExtranodalExtensionIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", - "rdfs:label": "TumorExtranodalExtensionIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" + "@id": "bts:Gabon" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Gambia" }, { - "@id": "bts:NO" + "@id": "bts:Georgia" }, { - "@id": "bts:YES" + "@id": "bts:Germany" }, { - "@id": "bts:Nosourcedocumentation" + "@id": "bts:Ghana" }, { - "@id": "bts:Notapplicable" + "@id": "bts:Gibraltar" }, { - "@id": "bts:Notsampledordissected" + "@id": "bts:Greece" }, { - "@id": "bts:Present" + "@id": "bts:Greenland" }, { - "@id": "bts:Present-extensive" + "@id": "bts:Grenada" }, { - "@id": "bts:Present-minimal" + "@id": "bts:Guadeloupe" }, { - "@id": "bts:UNKNOWN" + "@id": "bts:Guam" }, { - "@id": "bts:Unspecified" - } - ], - "sms:displayName": "Tumor Extranodal Extension Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", - "rdfs:label": "SatelliteMetastasisPresentIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:Guatemala" }, { - "@id": "bts:No" + "@id": "bts:Guernsey" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Satellite Metastasis Present Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherBiopsyResectionSite", - "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", - "rdfs:label": "OtherBiopsyResectionSite", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Biopsy Resection Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ExtentofTumorResection", - "@type": "rdfs:Class", - "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", - "rdfs:label": "ExtentofTumorResection", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:GrossTotalResection" + "@id": "bts:Guinea" }, { - "@id": "bts:OpenBiopsy" + "@id": "bts:Guinea-Bissau" }, { - "@id": "bts:SubtotalResection" + "@id": "bts:Guyana" }, { - "@id": "bts:ExtensiveSubtotal" + "@id": "bts:Haiti" }, { - "@id": "bts:Minor" + "@id": "bts:HolySee" }, { - "@id": "bts:Optimaldebulking" + "@id": "bts:Honduras" }, { - "@id": "bts:Other" + "@id": "bts:HongKong" }, { - "@id": "bts:Partialdebulking" + "@id": "bts:Hungary" }, { - "@id": "bts:Segmental" + "@id": "bts:Iceland" }, { - "@id": "bts:Suboptimal" + "@id": "bts:India" }, { - "@id": "bts:Suboptimaldebulking" + "@id": "bts:Indonesia" }, { - "@id": "bts:NTR" + "@id": "bts:Iran" }, { - "@id": "bts:Unknown" + "@id": "bts:Iraq" }, { - "@id": "bts:NotReported" + "@id": "bts:Ireland" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Extent of Tumor Resection", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PriorSitesofRadiation", - "@type": "rdfs:Class", - "rdfs:comment": "The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.", - "rdfs:label": "PriorSitesofRadiation", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Abdomentotal" + "@id": "bts:IsleofMan" }, { - "@id": "bts:AbdominalWall" + "@id": "bts:Israel" }, { - "@id": "bts:Acetabulum" + "@id": "bts:Italy" }, { - "@id": "bts:Adenoid" + "@id": "bts:Jamaica" }, { - "@id": "bts:Adipose" + "@id": "bts:Japan" }, { - "@id": "bts:Adrenal" + "@id": "bts:Jersey" }, { - "@id": "bts:AlveolarRidge" + "@id": "bts:Jordan" }, { - "@id": "bts:AmnioticFluid" + "@id": "bts:Kazakhstan" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:Kenya" }, { - "@id": "bts:AnalSphincter" + "@id": "bts:Kiribati" }, { - "@id": "bts:Ankle" + "@id": "bts:Kosovo" }, { - "@id": "bts:Anorectum" + "@id": "bts:Kuwait" }, { - "@id": "bts:AntecubitalFossa" + "@id": "bts:Kyrgyzstan" }, { - "@id": "bts:Antrum" + "@id": "bts:Laos" }, { - "@id": "bts:Anus" + "@id": "bts:Latvia" }, { - "@id": "bts:Aorta" + "@id": "bts:Lebanon" }, { - "@id": "bts:AorticBody" + "@id": "bts:Lesotho" }, { - "@id": "bts:Appendix" + "@id": "bts:Liberia" }, { - "@id": "bts:AqueousFluid" + "@id": "bts:Libya" }, { - "@id": "bts:Arm" + "@id": "bts:Liechtenstein" }, { - "@id": "bts:Artery" + "@id": "bts:Lithuania" }, { - "@id": "bts:AscendingColon" + "@id": "bts:Luxembourg" }, { - "@id": "bts:AscendingColonHepaticFlexure" + "@id": "bts:Macau" }, { - "@id": "bts:Ascites" + "@id": "bts:Madagascar" }, { - "@id": "bts:AuditoryCanal" + "@id": "bts:Malawi" }, { - "@id": "bts:AutonomicNervousSystem" + "@id": "bts:Malaysia" }, { - "@id": "bts:Axilla" + "@id": "bts:Maldives" }, { - "@id": "bts:Back" + "@id": "bts:Mali" }, { - "@id": "bts:BileDuct" + "@id": "bts:Malta" }, { - "@id": "bts:Bladder" + "@id": "bts:MarshallIslands" }, { - "@id": "bts:Blood" + "@id": "bts:Martinique" }, { - "@id": "bts:BloodVessel" + "@id": "bts:Mauritania" }, { - "@id": "bts:Bodytotal" + "@id": "bts:Mauritius" }, { - "@id": "bts:Bone" + "@id": "bts:Mayotte" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:Mexico" }, { - "@id": "bts:Bonenon-spine" + "@id": "bts:Moldova" }, { - "@id": "bts:Bowel" + "@id": "bts:Monaco" }, { - "@id": "bts:Brain" + "@id": "bts:Mongolia" }, { - "@id": "bts:BrainStem" + "@id": "bts:Montenegro" }, { - "@id": "bts:Breast" + "@id": "bts:Montserrat" }, { - "@id": "bts:BroadLigament" + "@id": "bts:Morocco" }, { - "@id": "bts:Bronchiole" + "@id": "bts:Mozambique" }, { - "@id": "bts:Bronchus" + "@id": "bts:Myanmar" }, { - "@id": "bts:Brow" + "@id": "bts:Namibia" }, { - "@id": "bts:BuccalCavity" + "@id": "bts:Nauru" }, { - "@id": "bts:BuccalMucosa" + "@id": "bts:Nepal" }, { - "@id": "bts:Buttock" + "@id": "bts:Netherlands" }, { - "@id": "bts:Calf" + "@id": "bts:NewCaledonia" }, { - "@id": "bts:Capillary" + "@id": "bts:NewZealand" }, { - "@id": "bts:Cardia" + "@id": "bts:Nicaragua" }, { - "@id": "bts:Carina" + "@id": "bts:Niger" }, { - "@id": "bts:CarotidArtery" + "@id": "bts:Nigeria" }, { - "@id": "bts:CarotidBody" + "@id": "bts:Niue" }, { - "@id": "bts:Cartilage" + "@id": "bts:NorthKorea" }, { - "@id": "bts:Cecum" + "@id": "bts:NorthMacedonia" }, { - "@id": "bts:Cell-Line" + "@id": "bts:NorthernMarianaIslands" }, { - "@id": "bts:CentralNervousSystem" + "@id": "bts:Norway" }, { - "@id": "bts:Cerebellum" + "@id": "bts:Oman" }, { - "@id": "bts:CerebralCortex" + "@id": "bts:Pakistan" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:Palau" }, { - "@id": "bts:Cerebrum" + "@id": "bts:Panama" }, { - "@id": "bts:CervicalSpine" + "@id": "bts:PapuaNewGuinea" }, { - "@id": "bts:Cervix" + "@id": "bts:Paraguay" }, { - "@id": "bts:Chest" + "@id": "bts:Peru" }, { - "@id": "bts:ChestWall" + "@id": "bts:Philippines" }, { - "@id": "bts:Chin" + "@id": "bts:Poland" }, { - "@id": "bts:Clavicle" + "@id": "bts:Portugal" }, { - "@id": "bts:Clitoris" + "@id": "bts:PuertoRico" }, { - "@id": "bts:Colon" + "@id": "bts:Qatar" }, { - "@id": "bts:ColonMucosaOnly" + "@id": "bts:Reunion" }, { - "@id": "bts:CommonDuct" + "@id": "bts:Romania" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:Russia" }, { - "@id": "bts:ConnectiveTissue" + "@id": "bts:Rwanda" }, { - "@id": "bts:Dermal" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:DescendingColon" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:Diaphragm" + "@id": "bts:SaintLucia" }, { - "@id": "bts:DistantSite" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:Duodenum" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:Ear" + "@id": "bts:Samoa" }, { - "@id": "bts:EarCanal" + "@id": "bts:SanMarino" }, { - "@id": "bts:EarPinna(External)" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:Elbow" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:EndocrineGland" + "@id": "bts:Senegal" }, { - "@id": "bts:Epididymis" + "@id": "bts:Serbia" }, { - "@id": "bts:EpiduralSpace" + "@id": "bts:Seychelles" }, { - "@id": "bts:Epitrochlear" + "@id": "bts:SierraLeone" }, { - "@id": "bts:EsophagogastricJunction" + "@id": "bts:Singapore" }, { - "@id": "bts:Esophagus" + "@id": "bts:Slovakia" }, { - "@id": "bts:EsophagusMucosaOnly" + "@id": "bts:Slovenia" }, { - "@id": "bts:Eye" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:FallopianTube" + "@id": "bts:Somalia" }, { - "@id": "bts:FemoralArtery" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:FemoralVein" + "@id": "bts:SouthKorea" }, { - "@id": "bts:Femur" + "@id": "bts:SouthSudan" }, { - "@id": "bts:Fibroblasts" + "@id": "bts:Spain" }, { - "@id": "bts:Fibula" + "@id": "bts:SriLanka" }, { - "@id": "bts:Finger" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:FloorofMouth" + "@id": "bts:Sudan" }, { - "@id": "bts:Fluid" + "@id": "bts:Suriname" }, { - "@id": "bts:Foot" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:Forearm" + "@id": "bts:Sweden" }, { - "@id": "bts:Forehead" + "@id": "bts:Switzerland" }, { - "@id": "bts:Foreskin" + "@id": "bts:Syria" }, { - "@id": "bts:FrontalCortex" + "@id": "bts:Taiwan" }, { - "@id": "bts:FrontalLobe" + "@id": "bts:Tajikistan" }, { - "@id": "bts:FundusofStomach" + "@id": "bts:Tanzania" }, { - "@id": "bts:Gallbladder" + "@id": "bts:Thailand" }, { - "@id": "bts:Ganglia" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:GastroesophagealJunction" + "@id": "bts:Togo" }, { - "@id": "bts:GastrointestinalTract" + "@id": "bts:Tokelau" }, { - "@id": "bts:GastrointestinalIntestine" + "@id": "bts:Tonga" }, { - "@id": "bts:GenitourinaryNOS" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:Groin" + "@id": "bts:Tunisia" }, { - "@id": "bts:Gum" + "@id": "bts:Turkey" }, { - "@id": "bts:Hand" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:HardPalate" + "@id": "bts:Tuvalu" }, { - "@id": "bts:HeadFaceOrNeckNos" + "@id": "bts:Uganda" }, { - "@id": "bts:HeadandNeck" + "@id": "bts:Ukraine" }, { - "@id": "bts:Heart" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:Hepatic" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:HepaticDuct" + "@id": "bts:UnitedStates" }, { - "@id": "bts:HepaticVein" + "@id": "bts:Uruguay" }, { - "@id": "bts:Hilar" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:Hip" + "@id": "bts:Vanuatu" }, { - "@id": "bts:Hippocampus" + "@id": "bts:Venezuela" }, { - "@id": "bts:Humerus" + "@id": "bts:Vietnam" }, { - "@id": "bts:Hypopharynx" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:IleocecalValve" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:Ileum" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:Ilium" + "@id": "bts:WesternSahara" }, { - "@id": "bts:IndexFinger" + "@id": "bts:Yemen" }, { - "@id": "bts:Ischium" + "@id": "bts:Zambia" }, { - "@id": "bts:IsletCells" + "@id": "bts:Zimbabwe" }, { - "@id": "bts:Jaw" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Country of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea", + "@type": "rdfs:Class", + "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", + "rdfs:label": "MedicallyUnderservedArea", + "rdfs:subClassOf": [ { - "@id": "bts:Jejunum" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Joint" + "@id": "bts:MedicallyUnderservedArea-Yes" }, { - "@id": "bts:Kidney" + "@id": "bts:MedicallyUnderservedArea-No" }, { - "@id": "bts:Knee" - }, + "@id": "bts:MedicallyUnderservedArea-Unknown" + } + ], + "sms:displayName": "Medically Underserved Area", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RuralvsUrban", + "@type": "rdfs:Class", + "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", + "rdfs:label": "RuralvsUrban", + "rdfs:subClassOf": [ { - "@id": "bts:LacrimalGland" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LargeBowel" + "@id": "bts:UrbanPopulation(population>50000)" }, { - "@id": "bts:Laryngopharynx" + "@id": "bts:UrbanCluster(population2500-50000)" }, { - "@id": "bts:Larynx" - }, + "@id": "bts:RuralPopulation(population<2500)" + } + ], + "sms:displayName": "Rural vs Urban", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidence", + "@type": "rdfs:Class", + "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", + "rdfs:label": "CancerIncidence", + "rdfs:subClassOf": [ { - "@id": "bts:Leg" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidenceLocation", + "@type": "rdfs:Class", + "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", + "rdfs:label": "CancerIncidenceLocation", + "rdfs:subClassOf": [ { - "@id": "bts:Leptomeninges" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Cancer related clinical data specific to SRRS", + "rdfs:label": "SRRSClinicalDataTier2", + "rdfs:subClassOf": [ { - "@id": "bts:Ligament" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Lip" + "@id": "bts:Component" }, { - "@id": "bts:Liver" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:LumbarSpine" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Lung" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:LymphNode" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:LymphNode(s)Axilla" + "@id": "bts:EducationLevel" }, { - "@id": "bts:LymphNode(s)Cervical" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:LymphNode(s)Distant" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:LymphNode(s)Epitrochlear" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:LymphNode(s)Femoral" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:LymphNode(s)Hilar" + "@id": "bts:CancerIncidenceLocation" }, { - "@id": "bts:LymphNode(s)Iliac-Common" + "@id": "bts:Ethnicity" }, { - "@id": "bts:LymphNode(s)Iliac-External" + "@id": "bts:Gender" }, { - "@id": "bts:LymphNode(s)Inguinal" + "@id": "bts:Race" }, { - "@id": "bts:LymphNode(s)InternalMammary" + "@id": "bts:VitalStatus" }, { - "@id": "bts:LymphNode(s)Mammary" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:LymphNode(s)Mediastinal" + "@id": "bts:DaystoLastFollowup" }, { - "@id": "bts:LymphNode(s)Mesenteric" + "@id": "bts:DaystoLastKnownDiseaseStatus" }, { - "@id": "bts:LymphNode(s)Occipital" + "@id": "bts:DaystoRecurrence" }, { - "@id": "bts:LymphNode(s)Paraaortic" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:LymphNode(s)Parotid" + "@id": "bts:Morphology" }, { - "@id": "bts:LymphNode(s)Pelvic" + "@id": "bts:PrimaryDiagnosis" }, { - "@id": "bts:LymphNode(s)Popliteal" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:LymphNode(s)Regional" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:LymphNode(s)Retroperitoneal" + "@id": "bts:TissueorOrganofOrigin" }, { - "@id": "bts:LymphNode(s)Scalene" + "@id": "bts:NCIAtlasCancerSite" }, { - "@id": "bts:LymphNode(s)Splenic" + "@id": "bts:TumorGrade" }, { - "@id": "bts:LymphNode(s)Subclavicular" + "@id": "bts:PackYearsSmoked" }, { - "@id": "bts:LymphNode(s)Submandibular" + "@id": "bts:YearsSmoked" }, { - "@id": "bts:LymphNode(s)Supraclavicular" + "@id": "bts:DaystoFollowUp" }, { - "@id": "bts:Mandible" + "@id": "bts:GeneSymbol" }, { - "@id": "bts:Mantle" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Maxilla" + "@id": "bts:TestResult" }, { - "@id": "bts:MediastinalSoftTissue" + "@id": "bts:TreatmentType" }, { - "@id": "bts:Mediastinum" - }, + "@id": "bts:TumorLargestDimensionDiameter" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Ethnicity", + "@type": "rdfs:Class", + "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "rdfs:label": "Ethnicity", + "rdfs:subClassOf": [ { - "@id": "bts:Mesentery" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Mesothelium" + "@id": "bts:Hispanicorlatino" }, { - "@id": "bts:MiddleFinger" + "@id": "bts:Nothispanicorlatino" }, { - "@id": "bts:Mitochondria" + "@id": "bts:Unknown" }, { - "@id": "bts:Muscle" + "@id": "bts:NotReported" }, { - "@id": "bts:Nails" - }, + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Ethnicity", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Gender", + "@type": "rdfs:Class", + "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "rdfs:label": "Gender", + "rdfs:subClassOf": [ { - "@id": "bts:NasalCavity" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NasalSoftTissue" + "@id": "bts:Female" }, { - "@id": "bts:Nasopharynx" + "@id": "bts:Male" }, { - "@id": "bts:Neck" + "@id": "bts:Unknown" }, { - "@id": "bts:Nerve" + "@id": "bts:Unspecified" }, { - "@id": "bts:Nerve(s)Cranial" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Gender", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Race", + "@type": "rdfs:Class", + "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "rdfs:label": "Race", + "rdfs:subClassOf": [ { - "@id": "bts:OccipitalCortex" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:OcularOrbits" + "@id": "bts:White" }, { - "@id": "bts:Omentum" + "@id": "bts:Americanindianoralaskanative" }, { - "@id": "bts:OralCavity" + "@id": "bts:Blackorafricanamerican" }, { - "@id": "bts:OralCavityMucosaOnly" + "@id": "bts:Asian" }, { - "@id": "bts:Oropharynx" + "@id": "bts:Nativehawaiianorotherpacificislander" }, { "@id": "bts:Other" }, { - "@id": "bts:Ovary" - }, - { - "@id": "bts:Palate" - }, - { - "@id": "bts:Pancreas" - }, - { - "@id": "bts:Parametrium" + "@id": "bts:Unknown" }, { - "@id": "bts:ParaspinalGanglion" + "@id": "bts:NotReported" }, { - "@id": "bts:Parathyroid" - }, + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Race", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:VitalStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", + "rdfs:subClassOf": [ { - "@id": "bts:ParotidGland" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Patella" + "@id": "bts:Alive" }, { - "@id": "bts:Pelvis" + "@id": "bts:Dead" }, { - "@id": "bts:Penis" + "@id": "bts:Unknown" }, { - "@id": "bts:Pericardium" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Vital Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label": "AgeatDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:PeriorbitalSoftTissue" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Age at Diagnosis", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoLastFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastFollowup", + "rdfs:subClassOf": [ { - "@id": "bts:PeritonealCavity" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Follow up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Peritoneum" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoRecurrence", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoRecurrence", + "rdfs:subClassOf": [ { - "@id": "bts:Pharynx" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:LastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", + "rdfs:label": "LastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Pineal" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:PinealGland" + "@id": "bts:Distantmetrecurrence/progression" }, { - "@id": "bts:PituitaryGland" + "@id": "bts:Loco-regionalrecurrence/progression" }, { - "@id": "bts:Placenta" + "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" }, { - "@id": "bts:Pleura" + "@id": "bts:Tumorfree" }, { - "@id": "bts:PoplitealFossa" + "@id": "bts:Unknowntumorstatus" }, { - "@id": "bts:Pouch" + "@id": "bts:Withtumor" }, { - "@id": "bts:PrimaryTumorField" + "@id": "bts:NotReported" }, { - "@id": "bts:Primarytumorsite" + "@id": "bts:NotAllowedToCollect" }, { - "@id": "bts:Prostate" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Morphology", + "@type": "rdfs:Class", + "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", + "rdfs:label": "Morphology", + "rdfs:subClassOf": [ { - "@id": "bts:ProstateBed" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Morphology", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "PrimaryDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:ProstateSeminalVesiclesandLymphNodes" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Pylorus" + "@id": "bts:Acinarcellcarcinoma" }, { - "@id": "bts:RectosigmoidJunction" + "@id": "bts:Acutebasophilicleukaemia" }, { - "@id": "bts:Rectum" + "@id": "bts:AcuteleukemiaBurkitttype" }, { - "@id": "bts:RegionalSite" + "@id": "bts:AcuteleukemiaNOS" }, { - "@id": "bts:Retina" + "@id": "bts:Acutelymphaticleukemia" }, { - "@id": "bts:Retro-OrbitalRegion" + "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" }, { - "@id": "bts:Retroperitoneum" + "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" }, { - "@id": "bts:Rib" + "@id": "bts:AcutelymphoblasticleukemiaNOS" }, { - "@id": "bts:RingFinger" + "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" }, { - "@id": "bts:RoundLigament" + "@id": "bts:Acutelymphocyticleukemia" }, { - "@id": "bts:Sacrum" + "@id": "bts:Acutelymphoidleukemia" }, { - "@id": "bts:SalivaryGland" + "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" }, { - "@id": "bts:Scalp" + "@id": "bts:AcutemyeloidleukemiaMLL" }, { - "@id": "bts:Scapula" + "@id": "bts:AcutemyeloidleukemiaNOS" }, { - "@id": "bts:SciaticNerve" + "@id": "bts:Acutemyelomonocyticleukemia" }, { - "@id": "bts:Scrotum" + "@id": "bts:AcutepromyelocyticleukemiaNOS" }, { - "@id": "bts:SeminalVesicle" + "@id": "bts:Adenocarcinoidtumor" }, { - "@id": "bts:Shoulder" + "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" }, { - "@id": "bts:SigmoidColon" + "@id": "bts:AdenocarcinomainapolypNOS" }, { - "@id": "bts:Sinus" + "@id": "bts:Adenocarcinomainadenomatouspolyp" }, { - "@id": "bts:Sinus(es)Maxillary" + "@id": "bts:Adenocarcinomainpolypoidadenoma" }, { - "@id": "bts:SkeletalMuscle" + "@id": "bts:AdenocarcinomainsituinapolypNOS" }, { - "@id": "bts:Skin" + "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" }, { - "@id": "bts:Skinlowerextremitylocal" + "@id": "bts:Adenocarcinomainsituintubularadenoma" }, { - "@id": "bts:Skintotal" + "@id": "bts:Adenocarcinomainsitumucinous" }, { - "@id": "bts:Skintrunklocal" + "@id": "bts:Adenocarcinomainsitunon-mucinous" }, { - "@id": "bts:Skinupperextremitylocal" + "@id": "bts:AdenocarcinomainsituNOS" }, { - "@id": "bts:Skull" + "@id": "bts:Adenocarcinomaintubularadenoma" }, { - "@id": "bts:SmallBowel" + "@id": "bts:Adenocarcinomainvillousadenoma" }, { - "@id": "bts:SmallBowelMucosaOnly" + "@id": "bts:Adenocarcinomaofanalducts" }, { - "@id": "bts:SmallFinger" + "@id": "bts:Adenocarcinomaofanalglands" }, { - "@id": "bts:SoftTissue" + "@id": "bts:Adenocarcinomadiffusetype" }, { - "@id": "bts:SpinalColumn" + "@id": "bts:Adenocarcinomaendocervicaltype" }, { - "@id": "bts:SpinalCord" + "@id": "bts:Adenocarcinomaintestinaltype" }, { - "@id": "bts:Spine" + "@id": "bts:AdenocarcinomametastaticNOS" }, { - "@id": "bts:Spleen" + "@id": "bts:AdenocarcinomaNOS" }, { - "@id": "bts:SplenicFlexure" + "@id": "bts:Adenocarcinomapancreatobiliarytype" }, { - "@id": "bts:Sternum" + "@id": "bts:Adultrhabdomyoma" }, { - "@id": "bts:Stomach" + "@id": "bts:AdultT-celllymphoma" }, { - "@id": "bts:StomachMucosaOnly" + "@id": "bts:AdultT-celllymphoma/leukemia" }, { - "@id": "bts:SubcutaneousTissue" + "@id": "bts:Astrocytomaanaplastic" }, { - "@id": "bts:Synovium" + "@id": "bts:Astrocytomalowgrade" }, { - "@id": "bts:TemporalCortex" + "@id": "bts:AstrocytomaNOS" }, { - "@id": "bts:Tendon" + "@id": "bts:BcelllymphomaNOS" }, { - "@id": "bts:Testis" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" }, { - "@id": "bts:Thigh" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" }, { - "@id": "bts:ThoracicSpine" + "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" }, { - "@id": "bts:Thorax" + "@id": "bts:B-ALL" }, { - "@id": "bts:Throat" + "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" }, { - "@id": "bts:Thumb" + "@id": "bts:Basalcelladenocarcinoma" }, { - "@id": "bts:Thymus" + "@id": "bts:Basalcelladenoma" }, { - "@id": "bts:Thyroid" + "@id": "bts:BasalcellcarcinomaNOS" }, { - "@id": "bts:Tibia" + "@id": "bts:Basalcellepithelioma" }, { - "@id": "bts:Tongue" + "@id": "bts:Basalcelltumor" }, { - "@id": "bts:Tonsil" + "@id": "bts:Basophiladenocarcinoma" }, { - "@id": "bts:Tonsil(Pharyngeal)" + "@id": "bts:Basophiladenoma" }, { - "@id": "bts:Trachea/MajorBronchi" + "@id": "bts:Basophilcarcinoma" }, { - "@id": "bts:TransverseColon" + "@id": "bts:Bileductadenocarcinoma" }, { - "@id": "bts:Trunk" + "@id": "bts:Bileductadenoma" }, { - "@id": "bts:UmbilicalCord" + "@id": "bts:Bileductcarcinoma" }, { - "@id": "bts:Unknown" + "@id": "bts:Bileductcystadenocarcinoma" }, { - "@id": "bts:Ureter" + "@id": "bts:Bileductcystadenoma" }, { - "@id": "bts:Urethra" + "@id": "bts:Bronchialadenomacarcinoid" }, { - "@id": "bts:UrinaryTract" + "@id": "bts:Bronchialadenomacylindroid" }, { - "@id": "bts:Uterus" + "@id": "bts:BronchialadenomaNOS" }, { - "@id": "bts:Uvula" + "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:Vagina" + "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" }, { - "@id": "bts:VasDeferens" + "@id": "bts:Bronchio-alveolarcarcinomamucinous" }, { - "@id": "bts:Vein" + "@id": "bts:Bronchiolaradenocarcinoma" }, { - "@id": "bts:Venous" + "@id": "bts:Bronchiolarcarcinoma" }, { - "@id": "bts:Vertebra" + "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" }, { - "@id": "bts:Vulva" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" }, { - "@id": "bts:WhiteBloodCells" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" }, { - "@id": "bts:Wrist" + "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Prior Sites of Radiation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Immunosuppression", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not immunosuppressive therapy was administered.", - "rdfs:label": "Immunosuppression", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + }, { - "@id": "bts:Yes" + "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" }, { - "@id": "bts:No" + "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Burkittcellleukemia" }, { - "@id": "bts:NotApplicable" + "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "Immunosuppression", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ConcomitantMedicationReceivedType", - "@type": "rdfs:Class", - "rdfs:comment": "An enumerated list of the type of concomitant medication received by the patient.", - "rdfs:label": "ConcomitantMedicationReceivedType", - "rdfs:subClassOf": [ + "@id": "bts:Burkitttumor" + }, { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Burkitt-likelymphoma" + }, { - "@id": "bts:Anticoagulantagents" + "@id": "bts:C-ALL" }, { - "@id": "bts:Anticonvulsant" + "@id": "bts:Cancer" }, { - "@id": "bts:Antifungal" + "@id": "bts:Capillaryhemangioma" }, { - "@id": "bts:Antiplateletagents" + "@id": "bts:Capillarylymphangioma" }, { - "@id": "bts:Antidepressants-ModerateCYP2D6inhibitors" + "@id": "bts:CarcinomainapolypNOS" }, { - "@id": "bts:Antidepressants-StrongCYP2D6inhibitors" + "@id": "bts:Carcinomainadenomatouspolyp" }, { - "@id": "bts:Antidepressants-weakCYP2D2inhibitorsornon-inhibitors" + "@id": "bts:Carcinomainpleomorphicadenoma" }, { - "@id": "bts:Anxiolyticsorsedatives" + "@id": "bts:CarcinomainsituinapolypNOS" }, { - "@id": "bts:Aspirin" + "@id": "bts:Carcinomainsituinadenomatouspolyp" }, { - "@id": "bts:Bisphosphonatesfortreatment/preventionofboneloss" + "@id": "bts:CarcinomainsituNOS" }, { - "@id": "bts:Corticosteroid" + "@id": "bts:CarcinomaanaplasticNOS" }, { - "@id": "bts:COX-2inhibitor" + "@id": "bts:Carcinomadiffusetype" }, { - "@id": "bts:Decadron" + "@id": "bts:Carcinomaintestinaltype" }, { - "@id": "bts:Diabetes-Insulin" + "@id": "bts:CarcinomametastaticNOS" }, { - "@id": "bts:Diabetes-Metformincontainingagents" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:Growthfactor" + "@id": "bts:CarcinosarcomaNOS" }, { - "@id": "bts:Intravaginalestrogenpreparations" + "@id": "bts:CarcinomaundifferentiatedNOS" }, { - "@id": "bts:Lipid-loweringdrugs" + "@id": "bts:CementomaNOS" }, { - "@id": "bts:Non-prescriptionsupplementsformemory" + "@id": "bts:Centralneuroblastoma" }, { - "@id": "bts:Non-prescriptionsupplementsforreliefofhotflashes" + "@id": "bts:Centralneurocytoma" }, { - "@id": "bts:Non-steroidalanti-inflammatoryagents" + "@id": "bts:Cerebellarliponeurocytoma" }, { - "@id": "bts:Opioids" + "@id": "bts:CerebellarsarcomaNOS" }, { - "@id": "bts:Other" + "@id": "bts:CervicalintraepithelialneoplasiagradeIII" }, { - "@id": "bts:Prescriptionmedicationsformemory" + "@id": "bts:Cervicalintraepithelialneoplasialowgrade" }, { - "@id": "bts:Prescriptionmedicationsforreliefofhotflashes" + "@id": "bts:ChondromaNOS" }, { - "@id": "bts:Prophylacticantiplatelettherapy" + "@id": "bts:Chondrosarcomagrade2/3" }, { - "@id": "bts:Tricyclicantidepressants" + "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" }, { - "@id": "bts:NotApplicable" + "@id": "bts:ChronicgranulocyticleukemiaNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Concomitant Medication Received Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", - "rdfs:label": "FamilyMemberVitalStatusIndicator", - "rdfs:subClassOf": [ + "@id": "bts:ChronicleukemiaNOS" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Chroniclymphaticleukemia" + }, { - "@id": "bts:VitalStatusAlive" + "@id": "bts:Chroniclymphocyticleukemia" }, { - "@id": "bts:VitalStatusDead" + "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" }, { - "@id": "bts:Unknown" + "@id": "bts:Chroniclymphoidleukemia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Family Member Vital Status Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19OccurrenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", - "rdfs:label": "COVID19OccurrenceIndicator", - "rdfs:subClassOf": [ + "@id": "bts:Chronicmonocyticleukemia" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ChronicmyelocyticleukemiaNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" }, { - "@id": "bts:No" + "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id": "bts:Unknown" + "@id": "bts:ChronicmyeloidleukemiaNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Occurrence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CurrentStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", - "rdfs:label": "COVID19CurrentStatus", - "rdfs:subClassOf": [ + "@id": "bts:ChronicmyelomonocyticleukemiaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ChronicmyelomonocyticleukemiaType1" + }, { - "@id": "bts:Patientcurrentlyhassymptoms" + "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" }, { - "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" + "@id": "bts:ChronicmyeloproliferativediseaseNOS" }, { - "@id": "bts:PatientneverhadanysymptomsofCOVID-19" + "@id": "bts:Chronicmyeloproliferativedisorder" }, { - "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" + "@id": "bts:Chronicneutrophilicleukemia" }, { - "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" }, { - "@id": "bts:Statusunknownduetootherreasons" - } - ], - "sms:displayName": "COVID19 Current Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", - "rdfs:label": "COVID19PositiveLabTestIndicator", - "rdfs:subClassOf": [ + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + }, { - "@id": "bts:Yes" + "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" }, { - "@id": "bts:No" + "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" }, { - "@id": "bts:NotApplicable" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Positive Lab Test Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19AntibodyTesting", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", - "rdfs:label": "COVID19AntibodyTesting", - "rdfs:subClassOf": [ + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + }, { - "@id": "bts:SARS-CoV-2IgMantibodypositive" + "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" }, { - "@id": "bts:SARS-CoV-2IgGantibodypositive" + "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" }, { - "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" + "@id": "bts:Combinedsmallcellcarcinoma" }, { - "@id": "bts:SARS-CoV-2IgMantibodynegative" + "@id": "bts:Combinedsmallcell-adenocarcinoma" }, { - "@id": "bts:SARS-CoV-2IgGantibodynegative" + "@id": "bts:Combinedsmallcell-largecarcinoma" }, { - "@id": "bts:SARS-CoV-2IgG/IgMantibodynegative" + "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" }, { - "@id": "bts:Unknown" + "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Antibody Testing", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19ComplicationsSeverity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.", - "rdfs:label": "COVID19ComplicationsSeverity", - "rdfs:subClassOf": [ + "@id": "bts:Dermalnevus" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DermatofibromaNOS" + }, { - "@id": "bts:Cardiaccomplications" + "@id": "bts:DiffuseastrocytomaIDH-mutant" }, { - "@id": "bts:Pulmonarycomplications" + "@id": "bts:DiffuseastrocytomaIDH-wildtype" }, { - "@id": "bts:Systemiccomplications" + "@id": "bts:Diffuseastrocytomalowgrade" }, { - "@id": "bts:Other" + "@id": "bts:DiffuselargeB-celllymphomaNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Diffusemelanocytosis" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "COVID19 Complications Severity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder", - "rdfs:label": "COVID19CancerTreatmentFollowup", - "rdfs:subClassOf": [ + "@id": "bts:DuctadenocarcinomaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DuctadenomaNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:Ductcarcinomadesmoplastictype" }, { - "@id": "bts:No" + "@id": "bts:DuctcarcinomaNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Ductcellcarcinoma" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "COVID19 Cancer Treatment Followup", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapeuse", - "@type": "rdfs:Class", - "rdfs:comment": "Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)", - "rdfs:label": "Ecigvapeuse", - "rdfs:subClassOf": [ + "@id": "bts:DuctalcarcinomainsituNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DuctalcarcinomaNOS" + }, { - "@id": "bts:Current" + "@id": "bts:Dysplasticnevus" }, { - "@id": "bts:Former" + "@id": "bts:EndometrialsarcomaNOS" }, { - "@id": "bts:Never" + "@id": "bts:EndometrioidadenocarcinomaNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ecig vape use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvape30dayusenum", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days e-cigarettes or vaping device was used in the last 30 days", - "rdfs:label": "Ecigvape30dayusenum", - "rdfs:subClassOf": [ + "@id": "bts:EndometrioidadenofibromaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape 30 day use num", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapetimesperday", - "@type": "rdfs:Class", - "rdfs:comment": "e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)", - "rdfs:label": "Ecigvapetimesperday", - "rdfs:subClassOf": [ + "@id": "bts:EndometrioidadenomaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape times per day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", - "rdfs:label": "Typeofsmokeexposurecumulativeyears", - "rdfs:subClassOf": [ + "@id": "bts:EndometrioidcarcinomaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Type of smoke exposure cumulative years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chewingtobaccodailyusecount", - "@type": "rdfs:Class", - "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", - "rdfs:label": "Chewingtobaccodailyusecount", - "rdfs:subClassOf": [ + "@id": "bts:Eosinophiladenocarcinoma" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Chewing tobacco daily use count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Secondhandsmokeexposureyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's exposure to second-hand cigarette smoke", - "rdfs:label": "Secondhandsmokeexposureyears", - "rdfs:subClassOf": [ + "@id": "bts:Eosinophiladenoma" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second hand smoke exposure years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KnownGeneticPredispositionMutation", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", - "rdfs:label": "KnownGeneticPredispositionMutation", - "rdfs:subClassOf": [ + "@id": "bts:Eosinophilcarcinoma" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Eosinophilicgranuloma" + }, { - "@id": "bts:Yes" + "@id": "bts:Eosinophilicleukemia" }, { - "@id": "bts:No" + "@id": "bts:EpendymomaNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Known Genetic Predisposition Mutation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HereditaryCancerPredispositionSyndrome", - "@type": "rdfs:Class", - "rdfs:comment": "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", - "rdfs:label": "HereditaryCancerPredispositionSyndrome", - "rdfs:subClassOf": [ + "@id": "bts:EpidermoidcarcinomainsituNOS" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:EpidermoidcarcinomaNOS" + }, { - "@id": "bts:Alpha-1antitrypsin" + "@id": "bts:Epithelialtumorbenign" }, { - "@id": "bts:Attenuatedfamilialadenomatouspolyposis" + "@id": "bts:Epithelialtumormalignant" }, { - "@id": "bts:BAP1mutantdisease" + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" }, { - "@id": "bts:Biliarydisorder" + "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" }, { - "@id": "bts:Birt-Hogg-Dubesyndrome" + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" }, { - "@id": "bts:Carneycomplex" + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" }, { - "@id": "bts:Cirrhosisunknownetiology" + "@id": "bts:Ewingsarcoma" }, { - "@id": "bts:Constitutionalmismatchrepairdeficiency" + "@id": "bts:GangliogliomaNOS" }, { "@id": "bts:Familialadenomatouspolyposis" }, { - "@id": "bts:Familialgastrointestinalstromaltumor" + "@id": "bts:Gastrincelltumor" }, { - "@id": "bts:Familialpancreaticcancer" + "@id": "bts:Gastrincelltumormalignant" }, { - "@id": "bts:Familialprostatecancer" + "@id": "bts:Gastrinomamalignant" }, { - "@id": "bts:Familialrenalcancer" + "@id": "bts:GastrinomaNOS" }, { - "@id": "bts:Fanconianemia" + "@id": "bts:Gastrointestinalstromaltumormalignant" }, { - "@id": "bts:GlycogenStorageDisease" + "@id": "bts:Glioblastoma" }, { - "@id": "bts:Gorlinsyndrome" + "@id": "bts:Gliomamalignant" }, { - "@id": "bts:Hereditarybreast–ovariancancersyndrome" + "@id": "bts:GliomaNOS" }, { - "@id": "bts:Hereditarydiffusegastriccancer" + "@id": "bts:Haemangioblastoma" }, { - "@id": "bts:Hereditaryleiomyoma-renalcellcarcinoma" + "@id": "bts:Haemangiosarcoma" }, { - "@id": "bts:Hereditarymelanoma" + "@id": "bts:Hepatocarcinoma" }, { - "@id": "bts:Hereditarymixedpolyposissyndrome" + "@id": "bts:Hepatocellularadenoma" }, { - "@id": "bts:HereditarypapillaryRCC" + "@id": "bts:HepatocellularcarcinomaNOS" }, { - "@id": "bts:Hereditarypapillaryrenalcellcarcinoma" + "@id": "bts:Hepatocholangiocarcinoma" }, { - "@id": "bts:Hereditaryparaganglioma–pheochromocytomasyndrome" + "@id": "bts:Hepatoidadenocarcinoma" }, { - "@id": "bts:Hereditaryrenaloncocytoma" + "@id": "bts:Hepatoidcarcinoma" }, { - "@id": "bts:Hereditaryretinoblastoma" + "@id": "bts:HodgkindiseaseNOS" }, { - "@id": "bts:Juvenilepolyposissyndrome" + "@id": "bts:Hodgkingranuloma" }, { - "@id": "bts:Li-Fraumenisyndrome" + "@id": "bts:HodgkinlymphomamixedcellularityNOS" }, { - "@id": "bts:Lynchsyndrome" + "@id": "bts:HodgkinlymphomanodularsclerosisNOS" }, { - "@id": "bts:Melanoma–astrocytomasyndrome" + "@id": "bts:HodgkinlymphomaNOS" }, { - "@id": "bts:MultipleendocrineneoplasiatypeI" + "@id": "bts:HodgkinparagranulomaNOS" }, { - "@id": "bts:MultipleendocrineneoplasiatypeII" + "@id": "bts:Hodgkinsarcoma" }, { - "@id": "bts:MUTYH-associatedpolyposis" + "@id": "bts:InfiltratingbasalcellcarcinomaNOS" }, { - "@id": "bts:Nevoidbasalcellcarcinomasyndrome" + "@id": "bts:InfiltratingductcarcinomaNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Infiltratingductandcolloidcarcinoma" }, { - "@id": "bts:NotReported" + "@id": "bts:Infiltratingductandcribriformcarcinoma" }, { - "@id": "bts:Peutz–Jegherssyndrome" + "@id": "bts:Inflammatoryadenocarcinoma" }, { - "@id": "bts:Cowdensyndrome" + "@id": "bts:Inflammatorycarcinoma" }, { - "@id": "bts:RhabdoidtumorpredispositionsyndrometypeI" + "@id": "bts:Interstitialcelltumorbenign" }, { - "@id": "bts:RhabdoidtumorpredispositionsyndrometypeII" + "@id": "bts:Interstitialcelltumormalignant" }, { - "@id": "bts:Rubinstein-Taybisyndrome" + "@id": "bts:InterstitialcelltumorNOS" }, { - "@id": "bts:SDHassociatedrenalcancer" + "@id": "bts:Intracysticpapilloma" }, { - "@id": "bts:Serratedpolyposissyndrome" + "@id": "bts:Intradermalnevus" }, { - "@id": "bts:Tuberoussclerosiscomplex" + "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" }, { - "@id": "bts:Turcotsyndrome" + "@id": "bts:Intraductalandlobularcarcinoma" }, { - "@id": "bts:Tyrosinemia" + "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" }, { - "@id": "bts:Unknown" + "@id": "bts:Intraductalcarcinomaclinging" }, { - "@id": "bts:VonHippel-LindauSyndrome" - } - ], - "sms:displayName": "Hereditary Cancer Predisposition Syndrome", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerAssociatedGeneMutations", - "@type": "rdfs:Class", - "rdfs:comment": "Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history", - "rdfs:label": "CancerAssociatedGeneMutations", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:APCmutation" + "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" }, { - "@id": "bts:ALKmutation" + "@id": "bts:IntraductalcarcinomaNOS" }, { - "@id": "bts:ARFmutation" + "@id": "bts:Intraductalcarcinomasolidtype" }, { - "@id": "bts:ATMmutation" + "@id": "bts:Intraductalmicropapillarycarcinoma" }, { - "@id": "bts:ATRXmutation" + "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" }, { - "@id": "bts:ACVR1mutation" + "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" }, { - "@id": "bts:BAP1mutation" + "@id": "bts:Intraductalpapillarycarcinoma" }, { - "@id": "bts:BMPR1Amutation" + "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" }, { - "@id": "bts:BLMmutation" + "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" }, { - "@id": "bts:BRCA1mutation" + "@id": "bts:Intraductaltubulopapillaryneoplasm" }, { - "@id": "bts:BRCA1and2mutation" + "@id": "bts:IntraepidermalcarcinomaNOS" }, { - "@id": "bts:BRCA2mutation" + "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" }, { - "@id": "bts:BRAFmutation" + "@id": "bts:IntravascularB-celllymphoma" }, { - "@id": "bts:CDH1mutation" + "@id": "bts:Juvenilemyelomonocyticleukemia" }, { - "@id": "bts:CDKN2Amutation" + "@id": "bts:Kaposisarcoma" }, { - "@id": "bts:CDKN2Aandp14ARFmutation" + "@id": "bts:LargecellcarcinomaNOS" }, { - "@id": "bts:CHKmutation" + "@id": "bts:Liposarcomadifferentiated" }, { - "@id": "bts:ETV6mutation" + "@id": "bts:LiposarcomaNOS" }, { - "@id": "bts:EGFRmutation" + "@id": "bts:Liposarcomawelldifferentiated" }, { - "@id": "bts:FHmutation" + "@id": "bts:Livercelladenoma" }, { - "@id": "bts:FLCNmutation" + "@id": "bts:Livercellcarcinoma" }, { - "@id": "bts:GREM1mutation" + "@id": "bts:Lobularadenocarcinoma" }, { - 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"@id": "bts:Gabon" + "@id": "bts:RhabdomyosarcomaNOS" }, { - "@id": "bts:Gambia" + "@id": "bts:Rhabdosarcoma" }, { - "@id": "bts:Georgia" + "@id": "bts:Rodentulcer" }, { - "@id": "bts:Germany" + "@id": "bts:SarcomaNOS" }, { - "@id": "bts:Ghana" + "@id": "bts:Sclerosinghemangioma" }, { - "@id": "bts:Gibraltar" + "@id": "bts:Sclerosinghepaticcarcinoma" }, { - "@id": "bts:Greece" + "@id": "bts:Secondarycarcinoma" }, { - "@id": "bts:Greenland" + "@id": "bts:Secretorycarcinomaofbreast" }, { - "@id": "bts:Grenada" + "@id": "bts:SerouscystadenocarcinomaNOS" }, { - "@id": "bts:Guadeloupe" + "@id": "bts:Seroussurfacepapillarycarcinoma" }, { - "@id": "bts:Guam" + "@id": "bts:High-gradeserouscarcinoma" }, { - "@id": "bts:Guatemala" + "@id": "bts:Skinappendagecarcinoma" }, { - "@id": "bts:Guernsey" + "@id": "bts:SmallcellcarcinomaNOS" }, { - "@id": "bts:Guinea" + "@id": "bts:Smallcellneuroendocrinecarcinoma" }, { - "@id": "bts:Guinea-Bissau" + "@id": "bts:Smallcellosteosarcoma" }, { - "@id": "bts:Guyana" + "@id": "bts:Smallcellsarcoma" }, { - "@id": "bts:Haiti" + "@id": "bts:Smallcongenitalnevus" }, { - "@id": "bts:HolySee" + "@id": "bts:SpindlecellcarcinomaNOS" }, { - "@id": "bts:Honduras" + "@id": "bts:SpindlecellmelanomaNOS" }, { - "@id": "bts:HongKong" + "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" }, { - "@id": "bts:Hungary" + "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" }, { - "@id": "bts:Iceland" + "@id": "bts:Spleniclymphomawithvillouslymphocytes" }, { - "@id": "bts:India" + "@id": "bts:SplenicmarginalzoneB-celllymphoma" }, { - "@id": "bts:Indonesia" + "@id": "bts:SplenicmarginalzonelymphomaNOS" }, { - "@id": "bts:Iran" + "@id": "bts:SquamouscellcarcinomainsituNOS" }, { - "@id": "bts:Iraq" + "@id": "bts:Squamouscellcarcinomaadenoid" }, { - "@id": "bts:Ireland" + "@id": "bts:Squamouscellcarcinomaclearcelltype" }, { - "@id": "bts:IsleofMan" + "@id": "bts:SquamouscellcarcinomaNOS" }, { - "@id": "bts:Israel" + "@id": "bts:Tlymphoblasticleukemia/lymphoma" }, { - "@id": "bts:Italy" + "@id": "bts:T-celllargegranularlymphocyticleukemia" }, { - "@id": "bts:Jamaica" + "@id": "bts:T-celllargegranularlymphocytosis" }, { - "@id": "bts:Japan" + "@id": "bts:T-celllymphomaNOS" }, { - "@id": "bts:Jersey" + "@id": "bts:TeratomamalignantNOS" }, { - "@id": "bts:Jordan" + "@id": "bts:TeratomaNOS" }, { - "@id": "bts:Kazakhstan" + "@id": "bts:Therapyrelatedmyeloidneoplasm" }, { - "@id": "bts:Kenya" + "@id": "bts:Transitionalcarcinoma" }, { - "@id": "bts:Kiribati" + "@id": "bts:Transitionalcellcarcinoma" }, { - "@id": "bts:Kosovo" + "@id": "bts:Transitionalcellcarcinomainsitu" }, { - "@id": "bts:Kuwait" + "@id": "bts:Tubularadenocarcinoma" }, { - "@id": "bts:Kyrgyzstan" + "@id": "bts:TubularadenomaNOS" }, { - "@id": "bts:Laos" + "@id": "bts:Tubularandroblastomawithlipidstorage" }, { - "@id": "bts:Latvia" + "@id": "bts:TubularandroblastomaNOS" }, { - "@id": "bts:Lebanon" + "@id": "bts:Tubularcarcinoid" }, { - "@id": "bts:Lesotho" + "@id": "bts:Tubularcarcinoma" }, { - "@id": "bts:Liberia" + "@id": "bts:Tubulo-papillaryadenoma" }, { - "@id": "bts:Libya" + "@id": "bts:Tubulocysticrenalcellcarcinoma" }, { - "@id": "bts:Liechtenstein" + "@id": "bts:Tubulolobularcarcinoma" }, { - "@id": "bts:Lithuania" + "@id": "bts:Tubulopapillaryadenocarcinoma" }, { - "@id": "bts:Luxembourg" + "@id": "bts:TubulovillousadenomaNOS" }, { - "@id": "bts:Macau" + "@id": "bts:Tumorcellsbenign" }, { - "@id": "bts:Madagascar" + "@id": "bts:Tumorcellsmalignant" }, { - "@id": "bts:Malawi" + "@id": "bts:TumorcellsNOS" }, { - "@id": "bts:Malaysia" + "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" }, { - "@id": "bts:Maldives" + "@id": "bts:Tumorembolus" }, { - "@id": "bts:Mali" + "@id": "bts:Tumorbenign" }, { - "@id": "bts:Malta" + "@id": "bts:TumormalignantNOS" }, { - "@id": "bts:MarshallIslands" + "@id": "bts:Tumormetastatic" }, { - "@id": "bts:Martinique" + "@id": "bts:TumorNOS" }, { - "@id": "bts:Mauritania" + "@id": "bts:Tumorsecondary" }, { - "@id": "bts:Mauritius" + "@id": "bts:Tumorletbenign" }, { - "@id": "bts:Mayotte" + "@id": "bts:Typicalcarcinoid" }, { - "@id": "bts:Mexico" + "@id": "bts:Unclassifiedtumorbenign" }, { - "@id": "bts:Moldova" + "@id": "bts:Unclassifiedtumorborderlinemalignancy" }, { - "@id": "bts:Monaco" + "@id": "bts:Unclassifiedtumormalignant" }, { - "@id": "bts:Mongolia" + "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" }, { - "@id": "bts:Montenegro" + "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" }, { - "@id": "bts:Montserrat" + "@id": "bts:Undifferentiatedepithelioidsarcoma" }, { - "@id": "bts:Morocco" + "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" }, { - "@id": "bts:Mozambique" + "@id": "bts:Undifferentiatedleukaemia" }, { - "@id": "bts:Myanmar" + "@id": "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id": "bts:Namibia" + "@id": "bts:Undifferentiatedroundcellsarcoma" }, { - "@id": "bts:Nauru" + "@id": "bts:Undifferentiatedsarcoma" }, { - "@id": "bts:Nepal" + "@id": "bts:Undifferentiatedspindlecellsarcoma" }, { - "@id": "bts:Netherlands" + "@id": "bts:Undifferentiateduterinesarcoma" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Primary Diagnosis", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProgressionorRecurrence", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", + "rdfs:label": "ProgressionorRecurrence", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-ProgressionorRecurrence" }, { - "@id": "bts:NewZealand" + "@id": "bts:No" }, { - "@id": "bts:Nicaragua" + "@id": "bts:Unknown" }, { - "@id": "bts:Niger" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Progression or Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SiteofResectionorBiopsy", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "SiteofResectionorBiopsy", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:Nigeria" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:Niue" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:NorthKorea" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Norway" + "@id": "bts:Analcanal" }, { - "@id": "bts:Oman" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:Pakistan" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:Palau" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Panama" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:Paraguay" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Peru" + "@id": "bts:AnusNOS" }, { - "@id": "bts:Philippines" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:Poland" + "@id": "bts:Appendix" }, { - "@id": "bts:Portugal" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:PuertoRico" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Qatar" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:Reunion" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:Romania" + "@id": "bts:Bladderneck" }, { - "@id": "bts:Russia" + "@id": "bts:BladderNOS" }, { - "@id": "bts:Rwanda" + "@id": "bts:Blood" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:SaintLucia" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:Samoa" + "@id": "bts:BoneNOS" }, { - "@id": "bts:SanMarino" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:Brainstem" }, { - "@id": "bts:Senegal" + "@id": "bts:BrainNOS" }, { - "@id": "bts:Serbia" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:Seychelles" + "@id": "bts:BreastNOS" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Broadligament" }, { - "@id": "bts:Singapore" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:Slovakia" + "@id": "bts:Carotidbody" }, { - "@id": "bts:Slovenia" + "@id": "bts:Caudaequina" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:Cecum" }, { - "@id": "bts:Somalia" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:SouthKorea" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:SouthSudan" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Spain" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:SriLanka" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:Choroid" }, { - "@id": "bts:Sudan" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:Suriname" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:ColonNOS" }, { - "@id": "bts:Sweden" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:Switzerland" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:Syria" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Taiwan" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:Tajikistan" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:Tanzania" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:Thailand" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Togo" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:Tokelau" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:Tonga" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:Tunisia" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:Turkey" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Tuvalu" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:Uganda" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Ukraine" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:Duodenum" }, { - "@id": "bts:UnitedStates" + "@id": "bts:Endocervix" }, { - "@id": "bts:Uruguay" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:Endometrium" }, { - "@id": "bts:Vanuatu" + "@id": "bts:Epididymis" }, { - "@id": "bts:Venezuela" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:Vietnam" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:Exocervix" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:Externalear" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:Yemen" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:Zambia" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:Zimbabwe" + "@id": "bts:EyeNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Country of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedArea", - "@type": "rdfs:Class", - "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", - "rdfs:label": "MedicallyUnderservedArea", - "rdfs:subClassOf": [ + "@id": "bts:Eyelid" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Fallopiantube" + }, { - "@id": "bts:MedicallyUnderservedArea-Yes" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:MedicallyUnderservedArea-No" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:MedicallyUnderservedArea-Unknown" - } - ], - "sms:displayName": "Medically Underserved Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RuralvsUrban", - "@type": "rdfs:Class", - "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", - "rdfs:label": "RuralvsUrban", - "rdfs:subClassOf": [ + "@id": "bts:Frontallobe" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Frontalsinus" + }, { - "@id": "bts:UrbanPopulation(population>50000)" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:UrbanCluster(population2500-50000)" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:RuralPopulation(population<2500)" - } - ], - "sms:displayName": "Rural vs Urban", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidence", - "@type": "rdfs:Class", - "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", - "rdfs:label": "CancerIncidence", - "rdfs:subClassOf": [ + "@id": "bts:Gallbladder" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidenceLocation", - "@type": "rdfs:Class", - "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", - "rdfs:label": "CancerIncidenceLocation", - "rdfs:subClassOf": [ + "@id": "bts:Gastricantrum" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Cancer related clinical data specific to SRRS", - "rdfs:label": "SRRSClinicalDataTier2", - "rdfs:subClassOf": [ + "@id": "bts:GastrointestinaltractNOS" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Glanspenis" + }, { - "@id": "bts:Component" + "@id": "bts:Glottis" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:GumNOS" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Hardpalate" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:EducationLevel" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:CountryofBirth" + "@id": "bts:Heart" }, { - "@id": "bts:MedicallyUnderservedArea" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:RuralvsUrban" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:CancerIncidenceLocation" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:Ethnicity" + "@id": "bts:Ileum" }, { - "@id": "bts:Gender" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:Race" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:VitalStatus" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:AgeatDiagnosis" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:DaystoLastFollowup" + "@id": "bts:Intrathoraciclymphnodes" }, { - "@id": "bts:DaystoLastKnownDiseaseStatus" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:DaystoRecurrence" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:Jejunum" }, { - "@id": "bts:Morphology" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:Labiummajus" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:Labiumminus" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:TissueorOrganofOrigin" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:NCIAtlasCancerSite" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:TumorGrade" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:PackYearsSmoked" + "@id": "bts:Lateralwallofbladder" }, { - "@id": "bts:YearsSmoked" + "@id": "bts:Lateralwallofnasopharynx" }, { - "@id": "bts:DaystoFollowUp" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:GeneSymbol" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:TestResult" + "@id": "bts:LipNOS" }, { - "@id": "bts:TreatmentType" + "@id": "bts:Liver" }, { - "@id": "bts:TumorLargestDimensionDiameter" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Ethnicity", - "@type": "rdfs:Class", - "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", - "rdfs:label": "Ethnicity", - "rdfs:subClassOf": [ + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + }, { - "@id": "bts:Hispanicorlatino" + "@id": "bts:Lowergum" }, { - "@id": "bts:Nothispanicorlatino" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:NotReported" + "@id": "bts:Lowerthirdofesophagus" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Ethnicity", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Gender", - "@type": "rdfs:Class", - "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", - "rdfs:label": "Gender", - "rdfs:subClassOf": [ + "@id": "bts:Lower-innerquadrantofbreast" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lower-outerquadrantofbreast" + }, { - "@id": "bts:Female" + "@id": "bts:LungNOS" }, { - "@id": "bts:Male" + "@id": "bts:LymphnodeNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Lymphnodesofaxillaorarm" }, { - "@id": "bts:Unspecified" + "@id": "bts:Lymphnodesofheadfaceandneck" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Gender", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Race", - "@type": "rdfs:Class", - "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", - "rdfs:label": "Race", - "rdfs:subClassOf": [ + "@id": "bts:Lymphnodesofinguinalregionorleg" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lymphnodesofmultipleregions" + }, { - "@id": "bts:White" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:Americanindianoralaskanative" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:Blackorafricanamerican" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:Asian" + "@id": "bts:Mandible" }, { - "@id": "bts:Nativehawaiianorotherpacificislander" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:Other" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:Unknown" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Race", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VitalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", - "rdfs:subClassOf": [ + "@id": "bts:MeningesNOS" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Middleear" + }, { - "@id": "bts:Alive" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:Dead" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:Unknown" + "@id": "bts:MouthNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vital Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", - "rdfs:label": "AgeatDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Age at Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoLastFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastFollowup", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Follow up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoLastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastKnownDiseaseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoRecurrence", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:LastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", - "rdfs:label": "LastKnownDiseaseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Distantmetrecurrence/progression" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:Loco-regionalrecurrence/progression" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:Tumorfree" + "@id": "bts:Myometrium" }, { - "@id": "bts:Unknowntumorstatus" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:Withtumor" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:Nipple" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Morphology", - "@type": "rdfs:Class", - "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", - "rdfs:label": "Morphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Morphology", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PrimaryDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "PrimaryDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Acinarcellcarcinoma" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:Acutebasophilicleukaemia" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:AcuteleukemiaBurkitttype" + "@id": "bts:Opticnerve" }, { - "@id": "bts:AcuteleukemiaNOS" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:Acutelymphaticleukemia" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" + "@id": "bts:Otherill-definedsites" }, { - "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id": "bts:AcutelymphoblasticleukemiaNOS" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" + "@id": "bts:Otherspecifiedpartsofpancreas" }, { - "@id": "bts:Acutelymphocyticleukemia" + "@id": "bts:Ovary" }, { - "@id": "bts:Acutelymphoidleukemia" + "@id": "bts:Overlappinglesionofaccessorysinuses" }, { - "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" + "@id": "bts:Overlappinglesionofbladder" }, { - "@id": "bts:AcutemyeloidleukemiaMLL" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" }, { - "@id": "bts:AcutemyeloidleukemiaNOS" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id": "bts:Acutemyelomonocyticleukemia" + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:AcutepromyelocyticleukemiaNOS" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:Adenocarcinoidtumor" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:AdenocarcinomainapolypNOS" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:Adenocarcinomainadenomatouspolyp" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:Adenocarcinomainpolypoidadenoma" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:AdenocarcinomainsituinapolypNOS" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:Adenocarcinomainsituintubularadenoma" + "@id": "bts:Overlappinglesionofesophagus" }, { - "@id": "bts:Adenocarcinomainsitumucinous" + "@id": "bts:Overlappinglesionofeyeandadnexa" }, { - "@id": "bts:Adenocarcinomainsitunon-mucinous" + "@id": "bts:Overlappinglesionoffemalegenitalorgans" }, { - "@id": "bts:AdenocarcinomainsituNOS" + "@id": "bts:Overlappinglesionoffloorofmouth" }, { - "@id": "bts:Adenocarcinomaintubularadenoma" + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" }, { - "@id": "bts:Adenocarcinomainvillousadenoma" + "@id": "bts:Overlappinglesionofhypopharynx" }, { - "@id": "bts:Adenocarcinomaofanalducts" + "@id": "bts:Overlappinglesionofill-definedsites" }, { - "@id": "bts:Adenocarcinomaofanalglands" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:Adenocarcinomadiffusetype" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:Adenocarcinomaendocervicaltype" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:Adenocarcinomaintestinaltype" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:AdenocarcinomametastaticNOS" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:AdenocarcinomaNOS" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:Adenocarcinomapancreatobiliarytype" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:Adultrhabdomyoma" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:AdultT-celllymphoma" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:AdultT-celllymphoma/leukemia" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:Astrocytomaanaplastic" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:Astrocytomalowgrade" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - "@id": "bts:AstrocytomaNOS" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:BcelllymphomaNOS" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + "@id": "bts:Overlappinglesionofskin" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" + "@id": "bts:Overlappinglesionofsmallintestine" }, { - "@id": "bts:B-ALL" + "@id": "bts:Overlappinglesionofstomach" }, { - "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" + "@id": "bts:Overlappinglesionoftongue" }, { - "@id": "bts:Basalcelladenocarcinoma" + "@id": "bts:Overlappinglesionoftonsil" }, { - "@id": "bts:Basalcelladenoma" + "@id": "bts:Overlappinglesionofurinaryorgans" }, { - "@id": "bts:BasalcellcarcinomaNOS" + "@id": "bts:Overlappinglesionofvulva" }, { - "@id": "bts:Basalcellepithelioma" + "@id": "bts:Overlappinglesionsoforopharynx" }, { - "@id": "bts:Basalcelltumor" + "@id": "bts:PalateNOS" }, { - "@id": "bts:Basophiladenocarcinoma" + "@id": "bts:PancreasNOS" }, { - "@id": "bts:Basophiladenoma" + "@id": "bts:Pancreaticduct" }, { - "@id": "bts:Basophilcarcinoma" + "@id": "bts:Parametrium" }, { - "@id": "bts:Bileductadenocarcinoma" + "@id": "bts:Paraspinal" }, { - "@id": "bts:Bileductadenoma" + "@id": "bts:Parathyroidgland" }, { - "@id": "bts:Bileductcarcinoma" + "@id": "bts:Paraurethralgland" }, { - "@id": "bts:Bileductcystadenocarcinoma" + "@id": "bts:Parietallobe" }, { - "@id": "bts:Bileductcystadenoma" + "@id": "bts:Parotidgland" }, { - "@id": "bts:Bronchialadenomacarcinoid" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:Bronchialadenomacylindroid" + "@id": "bts:Pelviclymphnodes" }, { - "@id": "bts:BronchialadenomaNOS" + "@id": "bts:PelvisNOS" }, { - "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" + "@id": "bts:PenisNOS" }, { - "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" }, { - "@id": "bts:Bronchio-alveolarcarcinomamucinous" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" }, { - "@id": "bts:Bronchiolaradenocarcinoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id": "bts:Bronchiolarcarcinoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" }, { - "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + "@id": "bts:Pinealgland" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" + "@id": "bts:Pituitarygland" }, { - "@id": "bts:Burkittcellleukemia" + "@id": "bts:Placenta" }, { - "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:Burkitttumor" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:Burkitt-likelymphoma" + "@id": "bts:Posteriormediastinum" }, { - "@id": "bts:C-ALL" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:Cancer" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:Capillaryhemangioma" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:Capillarylymphangioma" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:CarcinomainapolypNOS" + "@id": "bts:Prepuce" }, { - "@id": "bts:Carcinomainadenomatouspolyp" + "@id": "bts:Prostategland" }, { - "@id": "bts:Carcinomainpleomorphicadenoma" + "@id": "bts:Pylorus" }, { - "@id": "bts:CarcinomainsituinapolypNOS" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:Carcinomainsituinadenomatouspolyp" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:CarcinomainsituNOS" + "@id": "bts:RectumNOS" }, { - "@id": "bts:CarcinomaanaplasticNOS" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:Carcinomadiffusetype" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Carcinomaintestinaltype" + "@id": "bts:Retina" }, { - "@id": "bts:CarcinomametastaticNOS" + "@id": "bts:Retromolararea" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:CarcinosarcomaNOS" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:CarcinomaundifferentiatedNOS" + "@id": "bts:Roundligament" }, { - "@id": "bts:CementomaNOS" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:Centralneuroblastoma" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:Centralneurocytoma" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:Cerebellarliponeurocytoma" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:CerebellarsarcomaNOS" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:CervicalintraepithelialneoplasiagradeIII" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:Cervicalintraepithelialneoplasialowgrade" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:ChondromaNOS" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:Chondrosarcomagrade2/3" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:ChronicgranulocyticleukemiaNOS" + "@id": "bts:SkinNOS" }, { - "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:ChronicleukemiaNOS" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:Chroniclymphaticleukemia" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:Chroniclymphocyticleukemia" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:Chroniclymphoidleukemia" + "@id": "bts:Spinalcord" }, { - "@id": "bts:Chronicmonocyticleukemia" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:ChronicmyelocyticleukemiaNOS" + "@id": "bts:Spleen" }, { - "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:StomachNOS" }, { - "@id": "bts:ChronicmyeloidleukemiaNOS" + "@id": "bts:Subglottis" }, { - "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaNOS" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaType1" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" + "@id": "bts:Supraglottis" }, { - "@id": "bts:ChronicmyeloproliferativediseaseNOS" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:Chronicmyeloproliferativedisorder" + "@id": "bts:Temporallobe" }, { - "@id": "bts:Chronicneutrophilicleukemia" + "@id": "bts:TestisNOS" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + "@id": "bts:Thymus" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" + "@id": "bts:TongueNOS" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + "@id": "bts:Trachea" }, { - "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" + "@id": "bts:Transversecolon" }, { - "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:Combinedsmallcellcarcinoma" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:Combinedsmallcell-adenocarcinoma" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:Combinedsmallcell-largecarcinoma" + "@id": "bts:Uppergum" }, { - "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:Dermalnevus" + "@id": "bts:Upperthirdofesophagus" }, { - "@id": "bts:DermatofibromaNOS" + "@id": "bts:Upper-innerquadrantofbreast" }, { - "@id": "bts:DiffuseastrocytomaIDH-mutant" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:DiffuseastrocytomaIDH-wildtype" + "@id": "bts:Urachus" }, { - "@id": "bts:Diffuseastrocytomalowgrade" + "@id": "bts:Ureter" }, { - "@id": "bts:DiffuselargeB-celllymphomaNOS" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:Diffusemelanocytosis" + "@id": "bts:Urethra" }, { - "@id": "bts:DuctadenocarcinomaNOS" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:DuctadenomaNOS" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:Ductcarcinomadesmoplastictype" + "@id": "bts:UterusNOS" }, { - "@id": "bts:DuctcarcinomaNOS" + "@id": "bts:Uvula" }, { - "@id": "bts:Ductcellcarcinoma" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:DuctalcarcinomainsituNOS" + "@id": "bts:Vallecula" }, { - "@id": "bts:DuctalcarcinomaNOS" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:Dysplasticnevus" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:EndometrialsarcomaNOS" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:EndometrioidadenocarcinomaNOS" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:EndometrioidadenofibromaNOS" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:EndometrioidadenomaNOS" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:EndometrioidcarcinomaNOS" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:Eosinophiladenocarcinoma" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:Eosinophiladenoma" + "@id": "bts:Clitoris" }, { - "@id": "bts:Eosinophilcarcinoma" + "@id": "bts:Overlappinglesionofbiliarytract" }, { - "@id": "bts:Eosinophilicgranuloma" + "@id": "bts:Unknown" }, { - "@id": "bts:Eosinophilicleukemia" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Site of Resection or Biopsy", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TissueorOrganofOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "TissueorOrganofOrigin", + "rdfs:subClassOf": [ { - "@id": "bts:EpendymomaNOS" + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:EpidermoidcarcinomainsituNOS" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:EpidermoidcarcinomaNOS" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:Epithelialtumorbenign" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:Epithelialtumormalignant" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" + "@id": "bts:Analcanal" }, { - "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Ewingsarcoma" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:GangliogliomaNOS" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:Familialadenomatouspolyposis" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Gastrincelltumor" + "@id": "bts:AnusNOS" }, { - "@id": "bts:Gastrincelltumormalignant" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:Gastrinomamalignant" + "@id": "bts:Appendix" }, { - "@id": "bts:GastrinomaNOS" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:Gastrointestinalstromaltumormalignant" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Glioblastoma" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:Gliomamalignant" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:GliomaNOS" + "@id": "bts:Bladderneck" }, { - "@id": "bts:Haemangioblastoma" + "@id": "bts:BladderNOS" }, { - "@id": "bts:Haemangiosarcoma" + "@id": "bts:Blood" }, { - "@id": "bts:Hepatocarcinoma" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:Hepatocellularadenoma" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:HepatocellularcarcinomaNOS" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:Hepatocholangiocarcinoma" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Hepatoidadenocarcinoma" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:Hepatoidcarcinoma" + "@id": "bts:BoneNOS" }, { - "@id": "bts:HodgkindiseaseNOS" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:Hodgkingranuloma" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:HodgkinlymphomamixedcellularityNOS" + "@id": "bts:Brainstem" }, { - "@id": "bts:HodgkinlymphomanodularsclerosisNOS" + "@id": "bts:BrainNOS" }, { - "@id": "bts:HodgkinlymphomaNOS" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:HodgkinparagranulomaNOS" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Hodgkinsarcoma" + "@id": "bts:Broadligament" }, { - "@id": "bts:InfiltratingbasalcellcarcinomaNOS" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:InfiltratingductcarcinomaNOS" + "@id": "bts:Carotidbody" }, { - "@id": "bts:Infiltratingductandcolloidcarcinoma" + "@id": "bts:Caudaequina" }, { - "@id": "bts:Infiltratingductandcribriformcarcinoma" + "@id": "bts:Cecum" }, { - "@id": "bts:Inflammatoryadenocarcinoma" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:Inflammatorycarcinoma" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:Interstitialcelltumorbenign" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:Interstitialcelltumormalignant" + "@id": "bts:Cerebrum" }, { - "@id": "bts:InterstitialcelltumorNOS" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:Intracysticpapilloma" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:Intradermalnevus" + "@id": "bts:Choroid" }, { - "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:Intraductalandlobularcarcinoma" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" + "@id": "bts:ColonNOS" }, { - "@id": "bts:Intraductalcarcinomaclinging" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:IntraductalcarcinomaNOS" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Intraductalcarcinomasolidtype" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:Intraductalmicropapillarycarcinoma" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:Intraductalpapillarycarcinoma" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:Intraductaltubulopapillaryneoplasm" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:IntraepidermalcarcinomaNOS" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:IntravascularB-celllymphoma" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:Juvenilemyelomonocyticleukemia" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Kaposisarcoma" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:LargecellcarcinomaNOS" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Liposarcomadifferentiated" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:LiposarcomaNOS" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:Liposarcomawelldifferentiated" + "@id": "bts:Duodenum" }, { - "@id": "bts:Livercelladenoma" + "@id": "bts:Endocervix" }, { - "@id": "bts:Livercellcarcinoma" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:Lobularadenocarcinoma" + "@id": "bts:Endometrium" }, { - "@id": "bts:Lobularandductalcarcinoma" + "@id": "bts:Epididymis" }, { - "@id": "bts:LobularcarcinomainsituNOS" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:Lobularcarcinomanoninfiltrating" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:LobularcarcinomaNOS" + "@id": "bts:Exocervix" }, { - "@id": "bts:LymphaticleukemicNOS" + "@id": "bts:Externalear" }, { - "@id": "bts:LymphoblasticleukemiaNOS" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:Lymphoblastoma" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:LymphocyticleukemiaNOS" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:LymphomaNOS" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:Malignancy" + "@id": "bts:EyeNOS" }, { - "@id": "bts:MalignantlymphomadiffuseNOS" + "@id": "bts:Eyelid" }, { - "@id": "bts:MalignantlymphomaHodgkin" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:MalignantlymphomaimmunoblasticNOS" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:MalignantlymphomalargeB-cellNOS" + "@id": "bts:Frontallobe" }, { - "@id": "bts:MalignantlymphomalargecellNOS" + "@id": "bts:Frontalsinus" }, { - "@id": "bts:MalignantlymphomalymphoblasticNOS" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:MalignantlymphomalymphocyticdiffuseNOS" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:MalignantlymphomalymphocyticnodularNOS" + "@id": "bts:Gallbladder" }, { - "@id": "bts:MalignantlymphomalymphocyticNOS" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:Malignantlymphomamixedcelltypediffuse" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:Malignantlymphomamixedcelltypefollicular" + "@id": "bts:Glanspenis" }, { - "@id": "bts:Malignantlymphomamixedcelltypenodular" + "@id": "bts:Glottis" }, { - "@id": "bts:MalignantlymphomanodularNOS" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:Malignantlymphomanon-HodgkinNOS" + "@id": "bts:GumNOS" }, { - "@id": "bts:MalignantlymphomaNOS" + "@id": "bts:Hardpalate" }, { - "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:Malignantmelanomaingiantpigmentednevus" + "@id": "bts:Heart" }, { - "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:Malignantmelanomainjunctionalnevus" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:Malignantmelanomainprecancerousmelanosis" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:MalignantmelanomaNOS" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:Malignantmelanomaregressing" + "@id": "bts:Ileum" }, { - "@id": "bts:Mammarycarcinomainsitu" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:Medullaryadenocarcinoma" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:MedullarycarcinomaNOS" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:Medullaryosteosarcoma" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:MedulloblastomaNOS" + "@id": "bts:Intrathoraciclymphnodes" }, { - "@id": "bts:Melanoameloblastoma" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:Melanocyticnevus" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:Melanocytomaeyeball" + "@id": "bts:Jejunum" }, { - "@id": "bts:MelanocytomaNOS" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:Melanomainsitu" + "@id": "bts:Labiummajus" }, { - "@id": "bts:Melanomamalignantofsoftparts" + "@id": "bts:Labiumminus" }, { - "@id": "bts:MelanomaNOS" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:Melanoticmedulloblastoma" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:MelanoticMPNST" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:Melanoticneuroectodermaltumor" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:Melanoticneurofibroma" + "@id": "bts:Lateralwallofbladder" }, { - "@id": "bts:Melanoticprogonoma" + "@id": "bts:Lateralwallofnasopharynx" }, { - "@id": "bts:MelanoticpsammomatousMPNST" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:Melanoticschwannoma" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:Meningealmelanocytoma" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:Meningealmelanoma" + "@id": "bts:LipNOS" }, { - "@id": "bts:Meningiomaanaplastic" + "@id": "bts:Liver" }, { - "@id": "bts:Meningiomamalignant" + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:MeningiomaNOS" + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" }, { - "@id": "bts:MicropapillarycarcinomaNOS" + "@id": "bts:Lowergum" }, { - "@id": "bts:Mixedadenocarcinomaandepidermoidcarcinoma" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:Mixedmedullary-follicularcarcinoma" + "@id": "bts:Lowerthirdofesophagus" }, { - "@id": "bts:Mixedmedullary-papillarycarcinoma" + "@id": "bts:Lower-innerquadrantofbreast" }, { - "@id": "bts:Mixedpancreaticendocrineandexocrinetumormalignant" + "@id": "bts:Lower-outerquadrantofbreast" }, { - "@id": "bts:Mixedpinealtumor" + "@id": "bts:LungNOS" }, { - "@id": "bts:Mixedsmallcellcarcinoma" + "@id": "bts:LymphnodeNOS" }, { - "@id": "bts:Mixedsquamouscellandglandularpapilloma" + "@id": "bts:Lymphnodesofaxillaorarm" }, { - "@id": "bts:MixedtumormalignantNOS" + "@id": "bts:Lymphnodesofheadfaceandneck" }, { - "@id": "bts:MixedtumorNOS" + "@id": "bts:Lymphnodesofinguinalregionorleg" }, { - "@id": "bts:MonocyticleukemiaNOS" + "@id": "bts:Lymphnodesofmultipleregions" }, { - "@id": "bts:Mucosal-associatedlymphoidtissuelymphoma" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:Mucousadenocarcinoma" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:Multiplemyeloma" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:MyelocyticleukemiaNOS" + "@id": "bts:Mandible" }, { - "@id": "bts:MyeloidleukemiaNOS" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:MyelomaNOS" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:Myoepithelioma" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:Neoplasmbenign" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:Neoplasmmalignant" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:Neoplasmmalignantuncertainwhetherprimaryormetastatic" + "@id": "bts:Middleear" }, { - "@id": "bts:Neoplasmmetastatic" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:NeoplasmNOS" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:Neoplasmsecondary" + "@id": "bts:MouthNOS" }, { - "@id": "bts:Neoplasmuncertainwhetherbenignormalignant" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:NephroblastomaNOS" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:NeuroblastomaNOS" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:NeuroendocrinecarcinomaNOS" + "@id": "bts:Myometrium" }, { - "@id": "bts:NeuroepitheliomaNOS" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:NeurofibromaNOS" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:NeurofibromatosisNOS" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:Neurofibrosarcoma" + "@id": "bts:Nipple" }, { - "@id": "bts:Neurosarcoma" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:NevusNOS" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:Non-HodgkinlymphomaNOS" + "@id": "bts:Opticnerve" }, { - "@id": "bts:Non-invasivelowgradeserouscarcinoma" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:Non-lymphocyticleukemiaNOS" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:Non-smallcellcarcinoma" + "@id": "bts:Otherill-definedsites" }, { - "@id": "bts:Nonpigmentednevus" + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id": "bts:NotReported" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:Oatcellcarcinoma" + "@id": "bts:Otherspecifiedpartsofpancreas" }, { - "@id": "bts:Osteoblastomamalignant" + "@id": "bts:Ovary" }, { - "@id": "bts:OsteoblastomaNOS" + "@id": "bts:Overlappinglesionofaccessorysinuses" }, { - "@id": "bts:OsteosarcomaNOS" + "@id": "bts:Overlappinglesionofbladder" }, { - "@id": "bts:Pagetdiseaseandinfiltratingductcarcinomaofbreast" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" }, { - "@id": "bts:Pagetdiseaseandintraductalcarcinomaofbreast" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id": "bts:Pagetdiseaseofbreast" + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:Pagetdiseaseextramammary" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:Pagetdiseasemammary" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:Pagetoidreticulosis" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:Pancreaticendocrinetumorbenign" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:Pancreaticendocrinetumormalignant" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:Pancreaticendocrinetumornonfunctioning" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:PancreaticendocrinetumorNOS" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:Pancreaticmicroadenoma" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:Pancreatobiliaryneoplasmnon-invasive" + "@id": "bts:Overlappinglesionofesophagus" }, { - "@id": "bts:Pancreatobiliary-typecarcinoma" + "@id": "bts:Overlappinglesionofeyeandadnexa" }, { - "@id": "bts:Pancreatoblastoma" + "@id": "bts:Overlappinglesionoffemalegenitalorgans" }, { - "@id": "bts:Papillaryadenocarcinomafollicularvariant" + "@id": "bts:Overlappinglesionoffloorofmouth" }, { - "@id": "bts:PapillaryadenocarcinomaNOS" + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" }, { - "@id": "bts:Papillaryadenofibroma" + "@id": "bts:Overlappinglesionofhypopharynx" }, { - "@id": "bts:PapillaryadenomaNOS" + "@id": "bts:Overlappinglesionofill-definedsites" }, { - "@id": "bts:Papillaryandfollicularcarcinoma" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:Papillarycarcinomainsitu" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:PapillarycarcinomaNOS" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:PapillarycystadenomaNOS" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:Papillaryepidermoidcarcinoma" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:Papillaryglioneuronaltumor" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:Papillarymeningioma" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:Papillarymicrocarcinoma" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:Papillaryrenalcellcarcinoma" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:Papillaryserousadenocarcinoma" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:Papillaryserouscystadenocarcinoma" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:PapillaryserouscystadenomaNOS" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - "@id": "bts:Papillarysquamouscellcarcinoma" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:Papillarysquamouscellcarcinomainsitu" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:Papillarytransitionalcellcarcinoma" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:Papillarytumorofthepinealregion" + "@id": "bts:Overlappinglesionofskin" }, { - "@id": "bts:Papillaryurothelialcarcinoma" + "@id": "bts:Overlappinglesionofsmallintestine" }, { - "@id": "bts:Papillomaofbladder" + "@id": "bts:Overlappinglesionofstomach" }, { - "@id": "bts:PapillomaNOS" + "@id": "bts:Overlappinglesionoftongue" }, { - "@id": "bts:Papillomatosisglandular" + "@id": "bts:Overlappinglesionoftonsil" }, { - "@id": "bts:PapillomatosisNOS" + "@id": "bts:Overlappinglesionofurinaryorgans" }, { - "@id": "bts:Papillotubularadenocarcinoma" + "@id": "bts:Overlappinglesionofvulva" }, { - "@id": "bts:Papillotubularadenoma" + "@id": "bts:Overlappinglesionsoforopharynx" }, { - "@id": "bts:Paragangliomabenign" + "@id": "bts:PalateNOS" }, { - "@id": "bts:Paragangliomamalignant" + "@id": "bts:PancreasNOS" }, { - "@id": "bts:ParagangliomaNOS" + "@id": "bts:Pancreaticduct" }, { - "@id": "bts:PeripheralT-celllymphomalargecell" + "@id": "bts:Parametrium" }, { - "@id": "bts:PeripheralT-celllymphomaNOS" + "@id": "bts:Paraspinal" }, { - "@id": "bts:Pigmentedadenoma" + "@id": "bts:Parathyroidgland" }, { - "@id": "bts:Pigmentedbasalcellcarcinoma" + "@id": "bts:Paraurethralgland" }, { - "@id": "bts:PigmentednevusNOS" + "@id": "bts:Parietallobe" }, { - "@id": "bts:PituitaryadenomaNOS" + "@id": "bts:Parotidgland" }, { - "@id": "bts:PituitarycarcinomaNOS" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:Pleomorphicadenoma" + "@id": "bts:Pelviclymphnodes" }, { - "@id": "bts:Pleomorphiccarcinoma" + "@id": "bts:PelvisNOS" }, { - "@id": "bts:Pleomorphiclipoma" + "@id": "bts:PenisNOS" }, { - "@id": "bts:Pleomorphicliposarcoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" }, { - "@id": "bts:Pleomorphiclobularcarcinoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" }, { - "@id": "bts:Pleomorphiclobularcarcinomainsitu" + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id": "bts:PrecancerousmelanosisNOS" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" }, { - "@id": "bts:PrecursorB-celllymphoblasticleukemia" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" }, { - "@id": "bts:PrecursorB-celllymphoblasticlymphoma" + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" }, { - "@id": "bts:PrecursorcelllymphoblasticleukemiaNOS" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:PrecursorT-celllymphoblasticleukemia" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:PrecursorT-celllymphoblasticlymphoma" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:Preleukemia" + "@id": "bts:Pinealgland" }, { - "@id": "bts:Preleukemicsyndrome" + "@id": "bts:Pituitarygland" }, { - "@id": "bts:Primaryamyloidosis" + "@id": "bts:Placenta" }, { - "@id": "bts:Pro-BALL" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:Pro-TALL" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:ProstaticintraepithelialneoplasiagradeIII" + "@id": "bts:Posteriormediastinum" }, { - "@id": "bts:Pulmonaryadenomatosis" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:Pulmonaryarteryintimalsarcoma" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:Pulmonaryblastoma" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:Renalcarcinomacollectingducttype" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:Renalcelladenocarcinoma" + "@id": "bts:Prepuce" }, { - "@id": "bts:Renalcellcarcinomachromophobetype" + "@id": "bts:Prostategland" }, { - "@id": "bts:RenalcellcarcinomaNOS" + "@id": "bts:Pylorus" }, { - "@id": "bts:Renalcellcarcinomasarcomatoid" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:Renalcellcarcinomaspindlecell" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:Renalcellcarcinomaunclassified" + "@id": "bts:RectumNOS" }, { - "@id": "bts:Renalmedullarycarcinoma" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:Rhabdoidmeningioma" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Rhabdoidsarcoma" - }, - { - "@id": "bts:RhabdoidtumorNOS" - }, - { - "@id": "bts:RhabdomyomaNOS" - }, - { - "@id": "bts:Rhabdomyosarcomawithganglionicdifferentiation" + "@id": "bts:Retina" }, { - "@id": "bts:RhabdomyosarcomaNOS" + "@id": "bts:Retromolararea" }, { - "@id": "bts:Rhabdosarcoma" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:Rodentulcer" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:SarcomaNOS" + "@id": "bts:Roundligament" }, { - "@id": "bts:Sclerosinghemangioma" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:Sclerosinghepaticcarcinoma" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:Secondarycarcinoma" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:Secretorycarcinomaofbreast" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:SerouscystadenocarcinomaNOS" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:Seroussurfacepapillarycarcinoma" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:High-gradeserouscarcinoma" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:Skinappendagecarcinoma" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:SmallcellcarcinomaNOS" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:Smallcellneuroendocrinecarcinoma" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:Smallcellosteosarcoma" + "@id": "bts:SkinNOS" }, { - "@id": "bts:Smallcellsarcoma" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:Smallcongenitalnevus" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:SpindlecellcarcinomaNOS" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:SpindlecellmelanomaNOS" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" + "@id": "bts:Spinalcord" }, { - "@id": "bts:Spleniclymphomawithvillouslymphocytes" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:SplenicmarginalzoneB-celllymphoma" + "@id": "bts:Spleen" }, { - "@id": "bts:SplenicmarginalzonelymphomaNOS" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:SquamouscellcarcinomainsituNOS" + "@id": "bts:StomachNOS" }, { - "@id": "bts:Squamouscellcarcinomaadenoid" + "@id": "bts:Subglottis" }, { - "@id": "bts:Squamouscellcarcinomaclearcelltype" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:SquamouscellcarcinomaNOS" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:Tlymphoblasticleukemia/lymphoma" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:T-celllargegranularlymphocyticleukemia" + "@id": "bts:Supraglottis" }, { - "@id": "bts:T-celllargegranularlymphocytosis" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:T-celllymphomaNOS" + "@id": "bts:Temporallobe" }, { - "@id": "bts:TeratomamalignantNOS" + "@id": "bts:TestisNOS" }, { - "@id": "bts:TeratomaNOS" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:Therapyrelatedmyeloidneoplasm" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:Transitionalcarcinoma" + "@id": "bts:Thymus" }, { - "@id": "bts:Transitionalcellcarcinoma" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:Transitionalcellcarcinomainsitu" + "@id": "bts:TongueNOS" }, { - "@id": "bts:Tubularadenocarcinoma" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:TubularadenomaNOS" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:Tubularandroblastomawithlipidstorage" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:TubularandroblastomaNOS" + "@id": "bts:Trachea" }, { - "@id": "bts:Tubularcarcinoid" + "@id": "bts:Transversecolon" }, { - "@id": "bts:Tubularcarcinoma" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:Tubulo-papillaryadenoma" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:Tubulocysticrenalcellcarcinoma" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:Tubulolobularcarcinoma" + "@id": "bts:Uppergum" }, { - "@id": "bts:Tubulopapillaryadenocarcinoma" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:TubulovillousadenomaNOS" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:Tumorcellsbenign" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:Tumorcellsmalignant" + "@id": "bts:Upperthirdofesophagus" }, { - "@id": "bts:TumorcellsNOS" + "@id": "bts:Upper-innerquadrantofbreast" }, { - "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:Tumorembolus" + "@id": "bts:Urachus" }, { - "@id": "bts:Tumorbenign" + "@id": "bts:Ureter" }, { - "@id": "bts:TumormalignantNOS" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:Tumormetastatic" + "@id": "bts:Urethra" }, { - "@id": "bts:TumorNOS" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:Tumorsecondary" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:Tumorletbenign" + "@id": "bts:UterusNOS" }, { - "@id": "bts:Typicalcarcinoid" + "@id": "bts:Uvula" }, { - "@id": "bts:Unclassifiedtumorbenign" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:Unclassifiedtumorborderlinemalignancy" + "@id": "bts:Vallecula" }, { - "@id": "bts:Unclassifiedtumormalignant" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:Undifferentiatedepithelioidsarcoma" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:Undifferentiatedleukaemia" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:Undifferentiatedroundcellsarcoma" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:Undifferentiatedsarcoma" + "@id": "bts:Clitoris" }, { - "@id": "bts:Undifferentiatedspindlecellsarcoma" + "@id": "bts:Overlappinglesionofbiliarytract" }, { - "@id": "bts:Undifferentiateduterinesarcoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" } ], - "sms:displayName": "Primary Diagnosis", + "sms:displayName": "Tissue or Organ of Origin", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProgressionorRecurrence", + "@id": "bts:NCIAtlasCancerSite", "@type": "rdfs:Class", - "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", - "rdfs:label": "ProgressionorRecurrence", + "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", + "rdfs:label": "NCIAtlasCancerSite", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -11489,1028 +10492,1254 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-ProgressionorRecurrence" + "@id": "bts:Bladder" }, { - "@id": "bts:No" + "@id": "bts:BrainAndOtherNervousSystem" }, { - "@id": "bts:Unknown" + "@id": "bts:FemaleBreast" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Progression or Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteofResectionorBiopsy", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "SiteofResectionorBiopsy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" + "@id": "bts:InsituFemaleBreast" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:CervixUteri" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:LessThanAge" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:MalignantChildhoodNeoplasm" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:ColonAndRectum" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:Esophagus" }, { - "@id": "bts:Analcanal" + "@id": "bts:KidneyAndRenalPelvis" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:Leukemia" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:LiverAndBileDuct" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:LungAndBronchus" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:CutaneousMelanoma" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:Non-Hodgkin'sLymphoma" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:OralCavityAndPharynx" }, { - "@id": "bts:AnusNOS" + "@id": "bts:Ovary" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:Pancreas" }, { - "@id": "bts:Appendix" + "@id": "bts:ProstateGland" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:Stomach" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:ThyroidGland" }, { - "@id": "bts:Axillarytailofbreast" - }, + "@id": "bts:Uterus" + } + ], + "sms:displayName": "NCI Atlas Cancer Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorGrade", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", + "rdfs:label": "TumorGrade", + "rdfs:subClassOf": [ { - "@id": "bts:BaseoftongueNOS" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Bladderneck" + "@id": "bts:G1" }, { - "@id": "bts:BladderNOS" + "@id": "bts:G2" }, { - "@id": "bts:Blood" + "@id": "bts:G3" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:G4" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:GX" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:GB" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:HighGrade" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:IntermediateGrade" }, { - "@id": "bts:BoneNOS" + "@id": "bts:LowGrade" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:Unknown" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:NotReported" }, { - "@id": "bts:Brainstem" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Tumor Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PackYearsSmoked", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", + "rdfs:label": "PackYearsSmoked", + "rdfs:subClassOf": [ { - "@id": "bts:BrainNOS" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pack Years Smoked", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:YearsSmoked", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", + "rdfs:label": "YearsSmoked", + "rdfs:subClassOf": [ { - "@id": "bts:Branchialcleft" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Years Smoked", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoFollowUp", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoFollowUp", + "rdfs:subClassOf": [ { - "@id": "bts:BreastNOS" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Follow Up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:GeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "GeneSymbol", + "rdfs:subClassOf": [ { - "@id": "bts:Broadligament" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gene Symbol", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularAnalysisMethod", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularAnalysisMethod", + "rdfs:subClassOf": [ { - "@id": "bts:CardiaNOS" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Carotidbody" + "@id": "bts:ComparativeGenomicHybridization" }, { - "@id": "bts:Caudaequina" + "@id": "bts:CytogeneticsNOS" }, { - "@id": "bts:Cecum" + "@id": "bts:FISH" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:FlowCytometry" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:IHC" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:ISH" }, { - "@id": "bts:Cerebrum" + "@id": "bts:Karyotype" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:Microarray" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:MicrosatelliteAnalysis" }, { - "@id": "bts:Choroid" + "@id": "bts:NuclearStaining" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:Other" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:RNASequencing" }, { - "@id": "bts:ColonNOS" + "@id": "bts:RT-PCR" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:SequencingNOS" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:SouthernBlotting" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:TargetedSequencing" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:WGS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:WXS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:Unknown" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:NotReported" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Molecular Analysis Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TestResult", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestResult", + "rdfs:subClassOf": [ { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:AbnormalNOS" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:CopyNumberReported" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:Equivocal" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:High" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:Intermediate" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:LossofExpression" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:Low" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:Negative" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:Normal" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Overexpressed" }, { - "@id": "bts:Duodenum" + "@id": "bts:Positive" }, { - "@id": "bts:Endocervix" + "@id": "bts:TestValueReported" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Endometrium" + "@id": "bts:NotReported" }, { - "@id": "bts:Epididymis" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Test Result", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of treatment administered.", + "rdfs:label": "TreatmentType", + "rdfs:subClassOf": [ { - "@id": "bts:EsophagusNOS" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Ethmoidsinus" + "@id": "bts:AblationCryo" }, { - "@id": "bts:Exocervix" + "@id": "bts:AblationEthanolInjection" }, { - "@id": "bts:Externalear" + "@id": "bts:AblationMicrowave" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:AblationNOS" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:AblationRadiofrequency" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:AblationRadiosurgical" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:AncillaryTreatment" }, { - "@id": "bts:EyeNOS" + "@id": "bts:AntiseizureTreatment" }, { - "@id": "bts:Eyelid" + "@id": "bts:BisphosphonateTherapy" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:BlindedStudyTreatmentunknown" }, { - "@id": "bts:FemalegenitaltractNOS" + "@id": "bts:BrachytherapyHighDose" }, { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:BrachytherapyLowDose" }, { - "@id": "bts:Frontallobe" + "@id": "bts:BrachytherapyNOS" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:Chemoembolization" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:Chemoprotectant" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:Chemotherapy" }, { - "@id": "bts:Gallbladder" + "@id": "bts:ConcurrentChemoradiation" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:Cryoablation" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:Embolization" }, { - "@id": "bts:Glanspenis" + "@id": "bts:EthanolInjectionAblation" }, { - "@id": "bts:Glottis" + "@id": "bts:ExternalBeamRadiation" }, { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:HormoneTherapy" }, { - "@id": "bts:GumNOS" + "@id": "bts:I-131RadiationTherapy" }, { - "@id": "bts:Hardpalate" + "@id": "bts:InternalRadiation" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:Immunotherapy(IncludingVaccines)" }, { - "@id": "bts:HeadfaceorneckNOS" + "@id": "bts:IsolatedLimbPerfusion(ILP)" }, { - "@id": "bts:Heart" + "@id": "bts:OrganTransplantation" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:Other" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:PharmaceuticalTherapyNOS" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:Pleurodesis" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:Radiation2DConventional" }, { - "@id": "bts:Ileum" + "@id": "bts:Radiation3DConformal" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:RadiationCombination" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:RadiationCyberknife" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:RadiationExternalBeam" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:RadiationImplants" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:RadiationInternal" }, { - "@id": "bts:Isthmusuteri" + "@id": "bts:RadiationProtonBeam" }, { - "@id": "bts:Jejunum" + "@id": "bts:RadiationRadioisotope" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:RadiationStereotactic/GammaKnife/SRS" }, { - "@id": "bts:Labiummajus" + "@id": "bts:RadiationSystemic" }, { - "@id": "bts:Labiumminus" + "@id": "bts:RadiationTherapyNOS" }, { - "@id": "bts:Lacrimalgland" + "@id": "bts:RadioactiveIodineTherapy" }, { - "@id": "bts:Laryngealcartilage" + "@id": "bts:Radioembolization" }, { - "@id": "bts:LarynxNOS" + "@id": "bts:RadiosensitizingAgent" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:StemCellTreatment" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:StemCellTransplantationAutologous" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:StemCellTransplantationDoubleAutologous" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:StemCellTransplantationAllogeneic" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:StemCellTransplantationNon-Myeloablative" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:StemCellTransplantationSyngenic" }, { - "@id": "bts:LipNOS" + "@id": "bts:StemCellTransplantationHaploidentical" }, { - "@id": "bts:Liver" + "@id": "bts:StemCellTransplantationNOS" }, { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + "@id": "bts:StereotacticRadiosurgery" }, { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + "@id": "bts:SteroidTherapy" }, { - "@id": "bts:Lowergum" + "@id": "bts:Surgery" }, { - "@id": "bts:LowerlimbNOS" + "@id": "bts:TargetedMolecularTherapy" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:Unknown" }, { - "@id": "bts:Lowerthirdofesophagus" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [ + "list like" + ] + }, + { + "@id": "bts:TumorLargestDimensionDiameter", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", + "rdfs:label": "TumorLargestDimensionDiameter", + "rdfs:subClassOf": [ { - 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"@id": "bts:Temporallobe" + "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" }, { - "@id": "bts:TestisNOS" + "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" }, { - "@id": "bts:Thoracicesophagus" + "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" }, { - "@id": "bts:ThoraxNOS" + "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" }, { - "@id": "bts:Thymus" + "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" }, { - "@id": "bts:TongueNOS" + "@id": "bts:LLNOS(Leftlungnototherwisespecified)" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" }, { - "@id": "bts:Trachea" + "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" }, { - "@id": "bts:Transversecolon" + "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" }, { - "@id": "bts:Uppergum" + "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" }, { - "@id": "bts:Urachus" + "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" }, { - "@id": "bts:Ureter" + "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:LB6orificeAirwaywallbetweenLB6andLB6A/Bcarinae" }, { - "@id": "bts:Urethra" + "@id": "bts:LB1A/CCarinabetweentheapicalandlateralsubsegmentsoftheapicalsegmentleftupperlobe" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:LB1B/CCarinabetweenthemedialandlateralsubsegmentsoftheapicalsegmentoftheleftupperlobe" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:LB2A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheleftupperlobe" }, { - "@id": "bts:UterusNOS" + "@id": "bts:LB2A/CCarinabetweentheapicalandmedialsubsegmentsoftheposteriorsegmentoftheleftupperlobe" }, { - "@id": "bts:Uvula" + "@id": "bts:LB2B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentleftupperlobe" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:LB1+2/3Carinabetweentheapico-posteriorandanteriorsegmentsoftheleftupperlobe(CarinabetweenLB1+2orificeandLB3orifice)" }, { - "@id": "bts:Vallecula" + "@id": "bts:LB3A/BCarinabetweentheapicalandlateralsubsegmentsoftheanteriorsegmentoftheleftupperlobe" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:LULCarinabetweentheLULorificeandLLLorifice(airways)" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:LULorificeAirwaywallbetweenLULandLUDB" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:LB3orificeAnteriorsegmentleftupperlobe(airwaywallbetweenLB3andLB3A/Bcarinae)" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:LB4orificeSuperiorsegmentlingula(airwaywallbetweenLB4andLB4A/Bcarinae)" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:LB5orificeInferiorsegmentlingula(airwaywallbetweenLB5andLB5A/Bcarinae)" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:LLLorificeAirwaywallbetweenLULcarinaandLB6-10carinae" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:LB9orificeLateralsegmentleftlowerlobe(airwaywallbetweenLB9andLB9A/Bcarinae)" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:LB8orificeAnteriorsegmentleftlowerlobe(airwaywallbetweenLB8andLB8A/Bcarinae)" }, { - "@id": "bts:Clitoris" + "@id": "bts:LB10orificePosteriorsegmentleftlowerlobe(airwaywallbetweenLB10andLB10A/Bcarinae)" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -12519,18 +11748,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Site of Resection or Biopsy", - "sms:required": "sms:true", + "sms:displayName": "Lung Topography", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TissueorOrganofOrigin", + "@id": "bts:LungCancerHarboringGenomicAberrations", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "TissueorOrganofOrigin", + "rdfs:comment": "Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)", + "rdfs:label": "LungCancerHarboringGenomicAberrations", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -12538,1017 +11767,1699 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbdomenNOS" + "@id": "bts:G12AKRASmutation" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:G12CKRASmutation" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:G12DKRASmutation" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:G12RKRASmutation" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:G12SKRASmutation" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:G12VKRASmutation" }, { - "@id": "bts:Analcanal" + "@id": "bts:G13DKRASmutation" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:G13RKRASmutation" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:G13CKRASmutation" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:G13AKRASmutation" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:G13VKRASmutation" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:Q61LKRASmutation" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:Q61HKRASmutation" }, { - "@id": "bts:AnusNOS" + "@id": "bts:A146TKRASmutation" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:G719XEGFRmutation" }, { - "@id": "bts:Appendix" + "@id": "bts:T790MEGFRmutation" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:C797SEGFRmutation" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:L858REGFRmutation" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:L861QEGFRmutation" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:Exon19deletion" }, { - "@id": "bts:Bladderneck" + "@id": "bts:Exon20insertion" }, { - "@id": "bts:BladderNOS" + "@id": "bts:EML4-ALKtranslocation-variant1" }, { - "@id": "bts:Blood" + "@id": "bts:EML4-ALKtranslocation-variant2" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:EML4-ALKtranslocation-variant3" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:EML4-ALKtranslocation-variant4" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:EML4-ALKtranslocation-variant5" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:V600EBRAFmutation" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:V600DBRAFmutation" }, { - "@id": "bts:BoneNOS" + "@id": "bts:V600KBRAFmutation" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:V600RBRAFmutation" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:K601EBRAFmutation" }, { - "@id": "bts:Brainstem" + "@id": "bts:D963spliceMETmutation" }, { - "@id": "bts:BrainNOS" + "@id": "bts:D1010NMETmutation" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:D1010spliceMETmutation" }, { - "@id": "bts:BreastNOS" + "@id": "bts:Intron13mutation" }, { - "@id": "bts:Broadligament" + "@id": "bts:Intron14mutation" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:Exon14mutation" }, { - "@id": "bts:Carotidbody" + "@id": "bts:Exon14deletion" }, { - "@id": "bts:Caudaequina" + "@id": "bts:Other" }, { - "@id": "bts:Cecum" + "@id": "bts:Unknown" }, { - "@id": "bts:Centralportionofbreast" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ColorectalCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:CerebellumNOS" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Colorectal Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Cerebralmeninges" + "@id": "bts:Component" }, { - "@id": "bts:Cerebrum" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Choroid" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:ColorectalCancerDetectionMethodType" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:ColonNOS" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:PatientColonoscopyPerformedIndicator" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:ColorectalCancerTumorBorderConfiguration" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:MLH1PromoterMethylationStatus" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:ColorectalCancerKRASIndicator" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:ColonPolypOccurenceIndicator" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:FamilyHistoryColorectalPolyp" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:ColorectalPolypNewIndicator" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:ColorectalPolypShape" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:SizeofPolypRemoved" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:ColorectalPolypCount" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:ColorectalPolypType" }, { - "@id": "bts:Descendedtestis" - }, + "@id": "bts:ColorectalPolypAdenomaType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalCancerDetectionMethodType", + "@type": "rdfs:Class", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", + "rdfs:label": "ColorectalCancerDetectionMethodType", + "rdfs:subClassOf": [ { - "@id": "bts:Descendingcolon" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Domeofbladder" + "@id": "bts:Fecaloccultbloodtest" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Sigmoidoscopy" }, { - "@id": "bts:Duodenum" + "@id": "bts:Colonoscopy" }, { - "@id": "bts:Endocervix" + "@id": "bts:Virtualcolonoscopy" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:DNAstooltest" }, { - "@id": "bts:Endometrium" + "@id": "bts:Other" }, { - "@id": "bts:Epididymis" + "@id": "bts:Unknown" }, { - "@id": "bts:EsophagusNOS" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Colorectal Cancer Detection Method Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofPriorColonPolyps", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "HistoryofPriorColonPolyps", + "rdfs:subClassOf": [ { - "@id": "bts:Ethmoidsinus" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Exocervix" + "@id": "bts:Yes" }, { - "@id": "bts:Externalear" + "@id": "bts:No" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Externallowerlip" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "History of Prior Colon Polyps", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyColonCancerHistoryIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", + "rdfs:label": "FamilyColonCancerHistoryIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Externalupperlip" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:Yes" }, { - "@id": "bts:EyeNOS" + "@id": "bts:No" }, { - "@id": "bts:Eyelid" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Fallopiantube" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Family Colon Cancer History Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:FemalegenitaltractNOS" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:Yes" }, { - "@id": "bts:Frontallobe" + "@id": "bts:No" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Fundusofstomach" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", + "@type": "rdfs:Class", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", + "rdfs:subClassOf": [ { - "@id": "bts:Fundusuteri" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Gallbladder" + "@id": "bts:Beforeage50" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:Notbeforeage50" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Glanspenis" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Immediate Family History Endometrial Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmediateFamilyHistoryOvarianCancer", + "@type": "rdfs:Class", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", + "rdfs:subClassOf": [ { - "@id": "bts:Glottis" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:Beforeage50" }, { - "@id": "bts:GumNOS" + "@id": "bts:Notbeforeage50" }, { - "@id": "bts:Hardpalate" + "@id": "bts:Unknown" }, { - "@id": "bts:Headofpancreas" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Immediate Family History Ovarian Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", + "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "rdfs:subClassOf": [ { - "@id": "bts:HeadfaceorneckNOS" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Heart" + "@id": "bts:Yes-Crohn'sdisease" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:Yes-Ulcerativecolitis" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:No" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:Unknown" }, { - "@id": "bts:HypopharynxNOS" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PatientColonoscopyPerformedIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", + "rdfs:label": "PatientColonoscopyPerformedIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Ileum" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:Yes" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:No" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Intrahepaticbileduct" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Patient Colonoscopy Performed Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalCancerTumorBorderConfiguration", + "@type": "rdfs:Class", + "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", + "rdfs:label": "ColorectalCancerTumorBorderConfiguration", + "rdfs:subClassOf": [ { - 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Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. 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"@id": "bts:Roundligament" + "@id": "bts:Unknown" }, { - "@id": "bts:ScrotumNOS" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Cancer Assessment Tests", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerGenomicTestPerformed", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", + "rdfs:label": "BreastCancerGenomicTestPerformed", + "rdfs:subClassOf": [ { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:Oncotype" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:MammaPrint" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:Other" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:Unknown" }, { - "@id": "bts:Skinofscalpandneck" - }, + "@id": "bts:Notperformed" + } + ], + "sms:displayName": "Breast Cancer Genomic Test Performed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MammaprintRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "rdfs:label": "MammaprintRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:Skinoftrunk" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:Highrisk" }, { - "@id": "bts:SkinNOS" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:Lowrisk" }, { - "@id": "bts:SoftpalateNOS" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Specifiedpartsofperitoneum" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Mammaprint Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OncotypeRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "rdfs:label": "OncotypeRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:Spermaticcord" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Sphenoidsinus" + "@id": "bts:Highrisk" }, { - "@id": "bts:Spinalcord" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:Lowrisk" }, { - "@id": "bts:Spleen" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Splenicflexureofcolon" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Oncotype Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaEstrogenReceptorStatus", + "rdfs:subClassOf": [ { - "@id": "bts:StomachNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Subglottis" + "@id": "bts:Borderline" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:Equivocal" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Superiorwallofnasopharynx" + "@id": "bts:Negative" }, { - "@id": "bts:Supraglottis" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Tailofpancreas" + "@id": "bts:PerformedbutNotAvailable" }, { - "@id": "bts:Temporallobe" + "@id": "bts:Positive" }, { - "@id": "bts:TestisNOS" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Estrogen Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Thoracicesophagus" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ThoraxNOS" + "@id": "bts:Borderline" }, { - "@id": "bts:Thymus" + "@id": "bts:Equivocal" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:Indeterminate" }, { - "@id": "bts:TongueNOS" + "@id": "bts:Negative" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:PerformedbutNotAvailable" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:Positive" }, { - "@id": "bts:Trachea" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAllredEstrogenReceptorScore", + "@type": "rdfs:Class", + "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "rdfs:label": "BreastCancerAllredEstrogenReceptorScore", + "rdfs:subClassOf": [ { - "@id": "bts:Transversecolon" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Trigoneofbladder" + "@id": "bts:0" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:1" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:2" }, { - "@id": "bts:Uppergum" + "@id": "bts:3" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:4" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:5" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:6" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:7" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:8" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:10" }, { - "@id": "bts:Urachus" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Cancer Allred Estrogen Receptor Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorInvasiveBreastDisease", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate prior invasive breast condition in the participant", + "rdfs:label": "PriorInvasiveBreastDisease", + "rdfs:subClassOf": [ { - "@id": "bts:Ureter" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Uretericorifice" + "@id": "bts:DCIS" }, { - "@id": "bts:Urethra" + "@id": "bts:LCIS" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:Other" }, { - "@id": "bts:UterusNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Uvula" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Prior Invasive Breast Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaERStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStatusPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:VaginaNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma ER Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaPRStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStatusPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:Vallecula" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label": "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:subClassOf": [ { - "@id": "bts:VentralsurfaceoftongueNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaCentromere17CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", + "rdfs:label": "BreastCarcinomaCentromere17CopyNumber", + "rdfs:subClassOf": [ { - "@id": "bts:VentricleNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", + "rdfs:subClassOf": [ { - "@id": "bts:Vertebralcolumn" + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", + "@type": "rdfs:Class", + "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaSurgicalProcedureName", + "@type": "rdfs:Class", + "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "rdfs:label": "BreastCarcinomaSurgicalProcedureName", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Lumpectomy" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:Radicalmastectomy" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:Modifiedradicalmastectomy" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:Other" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:Partialmastectomy" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:Re-excision" }, { - "@id": "bts:Clitoris" + "@id": "bts:Simplemastectomy" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:Surgerynotperformed" }, { "@id": "bts:Unknown" - }, + } + ], + "sms:displayName": "Breast Carcinoma Surgical Procedure Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "HER2 ratio of the participant at diagnosis", + "rdfs:label": "BreastCarcinomaHER2RatioDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:BreastCancerTier3" } ], - "sms:displayName": "Tissue or Organ of Origin", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Ratio Diagnosis", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NCIAtlasCancerSite", + "@id": "bts:BreastCarcinomaHER2Status", "@type": "rdfs:Class", - "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", - "rdfs:label": "NCIAtlasCancerSite", + "rdfs:comment": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Status", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -13556,84 +13467,116 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Bladder" + "@id": "bts:Positive" }, { - "@id": "bts:BrainAndOtherNervousSystem" + "@id": "bts:Negative" }, { - "@id": "bts:FemaleBreast" + "@id": "bts:Amplified" }, { - "@id": "bts:InsituFemaleBreast" + "@id": "bts:Non-amplified" }, { - "@id": "bts:CervixUteri" + "@id": "bts:Equivocal" }, { - "@id": "bts:LessThanAge" + "@id": "bts:Indeterminate" }, { - "@id": "bts:MalignantChildhoodNeoplasm" + "@id": "bts:NotPerformed" }, { - "@id": "bts:ColonAndRectum" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma HER2 Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "Did the patient receive hormonal therapy for prevention of breast cancer?", + "rdfs:label": "HormoneTherapyBreastCancerPreventionIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Esophagus" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:KidneyAndRenalPelvis" + "@id": "bts:Yes" }, { - "@id": "bts:Leukemia" + "@id": "bts:No" }, { - "@id": "bts:LiverAndBileDuct" + "@id": "bts:Unknown" }, { - "@id": "bts:LungAndBronchus" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Hormone Therapy Breast Cancer Prevention Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaERStainingIntensity", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStainingIntensity", + "rdfs:subClassOf": [ { - "@id": "bts:CutaneousMelanoma" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Non-Hodgkin'sLymphoma" + "@id": "bts:Strong" }, { - "@id": "bts:OralCavityAndPharynx" + "@id": "bts:Moderate" }, { - "@id": "bts:Ovary" + "@id": "bts:Weak" }, { - "@id": "bts:Pancreas" + "@id": "bts:Weak-Moderate" }, { - "@id": "bts:ProstateGland" + "@id": "bts:Moderate-Strong" }, { - "@id": "bts:Stomach" + "@id": "bts:Weak-Strong" }, { - "@id": "bts:ThyroidGland" + "@id": "bts:Other" }, { - "@id": "bts:Uterus" + "@id": "bts:Unknown" } ], - "sms:displayName": "NCI Atlas Cancer Site", + "sms:displayName": "Breast Carcinoma ER Staining Intensity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorGrade", + "@id": "bts:BreastCarcinomaPRStainingIntensity", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", - "rdfs:label": "TumorGrade", + "rdfs:comment": "Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStainingIntensity", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -13641,124 +13584,164 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:G1" - }, - { - "@id": "bts:G2" - }, - { - "@id": "bts:G3" + "@id": "bts:Strong" }, { - "@id": "bts:G4" + "@id": "bts:Moderate" }, { - "@id": "bts:GX" + "@id": "bts:Weak" }, { - "@id": "bts:GB" + "@id": "bts:Weak-Moderate" }, { - "@id": "bts:HighGrade" + "@id": "bts:Moderate-Strong" }, { - "@id": "bts:IntermediateGrade" + "@id": "bts:Weak-Strong" }, { - "@id": "bts:LowGrade" + "@id": "bts:Other" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Tumor Grade", + "sms:displayName": "Breast Carcinoma PR Staining Intensity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PackYearsSmoked", + "@id": "bts:OncotypeScore", "@type": "rdfs:Class", - "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", - "rdfs:label": "PackYearsSmoked", + "rdfs:comment": "OncotypeDX recurrence score", + "rdfs:label": "OncotypeScore", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pack Years Smoked", - "sms:required": "sms:true", + "sms:displayName": "Oncotype Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearsSmoked", + "@id": "bts:BreastImagingPerformedType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", - "rdfs:label": "YearsSmoked", + "rdfs:comment": "The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).", + "rdfs:label": "BreastImagingPerformedType", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Years Smoked", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Mammogram" + }, + { + "@id": "bts:Ultrasound" + }, + { + "@id": "bts:MRI" + }, + { + "@id": "bts:PET/CT" + }, + { + "@id": "bts:CT" + }, + { + "@id": "bts:Multipleimagingmodalities" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Imaging Performed Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoFollowUp", + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoFollowUp", + "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.", + "rdfs:label": "MultifocalBreastCarcinomaPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Follow Up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Multifocal Breast Carcinoma Present Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:GeneSymbol", + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "GeneSymbol", + "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.", + "rdfs:label": "MulticentricBreastCarcinomaPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gene Symbol", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Multicentric Breast Carcinoma Present Indicator", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MolecularAnalysisMethod", + "@id": "bts:BIRADSMammographyBreastDensityCategory", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularAnalysisMethod", + "rdfs:comment": "The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.", + "rdfs:label": "BIRADSMammographyBreastDensityCategory", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -13766,81 +13749,88 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ComparativeGenomicHybridization" - }, - { - "@id": "bts:CytogeneticsNOS" - }, - { - "@id": "bts:FISH" - }, - { - "@id": "bts:FlowCytometry" + "@id": "bts:Predominantlyfatty" }, { - "@id": "bts:IHC" + "@id": "bts:Scatteredfibroglandulardensities" }, { - "@id": "bts:ISH" + "@id": "bts:Heterogeneouslydense" }, { - "@id": "bts:Karyotype" + "@id": "bts:Extremelydense" }, { - "@id": "bts:Microarray" + "@id": "bts:Unknown" }, { - "@id": "bts:MicrosatelliteAnalysis" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "BIRADS Mammography Breast Density Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NeuroblastomaandGliomaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Brain cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "NeuroblastomaandGliomaTier3", + "rdfs:subClassOf": [ { - "@id": "bts:NuclearStaining" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Neuroblastoma and Glioma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Other" + "@id": "bts:Component" }, { - "@id": "bts:RNASequencing" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:RT-PCR" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:SequencingNOS" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:SouthernBlotting" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:TargetedSequencing" + "@id": "bts:CNSTumorPrimaryAnatomicSite" }, { - "@id": "bts:WGS" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:WXS" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:Unknown" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:NotReported" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus" } ], - "sms:displayName": "Molecular Analysis Method", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TestResult", + "@id": "bts:CNSTumorPrimaryAnatomicSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestResult", + "rdfs:comment": "Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2", + "rdfs:label": "CNSTumorPrimaryAnatomicSite", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:NeuroblastomaandGliomaTier3" } ], "schema:isPartOf": { @@ -13848,63 +13838,72 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbnormalNOS" + "@id": "bts:Thalamus" }, { - "@id": "bts:CopyNumberReported" + "@id": "bts:Ventricles" }, { - "@id": "bts:Equivocal" + "@id": "bts:Intracranial/Leptomeningeal" }, { - "@id": "bts:High" + "@id": "bts:Suprasellar/Hypothalamic/Pituitary" }, { - "@id": "bts:Intermediate" + "@id": "bts:Cerebellar/Posteriorfossa" }, { - "@id": "bts:LossofExpression" + "@id": "bts:Brainstem-Medulla" }, { - "@id": "bts:Low" + "@id": "bts:Brainstem-Midbrain/Tectum" }, { - "@id": "bts:Negative" + "@id": "bts:Brainstem-Pons" }, { - "@id": "bts:Normal" + "@id": "bts:Spinalcord-Cervical" }, { - "@id": "bts:Overexpressed" + "@id": "bts:Spinalcord-Thoracic" }, { - "@id": "bts:Positive" + "@id": "bts:Spinalcord-Lumbar" }, { - "@id": "bts:TestValueReported" + "@id": "bts:Opticpathway" }, { - "@id": "bts:Unknown" + "@id": "bts:OtherlocationsNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:Paraspinalganglion" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Basalganglia" + }, + { + "@id": "bts:Hippocampus" + }, + { + "@id": "bts:Meninges/Dura" + }, + { + "@id": "bts:Otherlymphnodes" } ], - "sms:displayName": "Test Result", - "sms:required": "sms:true", + "sms:displayName": "CNS Tumor Primary Anatomic Site", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentType", + "@id": "bts:GliomaSpecificMetastasisSites", "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of treatment administered.", - "rdfs:label": "TreatmentType", + "rdfs:comment": "Evidence of active brain metastasis including leptomeningeal involvement", + "rdfs:label": "GliomaSpecificMetastasisSites", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:NeuroblastomaandGliomaTier3" } ], "schema:isPartOf": { @@ -13912,214 +13911,163 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AblationCryo" - }, - { - "@id": "bts:AblationEthanolInjection" - }, - { - "@id": "bts:AblationMicrowave" - }, - { - "@id": "bts:AblationNOS" - }, - { - "@id": "bts:AblationRadiofrequency" - }, - { - "@id": "bts:AblationRadiosurgical" - }, - { - "@id": "bts:AncillaryTreatment" - }, - { - "@id": "bts:AntiseizureTreatment" - }, - { - "@id": "bts:BisphosphonateTherapy" - }, - { - "@id": "bts:BlindedStudyTreatmentunknown" - }, - { - "@id": "bts:BrachytherapyHighDose" - }, - { - "@id": "bts:BrachytherapyLowDose" - }, - { - "@id": "bts:BrachytherapyNOS" - }, - { - "@id": "bts:Chemoembolization" - }, - { - "@id": "bts:Chemoprotectant" - }, - { - "@id": "bts:Chemotherapy" - }, - { - "@id": "bts:ConcurrentChemoradiation" - }, - { - "@id": "bts:Cryoablation" - }, - { - "@id": "bts:Embolization" - }, - { - "@id": "bts:EthanolInjectionAblation" - }, - { - "@id": "bts:ExternalBeamRadiation" - }, - { - "@id": "bts:HormoneTherapy" - }, - { - "@id": "bts:I-131RadiationTherapy" - }, - { - "@id": "bts:InternalRadiation" + "@id": "bts:CSF" }, { - "@id": "bts:Immunotherapy(IncludingVaccines)" + "@id": "bts:Spine" }, { - "@id": "bts:IsolatedLimbPerfusion(ILP)" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:OrganTransplantation" + "@id": "bts:Brain" }, { "@id": "bts:Other" }, { - "@id": "bts:PharmaceuticalTherapyNOS" - }, - { - "@id": "bts:Pleurodesis" - }, - { - "@id": "bts:Radiation2DConventional" - }, - { - "@id": "bts:Radiation3DConformal" - }, - { - "@id": "bts:RadiationCombination" - }, - { - "@id": "bts:RadiationCyberknife" - }, - { - "@id": "bts:RadiationExternalBeam" - }, - { - "@id": "bts:RadiationImplants" - }, - { - "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" - }, - { - "@id": "bts:RadiationInternal" - }, - { - "@id": "bts:RadiationProtonBeam" - }, - { - "@id": "bts:RadiationRadioisotope" - }, - { - "@id": "bts:RadiationStereotactic/GammaKnife/SRS" - }, - { - "@id": "bts:RadiationSystemic" - }, - { - "@id": "bts:RadiationTherapyNOS" + "@id": "bts:Leptomeningeal" }, { - "@id": "bts:RadioactiveIodineTherapy" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Glioma Specific Metastasis Sites", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GliomaSpecificRadiationField", + "@type": "rdfs:Class", + "rdfs:comment": "A description of the location on or within the CNS where radiation was administered in a partcipant with glioma", + "rdfs:label": "GliomaSpecificRadiationField", + "rdfs:subClassOf": [ { - "@id": "bts:Radioembolization" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RadiosensitizingAgent" + "@id": "bts:Craniospinal" }, { - "@id": "bts:StemCellTreatment" + "@id": "bts:Focal-tumorbed" }, { - "@id": "bts:StemCellTransplantationAutologous" + "@id": "bts:Unknown" }, { - "@id": "bts:StemCellTransplantationDoubleAutologous" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Glioma Specific Radiation Field", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the molecular subgroup in a supra tentorial ependymoma", + "rdfs:label": "SupraTentorialEpendymomaMolecularSubgroup", + "rdfs:subClassOf": [ { - "@id": "bts:StemCellTransplantationAllogeneic" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StemCellTransplantationNon-Myeloablative" + "@id": "bts:ST-EPN-RELA" }, { - "@id": "bts:StemCellTransplantationSyngenic" + "@id": "bts:ST-EPN-YAP1" }, { - "@id": "bts:StemCellTransplantationHaploidentical" + "@id": "bts:Unknown" }, { - "@id": "bts:StemCellTransplantationNOS" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Supra Tentorial Ependymoma Molecular Subgroup", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the molecular subgroup in a infra tentorial ependymoma", + "rdfs:label": "InfraTentorialEpendymomaMolecularSubgroup", + "rdfs:subClassOf": [ { - "@id": "bts:StereotacticRadiosurgery" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SteroidTherapy" + "@id": "bts:PF-EPN-A" }, { - "@id": "bts:Surgery" + "@id": "bts:PF-EPN-B" }, { - "@id": "bts:TargetedMolecularTherapy" + "@id": "bts:Myxopapillaryependymoma" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Treatment Type", + "sms:displayName": "Infra Tentorial Ependymoma Molecular Subgroup", "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] + "sms:validationRules": [] }, { - "@id": "bts:TumorLargestDimensionDiameter", + "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", - "rdfs:label": "TumorLargestDimensionDiameter", + "rdfs:comment": "Neuroblastoma MYCN amplification or over-expression status", + "rdfs:label": "NeuroblastomaMYCNGeneAmplificationStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:NeuroblastomaandGliomaTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Largest Dimension Diameter", + "schema:rangeIncludes": [ + { + "@id": "bts:Amplified" + }, + { + "@id": "bts:Notamplified" + }, + { + "@id": "bts:Notdone" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Neuroblastoma MYCN Gene Amplification Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerTier3", + "@id": "bts:AcuteLymphoblasticLeukemiaTier3", "@type": "rdfs:Class", - "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "LungCancerTier3", + "rdfs:comment": "Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3", + "rdfs:label": "AcuteLymphoblasticLeukemiaTier3", "rdfs:subClassOf": [ { "@id": "bts:Patient" @@ -14128,7 +14076,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lung Cancer Tier 3", + "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -14147,40 +14095,73 @@ "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:LungCancerDetectionMethodType" + "@id": "bts:SpecimenBlastCountPercentageValue" }, { - "@id": "bts:LungCancerParticipantProcedureHistory" + "@id": "bts:NCIALLRiskGroup" }, { - "@id": "bts:LungAdjacentHistologyType" + "@id": "bts:MRDALLDiagnosticSensitivity" }, { - "@id": "bts:LungTumorLocationAnatomicSite" - }, + "@id": "bts:CNSLeukemiaStatus" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SpecimenBlastCountPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis", + "rdfs:label": "SpecimenBlastCountPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:LungTumorLobeBronchialLocation" - }, + "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Specimen Blast Count Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NCIALLRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.", + "rdfs:label": "NCIALLRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:CurrentLungCancerSymptoms" + "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:NCIHighRisk" }, { - "@id": "bts:LungTopography" + "@id": "bts:NCIStandardRisk" }, { - "@id": "bts:LungCancerHarboringGenomicAberrations" + "@id": "bts:Unknown" } ], + "sms:displayName": "NCI ALL Risk Group", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerDetectionMethodType", + "@id": "bts:MRDALLDiagnosticSensitivity", "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", - "rdfs:label": "LungCancerDetectionMethodType", + "rdfs:comment": "The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.", + "rdfs:label": "MRDALLDiagnosticSensitivity", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:AcuteLymphoblasticLeukemiaTier3" } ], "schema:isPartOf": { @@ -14188,36 +14169,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:LowDoseComputedTomography(LDCT)" + "@id": "bts:Optimal" }, { - "@id": "bts:ChestX-ray" + "@id": "bts:Suboptimal" }, { - "@id": "bts:ChestCT" + "@id": "bts:Indeterminate" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - }, - { - "@id": "bts:Other" } ], - "sms:displayName": "Lung Cancer Detection Method Type", + "sms:displayName": "MRD ALL Diagnostic Sensitivity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerParticipantProcedureHistory", + "@id": "bts:CNSLeukemiaStatus", "@type": "rdfs:Class", - "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", - "rdfs:label": "LungCancerParticipantProcedureHistory", + "rdfs:comment": "The status of central nervous system leukemia at the time of diagnosis.", + "rdfs:label": "CNSLeukemiaStatus", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:AcuteLymphoblasticLeukemiaTier3" } ], "schema:isPartOf": { @@ -14225,69 +14200,94 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:LobectomyBilateral" + "@id": "bts:CNS1" }, { - "@id": "bts:LobectomyLeft" + "@id": "bts:CNS2" }, { - "@id": "bts:LobectomyRight" + "@id": "bts:CNS3" }, { - "@id": "bts:LungWedgeResectionBilateral" + "@id": "bts:CNS2a" }, { - "@id": "bts:LungWedgeResectionLeft" + "@id": "bts:CNS2b" }, { - "@id": "bts:LungWedgeResectionMultiple" + "@id": "bts:CNS2c" }, { - "@id": "bts:LungWedgeResectionRight" + "@id": "bts:CNS3a" }, { - "@id": "bts:PneumonectomyLeft" + "@id": "bts:CNS3b" }, { - "@id": "bts:PneumonectomyRight" + "@id": "bts:CNS3c" }, { - "@id": "bts:Endobronchialbiopsy" + "@id": "bts:Notevaluated" }, { - "@id": "bts:Mediastinoscopy" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "CNS Leukemia Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Ovarian cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "OvarianCancerTier3", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ovarian Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:VATSSclerosis" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Brainresection" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Segmentectomy" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Unknown" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Other" + "@id": "bts:OvarianCancerHistologicSubtype" }, { - "@id": "bts:NotReported" + "@id": "bts:OvarianCancerSurgicalOutcome" + }, + { + "@id": "bts:OvarianCancerPlatinumStatus" } ], - "sms:displayName": "Lung Cancer Participant Procedure History", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungAdjacentHistologyType", + "@id": "bts:OvarianCancerHistologicSubtype", "@type": "rdfs:Class", - "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", - "rdfs:label": "LungAdjacentHistologyType", + "rdfs:comment": "Text term to describe the histological subtype of ovarian cancer in the participant", + "rdfs:label": "OvarianCancerHistologicSubtype", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:OvarianCancerTier3" } ], "schema:isPartOf": { @@ -14295,43 +14295,28 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Lungadenocarcinoma" - }, - { - "@id": "bts:Adenosquamouscarcinoma" - }, - { - "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" - }, - { - "@id": "bts:Lungadenocarcinomainsitu" - }, - { - "@id": "bts:Largecelllungcarcinoma" - }, - { - "@id": "bts:Largecellneuroendocrinecarcinoma" + "@id": "bts:High-gradeserous" }, { - "@id": "bts:Lunglymphoepithelioma-likecarcinoma" + "@id": "bts:Low-gradeserous" }, { - "@id": "bts:Bronchioalveolarcarcinoma" + "@id": "bts:High-gradeendometrioid" }, { - "@id": "bts:ThoracicNUTcarcinoma" + "@id": "bts:Low-gradeendometrioid" }, { - "@id": "bts:Sarcomatoidcarcinoma" + "@id": "bts:Clearcell" }, { - "@id": "bts:Smallcelllungcarcinoma" + "@id": "bts:Mucinous" }, { - "@id": "bts:Squamouscelllungcarcinoma" + "@id": "bts:Sex-cordstromal" }, { - "@id": "bts:Lungsquamouscellcarcinomainsitu" + "@id": "bts:Germcell" }, { "@id": "bts:Other" @@ -14340,21 +14325,21 @@ "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Lung Adjacent Histology Type", + "sms:displayName": "Ovarian Cancer Histologic Subtype", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungTumorLocationAnatomicSite", + "@id": "bts:OvarianCancerSurgicalOutcome", "@type": "rdfs:Class", - "rdfs:comment": "Anatomic location of the tumor inside the lung", - "rdfs:label": "LungTumorLocationAnatomicSite", + "rdfs:comment": "Text term that describes the kind of surgical treatment administered.", + "rdfs:label": "OvarianCancerSurgicalOutcome", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:OvarianCancerTier3" } ], "schema:isPartOf": { @@ -14362,33 +14347,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Maincarina" + "@id": "bts:R0resection" }, { - "@id": "bts:Left" + "@id": "bts:Optimalcytoreduction" }, { - "@id": "bts:Right" + "@id": "bts:Sub-optimalcytoreduction" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Lung Tumor Location Anatomic Site", + "sms:displayName": "Ovarian Cancer Surgical Outcome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungTumorLobeBronchialLocation", + "@id": "bts:OvarianCancerPlatinumStatus", "@type": "rdfs:Class", - "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", - "rdfs:label": "LungTumorLobeBronchialLocation", + "rdfs:comment": "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", + "rdfs:label": "OvarianCancerPlatinumStatus", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:OvarianCancerTier3" } ], "schema:isPartOf": { @@ -14396,134 +14384,147 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Upperlobe" - }, - { - "@id": "bts:Middlelobe" + "@id": "bts:Platinum-refractory" }, { - "@id": "bts:Lowerlobe" + "@id": "bts:Platinum-sensitive" }, { - "@id": "bts:Stump" + "@id": "bts:Platinum-resistant" }, { - "@id": "bts:Bronchus" + "@id": "bts:Datanotavailable" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Tumor Lobe Bronchial Location", + "sms:displayName": "Ovarian Cancer Platinum Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CurrentLungCancerSymptoms", + "@id": "bts:ProstateCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", - "rdfs:label": "CurrentLungCancerSymptoms", + "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ProstateCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Prostate Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Asbestosis" + "@id": "bts:Component" }, { - "@id": "bts:Productivecough" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Non-productivecough" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Wheezing" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Rhonci" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Crackles" + "@id": "bts:LocationExtentExtraprostaticExtension" }, { - "@id": "bts:Hemoptysis" + "@id": "bts:LocationNaturePositiveMargins" }, { - "@id": "bts:Dyspnea" + "@id": "bts:SeminalVesicleInvasion" }, { - "@id": "bts:Unexplainedweightloss" + "@id": "bts:ProstateCarcinomaHistologicType" }, { - "@id": "bts:Unexplainedlossofenergy/fatigue" + "@id": "bts:ProstateCancerLocalExtent" }, { - "@id": "bts:Chestpainordiscomfort" + "@id": "bts:AdditonalFindingsUninvolvedProstate" }, { - "@id": "bts:Dysphagia" - }, + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:LocationExtentExtraprostaticExtension", + "@type": "rdfs:Class", + "rdfs:comment": "Location and extent of extraprostatic extension", + "rdfs:label": "LocationExtentExtraprostaticExtension", + "rdfs:subClassOf": [ { - "@id": "bts:Pneumonia" + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:LeftAnterior" }, { - "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" + "@id": "bts:LeftLateral" }, { - "@id": "bts:Airentrydecreased/fair/poor/diminished" + "@id": "bts:LeftPosterolateral" }, { - "@id": "bts:Fair/pooraeration" + "@id": "bts:LeftPosterior" }, { - "@id": "bts:Shallowinspiration" + "@id": "bts:LeftApex" }, { - "@id": "bts:Breathsoundscoarse/diminished" + "@id": "bts:LeftMid" }, { - "@id": "bts:Dullnesstopercussion" + "@id": "bts:LeftBase" }, { - "@id": "bts:Abnormalbreathsounds" + "@id": "bts:LeftFocal" }, { - "@id": "bts:Clearlungstoauscultationorpercussion" + "@id": "bts:LeftNon-focal(established)" }, { - "@id": "bts:Unlabored/normalbreathing" + "@id": "bts:RightAnterior" }, { - "@id": "bts:Coldsymptoms/flu/sinus/nasalcongestion" + "@id": "bts:RightLateral" }, { - "@id": "bts:Sinuspain/infection" + "@id": "bts:RightPosterolateral" }, { - "@id": "bts:Fingerclubbing" + "@id": "bts:RightPosterior" }, { - "@id": "bts:Noevidenceoflungcancerrecurrence" + "@id": "bts:RightApex" }, { - "@id": "bts:PatientisNED" + "@id": "bts:RightMid" }, { - "@id": "bts:Oxygensupplemental-portableO2atnightorcontinuous" + "@id": "bts:RightBase" }, { - "@id": "bts:Prolongedexpiration-long/forcedexpiratoryphase" + "@id": "bts:RightFocal" }, { - "@id": "bts:Other" + "@id": "bts:RightNon-focal(established)" }, { "@id": "bts:Unknown" @@ -14532,18 +14533,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Current Lung Cancer Symptoms", + "sms:displayName": "Location Extent Extraprostatic Extension", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungTopography", + "@id": "bts:LocationNaturePositiveMargins", "@type": "rdfs:Class", - "rdfs:comment": "Lung PCA specific topography (not covered in previous tiers)", - "rdfs:label": "LungTopography", + "rdfs:comment": "Location and nature of positive margins", + "rdfs:label": "LocationNaturePositiveMargins", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -14551,256 +14552,371 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MC-Carinabetweenrightandleftlungs(maincarina)" + "@id": "bts:LeftAnterior" }, { - "@id": "bts:TR-Trachea(airwaywallbetweentracheo-esophagealbifurcationandmaincarina)" + "@id": "bts:LeftLateral" }, { - "@id": "bts:CarinaNOS(Carinanototherwisespecified)" + "@id": "bts:LeftPosterolateral" }, { - "@id": "bts:LUDB-Carinabetweenthelingulaandupperdivisionleftupperlobe" + "@id": "bts:LeftPosterior" }, { - "@id": "bts:CarinabetweenLUDBorificeandlingulaorifice" + "@id": "bts:LeftApex" }, { - "@id": "bts:LUDB-orificeairwaywallbetweenLUDBandLB3(LB1+2carinae)" + "@id": "bts:LeftMid" }, { - "@id": "bts:LingulaorificeairwaywallbetweenLUDBandLB4/5carinae" + "@id": "bts:LeftBase" }, { - "@id": "bts:RMB-Rightmainstembronchus(airwaywallbetweenMC&RULcarina)" + "@id": "bts:LeftFocal" }, { - "@id": "bts:LMB-Leftmainstembronchus(airwaywallbetweenMC&LULcarina)" + "@id": "bts:LeftExtensive" }, { - "@id": "bts:RLNOS(Rightlungnototherwisespecified)" + "@id": "bts:LeftPositiveinanareaofextraprostaticextension(EPE)" }, { - "@id": "bts:RB1/2-Carinabetweenapicalandposteriorsegmentsrightupperlobe(CarinabetweenRB1orificeandRB2orifice)" + "@id": "bts:LeftPositiveinanareaofintraprostaticincision(II)" }, { - "@id": "bts:RB6A/B-CarinabetweenapicalandlateralsubsegmentssuperiorsegmentRLL" + "@id": "bts:LeftPositivewhereitisdifficulttodistinguishEPEvsII" }, { - "@id": "bts:RB6A/C-CarinabetweenapicalandmedialsubsegmentssuperiorsegmentRLL" + "@id": "bts:RightAnterior" }, { - "@id": "bts:RB6B/C-CarinabetweenmedialandlateralsubsegmentssuperiorsegmentRLL" + "@id": "bts:RightLateral" }, { - "@id": "bts:RB7A/B-CarinabetweenmedialandlateralsubsegmentsmedialbasalsegmentRLL" + "@id": "bts:RightPosterolateral" }, { - "@id": "bts:RB8/9-CarinabetweenanteriorandlateralsegmentsRLL(CarinabetweenRB8orificeandRB9orifice)" + "@id": "bts:RightPosterior" }, { - "@id": "bts:RB8A/B-CarinabetweenmedialandlateralsubsegmentsanteriorsegmentRLL" + "@id": "bts:RightApex" }, { - "@id": "bts:RB9/10-CarinabetweenlateralandposteriorsegmentsRLL" + "@id": "bts:RightMid" }, { - "@id": "bts:RB9A/B-CarinabetweenmedialandlateralsubsegmentslateralsegmentRLL" + "@id": "bts:RightBase" }, { - "@id": "bts:RB10A/B-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" + "@id": "bts:RightFocal" }, { - "@id": "bts:RB10A/C-CarinabetweenmedialandapicalsubsegmentsposteriorsegmentRLL" + "@id": "bts:RightExtensive" }, { - "@id": "bts:RB1A/B-CarinabetweenmedialandlateralsubsegmentsapicalsegmentRUL" + "@id": "bts:RightPositiveinanareaofextraprostaticextension(EPE)" }, { - "@id": "bts:RB10B/C-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" + "@id": "bts:RightPositiveinanareaofintraprostaticincision(II)" }, { - "@id": "bts:RB6-CarinaofsuperiorsegmentRLL(CarinabetweenRB6orificeandlowerportionofRLLorifice)" + "@id": "bts:RightPositivewhereitisdifficulttodistinguishEPEvsII" }, { - "@id": "bts:RB6orificeAirwaywallbetweenRB6andRB6A/B/Ccarinae" + "@id": "bts:Bladderneck(blockPUM)" }, { - "@id": "bts:BronchusIntermediusBronchus(airwaywall)betweenrightupperandrightmiddlelobes" + "@id": "bts:Vasdeferens" }, { - "@id": "bts:RB1/3-CarinabetweenapicalandanteriorsegmentsRUL(CarinabetweenRB1orificeandRB3orifice)" + "@id": "bts:Apicalmargin(blockDUM)" }, { - "@id": "bts:RB2/3-CarinabetweenanteriorandposteriorsegmentsRUL(CarinabetweenRB2orificeandRB3orifice)" + "@id": "bts:Unknown" }, { - "@id": "bts:RB2A/B-Carinabetweenthemedialandlateralsubsegmentsoftheposteriorsegment(RUL)" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Location Nature Positive Margins", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SeminalVesicleInvasion", + "@type": "rdfs:Class", + "rdfs:comment": "An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.", + "rdfs:label": "SeminalVesicleInvasion", + "rdfs:subClassOf": [ { - "@id": "bts:RB3A/B-CarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentRUL" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RB4/5-Carinabetweenthelateralandmedialsegmentsrightmiddlelobe(CarinabetweenRB4orificeandRB5orifice)" + "@id": "bts:None" }, { - "@id": "bts:RB4A/B-Carinabetweenthemedialandlateralsubsegmentsofthelateralsegmentoftherightmiddlelobe" + "@id": "bts:Left" }, { - "@id": "bts:RB5A/B-Carinabetweenthemedialandlateralsubsegmentsofthemedialsegmentoftherightmiddlelobe" + "@id": "bts:Right" }, { - "@id": "bts:RULCarinaebetweenRULorificeandbronchusintermedius" + "@id": "bts:Bothsides" }, { - "@id": "bts:RULorificeAirwaywallbetweenRULandRB1/RB2/RB3" + "@id": "bts:Unknown" }, { - "@id": "bts:RB1orificeApicalsegment-rightupperlobe(airwaywallbetweenRB1andRB1A/Bcarinae)" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Seminal Vesicle Invasion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCarcinomaHistologicType", + "@type": "rdfs:Class", + "rdfs:comment": "The diagnostic subclassification of an invasive prostate carcinoma.", + "rdfs:label": "ProstateCarcinomaHistologicType", + "rdfs:subClassOf": [ { - "@id": "bts:RB2orificePosteriorsegment-rightupperlobe(airwaywallbetweenRB2andRB2A/Bcarinae)" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RB3orificeAnteriorsegment-rightupperlobe(airwaywallbetweenRB3andRB3A/Bcarinae)" + "@id": "bts:Prostaticadenocarcinoma(conventionalNOS)" }, { - "@id": "bts:RML-CarinabetweenRMLorificeandRLLorifice" + "@id": "bts:Prostaticductadenocarcinoma" }, { - "@id": "bts:RMLorificeAirwaywallbetweenRMLandRB4/5" + "@id": "bts:Acinarprostatemucinous(colloid)adenocarcinoma" }, { - "@id": "bts:RB4orificeLateralsegmentrightmiddlelobe(airwaywallbetweenRB4andRB4A/Bcarinae)" + "@id": "bts:Acinarprostateadenocarcinoma-signet-ringvariant" }, { - "@id": "bts:RB5orificeMedialsegmentrightmiddlelobe(airwaywallbetweenRB5andRB5A/Bcarinae)" + "@id": "bts:Prostaticadenosquamouscarcinoma" }, { - "@id": "bts:RLLorificeAirwaywallbetweenRMLandRB6-10carinae" + "@id": "bts:Acinarprostatemucinousadenocarcinoma" }, { - "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" + "@id": "bts:Prostaticsmallcellcarcinoma" }, { - "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" + "@id": "bts:Acinarprostateadenocarcinoma-sarcomatoidvariant" }, { - "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" + "@id": "bts:UndifferentiatedcarcinomaNOS" }, { - "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Prostate Carcinoma Histologic Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCancerLocalExtent", + "@type": "rdfs:Class", + "rdfs:comment": "The response used to categorize the local extent of disease for prostate cancer.", + "rdfs:label": "ProstateCancerLocalExtent", + "rdfs:subClassOf": [ { - "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" + "@id": "bts:OrganConfined" }, { - "@id": "bts:LLNOS(Leftlungnototherwisespecified)" + "@id": "bts:Extraprostaticextension" }, { - "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" + "@id": "bts:Unknown" }, { - "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Prostate Cancer Local Extent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdditonalFindingsUninvolvedProstate", + "@type": "rdfs:Class", + "rdfs:comment": "Additional findings, uninvolved prostate", + "rdfs:label": "AdditonalFindingsUninvolvedProstate", + "rdfs:subClassOf": [ { - "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" + "@id": "bts:High-gradeprostaticintraepithelialneoplasia(PIN)" }, { - "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" + "@id": "bts:Inflammation" }, { - "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" + "@id": "bts:Benignprostatichyperplasia(BPH)" }, { - "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" + "@id": "bts:ProstaticIntraductaladenocarcinoma" }, { - "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" + "@id": "bts:Other" }, { - "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" + "@id": "bts:Unknown" }, { - "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Additonal Findings Uninvolved Prostate", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes various morphological and cytological subtypes in protate tumors.", + "rdfs:label": "ProstateCancerCytologicMorphologicSubtypes", + "rdfs:subClassOf": [ { - "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" + "@id": "bts:Prostaticbasalcellhyperplasia" }, { - "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + "@id": "bts:Prostaticclearcellcribiformhyperplasia" }, { - "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" + "@id": "bts:Prostaticatypicaladenomatoushyperplasia(adenosisorAAH)" }, { - "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + "@id": "bts:Lowgradeprostaticintraepithelialneoplasia(PIN)/(PINI)" }, { - "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" + "@id": "bts:Highgradeprostaticintraepithelialneoplasia(HGPIN)/(PINII&PINIII)" }, { - "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" + "@id": "bts:Other" }, { - "@id": "bts:LB6orificeAirwaywallbetweenLB6andLB6A/Bcarinae" + "@id": "bts:Unknown" }, { - "@id": "bts:LB1A/CCarinabetweentheapicalandlateralsubsegmentsoftheapicalsegmentleftupperlobe" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Prostate Cancer Cytologic Morphologic Subtypes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "SarcomaTier3", + "rdfs:subClassOf": [ { - "@id": "bts:LB1B/CCarinabetweenthemedialandlateralsubsegmentsoftheapicalsegmentoftheleftupperlobe" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sarcoma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:LB2A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + "@id": "bts:Component" }, { - "@id": "bts:LB2A/CCarinabetweentheapicalandmedialsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:LB2B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentleftupperlobe" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:LB1+2/3Carinabetweentheapico-posteriorandanteriorsegmentsoftheleftupperlobe(CarinabetweenLB1+2orificeandLB3orifice)" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:LB3A/BCarinabetweentheapicalandlateralsubsegmentsoftheanteriorsegmentoftheleftupperlobe" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:LULCarinabetweentheLULorificeandLLLorifice(airways)" + "@id": "bts:SarcomaSubtype" }, { - "@id": "bts:LULorificeAirwaywallbetweenLULandLUDB" + "@id": "bts:SarcomaDiagnosisClassificationCategory" }, { - "@id": "bts:LB3orificeAnteriorsegmentleftupperlobe(airwaywallbetweenLB3andLB3A/Bcarinae)" - }, + "@id": "bts:SarcomaTumorExtensionType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaSubtype", + "@type": "rdfs:Class", + "rdfs:comment": "The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.", + "rdfs:label": "SarcomaSubtype", + "rdfs:subClassOf": [ { - "@id": "bts:LB4orificeSuperiorsegmentlingula(airwaywallbetweenLB4andLB4A/Bcarinae)" + "@id": "bts:SarcomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id": "bts:LB5orificeInferiorsegmentlingula(airwaywallbetweenLB5andLB5A/Bcarinae)" + "@id": "bts:Leiomyosarcoma(uterineorextra-uterine)" }, { - "@id": "bts:LLLorificeAirwaywallbetweenLULcarinaandLB6-10carinae" + "@id": "bts:OtherSynovialSarcomaOrMalignantPeripheralNerveSheathTumorSarcoma" }, { - "@id": "bts:LB9orificeLateralsegmentleftlowerlobe(airwaywallbetweenLB9andLB9A/Bcarinae)" + "@id": "bts:GastrointestinalStromalTumor" }, { - "@id": "bts:LB8orificeAnteriorsegmentleftlowerlobe(airwaywallbetweenLB8andLB8A/Bcarinae)" + "@id": "bts:Liposarcoma" }, { - "@id": "bts:LB10orificePosteriorsegmentleftlowerlobe(airwaywallbetweenLB10andLB10A/Bcarinae)" + "@id": "bts:Undifferentiatedpleomorphicsarcomaormalignantfibroushistiosarcoma" }, { "@id": "bts:Other" @@ -14812,18 +14928,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Topography", + "sms:displayName": "Sarcoma Subtype", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerHarboringGenomicAberrations", + "@id": "bts:SarcomaDiagnosisClassificationCategory", "@type": "rdfs:Class", - "rdfs:comment": "Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)", - "rdfs:label": "LungCancerHarboringGenomicAberrations", + "rdfs:comment": "High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.", + "rdfs:label": "SarcomaDiagnosisClassificationCategory", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:SarcomaTier3" } ], "schema:isPartOf": { @@ -14831,118 +14947,191 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:G12AKRASmutation" + "@id": "bts:BoneSarcoma" }, { - "@id": "bts:G12CKRASmutation" + "@id": "bts:MusculoskeletalSarcoma" }, { - "@id": "bts:G12DKRASmutation" + "@id": "bts:SoftTissueSarcoma" }, { - "@id": "bts:G12RKRASmutation" + "@id": "bts:Unknown" }, { - "@id": "bts:G12SKRASmutation" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sarcoma Diagnosis Classification Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaTumorExtensionType", + "@type": "rdfs:Class", + "rdfs:comment": "The field to indicate the organs and structures to which the tumor has become adherent or has invaded.", + "rdfs:label": "SarcomaTumorExtensionType", + "rdfs:subClassOf": [ { - "@id": "bts:G12VKRASmutation" - }, + "@id": "bts:SarcomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:G13DKRASmutation" + "@id": "bts:Extraosseous" }, { - "@id": "bts:G13RKRASmutation" + "@id": "bts:Intracranial" }, { - "@id": "bts:G13CKRASmutation" + "@id": "bts:Lymphnodes" }, { - "@id": "bts:G13AKRASmutation" + "@id": "bts:Parameningeal" }, { - "@id": "bts:G13VKRASmutation" + "@id": "bts:Thoraciccavity" }, { - "@id": "bts:Q61LKRASmutation" + "@id": "bts:Other" }, { - "@id": "bts:Q61HKRASmutation" + "@id": "bts:Unknown" }, { - "@id": "bts:A146TKRASmutation" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sarcoma Tumor Extension Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Pancreatic cancer specific attributes in Clinical Tier Data 3", + "rdfs:label": "PancreaticCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:G719XEGFRmutation" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatic Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:T790MEGFRmutation" + "@id": "bts:Component" }, { - "@id": "bts:C797SEGFRmutation" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:L858REGFRmutation" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:L861QEGFRmutation" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Exon19deletion" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Exon20insertion" + "@id": "bts:PancreasPrecancerHistopathologicGrade" }, { - "@id": "bts:EML4-ALKtranslocation-variant1" + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" }, { - "@id": "bts:EML4-ALKtranslocation-variant2" - }, + "@id": "bts:PancreaticDuctFinalPathologyType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PancreasPrecancerHistopathologicGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.", + "rdfs:label": "PancreasPrecancerHistopathologicGrade", + "rdfs:subClassOf": [ { - "@id": "bts:EML4-ALKtranslocation-variant3" - }, + "@id": "bts:PancreaticCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:EML4-ALKtranslocation-variant4" + "@id": "bts:IPMN-Adenoma" }, { - "@id": "bts:EML4-ALKtranslocation-variant5" + "@id": "bts:IPMN-Borderline" }, { - "@id": "bts:V600EBRAFmutation" + "@id": "bts:IPMN-Carcinomainsitu" }, { - "@id": "bts:V600DBRAFmutation" + "@id": "bts:IPMN-Invasivecarcinoma" }, { - "@id": "bts:V600KBRAFmutation" + "@id": "bts:PanIN1" }, { - "@id": "bts:V600RBRAFmutation" + "@id": "bts:PanIN1A" }, { - "@id": "bts:K601EBRAFmutation" + "@id": "bts:PanIN1B" }, { - "@id": "bts:D963spliceMETmutation" + "@id": "bts:PanIN2" }, { - "@id": "bts:D1010NMETmutation" + "@id": "bts:PanIN3" }, { - "@id": "bts:D1010spliceMETmutation" + "@id": "bts:Unknown" }, { - "@id": "bts:Intron13mutation" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreas Precancer Histopathologic Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype", + "@type": "rdfs:Class", + "rdfs:comment": "The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen", + "rdfs:label": "PancreaticIPMNPathologyEpithelialSubtype", + "rdfs:subClassOf": [ + { + "@id": "bts:PancreaticCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GastricFoveolar" }, { - "@id": "bts:Intron14mutation" + "@id": "bts:Intestinal" }, { - "@id": "bts:Exon14mutation" + "@id": "bts:IntraductalTubopapillary" }, { - "@id": "bts:Exon14deletion" + "@id": "bts:Pancreatobiliary" + }, + { + "@id": "bts:Oncocytic" }, { "@id": "bts:Other" @@ -14954,109 +15143,131 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", + "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerTier3", + "@id": "bts:PancreaticDuctFinalPathologyType", "@type": "rdfs:Class", - "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ColorectalCancerTier3", + "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", + "rdfs:label": "PancreaticDuctFinalPathologyType", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:PancreaticCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Colorectal Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Side-Branch" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:MainDuct" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Mixed" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:NotSpecified" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:None" }, { - "@id": "bts:ColorectalCancerDetectionMethodType" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreatic Duct Final Pathology Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "MelanomaTier3", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Melanoma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:CutaneousMelanomaTumorRegressionRange" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:MelanomaSpecimenClarkLevelValue" }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" + "@id": "bts:CutaneousMelanomaSurgicalMargins" }, { - "@id": "bts:MLH1PromoterMethylationStatus" + "@id": "bts:MelanomaLesionSize" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:HistoryofAtypicalNevi" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:FitzpatrickSkinTone" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:HistoryofChronicUVExposure" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:HistoryofBlisteringSunburn" }, { - "@id": "bts:ColorectalPolypShape" + "@id": "bts:HistoryofTanningBedUse" }, { - "@id": "bts:SizeofPolypRemoved" + "@id": "bts:ImmediateFamilyHistoryMelanoma" }, { - "@id": "bts:ColorectalPolypCount" + "@id": "bts:MelanomaBiopsyResectionSites" }, { - "@id": "bts:ColorectalPolypType" + "@id": "bts:CutaneousMelanomaUlceration" }, { - "@id": "bts:ColorectalPolypAdenomaType" + "@id": "bts:CutaneousMelanomaAdditionalFindings" } ], "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerDetectionMethodType", + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes", "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", - "rdfs:label": "ColorectalCancerDetectionMethodType", + "rdfs:comment": "Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaTumorInfiltratingLymphocytes", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15064,42 +15275,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Fecaloccultbloodtest" - }, - { - "@id": "bts:Sigmoidoscopy" - }, - { - "@id": "bts:Colonoscopy" - }, - { - "@id": "bts:Virtualcolonoscopy" + "@id": "bts:Absent" }, { - "@id": "bts:DNAstooltest" + "@id": "bts:Brisk" }, { - "@id": "bts:Other" + "@id": "bts:Nonbrisk" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Colorectal Cancer Detection Method Type", + "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofPriorColonPolyps", + "@id": "bts:CutaneousMelanomaTumorRegressionRange", "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "HistoryofPriorColonPolyps", + "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", + "rdfs:label": "CutaneousMelanomaTumorRegressionRange", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15107,30 +15306,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Absent" }, { - "@id": "bts:No" + "@id": "bts:Presentinvolving75%ormore" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Presentinvolvinglessthan75%" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "History of Prior Colon Polyps", + "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FamilyColonCancerHistoryIndicator", + "@id": "bts:MelanomaSpecimenClarkLevelValue", "@type": "rdfs:Class", - "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", - "rdfs:label": "FamilyColonCancerHistoryIndicator", + "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", + "rdfs:label": "MelanomaSpecimenClarkLevelValue", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15138,61 +15337,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:I" }, { - "@id": "bts:No" + "@id": "bts:II" }, { - "@id": "bts:NotApplicable" + "@id": "bts:III" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Colon Cancer History Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:IV" }, { - "@id": "bts:No" + "@id": "bts:V" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NoSourceDocumentation" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", + "sms:displayName": "Melanoma Specimen Clark Level Value", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", + "@id": "bts:CutaneousMelanomaSurgicalMargins", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", + "rdfs:comment": "Text term to indicate presence of tumor at resection margins", + "rdfs:label": "CutaneousMelanomaSurgicalMargins", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15200,61 +15377,47 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Beforeage50" + "@id": "bts:Positive" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:Negative" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Immediate Family History Endometrial Cancer", + "sms:displayName": "Cutaneous Melanoma Surgical Margins", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer", + "@id": "bts:MelanomaLesionSize", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", + "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", + "rdfs:label": "MelanomaLesionSize", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beforeage50" - }, - { - "@id": "bts:Notbeforeage50" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Ovarian Cancer", + "sms:displayName": "Melanoma Lesion Size", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "@id": "bts:HistoryofAtypicalNevi", "@type": "rdfs:Class", - "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", - "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "rdfs:comment": "Patient has a history of atypical nevi", + "rdfs:label": "HistoryofAtypicalNevi", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15262,10 +15425,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-Crohn'sdisease" + "@id": "bts:Yes(morethan50)" }, { - "@id": "bts:Yes-Ulcerativecolitis" + "@id": "bts:Yes(lessthan50)" }, { "@id": "bts:No" @@ -15274,21 +15437,21 @@ "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", + "sms:displayName": "History of Atypical Nevi", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PatientColonoscopyPerformedIndicator", + "@id": "bts:FitzpatrickSkinTone", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", - "rdfs:label": "PatientColonoscopyPerformedIndicator", + "rdfs:comment": "The Fitzpatrick classification of skin phototype", + "rdfs:label": "FitzpatrickSkinTone", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15296,30 +15459,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:I" }, { - "@id": "bts:No" + "@id": "bts:II" }, { - "@id": "bts:NotApplicable" + "@id": "bts:III" + }, + { + "@id": "bts:IV" + }, + { + "@id": "bts:V" + }, + { + "@id": "bts:VI" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Patient Colonoscopy Performed Indicator", + "sms:displayName": "Fitzpatrick Skin Tone", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration", + "@id": "bts:HistoryofChronicUVExposure", "@type": "rdfs:Class", - "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", - "rdfs:label": "ColorectalCancerTumorBorderConfiguration", + "rdfs:comment": "History of chronic UV exposure", + "rdfs:label": "HistoryofChronicUVExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15327,33 +15502,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Indeterminate" + "@id": "bts:Outdooroccupational" }, { - "@id": "bts:Infiltrating" + "@id": "bts:Outdoorrecreational" }, { - "@id": "bts:Other" + "@id": "bts:Therapeutic" }, { - "@id": "bts:Pushing" + "@id": "bts:None" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Colorectal Cancer Tumor Border Configuration", + "sms:displayName": "History of Chronic UV Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MLH1PromoterMethylationStatus", + "@id": "bts:HistoryofBlisteringSunburn", "@type": "rdfs:Class", - "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", - "rdfs:label": "MLH1PromoterMethylationStatus", + "rdfs:comment": "Patient has history of blistering sunburn", + "rdfs:label": "HistoryofBlisteringSunburn", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15361,30 +15536,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:Yes" }, { - "@id": "bts:Indeterminate" + "@id": "bts:No" }, { - "@id": "bts:NotAssessed" + "@id": "bts:Unknown" }, { - "@id": "bts:Present" + "@id": "bts:NotReported" } ], - "sms:displayName": "MLH1 Promoter Methylation Status", + "sms:displayName": "History of Blistering Sunburn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerKRASIndicator", + "@id": "bts:HistoryofTanningBedUse", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", - "rdfs:label": "ColorectalCancerKRASIndicator", + "rdfs:comment": "History of tanning bed use of the patient", + "rdfs:label": "HistoryofTanningBedUse", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15392,30 +15567,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Never" }, { - "@id": "bts:No" + "@id": "bts:Lessthan10times" }, { - "@id": "bts:Unknown" + "@id": "bts:10-50times" }, { - "@id": "bts:NotApplicable" + "@id": "bts:50-100times" + }, + { + "@id": "bts:Morethan100times" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Colorectal Cancer KRAS Indicator", + "sms:displayName": "History of Tanning Bed Use", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColonPolypOccurenceIndicator", + "@id": "bts:ImmediateFamilyHistoryMelanoma", "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "ColonPolypOccurenceIndicator", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryMelanoma", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15423,30 +15604,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Beforeage50" }, { - "@id": "bts:No" + "@id": "bts:Notbeforeage50" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Colon Polyp Occurence Indicator", + "sms:displayName": "Immediate Family History Melanoma", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FamilyHistoryColorectalPolyp", + "@id": "bts:MelanomaBiopsyResectionSites", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyHistoryColorectalPolyp", + "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", + "rdfs:label": "MelanomaBiopsyResectionSites", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15454,30 +15632,84 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Skinofscalp" }, { - "@id": "bts:No" + "@id": "bts:Skinofeyelid" }, { - "@id": "bts:Unknown" + "@id": "bts:Skinofnose" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Skinoflip" + }, + { + "@id": "bts:Skinofear" + }, + { + "@id": "bts:Skinofneck" + }, + { + "@id": "bts:Skinofotherpartsofface" + }, + { + "@id": "bts:Skinofchest" + }, + { + "@id": "bts:Skinofback" + }, + { + "@id": "bts:Skinofabdomen" + }, + { + "@id": "bts:Skinoftrunk-other" + }, + { + "@id": "bts:Skinofbreast" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:Skinofpalm" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:Skinother" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Family History Colorectal Polyp", + "sms:displayName": "Melanoma Biopsy Resection Sites", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalPolypNewIndicator", + "@id": "bts:CutaneousMelanomaUlceration", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", - "rdfs:label": "ColorectalPolypNewIndicator", + "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaUlceration", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15485,30 +15717,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Absent" }, { - "@id": "bts:No" + "@id": "bts:Present" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Colorectal Polyp New Indicator", + "sms:displayName": "Cutaneous Melanoma Ulceration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalPolypShape", + "@id": "bts:CutaneousMelanomaAdditionalFindings", "@type": "rdfs:Class", - "rdfs:comment": "Shape of polyp identified in the participant", - "rdfs:label": "ColorectalPolypShape", + "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaAdditionalFindings", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -15516,67 +15748,67 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pedunculated" + "@id": "bts:ActinicKeratosis" }, { - "@id": "bts:Sessile" + "@id": "bts:NevusRemnant" }, { - "@id": "bts:Flat" + "@id": "bts:SolarElastosis" }, { - "@id": "bts:Notstated" + "@id": "bts:FibrosingRegression" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Shape", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeofPolypRemoved", - "@type": "rdfs:Class", - "rdfs:comment": "Size of the polyp removed in cm", - "rdfs:label": "SizeofPolypRemoved", - "rdfs:subClassOf": [ + "@id": "bts:NestingMelanoma" + }, { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:PagetoidSpread" + }, + { + "@id": "bts:VascularProliferation" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size of Polyp Removed", + "sms:displayName": "Cutaneous Melanoma Additional Findings", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalPolypCount", + "@id": "bts:DaystoBirth", "@type": "rdfs:Class", - "rdfs:comment": "The total number of polyps detected", - "rdfs:label": "ColorectalPolypCount", + "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoBirth", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Colorectal Polyp Count", + "sms:displayName": "Days to Birth", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:ColorectalPolypType", + "@id": "bts:CountryofResidence", "@type": "rdfs:Class", - "rdfs:comment": "Type of polyp found in the participant", - "rdfs:label": "ColorectalPolypType", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -15584,1166 +15816,714 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Adenoma" + "@id": "bts:Afghanistan" }, { - "@id": "bts:Hyperplastic" + "@id": "bts:Albania" }, { - "@id": "bts:Mixed" + "@id": "bts:Algeria" }, { - "@id": "bts:Papillomatous" + "@id": "bts:Andorra" }, { - "@id": "bts:Normal" + "@id": "bts:Angola" }, { - "@id": "bts:Cancer" + "@id": "bts:Anguilla" }, { - "@id": "bts:Other" + "@id": "bts:AntiguaandBarbuda" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Colorectal Polyp Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypAdenomaType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of adenoma associated with the polyp", - "rdfs:label": "ColorectalPolypAdenomaType", - "rdfs:subClassOf": [ + "@id": "bts:Argentina" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Armenia" + }, { - "@id": "bts:Tubular" + "@id": "bts:Aruba" }, { - "@id": "bts:Villous" + "@id": "bts:Australia" }, { - "@id": "bts:Tubulovillous" + "@id": "bts:Austria" }, { - "@id": "bts:Sessileserrated" + "@id": "bts:Azerbaijan" }, { - "@id": "bts:Traditionalserrated" + "@id": "bts:Bahamas" }, { - "@id": "bts:Serratednotspecified" + "@id": "bts:Bahrain" }, { - "@id": "bts:Notstated" + "@id": "bts:Bangladesh" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Adenoma Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "BreastCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:Barbados" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Belarus" + }, { - "@id": "bts:Component" + "@id": "bts:Belgium" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Belize" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Benin" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Bermuda" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Bhutan" }, { - "@id": "bts:BreastCarcinomaDetectionMethodType" + "@id": "bts:Bolivia" }, { - "@id": "bts:BreastCarcinomaHistologyCategory" + "@id": "bts:BosniaandHerzegovina" }, { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + "@id": "bts:Botswana" }, { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + "@id": "bts:Brazil" }, { - "@id": "bts:BreastBiopsyProcedureFindingType" + "@id": "bts:Brunei" }, { - "@id": "bts:BreastQuadrantSite" + "@id": "bts:Bulgaria" }, { - "@id": "bts:BreastCancerAssessmentTests" + "@id": "bts:BurkinaFaso" }, { - "@id": "bts:BreastCancerGenomicTestPerformed" + "@id": "bts:Burundi" }, { - "@id": "bts:MammaprintRiskGroup" + "@id": "bts:Cambodia" }, { - "@id": "bts:OncotypeRiskGroup" + "@id": "bts:Cameroon" }, { - "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" + "@id": "bts:Canada" }, { - "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" + "@id": "bts:CapeVerde" }, { - "@id": "bts:BreastCancerAllredEstrogenReceptorScore" + "@id": "bts:CaymanIslands" }, { - "@id": "bts:PriorInvasiveBreastDisease" + "@id": "bts:CentralAfricanRepublic" }, { - "@id": "bts:BreastCarcinomaERStatusPercentageValue" + "@id": "bts:Chad" }, { - "@id": "bts:BreastCarcinomaPRStatusPercentageValue" + "@id": "bts:Chile" }, { - "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" + "@id": "bts:China" }, { - "@id": "bts:BreastCarcinomaCentromere17CopyNumber" + "@id": "bts:Colombia" }, { - "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" + "@id": "bts:Comoros" }, { - "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" + "@id": "bts:Congo" }, { - "@id": "bts:BreastCarcinomaSurgicalProcedureName" + "@id": "bts:CookIslands" }, { - "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" + "@id": "bts:CostaRica" }, { - "@id": "bts:BreastCarcinomaHER2Status" + "@id": "bts:Coted'Ivoire" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:Croatia" }, { - "@id": "bts:BreastCarcinomaERStainingIntensity" + "@id": "bts:Cuba" }, { - "@id": "bts:BreastCarcinomaPRStainingIntensity" + "@id": "bts:Curacao" }, { - "@id": "bts:OncotypeScore" + "@id": "bts:Cyprus" }, { - "@id": "bts:BreastImagingPerformedType" + "@id": "bts:CzechRepublic(Czechia)" }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id": "bts:DemocraticRepublicoftheCongo" }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + "@id": "bts:Denmark" }, { - "@id": "bts:BIRADSMammographyBreastDensityCategory" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", - "rdfs:label": "BreastCarcinomaDetectionMethodType", - "rdfs:subClassOf": [ + "@id": "bts:Djibouti" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Dominica" + }, { - "@id": "bts:ClinicalExam" + "@id": "bts:DominicanRepublic" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Ecuador" }, { - "@id": "bts:NippleDischarge" + "@id": "bts:Egypt" }, { - "@id": "bts:Other" + "@id": "bts:ElSalvador" }, { - "@id": "bts:ScreeningMammography" + "@id": "bts:EquatorialGuinea" }, { - "@id": "bts:ScreeningMRI" + "@id": "bts:Eritrea" }, { - "@id": "bts:Selfexam" + "@id": "bts:Estonia" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaHistologyCategory", - "@type": "rdfs:Class", - "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", - "rdfs:label": "BreastCarcinomaHistologyCategory", - "rdfs:subClassOf": [ + "@id": "bts:Eswatini" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ethiopia" + }, { - "@id": "bts:Infiltratingductalcarcinoma" + "@id": "bts:FalklandIslands(Malvinas)" }, { - "@id": "bts:Infiltratinglobularcarcinoma" + "@id": "bts:FaroeIslands" }, { - "@id": "bts:InvasivemammarycarcinomaNOS" + "@id": "bts:FederatedStatesofMicronesia" }, { - "@id": "bts:Invasivemixedductalandlobularcarcinoma" + "@id": "bts:Fiji" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Breast Carcinoma Histology Category", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", - "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", - "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", - "rdfs:subClassOf": [ + "@id": "bts:Finland" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:France" + }, { - "@id": "bts:Alveolartype" + "@id": "bts:FrenchGuiana" }, { - "@id": "bts:Classicaltype" + "@id": "bts:FrenchPolynesia" }, { - 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"rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", - "rdfs:subClassOf": [ + "@id": "bts:Mozambique" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Myanmar" + }, { - "@id": "bts:Borderline" + "@id": "bts:Namibia" }, { - "@id": "bts:Equivocal" + "@id": "bts:Nauru" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Nepal" }, { - "@id": "bts:Negative" + "@id": "bts:Netherlands" }, { - "@id": "bts:NotPerformed" + "@id": "bts:NewCaledonia" }, { - "@id": "bts:PerformedbutNotAvailable" + "@id": "bts:NewZealand" }, { - "@id": "bts:Positive" + "@id": "bts:Nicaragua" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerAllredEstrogenReceptorScore", - "@type": "rdfs:Class", - "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", - 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"rdfs:label": "HER2BreastCarcinomaCopyNumberTotal", - "rdfs:subClassOf": [ + "@id": "bts:Russia" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaCentromere17CopyNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", - "rdfs:label": "BreastCarcinomaCentromere17CopyNumber", - "rdfs:subClassOf": [ + "@id": "bts:Rwanda" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", - "@type": "rdfs:Class", - "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", - "rdfs:subClassOf": [ + "@id": "bts:SaintHelenaAscensionandTristandaCunha" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", - "@type": "rdfs:Class", - "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", - "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", - "rdfs:subClassOf": [ + "@id": "bts:SaintKittsandNevis" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", - "sms:required": "sms:false", - 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} - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Slovakia" + }, { - "@id": "bts:Positive" + "@id": "bts:Slovenia" }, { - "@id": "bts:Negative" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:Amplified" + "@id": "bts:Somalia" }, { - "@id": "bts:Non-amplified" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:Equivocal" + "@id": "bts:SouthKorea" }, { - "@id": "bts:Indeterminate" + "@id": "bts:SouthSudan" }, { - "@id": "bts:NotPerformed" + "@id": "bts:Spain" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma HER2 Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "Did the patient receive hormonal therapy for prevention of breast cancer?", - "rdfs:label": "HormoneTherapyBreastCancerPreventionIndicator", - "rdfs:subClassOf": [ + "@id": "bts:SriLanka" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StateofPalestine" + }, { - "@id": "bts:Yes" + "@id": "bts:Sudan" }, { - "@id": "bts:No" + "@id": "bts:Suriname" }, { - "@id": "bts:Unknown" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Hormone Therapy Breast Cancer Prevention Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaERStainingIntensity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaERStainingIntensity", - "rdfs:subClassOf": [ + "@id": "bts:Sweden" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Switzerland" + }, { - "@id": "bts:Strong" + "@id": "bts:Syria" }, { - "@id": "bts:Moderate" + "@id": "bts:Taiwan" }, { - "@id": "bts:Weak" + "@id": "bts:Tajikistan" }, { - "@id": "bts:Weak-Moderate" + "@id": "bts:Tanzania" }, { - "@id": "bts:Moderate-Strong" + "@id": "bts:Thailand" }, { - "@id": "bts:Weak-Strong" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:Other" + "@id": "bts:Togo" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma ER Staining Intensity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaPRStainingIntensity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaPRStainingIntensity", - "rdfs:subClassOf": [ + "@id": "bts:Tokelau" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Tonga" + }, { - "@id": "bts:Strong" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:Moderate" + "@id": "bts:Tunisia" }, { - "@id": "bts:Weak" + "@id": "bts:Turkey" }, { - "@id": "bts:Weak-Moderate" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:Moderate-Strong" + "@id": "bts:Tuvalu" }, { - "@id": "bts:Weak-Strong" + "@id": "bts:Uganda" }, { - "@id": "bts:Other" + "@id": "bts:Ukraine" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma PR Staining Intensity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OncotypeScore", - "@type": "rdfs:Class", - "rdfs:comment": "OncotypeDX recurrence score", - "rdfs:label": "OncotypeScore", - "rdfs:subClassOf": [ + "@id": "bts:UnitedArabEmirates" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Oncotype Score", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastImagingPerformedType", - "@type": "rdfs:Class", - "rdfs:comment": "The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).", - "rdfs:label": "BreastImagingPerformedType", - "rdfs:subClassOf": [ + "@id": "bts:UnitedKingdom" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:UnitedStates" + }, { - "@id": "bts:Mammogram" + "@id": "bts:Uruguay" }, { - "@id": "bts:Ultrasound" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:MRI" + "@id": "bts:Vanuatu" }, { - "@id": "bts:PET/CT" + "@id": "bts:Venezuela" }, { - "@id": "bts:CT" + "@id": "bts:Vietnam" }, { - "@id": "bts:Multipleimagingmodalities" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:Unknown" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:Datanotavailable" + "@id": "bts:WallisandFutuna" + }, + { + "@id": "bts:WesternSahara" + }, + { + "@id": "bts:Yemen" + }, + { + "@id": "bts:Zambia" + }, + { + "@id": "bts:Zimbabwe" } ], - "sms:displayName": "Breast Imaging Performed Type", + "sms:displayName": "Country of Residence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator", + "@id": "bts:AgeIsObfuscated", "@type": "rdfs:Class", - "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.", - "rdfs:label": "MultifocalBreastCarcinomaPresentIndicator", + "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "rdfs:label": "AgeIsObfuscated", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -16751,223 +16531,106 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" + "@id": "bts:True" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:False" } ], - "sms:displayName": "Multifocal Breast Carcinoma Present Indicator", + "sms:displayName": "Age Is Obfuscated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator", + "@id": "bts:YearOfBirth", "@type": "rdfs:Class", - "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.", - "rdfs:label": "MulticentricBreastCarcinomaPresentIndicator", + "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label": "YearOfBirth", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Multicentric Breast Carcinoma Present Indicator", + "sms:displayName": "Year Of Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BIRADSMammographyBreastDensityCategory", + "@id": "bts:OccupationDurationYears", "@type": "rdfs:Class", - "rdfs:comment": "The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.", - "rdfs:label": "BIRADSMammographyBreastDensityCategory", + "rdfs:comment": "The number of years a patient worked in a specific occupation.", + "rdfs:label": "OccupationDurationYears", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Predominantlyfatty" - }, - { - "@id": "bts:Scatteredfibroglandulardensities" - }, - { - "@id": "bts:Heterogeneouslydense" - }, - { - "@id": "bts:Extremelydense" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "BIRADS Mammography Breast Density Category", + "sms:displayName": "Occupation Duration Years", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NeuroblastomaandGliomaTier3", + "@id": "bts:PrematureAtBirth", "@type": "rdfs:Class", - "rdfs:comment": "Brain cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "NeuroblastomaandGliomaTier3", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", + "rdfs:label": "PrematureAtBirth", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Neuroblastoma and Glioma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:CNSTumorPrimaryAnatomicSite" - }, - { - "@id": "bts:GliomaSpecificMetastasisSites" - }, + "schema:rangeIncludes": [ { - "@id": "bts:GliomaSpecificRadiationField" + "@id": "bts:Yes" }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:No" }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:Unknown" }, { - "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus" + "@id": "bts:NotReported" } ], + "sms:displayName": "Premature At Birth", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CNSTumorPrimaryAnatomicSite", + "@id": "bts:WeeksGestationatBirth", "@type": "rdfs:Class", - "rdfs:comment": "Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2", - "rdfs:label": "CNSTumorPrimaryAnatomicSite", + "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", + "rdfs:label": "WeeksGestationatBirth", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Thalamus" - }, - { - "@id": "bts:Ventricles" - }, - { - "@id": "bts:Intracranial/Leptomeningeal" - }, - { - "@id": "bts:Suprasellar/Hypothalamic/Pituitary" - }, - { - "@id": "bts:Cerebellar/Posteriorfossa" - }, - { - "@id": "bts:Brainstem-Medulla" - }, - { - "@id": "bts:Brainstem-Midbrain/Tectum" - }, - { - "@id": "bts:Brainstem-Pons" - }, - { - "@id": "bts:Spinalcord-Cervical" - }, - { - "@id": "bts:Spinalcord-Thoracic" - }, - { - "@id": "bts:Spinalcord-Lumbar" - }, - { - "@id": "bts:Opticpathway" - }, - { - "@id": "bts:OtherlocationsNOS" - }, - { - "@id": "bts:Paraspinalganglion" - }, - { - "@id": "bts:Basalganglia" - }, - { - "@id": "bts:Hippocampus" - }, - { - "@id": "bts:Meninges/Dura" - }, - { - "@id": "bts:Otherlymphnodes" - } - ], - "sms:displayName": "CNS Tumor Primary Anatomic Site", + "sms:displayName": "Weeks Gestation at Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GliomaSpecificMetastasisSites", + "@id": "bts:RelativewithCancerHistory", "@type": "rdfs:Class", - "rdfs:comment": "Evidence of active brain metastasis including leptomeningeal involvement", - "rdfs:label": "GliomaSpecificMetastasisSites", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "rdfs:label": "RelativewithCancerHistory", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:FamilyHistory" } ], "schema:isPartOf": { @@ -16975,39 +16638,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CSF" - }, - { - "@id": "bts:Spine" - }, - { - "@id": "bts:Bonemarrow" - }, - { - "@id": "bts:Brain" + "@id": "bts:Yes-CancerHistoryRelative" }, { - "@id": "bts:Other" + "@id": "bts:None" }, { - "@id": "bts:Leptomeningeal" + "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Glioma Specific Metastasis Sites", + "sms:displayName": "Relative with Cancer History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GliomaSpecificRadiationField", + "@id": "bts:SmokingExposure", "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the CNS where radiation was administered in a partcipant with glioma", - "rdfs:label": "GliomaSpecificRadiationField", + "rdfs:comment": "Indicate if individual has smoking exposure", + "rdfs:label": "SmokingExposure", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -17015,30 +16669,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Craniospinal" - }, - { - "@id": "bts:Focal-tumorbed" + "@id": "bts:Yes-SmokingExposure" }, { - "@id": "bts:Unknown" + "@id": "bts:No-SmokingExposure" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Glioma Specific Radiation Field", - "sms:required": "sms:false", + "sms:displayName": "Smoking Exposure", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:AlcoholExposure", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a supra tentorial ependymoma", - "rdfs:label": "SupraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "Indicate if individual has alcohol exposure", + "rdfs:label": "AlcoholExposure", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -17046,30 +16697,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ST-EPN-RELA" - }, - { - "@id": "bts:ST-EPN-YAP1" + "@id": "bts:Yes-AlcoholExposure" }, { - "@id": "bts:Unknown" + "@id": "bts:No-AlcoholExposure" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Supra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", + "sms:displayName": "Alcohol Exposure", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:AsbestosExposure", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a infra tentorial ependymoma", - "rdfs:label": "InfraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", + "rdfs:label": "AsbestosExposure", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -17077,33 +16725,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:PF-EPN-A" - }, - { - "@id": "bts:PF-EPN-B" + "@id": "bts:Yes" }, { - "@id": "bts:Myxopapillaryependymoma" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Infra Tentorial Ependymoma Molecular Subgroup", + "sms:displayName": "Asbestos Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus", + "@id": "bts:CoalDustExposure", "@type": "rdfs:Class", - "rdfs:comment": "Neuroblastoma MYCN amplification or over-expression status", - "rdfs:label": "NeuroblastomaMYCNGeneAmplificationStatus", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", + "rdfs:label": "CoalDustExposure", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -17111,93 +16756,55 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Amplified" - }, - { - "@id": "bts:Notamplified" + "@id": "bts:Yes" }, { - "@id": "bts:Notdone" + "@id": "bts:No" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Neuroblastoma MYCN Gene Amplification Status", + "sms:displayName": "Coal Dust Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3", + "@id": "bts:EnvironmentalTobaccoSmokeExposure", "@type": "rdfs:Class", - "rdfs:comment": "Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3", - "rdfs:label": "AcuteLymphoblasticLeukemiaTier3", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", + "rdfs:label": "EnvironmentalTobaccoSmokeExposure", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:SpecimenBlastCountPercentageValue" - }, + "schema:rangeIncludes": [ { - "@id": "bts:NCIALLRiskGroup" + "@id": "bts:Yes" }, { - "@id": "bts:MRDALLDiagnosticSensitivity" + "@id": "bts:No" }, { - "@id": "bts:CNSLeukemiaStatus" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SpecimenBlastCountPercentageValue", - "@type": "rdfs:Class", - "rdfs:comment": "The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis", - "rdfs:label": "SpecimenBlastCountPercentageValue", - "rdfs:subClassOf": [ - { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Specimen Blast Count Percentage Value", + "sms:displayName": "Environmental Tobacco Smoke Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NCIALLRiskGroup", + "@id": "bts:RadonExposure", "@type": "rdfs:Class", - "rdfs:comment": "The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.", - "rdfs:label": "NCIALLRiskGroup", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", + "rdfs:label": "RadonExposure", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -17205,27 +16812,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NCIHighRisk" + "@id": "bts:Yes" }, { - "@id": "bts:NCIStandardRisk" + "@id": "bts:No" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "NCI ALL Risk Group", + "sms:displayName": "Radon Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MRDALLDiagnosticSensitivity", + "@id": "bts:RespirableCrystallineSilicaExposure", "@type": "rdfs:Class", - "rdfs:comment": "The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.", - "rdfs:label": "MRDALLDiagnosticSensitivity", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", + "rdfs:label": "RespirableCrystallineSilicaExposure", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -17233,30 +16843,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Optimal" - }, - { - "@id": "bts:Suboptimal" + "@id": "bts:Yes" }, { - "@id": "bts:Indeterminate" + "@id": "bts:No" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "MRD ALL Diagnostic Sensitivity", + "sms:displayName": "Respirable Crystalline Silica Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CNSLeukemiaStatus", + "@id": "bts:AdverseEvent", "@type": "rdfs:Class", - "rdfs:comment": "The status of central nervous system leukemia at the time of diagnosis.", - "rdfs:label": "CNSLeukemiaStatus", + "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", + "rdfs:label": "AdverseEvent", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -17264,5884 +16871,5755 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CNS1" + "@id": "bts:AbdominalDistension" }, { - "@id": "bts:CNS2" + "@id": "bts:AbdominalInfection" }, { - "@id": "bts:CNS3" + "@id": "bts:AbdominalPain" }, { - "@id": "bts:CNS2a" + "@id": "bts:AbdominalSoftTissueNecrosis" }, { - "@id": "bts:CNS2b" + "@id": "bts:AbducensNerveDisorder" }, { - "@id": "bts:CNS2c" + "@id": "bts:AccessoryNerveDisorder" }, { - "@id": "bts:CNS3a" + "@id": "bts:Acidosis" }, { - "@id": "bts:CNS3b" + "@id": "bts:AcousticNerveDisorderNOS" }, { - "@id": "bts:CNS3c" + "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" }, { - "@id": "bts:Notevaluated" + "@id": "bts:AcuteCoronarySyndrome" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "CNS Leukemia Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Ovarian cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "OvarianCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ovarian Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:AcuteKidneyInjury" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:AdrenalInsufficiency" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:AdultRespiratoryDistressSyndrome" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Agitation" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Akathisia" }, { - "@id": "bts:OvarianCancerHistologicSubtype" + "@id": "bts:AlanineAminotransferaseIncreased" }, { - "@id": "bts:OvarianCancerSurgicalOutcome" + "@id": "bts:AlcoholIntolerance" }, { - "@id": "bts:OvarianCancerPlatinumStatus" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerHistologicSubtype", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to describe the histological subtype of ovarian cancer in the participant", - "rdfs:label": "OvarianCancerHistologicSubtype", - "rdfs:subClassOf": [ - { - "@id": "bts:OvarianCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AlkalinePhosphataseIncreased" + }, { - "@id": "bts:High-gradeserous" + "@id": "bts:Alkalosis" }, { - "@id": "bts:Low-gradeserous" + "@id": "bts:AllergicReaction" }, { - "@id": "bts:High-gradeendometrioid" + "@id": "bts:AllergicRhinitis" }, { - "@id": "bts:Low-gradeendometrioid" + "@id": "bts:Alopecia" }, { - "@id": "bts:Clearcell" + "@id": "bts:Amnesia" }, { - "@id": "bts:Mucinous" + "@id": "bts:AnalFistula" }, { - "@id": "bts:Sex-cordstromal" + "@id": "bts:AnalHemorrhage" }, { - "@id": "bts:Germcell" + "@id": "bts:AnalMucositis" }, { - "@id": "bts:Other" + "@id": "bts:AnalNecrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:AnalPain" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Ovarian Cancer Histologic Subtype", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerSurgicalOutcome", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of surgical treatment administered.", - "rdfs:label": "OvarianCancerSurgicalOutcome", - "rdfs:subClassOf": [ + "@id": "bts:AnalStenosis" + }, { - "@id": "bts:OvarianCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AnalUlcer" + }, { - "@id": "bts:R0resection" + "@id": "bts:Anaphylaxis" }, { - "@id": "bts:Optimalcytoreduction" + "@id": "bts:Anemia" }, { - "@id": "bts:Sub-optimalcytoreduction" + "@id": "bts:AnkleFracture" }, { - "@id": "bts:Other" + "@id": "bts:AnorectalInfection" }, { - "@id": "bts:Unknown" + "@id": "bts:Anorexia" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Ovarian Cancer Surgical Outcome", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerPlatinumStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", - "rdfs:label": "OvarianCancerPlatinumStatus", - "rdfs:subClassOf": [ + "@id": "bts:Anorgasmia" + }, { - "@id": "bts:OvarianCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Anxiety" + }, { - "@id": "bts:Platinum-refractory" + "@id": "bts:AorticInjury" }, { - "@id": "bts:Platinum-sensitive" + "@id": "bts:AorticValveDisease" }, { - "@id": "bts:Platinum-resistant" + "@id": "bts:Aphonia" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Apnea" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ovarian Cancer Platinum Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ProstateCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:Appendicitis" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Prostate Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:AppendicitisPerforated" + }, { - "@id": "bts:Component" + "@id": "bts:Arachnoiditis" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:ArterialInjury" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:ArteritisInfective" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Arthralgia" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Arthritis" }, { - "@id": "bts:LocationExtentExtraprostaticExtension" + "@id": "bts:Ascites" }, { - "@id": "bts:LocationNaturePositiveMargins" + "@id": "bts:AspartateAminotransferaseIncreased" }, { - "@id": "bts:SeminalVesicleInvasion" + "@id": "bts:Aspiration" }, { - "@id": "bts:ProstateCarcinomaHistologicType" + "@id": "bts:Asystole" }, { - "@id": "bts:ProstateCancerLocalExtent" + "@id": "bts:Ataxia" }, { - "@id": "bts:AdditonalFindingsUninvolvedProstate" + "@id": "bts:Atelectasis" }, { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:LocationExtentExtraprostaticExtension", - "@type": "rdfs:Class", - "rdfs:comment": "Location and extent of extraprostatic extension", - "rdfs:label": "LocationExtentExtraprostaticExtension", - "rdfs:subClassOf": [ + "@id": "bts:AtrialFibrillation" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AtrialFlutter" + }, { - "@id": "bts:LeftAnterior" + "@id": "bts:AtrioventricularBlockComplete" }, { - "@id": "bts:LeftLateral" + "@id": "bts:AtrioventricularBlockFirstDegree" }, { - "@id": "bts:LeftPosterolateral" + "@id": "bts:AutoimmuneDisorder" }, { - "@id": "bts:LeftPosterior" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:LeftApex" + "@id": "bts:Azoospermia" }, { - "@id": "bts:LeftMid" + "@id": "bts:BackPain" }, { - "@id": "bts:LeftBase" + "@id": "bts:BileDuctStenosis" }, { - "@id": "bts:LeftFocal" + "@id": "bts:BiliaryAnastomoticLeak" }, { - "@id": "bts:LeftNon-focal(established)" + "@id": "bts:BiliaryFistula" }, { - "@id": "bts:RightAnterior" + "@id": "bts:BiliaryTractInfection" }, { - "@id": "bts:RightLateral" + "@id": "bts:BladderAnastomoticLeak" }, { - "@id": "bts:RightPosterolateral" + "@id": "bts:BladderInfection" }, { - "@id": "bts:RightPosterior" + "@id": "bts:BladderPerforation" }, { - "@id": "bts:RightApex" + "@id": "bts:BladderSpasm" }, { - "@id": "bts:RightMid" + "@id": "bts:Bloating" }, { - "@id": "bts:RightBase" + "@id": "bts:BloodandLymphaticSystemDisordersOther" }, { - "@id": "bts:RightFocal" + "@id": "bts:BloodAntidiureticHormoneAbnormal" }, { - "@id": "bts:RightNon-focal(established)" + "@id": "bts:BloodBilirubinIncreased" }, { - "@id": "bts:Unknown" + "@id": "bts:BloodCorticotrophinDecreased" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Location Extent Extraprostatic Extension", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LocationNaturePositiveMargins", - "@type": "rdfs:Class", - "rdfs:comment": "Location and nature of positive margins", - "rdfs:label": "LocationNaturePositiveMargins", - "rdfs:subClassOf": [ + "@id": "bts:BloodGonadotrophinAbnormal" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BloodProlactinAbnormal" + }, { - "@id": "bts:LeftAnterior" + "@id": "bts:BlurredVision" }, { - "@id": "bts:LeftLateral" + "@id": "bts:BodyOdor" }, { - "@id": "bts:LeftPosterolateral" + "@id": "bts:BoneInfection" }, { - "@id": "bts:LeftPosterior" + "@id": "bts:BoneMarrowHypocellular" }, { - "@id": "bts:LeftApex" + "@id": "bts:BonePain" }, { - "@id": "bts:LeftMid" + "@id": "bts:BrachialPlexopathy" }, { - "@id": "bts:LeftBase" + "@id": "bts:BreastAtrophy" }, { - "@id": "bts:LeftFocal" + "@id": "bts:BreastInfection" }, { - "@id": "bts:LeftExtensive" + "@id": "bts:BreastPain" }, { - "@id": "bts:LeftPositiveinanareaofextraprostaticextension(EPE)" + "@id": "bts:BronchialFistula" }, { - "@id": "bts:LeftPositiveinanareaofintraprostaticincision(II)" + "@id": "bts:BronchialInfection" }, { - "@id": "bts:LeftPositivewhereitisdifficulttodistinguishEPEvsII" + "@id": "bts:BronchialObstruction" }, { - "@id": "bts:RightAnterior" + "@id": "bts:BronchialStricture" }, { - "@id": "bts:RightLateral" + "@id": "bts:BronchopleuralFistula" }, { - "@id": "bts:RightPosterolateral" + "@id": "bts:BronchopulmonaryHemorrhage" }, { - "@id": "bts:RightPosterior" + "@id": "bts:Bronchospasm" }, { - "@id": "bts:RightApex" + "@id": "bts:Bruising" }, { - "@id": "bts:RightMid" + "@id": "bts:BullousDermatitis" }, { - "@id": "bts:RightBase" + "@id": "bts:Burn" }, { - "@id": "bts:RightFocal" + "@id": "bts:ButtockPain" }, { - "@id": "bts:RightExtensive" + "@id": "bts:CapillaryLeakSyndrome" }, { - "@id": "bts:RightPositiveinanareaofextraprostaticextension(EPE)" + "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" }, { - "@id": "bts:RightPositiveinanareaofintraprostaticincision(II)" + "@id": "bts:CardiacArrest" }, { - "@id": "bts:RightPositivewhereitisdifficulttodistinguishEPEvsII" + "@id": "bts:CardiacDisordersOther" }, { - "@id": "bts:Bladderneck(blockPUM)" + "@id": "bts:CardiacTroponinIIncreased" }, { - "@id": "bts:Vasdeferens" + "@id": "bts:CardiacTroponinTIncreased" }, { - "@id": "bts:Apicalmargin(blockDUM)" + "@id": "bts:Cataract" }, { - "@id": "bts:Unknown" + "@id": "bts:CatheterRelatedInfection" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Location Nature Positive Margins", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SeminalVesicleInvasion", - "@type": "rdfs:Class", - "rdfs:comment": "An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.", - "rdfs:label": "SeminalVesicleInvasion", - "rdfs:subClassOf": [ + "@id": "bts:CD4LymphocytesDecreased" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CecalHemorrhage" + }, { - "@id": "bts:None" + "@id": "bts:CecalInfection" }, { - "@id": "bts:Left" + "@id": "bts:CentralNervousSystemNecrosis" }, { - "@id": "bts:Right" + "@id": "bts:CerebrospinalFluidLeakage" }, { - "@id": "bts:Bothsides" + "@id": "bts:CervicitisInfection" }, { - "@id": "bts:Unknown" + "@id": "bts:Cheilitis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Seminal Vesicle Invasion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCarcinomaHistologicType", - "@type": "rdfs:Class", - "rdfs:comment": "The diagnostic subclassification of an invasive prostate carcinoma.", - "rdfs:label": "ProstateCarcinomaHistologicType", - "rdfs:subClassOf": [ + "@id": "bts:ChestPainCardiac" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ChestWallPain" + }, { - "@id": "bts:Prostaticadenocarcinoma(conventionalNOS)" + "@id": "bts:Chills" }, { - "@id": "bts:Prostaticductadenocarcinoma" + "@id": "bts:Cholecystitis" }, { - "@id": "bts:Acinarprostatemucinous(colloid)adenocarcinoma" + "@id": "bts:CholesterolHigh" }, { - "@id": "bts:Acinarprostateadenocarcinoma-signet-ringvariant" + "@id": "bts:ChronicKidneyDisease" }, { - "@id": "bts:Prostaticadenosquamouscarcinoma" + "@id": "bts:Chylothorax" }, { - "@id": "bts:Acinarprostatemucinousadenocarcinoma" + "@id": "bts:CognitiveDisturbance" }, { - "@id": "bts:Prostaticsmallcellcarcinoma" + "@id": "bts:Colitis" }, { - "@id": "bts:Acinarprostateadenocarcinoma-sarcomatoidvariant" + "@id": "bts:ColonicFistula" }, { - "@id": "bts:UndifferentiatedcarcinomaNOS" + "@id": "bts:ColonicHemorrhage" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Prostate Carcinoma Histologic Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerLocalExtent", - "@type": "rdfs:Class", - "rdfs:comment": "The response used to categorize the local extent of disease for prostate cancer.", - "rdfs:label": "ProstateCancerLocalExtent", - "rdfs:subClassOf": [ + "@id": "bts:ColonicObstruction" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ColonicPerforation" + }, { - "@id": "bts:OrganConfined" + "@id": "bts:ColonicStenosis" }, { - "@id": "bts:Extraprostaticextension" + "@id": "bts:ColonicUlcer" }, { - "@id": "bts:Unknown" + "@id": "bts:ConcentrationImpairment" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Prostate Cancer Local Extent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdditonalFindingsUninvolvedProstate", - "@type": "rdfs:Class", - "rdfs:comment": "Additional findings, uninvolved prostate", - "rdfs:label": "AdditonalFindingsUninvolvedProstate", - "rdfs:subClassOf": [ + "@id": "bts:ConductionDisorder" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Confusion" + }, { - "@id": "bts:High-gradeprostaticintraepithelialneoplasia(PIN)" + "@id": "bts:Congenital" }, { - "@id": "bts:Inflammation" + "@id": "bts:FamilialandGeneticDisordersOther" }, { - "@id": "bts:Benignprostatichyperplasia(BPH)" + "@id": "bts:Conjunctivitis" }, { - "@id": "bts:ProstaticIntraductaladenocarcinoma" + "@id": "bts:ConjunctivitisInfective" }, { - "@id": "bts:Other" + "@id": "bts:Constipation" }, { - "@id": "bts:Unknown" + "@id": "bts:ConstrictivePericarditis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Additonal Findings Uninvolved Prostate", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes various morphological and cytological subtypes in protate tumors.", - "rdfs:label": "ProstateCancerCytologicMorphologicSubtypes", - "rdfs:subClassOf": [ + "@id": "bts:CornealInfection" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CornealUlcer" + }, { - "@id": "bts:Prostaticbasalcellhyperplasia" + "@id": "bts:Cough" }, { - "@id": "bts:Prostaticclearcellcribiformhyperplasia" + "@id": "bts:CPKIncreased" }, { - "@id": "bts:Prostaticatypicaladenomatoushyperplasia(adenosisorAAH)" + "@id": "bts:CranialNerveInfection" }, { - "@id": "bts:Lowgradeprostaticintraepithelialneoplasia(PIN)/(PINI)" + "@id": "bts:CreatinineIncreased" }, { - "@id": "bts:Highgradeprostaticintraepithelialneoplasia(HGPIN)/(PINII&PINIII)" + "@id": "bts:Cushingoid" }, { - "@id": "bts:Other" + "@id": "bts:CystitisNoninfective" }, { - "@id": "bts:Unknown" + "@id": "bts:CytokineReleaseSyndrome" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Prostate Cancer Cytologic Morphologic Subtypes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SarcomaTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", - "rdfs:label": "SarcomaTier3", - "rdfs:subClassOf": [ + "@id": "bts:DeathNeonatal" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sarcoma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:DeathNOS" + }, { - "@id": "bts:Component" + "@id": "bts:Dehydration" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:DelayedOrgasm" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:DelayedPuberty" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Delirium" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Delusions" }, { - "@id": "bts:SarcomaSubtype" + "@id": "bts:DentalCaries" }, { - "@id": "bts:SarcomaDiagnosisClassificationCategory" + "@id": "bts:DepressedLevelofConsciousness" }, { - "@id": "bts:SarcomaTumorExtensionType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SarcomaSubtype", - "@type": "rdfs:Class", - "rdfs:comment": "The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.", - "rdfs:label": "SarcomaSubtype", - "rdfs:subClassOf": [ + "@id": "bts:Depression" + }, { - 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"@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HeadSoftTissueNecrosis" + }, { - "@id": "bts:Never" + "@id": "bts:Headache" }, { - "@id": "bts:Lessthan10times" + "@id": "bts:HearingImpaired" }, { - "@id": "bts:10-50times" + "@id": "bts:HeartFailure" }, { - "@id": "bts:50-100times" + "@id": "bts:Hematoma" }, { - "@id": "bts:Morethan100times" + "@id": "bts:Hematosalpinx" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Tanning Bed Use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryMelanoma", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryMelanoma", - "rdfs:subClassOf": [ + "@id": "bts:Hematuria" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HemoglobinIncreased" + }, { - "@id": "bts:Beforeage50" + "@id": "bts:Hemoglobinuria" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:Hemolysis" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Immediate Family History Melanoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaBiopsyResectionSites", - "@type": "rdfs:Class", - "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", - "rdfs:label": "MelanomaBiopsyResectionSites", - "rdfs:subClassOf": [ + "@id": "bts:HemolyticUremicSyndrome" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HemorrhoidalHemorrhage" + }, { - "@id": "bts:Skinofscalp" + "@id": "bts:Hemorrhoids" }, { - "@id": "bts:Skinofeyelid" + "@id": "bts:HepaticFailure" }, { - "@id": "bts:Skinofnose" + "@id": "bts:HepaticHemorrhage" }, { - "@id": "bts:Skinoflip" + "@id": "bts:HepaticInfection" }, { - "@id": "bts:Skinofear" + "@id": "bts:HepaticNecrosis" }, { - "@id": "bts:Skinofneck" + "@id": "bts:HepaticPain" }, { - "@id": "bts:Skinofotherpartsofface" + "@id": "bts:HepatitisViral" }, { - "@id": "bts:Skinofchest" + "@id": "bts:HepatobiliaryDisordersOther" }, { - "@id": "bts:Skinofback" + "@id": "bts:Hiccups" }, { - "@id": "bts:Skinofabdomen" + "@id": "bts:HipFracture" }, { - "@id": "bts:Skinoftrunk-other" + "@id": "bts:Hirsutism" }, { - "@id": "bts:Skinofbreast" + "@id": "bts:Hoarseness" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:HotFlashes" }, { - "@id": "bts:Skinofpalm" + "@id": "bts:Hydrocephalus" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:Skinofsole" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:Skinofpenis" + "@id": "bts:Hyperhidrosis" }, { - "@id": "bts:Skinofscrotum" + "@id": "bts:Hyperkalemia" }, { - "@id": "bts:Skinofvulva" + "@id": "bts:Hypermagnesemia" }, { - "@id": "bts:Skinother" + "@id": "bts:Hypernatremia" }, { - "@id": "bts:SkinNOS" + "@id": "bts:Hyperparathyroidism" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Melanoma Biopsy Resection Sites", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaUlceration", - "@type": "rdfs:Class", - "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaUlceration", - "rdfs:subClassOf": [ + "@id": "bts:Hypersomnia" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hypertension" + }, { - "@id": "bts:Absent" + "@id": "bts:Hyperthyroidism" }, { - "@id": "bts:Present" + "@id": "bts:Hypertrichosis" }, { - "@id": "bts:Unknown" + "@id": "bts:Hypertriglyceridemia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Cutaneous Melanoma Ulceration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaAdditionalFindings", - "@type": "rdfs:Class", - "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaAdditionalFindings", - "rdfs:subClassOf": [ + "@id": "bts:Hyperuricemia" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hypoalbuminemia" + }, { - "@id": "bts:ActinicKeratosis" + "@id": "bts:Hypocalcemia" }, { - "@id": "bts:NevusRemnant" + "@id": "bts:HypoglossalNerveDisorder" }, { - "@id": "bts:SolarElastosis" + "@id": "bts:Hypoglycemia" }, { - "@id": "bts:FibrosingRegression" + "@id": "bts:Hypohidrosis" }, { - "@id": "bts:NestingMelanoma" + "@id": "bts:Hypokalemia" }, { - "@id": "bts:PagetoidSpread" + "@id": "bts:Hypomagnesemia" }, { - "@id": "bts:VascularProliferation" + "@id": "bts:Hyponatremia" }, { - "@id": "bts:Other" + "@id": "bts:Hypoparathyroidism" }, { - "@id": "bts:Unknown" + "@id": "bts:Hypophosphatemia" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Cutaneous Melanoma Additional Findings", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoBirth", - "rdfs:subClassOf": [ + "@id": "bts:Hypotension" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Birth", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:CountryofResidence", - "@type": "rdfs:Class", - "rdfs:comment": "Country of Residence at enrollment", - "rdfs:label": "CountryofResidence", - "rdfs:subClassOf": [ + "@id": "bts:Hypothermia" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hypothyroidism" + }, { - "@id": "bts:Afghanistan" + "@id": "bts:Hypoxia" }, { - "@id": "bts:Albania" + "@id": "bts:IlealFistula" }, { - "@id": "bts:Algeria" + "@id": "bts:IlealHemorrhage" }, { - "@id": "bts:Andorra" + "@id": "bts:IlealObstruction" }, { - "@id": "bts:Angola" + "@id": "bts:IlealPerforation" }, { - "@id": "bts:Anguilla" + "@id": "bts:IlealStenosis" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:IlealUlcer" }, { - "@id": "bts:Argentina" + "@id": "bts:Ileus" }, { - "@id": "bts:Armenia" + "@id": "bts:ImmuneSystemDisordersOther" }, { - "@id": "bts:Aruba" + "@id": "bts:InfectionsandInfestationsOther" }, { - "@id": "bts:Australia" + "@id": "bts:InfectiveMyositis" }, { - "@id": "bts:Austria" + "@id": "bts:InfusionRelatedReaction" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:InfusionSiteExtravasation" }, { - "@id": "bts:Bahamas" + "@id": "bts:InjectionSiteReaction" }, { - "@id": "bts:Bahrain" + "@id": "bts:InjurytoCarotidArtery" }, { - "@id": "bts:Bangladesh" + "@id": "bts:InjurytoInferiorVenaCava" }, { - "@id": "bts:Barbados" + "@id": "bts:InjurytoJugularVein" }, { - "@id": "bts:Belarus" + "@id": "bts:InjurytoSuperiorVenaCava" }, { - "@id": "bts:Belgium" + "@id": "bts:Injury" }, { - "@id": "bts:Belize" + "@id": "bts:PoisoningandProceduralComplicationsOther" }, { - "@id": "bts:Benin" + "@id": "bts:INRIncreased" }, { - "@id": "bts:Bermuda" + "@id": "bts:Insomnia" }, { - "@id": "bts:Bhutan" + "@id": "bts:IntestinalStomaLeak" }, { - "@id": "bts:Bolivia" + "@id": "bts:IntestinalStomaObstruction" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:IntestinalStomaSiteBleeding" }, { - "@id": "bts:Botswana" + "@id": "bts:Intra-AbdominalHemorrhage" }, { - "@id": "bts:Brazil" + "@id": "bts:IntracranialHemorrhage" }, { - "@id": "bts:Brunei" + "@id": "bts:IntraoperativeArterialInjury" }, { - "@id": "bts:Bulgaria" + "@id": "bts:IntraoperativeBreastInjury" }, { - "@id": "bts:BurkinaFaso" + "@id": "bts:IntraoperativeCardiacInjury" }, { - "@id": "bts:Burundi" + "@id": "bts:IntraoperativeEarInjury" }, { - "@id": "bts:Cambodia" + "@id": "bts:IntraoperativeEndocrineInjury" }, { - "@id": "bts:Cameroon" + "@id": "bts:IntraoperativeGastrointestinalInjury" }, { - "@id": "bts:Canada" + "@id": "bts:IntraoperativeHeadandNeckInjury" }, { - "@id": "bts:CapeVerde" + "@id": "bts:IntraoperativeHemorrhage" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:IntraoperativeHepatobiliaryInjury" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:IntraoperativeMusculoskeletalInjury" }, { - "@id": "bts:Chad" + "@id": "bts:IntraoperativeNeurologicalInjury" }, { - "@id": "bts:Chile" + "@id": "bts:IntraoperativeOcularInjury" }, { - "@id": "bts:China" + "@id": "bts:IntraoperativeRenalInjury" }, { - "@id": "bts:Colombia" + "@id": "bts:IntraoperativeReproductiveTractInjury" }, { - "@id": "bts:Comoros" + "@id": "bts:IntraoperativeRespiratoryInjury" }, { - "@id": "bts:Congo" + "@id": "bts:IntraoperativeSkinInjury" }, { - "@id": "bts:CookIslands" + "@id": "bts:IntraoperativeSplenicInjury" }, { - "@id": "bts:CostaRica" + "@id": "bts:IntraoperativeUrinaryInjury" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:IntraoperativeVenousInjury" }, { - "@id": "bts:Croatia" + "@id": "bts:InvestigationsOther" }, { - "@id": "bts:Cuba" + "@id": "bts:IronOverload" }, { - "@id": "bts:Curacao" + "@id": "bts:IrregularMenstruation" }, { - "@id": "bts:Cyprus" + "@id": "bts:Irritability" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:IschemiaCerebrovascular" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:IVthNerveDisorder" }, { - "@id": "bts:Denmark" + "@id": "bts:JejunalFistula" }, { - "@id": "bts:Djibouti" + "@id": "bts:JejunalHemorrhage" }, { - "@id": "bts:Dominica" + "@id": "bts:JejunalObstruction" }, { - "@id": "bts:DominicanRepublic" + "@id": "bts:JejunalPerforation" }, { - "@id": "bts:Ecuador" + "@id": "bts:JejunalStenosis" }, { - "@id": "bts:Egypt" + "@id": "bts:JejunalUlcer" }, { - "@id": "bts:ElSalvador" + "@id": "bts:JointEffusion" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:JointInfection" }, { - "@id": "bts:Eritrea" + "@id": "bts:JointRangeofMotionDecreased" }, { - "@id": "bts:Estonia" + "@id": "bts:JointRangeofMotionDecreasedCervicalSpine" }, { - "@id": "bts:Eswatini" + "@id": "bts:JointRangeofMotionDecreasedLumbarSpine" }, { - "@id": "bts:Ethiopia" + "@id": "bts:Keratitis" }, { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:KidneyAnastomoticLeak" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:KidneyInfection" }, { - "@id": "bts:FederatedStatesofMicronesia" + "@id": "bts:Kyphosis" }, { - "@id": "bts:Fiji" + "@id": "bts:LactationDisorder" }, { - "@id": "bts:Finland" + "@id": "bts:LargeIntestinalAnastomoticLeak" }, { - "@id": "bts:France" + "@id": "bts:LaryngealEdema" }, { - "@id": "bts:FrenchGuiana" + "@id": "bts:LaryngealFistula" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:LaryngealHemorrhage" }, { - "@id": "bts:Gabon" + "@id": "bts:LaryngealInflammation" }, { - "@id": "bts:Gambia" + "@id": "bts:LaryngealMucositis" }, { - "@id": "bts:Georgia" + "@id": "bts:LaryngealObstruction" }, { - "@id": "bts:Germany" + "@id": "bts:LaryngealStenosis" }, { - "@id": "bts:Ghana" + "@id": "bts:Laryngitis" }, { - "@id": "bts:Gibraltar" + "@id": "bts:LaryngopharyngealDysesthesia" }, { - "@id": "bts:Greece" + "@id": "bts:Laryngospasm" }, { - "@id": "bts:Greenland" + "@id": "bts:LeftVentricularSystolicDysfunction" }, { - "@id": "bts:Grenada" + "@id": "bts:Lethargy" }, { - "@id": "bts:Guadeloupe" + "@id": "bts:LeukemiaSecondarytoOncologyChemotherapy" }, { - "@id": "bts:Guam" + "@id": "bts:Leukocytosis" }, { - "@id": "bts:Guatemala" + "@id": "bts:Leukoencephalopathy" }, { - "@id": "bts:Guernsey" + "@id": "bts:LibidoDecreased" }, { - "@id": "bts:Guinea" + "@id": "bts:LibidoIncreased" }, { - "@id": "bts:Guinea-Bissau" + "@id": "bts:LipInfection" }, { - "@id": "bts:Guyana" + "@id": "bts:LipPain" }, { - "@id": "bts:Haiti" + "@id": "bts:LipaseIncreased" }, { - "@id": "bts:HolySee" + "@id": "bts:Lipohypertrophy" }, { - "@id": "bts:Honduras" + "@id": "bts:LocalizedEdema" }, { - "@id": "bts:HongKong" + "@id": "bts:Lordosis" }, { - "@id": "bts:Hungary" + "@id": "bts:LowerGastrointestinalHemorrhage" }, { - "@id": "bts:Iceland" + "@id": "bts:LungInfection" }, { - "@id": "bts:India" + "@id": "bts:LymphGlandInfection" }, { - "@id": "bts:Indonesia" + "@id": "bts:LymphLeakage" }, { - "@id": "bts:Iran" + "@id": "bts:LymphNodePain" }, { - "@id": "bts:Iraq" + "@id": "bts:Lymphedema" }, { - "@id": "bts:Ireland" + "@id": "bts:Lymphocele" }, { - "@id": "bts:IsleofMan" + "@id": "bts:LymphocyteCountDecreased" }, { - "@id": "bts:Israel" + "@id": "bts:LymphocyteCountIncreased" }, { - "@id": "bts:Italy" + "@id": "bts:Malabsorption" }, { - "@id": "bts:Jamaica" + "@id": "bts:Malaise" }, { - "@id": "bts:Japan" + "@id": "bts:Mania" }, { - "@id": "bts:Jersey" + "@id": "bts:MediastinalHemorrhage" }, { - "@id": "bts:Jordan" + "@id": "bts:MediastinalInfection" }, { - "@id": "bts:Kazakhstan" + "@id": "bts:MemoryImpairment" }, { - "@id": "bts:Kenya" + "@id": "bts:Meningismus" }, { - "@id": "bts:Kiribati" + "@id": "bts:Meningitis" }, { - "@id": "bts:Kosovo" + "@id": "bts:Menopause" }, { - "@id": "bts:Kuwait" + "@id": "bts:Menorrhagia" }, { - "@id": "bts:Kyrgyzstan" + "@id": "bts:MetabolismandNutritionDisordersOther" }, { - "@id": "bts:Laos" + "@id": "bts:MiddleEarInflammation" }, { - "@id": "bts:Latvia" + "@id": "bts:MitralValveDisease" }, { - "@id": "bts:Lebanon" + "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" }, { - "@id": "bts:Lesotho" + "@id": "bts:MobitzTypeI" }, { - "@id": "bts:Liberia" + "@id": "bts:MovementsInvoluntary" }, { - "@id": "bts:Libya" + "@id": "bts:MucosalInfection" }, { - "@id": "bts:Liechtenstein" + "@id": "bts:MucositisOral" }, { - "@id": "bts:Lithuania" + "@id": "bts:Multi-OrganFailure" }, { - "@id": "bts:Luxembourg" + "@id": "bts:MuscleWeaknessLeft-Sided" }, { - "@id": "bts:Macau" + "@id": "bts:MuscleWeaknessLowerLimb" }, { - "@id": "bts:Madagascar" + "@id": "bts:MuscleWeaknessRight-Sided" }, { - "@id": "bts:Malawi" + "@id": "bts:MuscleWeaknessTrunk" }, { - "@id": "bts:Malaysia" + "@id": "bts:MuscleWeaknessUpperLimb" }, { - "@id": "bts:Maldives" + "@id": "bts:MusculoskeletalandConnectiveTissueDisordersOther" }, { - "@id": "bts:Mali" + "@id": "bts:MusculoskeletalDeformity" }, { - "@id": "bts:Malta" + "@id": "bts:Myalgia" }, { - "@id": "bts:MarshallIslands" + "@id": "bts:Myelitis" }, { - "@id": "bts:Martinique" + "@id": "bts:MyelodysplasticSyndrome" }, { - "@id": "bts:Mauritania" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:Mauritius" + "@id": "bts:Myocarditis" }, { - "@id": "bts:Mayotte" + "@id": "bts:Myositis" }, { - "@id": "bts:Mexico" + "@id": "bts:NailDiscoloration" }, { - "@id": "bts:Moldova" + "@id": "bts:NailInfection" }, { - "@id": "bts:Monaco" + "@id": "bts:NailLoss" }, { - "@id": "bts:Mongolia" + "@id": "bts:NailRidging" }, { - "@id": "bts:Montenegro" + "@id": "bts:NasalCongestion" }, { - "@id": "bts:Montserrat" + "@id": "bts:Nausea" }, { - "@id": "bts:Morocco" + "@id": "bts:NeckEdema" }, { - "@id": "bts:Mozambique" + "@id": "bts:NeckPain" }, { - "@id": "bts:Myanmar" + "@id": "bts:NeckSoftTissueNecrosis" }, { - "@id": "bts:Namibia" + "@id": "bts:NeoplasmsBenign" }, { - "@id": "bts:Nauru" + "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" }, { - "@id": "bts:Nepal" + "@id": "bts:NervousSystemDisordersOther" }, { - "@id": "bts:Netherlands" + "@id": "bts:Neuralgia" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:NeutrophilCountDecreased" }, { - "@id": "bts:NewZealand" + "@id": "bts:NightBlindness" }, { - "@id": "bts:Nicaragua" + "@id": "bts:NippleDeformity" }, { - "@id": "bts:Niger" + "@id": "bts:Non-CardiacChestPain" }, { - "@id": "bts:Nigeria" + "@id": "bts:Nystagmus" }, { - "@id": "bts:Niue" + "@id": "bts:Obesity" }, { - "@id": "bts:NorthKorea" + "@id": "bts:ObstructionGastric" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:OculomotorNerveDisorder" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:OlfactoryNerveDisorder" }, { - "@id": "bts:Norway" + "@id": "bts:Oligospermia" }, { - "@id": "bts:Oman" + "@id": "bts:OpticNerveDisorder" }, { - "@id": "bts:Pakistan" + "@id": "bts:OralCavityFistula" }, { - "@id": "bts:Palau" + "@id": "bts:OralDysesthesia" }, { - "@id": "bts:Panama" + "@id": "bts:OralHemorrhage" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:OralPain" }, { - "@id": "bts:Paraguay" + "@id": "bts:OsteonecrosisofJaw" }, { - "@id": "bts:Peru" + "@id": "bts:Osteoporosis" }, { - "@id": "bts:Philippines" + "@id": "bts:OtitisExterna" }, { - "@id": "bts:Poland" + "@id": "bts:OtitisMedia" }, { - "@id": "bts:Portugal" + "@id": "bts:OvarianHemorrhage" }, { - "@id": "bts:PuertoRico" + "@id": "bts:OvarianInfection" }, { - "@id": "bts:Qatar" + "@id": "bts:OvarianRupture" }, { - "@id": "bts:Reunion" + "@id": "bts:OvulationPain" }, { - "@id": "bts:Romania" + "@id": "bts:Pain" }, { - "@id": "bts:Russia" + "@id": "bts:PaininExtremity" }, { - "@id": "bts:Rwanda" + "@id": "bts:PainofSkin" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Palmar-PlantarErythrodysesthesiaSyndrome" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:Palpitations" }, { - "@id": "bts:SaintLucia" + "@id": "bts:PancreasInfection" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:PancreaticAnastomoticLeak" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:PancreaticDuctStenosis" }, { - "@id": "bts:Samoa" + "@id": "bts:PancreaticEnzymesDecreased" }, { - "@id": "bts:SanMarino" + "@id": "bts:PancreaticFistula" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:PancreaticHemorrhage" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:PancreaticNecrosis" }, { - "@id": "bts:Senegal" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:Serbia" + "@id": "bts:Papilledema" }, { - "@id": "bts:Seychelles" + "@id": "bts:PapulopustularRash" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Paresthesia" }, { - "@id": "bts:Singapore" + "@id": "bts:Paronychia" }, { - "@id": "bts:Slovakia" + "@id": "bts:ParoxysmalAtrialTachycardia" }, { - "@id": "bts:Slovenia" + "@id": "bts:PelvicFloorMuscleWeakness" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:PelvicInfection" }, { - "@id": "bts:Somalia" + "@id": "bts:PelvicPain" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:PelvicSoftTissueNecrosis" }, { - "@id": "bts:SouthKorea" + "@id": "bts:PenileInfection" }, { - "@id": "bts:SouthSudan" + "@id": "bts:PenilePain" }, { - "@id": "bts:Spain" + "@id": "bts:PerforationBileDuct" }, { - "@id": "bts:SriLanka" + "@id": "bts:PericardialEffusion" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:PericardialTamponade" }, { - "@id": "bts:Sudan" + "@id": "bts:Pericarditis" }, { - "@id": "bts:Suriname" + "@id": "bts:PerinealPain" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:PeriodontalDisease" }, { - "@id": "bts:Sweden" + "@id": "bts:PeriorbitalEdema" }, { - "@id": "bts:Switzerland" + "@id": "bts:PeriorbitalInfection" }, { - "@id": "bts:Syria" + "@id": "bts:PeripheralIschemia" }, { - "@id": "bts:Taiwan" + "@id": "bts:PeripheralMotorNeuropathy" }, { - "@id": "bts:Tajikistan" + "@id": "bts:PeripheralNerveInfection" }, { - "@id": "bts:Tanzania" + "@id": "bts:PeripheralSensoryNeuropathy" }, { - "@id": "bts:Thailand" + "@id": "bts:PeritonealInfection" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:PeritonealNecrosis" }, { - "@id": "bts:Togo" + "@id": "bts:PersonalityChange" }, { - "@id": "bts:Tokelau" + "@id": "bts:PhantomPain" }, { - "@id": "bts:Tonga" + "@id": "bts:PharyngealAnastomoticLeak" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:PharyngealFistula" }, { - "@id": "bts:Tunisia" + "@id": "bts:PharyngealHemorrhage" }, { - "@id": "bts:Turkey" + "@id": "bts:PharyngealMucositis" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:PharyngealNecrosis" }, { - "@id": "bts:Tuvalu" + "@id": "bts:PharyngealStenosis" }, { - "@id": "bts:Uganda" + "@id": "bts:Pharyngitis" }, { - "@id": "bts:Ukraine" + "@id": "bts:PharyngolaryngealPain" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:Phlebitis" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:PhlebitisInfective" }, { - "@id": "bts:UnitedStates" + "@id": "bts:Photophobia" }, { - "@id": "bts:Uruguay" + "@id": "bts:Photosensitivity" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:PlateletCountDecreased" }, { - "@id": "bts:Vanuatu" + "@id": "bts:PleuralEffusion" }, { - "@id": "bts:Venezuela" + "@id": "bts:PleuralHemorrhage" }, { - "@id": "bts:Vietnam" + "@id": "bts:PleuralInfection" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:PleuriticPain" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:Pneumonitis" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:Pneumothorax" }, { - "@id": "bts:WesternSahara" + "@id": "bts:PortalHypertension" }, { - "@id": "bts:Yemen" + "@id": "bts:PortalVeinThrombosis" }, { - "@id": "bts:Zambia" + "@id": "bts:PostnasalDrip" }, { - "@id": "bts:Zimbabwe" - } - ], - "sms:displayName": "Country of Residence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeIsObfuscated", - "@type": "rdfs:Class", - "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "rdfs:label": "AgeIsObfuscated", - "rdfs:subClassOf": [ + "@id": "bts:PostoperativeHemorrhage" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PostoperativeThoracicProcedureComplication" + }, { - "@id": "bts:True" + "@id": "bts:PrecociousPuberty" }, { - "@id": "bts:False" - } - ], - "sms:displayName": "Age Is Obfuscated", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:YearOfBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label": "YearOfBirth", - "rdfs:subClassOf": [ + "@id": "bts:Pregnancy" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Year Of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OccupationDurationYears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", - "rdfs:subClassOf": [ + "@id": "bts:PuerperiumandPerinatalConditionsOther" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Occupation Duration Years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PrematureAtBirth", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", - "rdfs:subClassOf": [ + "@id": "bts:PrematureDelivery" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PrematureMenopause" + }, { - "@id": "bts:Yes" + "@id": "bts:Presyncope" }, { - "@id": "bts:No" + "@id": "bts:Proctitis" }, { - "@id": "bts:Unknown" + "@id": "bts:ProductiveCough" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Premature At Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WeeksGestationatBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", - "rdfs:subClassOf": [ + "@id": "bts:ProlapseofIntestinalStoma" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weeks Gestation at Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RelativewithCancerHistory", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", - "rdfs:subClassOf": [ + "@id": "bts:ProlapseofUrostomy" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ProstateInfection" + }, { - "@id": "bts:Yes-CancerHistoryRelative" + "@id": "bts:ProstaticHemorrhage" }, { - "@id": "bts:None" + "@id": "bts:ProstaticObstruction" }, { - "@id": "bts:Unknown" + "@id": "bts:ProstaticPain" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relative with Cancer History", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokingExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", - "rdfs:subClassOf": [ + "@id": "bts:Proteinuria" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Pruritus" + }, { - "@id": "bts:Yes-SmokingExposure" + "@id": "bts:PsychiatricDisordersOther" }, { - "@id": "bts:No-SmokingExposure" + "@id": "bts:Psychosis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AlcoholExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", - "rdfs:subClassOf": [ + "@id": "bts:PulmonaryEdema" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PulmonaryFibrosis" + }, { - "@id": "bts:Yes-AlcoholExposure" + "@id": "bts:PulmonaryFistula" }, { - "@id": "bts:No-AlcoholExposure" + "@id": "bts:PulmonaryHypertension" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AsbestosExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", - "rdfs:subClassOf": [ + "@id": "bts:PulmonaryValveDisease" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Purpura" + }, { - "@id": "bts:Yes" + "@id": "bts:PyramidalTractSyndrome" }, { - "@id": "bts:No" + "@id": "bts:RadiationRecallReaction(Dermatologic)" }, { - "@id": "bts:Unknown" + "@id": "bts:Radiculitis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Asbestos Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CoalDustExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", - "rdfs:subClassOf": [ + "@id": "bts:RashAcneiform" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RashMaculo-Papular" + }, { - "@id": "bts:Yes" + "@id": "bts:RashPustular" }, { - "@id": "bts:No" + "@id": "bts:RectalAnastomoticLeak" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Coal Dust Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:RectalFistula" }, { - "@id": "bts:No" + "@id": "bts:RectalHemorrhage" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RadonExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:RectalMucositis" }, { - "@id": "bts:No" + "@id": "bts:RectalNecrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:RectalObstruction" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Radon Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RespirableCrystallineSilicaExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:RectalPain" }, { - "@id": "bts:No" + "@id": "bts:RectalPerforation" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Respirable Crystalline Silica Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdverseEvent", - "@type": "rdfs:Class", - "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", - "rdfs:label": "AdverseEvent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdominalDistension" + "@id": "bts:RectalStenosis" }, { - "@id": "bts:AbdominalInfection" + "@id": "bts:RectalUlcer" }, { - "@id": "bts:AbdominalPain" + "@id": "bts:RecurrentLaryngealNervePalsy" }, { - "@id": "bts:AbdominalSoftTissueNecrosis" + "@id": "bts:RenalandUrinaryDisordersOther" }, { - "@id": "bts:AbducensNerveDisorder" + "@id": "bts:RenalCalculi" }, { - "@id": "bts:AccessoryNerveDisorder" + "@id": "bts:RenalColic" }, { - "@id": "bts:Acidosis" + "@id": "bts:RenalHemorrhage" }, { - "@id": "bts:AcousticNerveDisorderNOS" + "@id": "bts:ReproductiveSystemandBreastDisordersOther" }, { - "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" + "@id": "bts:RespiratoryFailure" }, { - "@id": "bts:AcuteCoronarySyndrome" + "@id": "bts:Respiratory" }, { - "@id": "bts:AcuteKidneyInjury" + "@id": "bts:ThoracicandMediastinalDisordersOther" }, { - "@id": "bts:AdrenalInsufficiency" + "@id": "bts:Restlessness" }, { - "@id": "bts:AdultRespiratoryDistressSyndrome" + "@id": "bts:RestrictiveCardiomyopathy" }, { - "@id": "bts:Agitation" + "@id": "bts:RetinalDetachment" }, { - "@id": "bts:Akathisia" + "@id": "bts:RetinalTear" }, { - "@id": "bts:AlanineAminotransferaseIncreased" + "@id": "bts:RetinalVascularDisorder" }, { - "@id": "bts:AlcoholIntolerance" + "@id": "bts:RetinoicAcidSyndrome" }, { - "@id": "bts:AlkalinePhosphataseIncreased" + "@id": "bts:Retinopathy" }, { - "@id": "bts:Alkalosis" + "@id": "bts:RetroperitonealHemorrhage" }, { - "@id": "bts:AllergicReaction" + "@id": "bts:ReversiblePosteriorLeukoencephalopathySyndrome" }, { - "@id": "bts:AllergicRhinitis" + "@id": "bts:RhinitisInfective" }, { - "@id": "bts:Alopecia" + "@id": "bts:RightVentricularDysfunction" }, { - "@id": "bts:Amnesia" + "@id": "bts:SalivaryDuctInflammation" }, { - "@id": "bts:AnalFistula" + "@id": "bts:SalivaryGlandFistula" }, { - "@id": "bts:AnalHemorrhage" + "@id": "bts:SalivaryGlandInfection" }, { - "@id": "bts:AnalMucositis" + "@id": "bts:ScalpPain" }, { - "@id": "bts:AnalNecrosis" + "@id": "bts:ScleralDisorder" }, { - "@id": "bts:AnalPain" + "@id": "bts:Scoliosis" }, { - "@id": "bts:AnalStenosis" + "@id": "bts:ScrotalInfection" }, { - "@id": "bts:AnalUlcer" + "@id": "bts:ScrotalPain" }, { - "@id": "bts:Anaphylaxis" + "@id": "bts:Seizure" }, { - "@id": "bts:Anemia" + "@id": "bts:Sepsis" }, { - "@id": "bts:AnkleFracture" + "@id": "bts:Seroma" }, { - "@id": "bts:AnorectalInfection" + "@id": "bts:SerumAmylaseIncreased" }, { - "@id": "bts:Anorexia" + "@id": "bts:SerumSickness" }, { - "@id": "bts:Anorgasmia" + "@id": "bts:SickSinusSyndrome" }, { - "@id": "bts:Anxiety" + "@id": "bts:SinusBradycardia" }, { - "@id": "bts:AorticInjury" + "@id": "bts:SinusDisorder" }, { - "@id": "bts:AorticValveDisease" + "@id": "bts:SinusPain" }, { - "@id": "bts:Aphonia" + "@id": "bts:SinusTachycardia" }, { - "@id": "bts:Apnea" + "@id": "bts:Sinusitis" }, { - "@id": "bts:Appendicitis" + "@id": "bts:SkinandSubcutaneousTissueDisordersOther" }, { - "@id": "bts:AppendicitisPerforated" + "@id": "bts:SkinAtrophy" }, { - "@id": "bts:Arachnoiditis" + "@id": "bts:SkinHyperpigmentation" }, { - "@id": "bts:ArterialInjury" + "@id": "bts:SkinHypopigmentation" }, { - "@id": "bts:ArteritisInfective" + "@id": "bts:SkinInduration" }, { - "@id": "bts:Arthralgia" + "@id": "bts:SkinInfection" }, { - "@id": "bts:Arthritis" + "@id": "bts:SkinUlceration" }, { - "@id": "bts:Ascites" + "@id": "bts:SleepApnea" }, { - "@id": "bts:AspartateAminotransferaseIncreased" + "@id": "bts:SmallIntestinalAnastomoticLeak" }, { - "@id": "bts:Aspiration" + "@id": "bts:SmallIntestinalMucositis" }, { - "@id": "bts:Asystole" + "@id": "bts:SmallIntestinalObstruction" }, { - "@id": "bts:Ataxia" + "@id": "bts:SmallIntestinalPerforation" }, { - "@id": "bts:Atelectasis" + "@id": "bts:SmallIntestinalStenosis" }, { - "@id": "bts:AtrialFibrillation" + "@id": "bts:SmallIntestineInfection" }, { - "@id": "bts:AtrialFlutter" + "@id": "bts:SmallIntestineUlcer" }, { - "@id": "bts:AtrioventricularBlockComplete" + "@id": "bts:Sneezing" }, { - "@id": "bts:AtrioventricularBlockFirstDegree" + "@id": "bts:SocialCircumstancesOther" }, { - "@id": "bts:AutoimmuneDisorder" + "@id": "bts:SoftTissueInfection" }, { - "@id": "bts:AvascularNecrosis" + "@id": "bts:SoftTissueNecrosisLowerLimb" }, { - "@id": "bts:Azoospermia" + "@id": "bts:SoftTissueNecrosisUpperLimb" }, { - "@id": "bts:BackPain" + "@id": "bts:Somnolence" }, { - "@id": "bts:BileDuctStenosis" + "@id": "bts:SoreThroat" }, { - "@id": "bts:BiliaryAnastomoticLeak" + "@id": "bts:Spasticity" }, { - "@id": "bts:BiliaryFistula" + "@id": "bts:SpermaticCordAnastomoticLeak" }, { - "@id": "bts:BiliaryTractInfection" + "@id": "bts:SpermaticCordHemorrhage" }, { - "@id": "bts:BladderAnastomoticLeak" + "@id": "bts:SpermaticCordObstruction" }, { - "@id": "bts:BladderInfection" + "@id": "bts:SpinalFracture" }, { - "@id": "bts:BladderPerforation" + "@id": "bts:SpleenDisorder" }, { - "@id": "bts:BladderSpasm" + "@id": "bts:SplenicInfection" }, { - "@id": "bts:Bloating" + "@id": "bts:StenosisofGastrointestinalStoma" }, { - "@id": "bts:BloodandLymphaticSystemDisordersOther" + "@id": "bts:Stevens-JohnsonSyndrome" }, { - "@id": "bts:BloodAntidiureticHormoneAbnormal" + "@id": "bts:StomaSiteInfection" }, { - "@id": "bts:BloodBilirubinIncreased" + "@id": "bts:StomachPain" }, { - "@id": "bts:BloodCorticotrophinDecreased" + "@id": "bts:StomalUlcer" }, { - "@id": "bts:BloodGonadotrophinAbnormal" + "@id": "bts:Stridor" }, { - "@id": "bts:BloodProlactinAbnormal" + "@id": "bts:Stroke" }, { - "@id": "bts:BlurredVision" + "@id": "bts:SuddenDeathNOS" }, { - "@id": "bts:BodyOdor" + "@id": "bts:SuicidalIdeation" }, { - "@id": "bts:BoneInfection" + "@id": "bts:SuicideAttempt" }, { - "@id": "bts:BoneMarrowHypocellular" + "@id": "bts:SuperficialSoftTissueFibrosis" }, { - "@id": "bts:BonePain" + "@id": "bts:SuperficialThrombophlebitis" }, { - "@id": "bts:BrachialPlexopathy" + "@id": "bts:SuperiorVenaCavaSyndrome" }, { - "@id": "bts:BreastAtrophy" + "@id": "bts:SupraventricularTachycardia" }, { - "@id": "bts:BreastInfection" + "@id": "bts:SurgicalandMedicalProceduresOther" }, { - "@id": "bts:BreastPain" + "@id": "bts:Syncope" }, { - "@id": "bts:BronchialFistula" + "@id": "bts:Telangiectasia" }, { - "@id": "bts:BronchialInfection" + "@id": "bts:TesticularDisorder" }, { - "@id": "bts:BronchialObstruction" + "@id": "bts:TesticularHemorrhage" }, { - "@id": "bts:BronchialStricture" + "@id": "bts:TesticularPain" }, { - "@id": "bts:BronchopleuralFistula" + "@id": "bts:ThromboembolicEvent" }, { - "@id": "bts:BronchopulmonaryHemorrhage" + "@id": "bts:ThromboticThrombocytopenicPurpura" }, { - "@id": "bts:Bronchospasm" + "@id": "bts:Tinnitus" }, { - "@id": "bts:Bruising" + "@id": "bts:ToothDevelopmentDisorder" }, { - "@id": "bts:BullousDermatitis" + "@id": "bts:ToothDiscoloration" }, { - "@id": "bts:Burn" + "@id": "bts:ToothInfection" }, { - "@id": "bts:ButtockPain" + "@id": "bts:Toothache" }, { - "@id": "bts:CapillaryLeakSyndrome" + "@id": "bts:ToxicEpidermalNecrolysis" }, { - "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" + "@id": "bts:TrachealFistula" }, { - "@id": "bts:CardiacArrest" + "@id": "bts:TrachealHemorrhage" }, { - "@id": "bts:CardiacDisordersOther" + "@id": "bts:TrachealMucositis" }, { - "@id": "bts:CardiacTroponinIIncreased" + "@id": "bts:TrachealObstruction" }, { - "@id": "bts:CardiacTroponinTIncreased" + "@id": "bts:TrachealStenosis" }, { - "@id": "bts:Cataract" + "@id": "bts:Tracheitis" }, { - "@id": "bts:CatheterRelatedInfection" + "@id": "bts:TracheostomySiteBleeding" }, { - "@id": "bts:CD4LymphocytesDecreased" + "@id": "bts:TransientIschemicAttacks" }, { - "@id": "bts:CecalHemorrhage" + "@id": "bts:TreatmentRelatedSecondaryMalignancy" }, { - "@id": "bts:CecalInfection" + "@id": "bts:Tremor" }, { - "@id": "bts:CentralNervousSystemNecrosis" + "@id": "bts:TricuspidValveDisease" }, { - "@id": "bts:CerebrospinalFluidLeakage" + "@id": "bts:TrigeminalNerveDisorder" }, { - "@id": "bts:CervicitisInfection" + "@id": "bts:Trismus" }, { - "@id": "bts:Cheilitis" + "@id": "bts:TumorLysisSyndrome" }, { - "@id": "bts:ChestPainCardiac" + "@id": "bts:TumorPain" }, { - "@id": "bts:ChestWallPain" + "@id": "bts:Typhlitis" }, { - "@id": "bts:Chills" + "@id": "bts:UnequalLimbLength" }, { - "@id": "bts:Cholecystitis" + "@id": "bts:UnintendedPregnancy" }, { - "@id": "bts:CholesterolHigh" + "@id": "bts:UpperGastrointestinalHemorrhage" }, { - "@id": "bts:ChronicKidneyDisease" + "@id": "bts:UpperRespiratoryInfection" }, { - "@id": "bts:Chylothorax" + "@id": "bts:UretericAnastomoticLeak" }, { - "@id": "bts:CognitiveDisturbance" + "@id": "bts:UrethralAnastomoticLeak" }, { - "@id": "bts:Colitis" + "@id": "bts:UrethralInfection" }, { - "@id": "bts:ColonicFistula" + "@id": "bts:UrinaryFistula" }, { - "@id": "bts:ColonicHemorrhage" + "@id": "bts:UrinaryFrequency" }, { - "@id": "bts:ColonicObstruction" + "@id": "bts:UrinaryIncontinence" }, { - "@id": "bts:ColonicPerforation" + "@id": "bts:UrinaryRetention" }, { - "@id": "bts:ColonicStenosis" + "@id": "bts:UrinaryTractInfection" }, { - "@id": "bts:ColonicUlcer" + "@id": "bts:UrinaryTractObstruction" }, { - "@id": "bts:ConcentrationImpairment" + "@id": "bts:UrinaryTractPain" }, { - "@id": "bts:ConductionDisorder" + "@id": "bts:UrinaryUrgency" }, { - "@id": "bts:Confusion" + "@id": "bts:UrineDiscoloration" }, { - "@id": "bts:Congenital" + "@id": "bts:UrineOutputDecreased" }, { - "@id": "bts:FamilialandGeneticDisordersOther" + "@id": "bts:UrostomyLeak" }, { - "@id": "bts:Conjunctivitis" + "@id": "bts:UrostomyObstruction" }, { - "@id": "bts:ConjunctivitisInfective" + "@id": "bts:UrostomySiteBleeding" }, { - "@id": "bts:Constipation" + "@id": "bts:UrostomyStenosis" }, { - "@id": "bts:ConstrictivePericarditis" + "@id": "bts:Urticaria" }, { - "@id": "bts:CornealInfection" + "@id": "bts:UterineAnastomoticLeak" }, { - "@id": "bts:CornealUlcer" + "@id": "bts:UterineFistula" }, { - "@id": "bts:Cough" + "@id": "bts:UterineHemorrhage" }, { - "@id": "bts:CPKIncreased" + "@id": "bts:UterineInfection" }, { - "@id": "bts:CranialNerveInfection" + "@id": "bts:UterineObstruction" }, { - "@id": "bts:CreatinineIncreased" + "@id": "bts:UterinePain" }, { - "@id": "bts:Cushingoid" + "@id": "bts:UterinePerforation" }, { - "@id": "bts:CystitisNoninfective" + "@id": "bts:Uveitis" }, { - "@id": "bts:CytokineReleaseSyndrome" + "@id": "bts:VaginalAnastomoticLeak" }, { - "@id": "bts:DeathNeonatal" + "@id": "bts:VaginalDischarge" }, { - "@id": "bts:DeathNOS" + "@id": "bts:VaginalDryness" }, { - "@id": "bts:Dehydration" + "@id": "bts:VaginalFistula" }, { - "@id": "bts:DelayedOrgasm" + "@id": "bts:VaginalHemorrhage" }, { - "@id": "bts:DelayedPuberty" + "@id": "bts:VaginalInfection" }, { - "@id": "bts:Delirium" + "@id": "bts:VaginalInflammation" }, { - "@id": "bts:Delusions" + "@id": "bts:VaginalObstruction" }, { - "@id": "bts:DentalCaries" + "@id": "bts:VaginalPain" }, { - "@id": "bts:DepressedLevelofConsciousness" + "@id": "bts:VaginalPerforation" }, { - "@id": "bts:Depression" + "@id": "bts:VaginalStricture" }, { - "@id": "bts:DermatitisRadiation" + "@id": "bts:Vaginismus" }, { - "@id": "bts:DeviceRelatedInfection" + "@id": "bts:VagusNerveDisorder" }, { - "@id": "bts:Diarrhea" + "@id": "bts:VasDeferensAnastomoticLeak" }, { - "@id": "bts:DisseminatedIntravascularCoagulation" + "@id": "bts:VascularAccessComplication" }, { - "@id": "bts:Dizziness" + "@id": "bts:VascularDisordersOther" }, { - "@id": "bts:DryEye" + "@id": "bts:Vasculitis" }, { - "@id": "bts:DryMouth" + "@id": "bts:VasovagalReaction" }, { - "@id": "bts:DrySkin" + "@id": "bts:VenousInjury" }, { - "@id": "bts:DuodenalFistula" + "@id": "bts:VentricularArrhythmia" }, { - "@id": "bts:DuodenalHemorrhage" + "@id": "bts:VentricularFibrillation" }, { - "@id": "bts:DuodenalInfection" + "@id": "bts:VentricularTachycardia" }, { - "@id": "bts:DuodenalObstruction" + "@id": "bts:Vertigo" }, { - "@id": "bts:DuodenalPerforation" + "@id": "bts:VestibularDisorder" }, { - "@id": "bts:DuodenalStenosis" + "@id": "bts:Virilization" }, { - "@id": "bts:DuodenalUlcer" + "@id": "bts:VisceralArterialIschemia" }, { - "@id": "bts:Dysarthria" + "@id": "bts:VitalCapacityAbnormal" }, { - "@id": "bts:Dysesthesia" + "@id": "bts:VitreousHemorrhage" }, { - "@id": "bts:Dysgeusia" + "@id": "bts:VoiceAlteration" }, { - "@id": "bts:Dysmenorrhea" + "@id": "bts:Vomiting" }, { - "@id": "bts:Dyspareunia" + "@id": "bts:VulvalInfection" }, { - "@id": "bts:Dyspepsia" + "@id": "bts:WateringEyes" }, { - "@id": "bts:Dysphagia" + "@id": "bts:WeightGain" }, { - "@id": "bts:Dysphasia" + "@id": "bts:WeightLoss" }, { - "@id": "bts:Dyspnea" + "@id": "bts:Wheezing" }, { - "@id": "bts:EarandLabyrinthDisordersOther" + "@id": "bts:WhiteBloodCellDecreased" }, { - "@id": "bts:EarPain" + "@id": "bts:Wolff-Parkinson-WhiteSyndrome" }, { - "@id": "bts:EdemaCerebral" + "@id": "bts:WoundComplication" }, { - "@id": "bts:EdemaFace" + "@id": "bts:WoundDehiscence" }, { - "@id": "bts:EdemaLimbs" + "@id": "bts:WoundInfection" }, { - "@id": "bts:EdemaTrunk" - }, + "@id": "bts:WristFracture" + } + ], + "sms:displayName": "Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", + "rdfs:label": "BarrettsEsophagusGobletCellsPresent", + "rdfs:subClassOf": [ { - "@id": "bts:EjaculationDisorder" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:EjectionFractionDecreased" + "@id": "bts:Yes" }, { - "@id": "bts:ElectrocardiogramQTCorrectedIntervalProlonged" - }, + "@id": "bts:No" + } + ], + "sms:displayName": "Barretts Esophagus Goblet Cells Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BMI", + "@type": "rdfs:Class", + "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", + "rdfs:label": "BMI", + "rdfs:subClassOf": [ { - "@id": "bts:EncephalitisInfection" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "BMI", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CauseofResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", + "rdfs:label": "CauseofResponse", + "rdfs:subClassOf": [ { - "@id": "bts:EncephalomyelitisInfection" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cause of Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Comorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", + "rdfs:label": "Comorbidity", + "rdfs:subClassOf": [ { - "@id": "bts:Encephalopathy" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:EndocarditisInfective" + "@id": "bts:AcuteRenalFailure" }, { - "@id": "bts:EndocrineDisordersOther" + "@id": "bts:Adenocarcinoma" }, { - "@id": "bts:Endophthalmitis" + "@id": "bts:AdrenocorticalInsufficiency" }, { - "@id": "bts:Enterocolitis" + "@id": "bts:AdenomatousPolyposisColi" }, { - "@id": "bts:EnterocolitisInfectious" + "@id": "bts:Allergies" }, { - "@id": "bts:EnterovesicalFistula" + "@id": "bts:Alpha-1Antitrypsin" }, { - "@id": "bts:Epistaxis" + "@id": "bts:Anemia" }, { - "@id": "bts:ErectileDysfunction" + "@id": "bts:Anxiety" }, { - "@id": "bts:ErythemaMultiforme" + "@id": "bts:Arrhythmia" }, { - "@id": "bts:Erythroderma" + "@id": "bts:Arthritis" }, { - "@id": "bts:EsophagealAnastomoticLeak" + "@id": "bts:Asthma" }, { - "@id": "bts:EsophagealFistula" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:EsophagealHemorrhage" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:EsophagealInfection" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:EsophagealNecrosis" + "@id": "bts:BasalCellCarcinoma" }, { - "@id": "bts:EsophagealObstruction" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:EsophagealPain" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:EsophagealPerforation" + "@id": "bts:BiliaryDisorder" }, { - "@id": "bts:EsophagealStenosis" + "@id": "bts:BloodClots" }, { - "@id": "bts:EsophagealUlcer" + "@id": "bts:BoneFracture(s)" }, { - "@id": "bts:EsophagealVaricesHemorrhage" + "@id": "bts:Bronchitis" }, { - "@id": "bts:Esophagitis" + "@id": "bts:CalciumChannelBlockers" }, { - "@id": "bts:Euphoria" + "@id": "bts:Cancer" }, { - "@id": "bts:Exostosis" + "@id": "bts:Cataracts" }, { - "@id": "bts:ExternalEarInflammation" + "@id": "bts:CeliacDisease" }, { - "@id": "bts:ExternalEarPain" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:ExtraocularMuscleParesis" + "@id": "bts:UnknownEtiology" }, { - "@id": "bts:ExtrapyramidalDisorder" + "@id": "bts:CerebrovascularDisease" }, { - "@id": "bts:EyeDisordersOther" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:EyeInfection" + "@id": "bts:ChronicRenalFailure" }, { - "@id": "bts:EyePain" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:EyelidFunctionDisorder" + "@id": "bts:CommonVariableImmunodeficiency" }, { - "@id": "bts:FacialMuscleWeakness" + "@id": "bts:CongestiveHeartFailure(CHF)" }, { - "@id": "bts:FacialNerveDisorder" + "@id": "bts:ConnectiveTissueDisorder" }, { - "@id": "bts:FacialPain" + "@id": "bts:COPD" }, { - "@id": "bts:Fall" + "@id": "bts:CoronaryArteryDisease" }, { - "@id": "bts:FallopianTubeAnastomoticLeak" + "@id": "bts:Crohn'sDisease" }, { - "@id": "bts:FallopianTubeObstruction" + "@id": "bts:CryptogenicOrganizingPneumonia" }, { - "@id": "bts:FallopianTubePerforation" + "@id": "bts:DeepVeinThrombosis/Thromboembolism" }, { - "@id": "bts:FallopianTubeStenosis" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:FatAtrophy" + "@id": "bts:Depression" }, { - "@id": "bts:Fatigue" + "@id": "bts:Diabetes" }, { - "@id": "bts:FebrileNeutropenia" + "@id": "bts:TypeII" }, { - "@id": "bts:FecalIncontinence" + "@id": "bts:DiabeticNeuropathy" }, { - "@id": "bts:FemaleGenitalTractFistula" + "@id": "bts:DietControlledDiabetes" }, { - "@id": "bts:FeminizationAcquired" + "@id": "bts:Diverticulitis" }, { - "@id": "bts:FetalDeath" + "@id": "bts:DVT/PE" }, { - "@id": "bts:FetalGrowthRetardation" + "@id": "bts:Dyslipidemia" }, { - "@id": "bts:Fever" + "@id": "bts:Epilepsy" }, { - "@id": "bts:FibrinogenDecreased" + "@id": "bts:Eczema" }, { - "@id": "bts:FibrosisDeepConnectiveTissue" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:FlankPain" + "@id": "bts:FamilialAdenomatousPolyposis" }, { - "@id": "bts:FlashingLights" + "@id": "bts:FanconiAnemia" }, { - "@id": "bts:Flatulence" + "@id": "bts:Fibrosis" }, { - "@id": "bts:Floaters" + "@id": "bts:GastroesophagealRefluxDisease" }, { - "@id": "bts:FluLikeSymptoms" + "@id": "bts:GERD" }, { - "@id": "bts:Flushing" + "@id": "bts:Glaucoma" }, { - "@id": "bts:ForcedExpiratoryVolumeDecreased" + "@id": "bts:GlycogenStorageDisease" }, { - "@id": "bts:Fracture" + "@id": "bts:Gout" }, { - "@id": "bts:GaitDisturbance" + "@id": "bts:GonadalDysfunction" }, { - "@id": "bts:GallbladderFistula" + "@id": "bts:GorlinSyndrome" }, { - "@id": "bts:GallbladderInfection" + "@id": "bts:H.pyloriInfection" }, { - "@id": "bts:GallbladderNecrosis" + "@id": "bts:Hashimoto'sThyroiditis" }, { - "@id": "bts:GallbladderObstruction" + "@id": "bts:Headache" }, { - "@id": "bts:GallbladderPain" + "@id": "bts:HeartDisease" }, { - "@id": "bts:GallbladderPerforation" + "@id": "bts:Hemihypertrophy" }, { - "@id": "bts:GastricAnastomoticLeak" + "@id": "bts:HemorrhagicCystitis" }, { - "@id": "bts:GastricFistula" + "@id": "bts:Hepatitis" }, { - "@id": "bts:GastricHemorrhage" + "@id": "bts:HepatitisAInfection" }, { - "@id": "bts:GastricNecrosis" + "@id": "bts:HepatitisBInfection" }, { - "@id": "bts:GastricPerforation" + "@id": "bts:HepatitisCInfection" }, { - "@id": "bts:GastricStenosis" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:GastricUlcer" + "@id": "bts:HereditaryNon-polyposisColonCancer" }, { - "@id": "bts:Gastritis" + "@id": "bts:Herpes" }, { - "@id": "bts:GastroesophagealRefluxDisease" + "@id": "bts:HighGradeLiverDysplasticNodule" }, { - "@id": "bts:GastrointestinalAnastomoticLeak" + "@id": "bts:HIV/AIDS" }, { - "@id": "bts:GastrointestinalDisordersOther" + "@id": "bts:HumanPapillomavirusInfection" }, { - "@id": "bts:GastrointestinalFistula" + "@id": "bts:HUS/TTP" }, { - "@id": "bts:GastrointestinalPain" + "@id": "bts:Hypercholesterolemia" }, { - "@id": "bts:GastrointestinalStomaNecrosis" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:Gastroparesis" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:GeneralDisordersandAdministrationSiteConditionsOther" + "@id": "bts:Hyperlipidemia" }, { - "@id": "bts:GeneralizedMuscleWeakness" + "@id": "bts:Hypertension" }, { - "@id": "bts:GenitalEdema" + "@id": "bts:Hypospadias" }, { - "@id": "bts:GGTIncreased" + "@id": "bts:Hypothyroidism" }, { - "@id": "bts:GingivalPain" + "@id": "bts:InflammatoryBowelDisease" }, { - "@id": "bts:Glaucoma" + "@id": "bts:InsulinControlledDiabetes" }, { - "@id": "bts:GlossopharyngealNerveDisorder" + "@id": "bts:InterstitialPneumontisorARDS" }, { - "@id": "bts:GlucoseIntolerance" + "@id": "bts:IntraductalPapillaryMucinousNeoplasm" }, { - "@id": "bts:GrowthAccelerated" + "@id": "bts:IronOverload" }, { - "@id": "bts:GrowthHormoneAbnormal" + "@id": "bts:IschemicHeartDisease" }, { - "@id": "bts:GrowthSuppression" + "@id": "bts:ITP" }, { - "@id": "bts:GumInfection" + "@id": "bts:JointReplacement" }, { - "@id": "bts:Gynecomastia" + "@id": "bts:KidneyDisease" }, { - "@id": "bts:Hallucinations" + "@id": "bts:LiverCirrhosis(LiverDisease)" }, { - "@id": "bts:HaptoglobinDecreased" + "@id": "bts:LiverToxicity(Non-Infectious)" }, { - "@id": "bts:HeadSoftTissueNecrosis" + "@id": "bts:Li-FraumeniSyndrome" }, { - "@id": "bts:Headache" + "@id": "bts:LowGradeLiverDysplasticNodule" }, { - "@id": "bts:HearingImpaired" + "@id": "bts:Lupus" }, { - "@id": "bts:HeartFailure" + "@id": "bts:LynchSyndrome" }, { - "@id": "bts:Hematoma" + "@id": "bts:MAI" }, { - "@id": "bts:Hematosalpinx" + "@id": "bts:MyastheniaGravis" }, { - "@id": "bts:Hematuria" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:HemoglobinIncreased" + "@id": "bts:NeuroendocrineTumor" }, { - "@id": "bts:Hemoglobinuria" + "@id": "bts:NonalcoholicSteatohepatitis" }, { - "@id": "bts:Hemolysis" + "@id": "bts:Obesity" }, { - "@id": "bts:HemolyticUremicSyndrome" + "@id": "bts:Organtransplant(site)" }, { - "@id": "bts:HemorrhoidalHemorrhage" + "@id": "bts:Osteoarthritis" }, { - "@id": "bts:Hemorrhoids" + "@id": "bts:OsteoporosisorOsteopenia" }, { - "@id": "bts:HepaticFailure" + "@id": "bts:Other" }, { - "@id": "bts:HepaticHemorrhage" + "@id": "bts:OtherCancerWithin5Years" }, { - "@id": "bts:HepaticInfection" + "@id": "bts:OtherNonmalignantSystemicDisease" }, { - "@id": "bts:HepaticNecrosis" + "@id": "bts:OtherPulmonaryComplications" }, { - "@id": "bts:HepaticPain" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:HepatitisViral" + "@id": "bts:Pain(Various)" }, { - "@id": "bts:HepatobiliaryDisordersOther" + "@id": "bts:PepticUlcer(Ulcer)" }, { - "@id": "bts:Hiccups" + "@id": "bts:PeripheralNeuropathy" }, { - "@id": "bts:HipFracture" + "@id": "bts:PeripheralVascularDisease" }, { - "@id": "bts:Hirsutism" + "@id": "bts:Peutz-JeghersDisease" }, { - "@id": "bts:Hoarseness" + "@id": "bts:PregnancyinPatientorPartner" }, { - "@id": "bts:HotFlashes" + "@id": "bts:PrimarySclerosingCholangitis" }, { - "@id": "bts:Hydrocephalus" + "@id": "bts:Psoriasis" }, { - "@id": "bts:Hypercalcemia" + "@id": "bts:PulmonaryFibrosis" }, { - "@id": "bts:Hyperglycemia" + "@id": "bts:PulmonaryHemorrhage" }, { - "@id": "bts:Hyperhidrosis" + "@id": "bts:RenalFailure(RequiringDialysis)" }, { - "@id": "bts:Hyperkalemia" + "@id": "bts:RenalDialysis" }, { - "@id": "bts:Hypermagnesemia" + "@id": "bts:RenalInsufficiency" }, { - "@id": "bts:Hypernatremia" + "@id": "bts:RheumatologicDisease" }, { - "@id": "bts:Hyperparathyroidism" + "@id": "bts:RheumatoidArthritis" }, { - "@id": "bts:Hypersomnia" + "@id": "bts:Rubinstein-TaybiSyndrome" }, { - "@id": "bts:Hypertension" + "@id": "bts:Sarcoidosis" }, { - "@id": "bts:Hyperthyroidism" + "@id": "bts:Seizure" }, { - "@id": "bts:Hypertrichosis" + "@id": "bts:Sleepapnea" }, { - "@id": "bts:Hypertriglyceridemia" + "@id": "bts:Smoking" }, { - "@id": "bts:Hyperuricemia" + "@id": "bts:Steatosis" }, { - "@id": "bts:Hypoalbuminemia" + "@id": "bts:Stroke" }, { - "@id": "bts:Hypocalcemia" + "@id": "bts:TransientIschemicAttack" }, { - "@id": "bts:HypoglossalNerveDisorder" + "@id": "bts:Tuberculosis" }, { - "@id": "bts:Hypoglycemia" + "@id": "bts:TurcotSyndrome" }, { - "@id": "bts:Hypohidrosis" + "@id": "bts:Tyrosinemia" }, { - "@id": "bts:Hypokalemia" + "@id": "bts:UlcerativeColitis" }, { - "@id": "bts:Hypomagnesemia" + "@id": "bts:WagrSyndrome" }, { - "@id": "bts:Hyponatremia" + "@id": "bts:Unknown" }, { - "@id": "bts:Hypoparathyroidism" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Comorbidity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ComorbidityMethodofDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", + "rdfs:label": "ComorbidityMethodofDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:Hypophosphatemia" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Hypotension" + "@id": "bts:Histology" }, { - "@id": "bts:Hypothermia" + "@id": "bts:Pathology" }, { - "@id": "bts:Hypothyroidism" + "@id": "bts:Radiology" }, { - "@id": "bts:Hypoxia" + "@id": "bts:Unknown" }, { - "@id": "bts:IlealFistula" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Comorbidity Method of Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoAdverseEvent", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoAdverseEvent", + "rdfs:subClassOf": [ { - "@id": "bts:IlealHemorrhage" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoComorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoComorbidity", + "rdfs:subClassOf": [ { - "@id": "bts:IlealObstruction" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Comorbidity", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DiabetesTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", + "rdfs:label": "DiabetesTreatmentType", + "rdfs:subClassOf": [ { - "@id": "bts:IlealPerforation" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:IlealStenosis" + "@id": "bts:Alpha-GlucosidaseInhibitor" }, { - "@id": "bts:IlealUlcer" + "@id": "bts:Biguanide" }, { - "@id": "bts:Ileus" + "@id": "bts:Diet" }, { - "@id": "bts:ImmuneSystemDisordersOther" + "@id": "bts:InjectedInsulin" }, { - "@id": "bts:InfectionsandInfestationsOther" + "@id": "bts:Insulin" }, { - "@id": "bts:InfectiveMyositis" + "@id": "bts:OralHypoglycemic" }, { - "@id": "bts:InfusionRelatedReaction" + "@id": "bts:Sulfonylurea" }, { - "@id": "bts:InfusionSiteExtravasation" + "@id": "bts:Thiazolidinedione" }, { - "@id": "bts:InjectionSiteReaction" + "@id": "bts:Other" }, { - "@id": "bts:InjurytoCarotidArtery" + "@id": "bts:Unknown" }, { - "@id": "bts:InjurytoInferiorVenaCava" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Diabetes Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DiseaseResponse", + "@type": "rdfs:Class", + "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", + "rdfs:label": "DiseaseResponse", + "rdfs:subClassOf": [ { - "@id": "bts:InjurytoJugularVein" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:InjurytoSuperiorVenaCava" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:Injury" + "@id": "bts:BED-BiochemicalEvidenceofDisease" }, { - "@id": "bts:PoisoningandProceduralComplicationsOther" + "@id": "bts:CPD-ClinicalProgression" }, { - "@id": "bts:INRIncreased" + "@id": "bts:CR-CompleteResponse" }, { - "@id": "bts:Insomnia" + "@id": "bts:CRU-CompleteResponseUnconfirmed" }, { - "@id": "bts:IntestinalStomaLeak" + "@id": "bts:DU-DiseaseUnchanged" }, { - "@id": "bts:IntestinalStomaObstruction" + "@id": "bts:IMR-Immunoresponse" }, { - "@id": "bts:IntestinalStomaSiteBleeding" + "@id": "bts:IPD-Immunoprogression" }, { - "@id": "bts:Intra-AbdominalHemorrhage" + "@id": "bts:MR-Minimal/Marginalresponse" }, { - "@id": "bts:IntracranialHemorrhage" + "@id": "bts:MX-MixedResponse" }, { - "@id": "bts:IntraoperativeArterialInjury" + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" }, { - "@id": "bts:IntraoperativeBreastInjury" + "@id": "bts:NPB-NoPalliativeBenefit" }, { - "@id": "bts:IntraoperativeCardiacInjury" + "@id": "bts:NR-NoResponse" }, { - "@id": "bts:IntraoperativeEarInjury" + "@id": "bts:PA-PalliativeTherapy" }, { - "@id": "bts:IntraoperativeEndocrineInjury" + "@id": "bts:PB-PalliativeBenefit" }, { - "@id": "bts:IntraoperativeGastrointestinalInjury" + "@id": "bts:PD-ProgressiveDisease" }, { - "@id": "bts:IntraoperativeHeadandNeckInjury" + "@id": "bts:PDM-PersistentDistantMetastasis" }, { - "@id": "bts:IntraoperativeHemorrhage" + "@id": "bts:PLD-PersistentLocoregionalDisease" }, { - "@id": "bts:IntraoperativeHepatobiliaryInjury" + "@id": "bts:PPD-Pseudoprogression" }, { - "@id": "bts:IntraoperativeMusculoskeletalInjury" + "@id": "bts:PR-PartialResponse" }, { - "@id": "bts:IntraoperativeNeurologicalInjury" + "@id": "bts:PSR-Pseudoresponse" }, { - "@id": "bts:IntraoperativeOcularInjury" + "@id": "bts:RD-ResponsiveDisease" }, { - "@id": "bts:IntraoperativeRenalInjury" + "@id": "bts:RP-Response" }, { - "@id": "bts:IntraoperativeReproductiveTractInjury" + "@id": "bts:RPD-RadiographicProgressiveDisease" }, { - "@id": "bts:IntraoperativeRespiratoryInjury" - }, - { - "@id": "bts:IntraoperativeSkinInjury" + "@id": "bts:SCR-StringentCompleteResponse" }, { - "@id": "bts:IntraoperativeSplenicInjury" + "@id": "bts:SD-StableDisease" }, { - "@id": "bts:IntraoperativeUrinaryInjury" + "@id": "bts:SPD-SurgicalProgression" }, { - "@id": "bts:IntraoperativeVenousInjury" + "@id": "bts:TE-TooEarly" }, { - "@id": "bts:InvestigationsOther" + "@id": "bts:TF-TumorFree" }, { - "@id": "bts:IronOverload" + "@id": "bts:VGPR-VeryGoodPartialResponse" }, { - "@id": "bts:IrregularMenstruation" + "@id": "bts:WT-WithTumor" }, { - "@id": "bts:Irritability" + "@id": "bts:Unknown" }, { - "@id": "bts:IschemiaCerebrovascular" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Disease Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DLCORefPredictivePercent", + "@type": "rdfs:Class", + "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", + "rdfs:label": "DLCORefPredictivePercent", + "rdfs:subClassOf": [ { - "@id": "bts:IVthNerveDisorder" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DLCO Ref Predictive Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ECOGPerformanceStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The ECOG functional performance status of the patient/participant.", + "rdfs:label": "ECOGPerformanceStatus", + "rdfs:subClassOf": [ { - "@id": "bts:JejunalFistula" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:JejunalHemorrhage" + "@id": "bts:\"0\"" }, { - "@id": "bts:JejunalObstruction" + "@id": "bts:\"1\"" }, { - "@id": "bts:JejunalPerforation" + "@id": "bts:\"2\"" }, { - "@id": "bts:JejunalStenosis" + "@id": "bts:\"3\"" }, { - "@id": "bts:JejunalUlcer" + "@id": "bts:\"4\"" }, { - "@id": "bts:JointEffusion" + "@id": "bts:\"5\"" }, { - "@id": "bts:JointInfection" + "@id": "bts:\"0.0\"" }, { - "@id": "bts:JointRangeofMotionDecreased" + "@id": "bts:\"1.0\"" }, { - "@id": "bts:JointRangeofMotionDecreasedCervicalSpine" + "@id": "bts:\"2.0\"" }, { - "@id": "bts:JointRangeofMotionDecreasedLumbarSpine" + "@id": "bts:\"3.0\"" }, { - "@id": "bts:Keratitis" + "@id": "bts:\"4.0\"" }, { - "@id": "bts:KidneyAnastomoticLeak" + "@id": "bts:\"5.0\"" }, { - "@id": "bts:KidneyInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:Kyphosis" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "ECOG Performance Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1FVCPostBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", + "rdfs:label": "FEV1FVCPostBronchPercent", + "rdfs:subClassOf": [ { - "@id": "bts:LactationDisorder" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 FVC Post Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1FVCPreBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", + "rdfs:label": "FEV1FVCPreBronchPercent", + "rdfs:subClassOf": [ { - "@id": "bts:LargeIntestinalAnastomoticLeak" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV 1 FVC Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1RefPostBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", + "rdfs:label": "FEV1RefPostBronchPercent", + "rdfs:subClassOf": [ { - "@id": "bts:LaryngealEdema" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 Ref Post Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1RefPreBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", + "rdfs:label": "FEV1RefPreBronchPercent", + "rdfs:subClassOf": [ { - "@id": "bts:LaryngealFistula" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 Ref Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Height", + "@type": "rdfs:Class", + "rdfs:comment": "The height of the patient in centimeters.", + "rdfs:label": "Height", + "rdfs:subClassOf": [ { - "@id": "bts:LaryngealHemorrhage" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Height", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HepatitisSustainedVirologicalResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "HepatitisSustainedVirologicalResponse", + "rdfs:subClassOf": [ { - "@id": "bts:LaryngealInflammation" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LaryngealMucositis" + "@id": "bts:Yes" }, { - "@id": "bts:LaryngealObstruction" + "@id": "bts:No" }, { - "@id": "bts:LaryngealStenosis" + "@id": "bts:Unknown" }, { - "@id": "bts:Laryngitis" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Hepatitis Sustained Virological Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HPVPositiveType", + "@type": "rdfs:Class", + "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", + "rdfs:label": "HPVPositiveType", + "rdfs:subClassOf": [ { - "@id": "bts:LaryngopharyngealDysesthesia" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Laryngospasm" + "@id": "bts:\"16\"" }, { - "@id": "bts:LeftVentricularSystolicDysfunction" + "@id": "bts:\"18\"" }, { - "@id": "bts:Lethargy" + "@id": "bts:\"26\"" }, { - "@id": "bts:LeukemiaSecondarytoOncologyChemotherapy" + "@id": "bts:\"31\"" }, { - "@id": "bts:Leukocytosis" + "@id": "bts:\"33\"" }, { - "@id": "bts:Leukoencephalopathy" + "@id": "bts:\"35\"" }, { - "@id": "bts:LibidoDecreased" + "@id": "bts:\"39\"" }, { - "@id": "bts:LibidoIncreased" + "@id": "bts:\"45\"" }, { - "@id": "bts:LipInfection" + "@id": "bts:\"51\"" }, { - "@id": "bts:LipPain" + "@id": "bts:\"52\"" }, { - "@id": "bts:LipaseIncreased" + "@id": "bts:\"53\"" }, { - "@id": "bts:Lipohypertrophy" + "@id": "bts:\"56\"" }, { - "@id": "bts:LocalizedEdema" + "@id": "bts:\"58\"" }, { - "@id": "bts:Lordosis" + "@id": "bts:\"59\"" }, { - "@id": "bts:LowerGastrointestinalHemorrhage" + "@id": "bts:\"63\"" }, { - "@id": "bts:LungInfection" + "@id": "bts:\"66\"" }, { - "@id": "bts:LymphGlandInfection" + "@id": "bts:\"68\"" }, { - "@id": "bts:LymphLeakage" + "@id": "bts:\"70\"" }, { - "@id": "bts:LymphNodePain" + "@id": "bts:\"73\"" }, { - "@id": "bts:Lymphedema" + "@id": "bts:\"82\"" }, { - "@id": "bts:Lymphocele" + "@id": "bts:Other" }, { - "@id": "bts:LymphocyteCountDecreased" + "@id": "bts:Unknown" }, { - "@id": "bts:LymphocyteCountIncreased" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HPV Positive Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KarnofskyPerformanceStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", + "rdfs:label": "KarnofskyPerformanceStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Malabsorption" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Malaise" + "@id": "bts:\"0\"" }, { - "@id": "bts:Mania" + "@id": "bts:\"10\"" }, { - "@id": "bts:MediastinalHemorrhage" + "@id": "bts:\"20\"" }, { - "@id": "bts:MediastinalInfection" + "@id": "bts:\"30\"" }, { - "@id": "bts:MemoryImpairment" + "@id": "bts:\"40\"" }, { - "@id": "bts:Meningismus" + "@id": "bts:\"50\"" }, { - "@id": "bts:Meningitis" + "@id": "bts:\"60\"" }, { - "@id": "bts:Menopause" + "@id": "bts:\"70\"" }, { - "@id": "bts:Menorrhagia" + "@id": "bts:\"80\"" }, { - "@id": "bts:MetabolismandNutritionDisordersOther" + "@id": "bts:\"90\"" }, { - "@id": "bts:MiddleEarInflammation" + "@id": "bts:\"100\"" }, { - "@id": "bts:MitralValveDisease" + "@id": "bts:Unknown" }, { - "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Karnofsky Performance Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MenopauseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's menopause status.", + "rdfs:label": "MenopauseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:MobitzTypeI" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MovementsInvoluntary" + "@id": "bts:Premenopausal" }, { - "@id": "bts:MucosalInfection" + "@id": "bts:Perimenopausal" }, { - "@id": "bts:MucositisOral" + "@id": "bts:Postmenopausal" }, { - "@id": "bts:Multi-OrganFailure" + "@id": "bts:Unknown" }, { - "@id": "bts:MuscleWeaknessLeft-Sided" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Menopause Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreatitisOnsetYear", + "@type": "rdfs:Class", + "rdfs:comment": "Date of onset of pancreatitis.", + "rdfs:label": "PancreatitisOnsetYear", + "rdfs:subClassOf": [ { - "@id": "bts:MuscleWeaknessLowerLimb" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatitis Onset Year", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:RefluxTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", + "rdfs:label": "RefluxTreatmentType", + "rdfs:subClassOf": [ { - "@id": "bts:MuscleWeaknessRight-Sided" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MuscleWeaknessTrunk" + "@id": "bts:Antacids" }, { - "@id": "bts:MuscleWeaknessUpperLimb" + "@id": "bts:H2Blockers" }, { - "@id": "bts:MusculoskeletalandConnectiveTissueDisordersOther" + "@id": "bts:MedicallyTreated" }, { - "@id": "bts:MusculoskeletalDeformity" + "@id": "bts:NoTreatment" }, { - "@id": "bts:Myalgia" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Myelitis" + "@id": "bts:NotReported" }, { - "@id": "bts:MyelodysplasticSyndrome" + "@id": "bts:ProtonPumpInhibitors" }, { - "@id": "bts:MyocardialInfarction" + "@id": "bts:SurgicallyTreated" }, { - "@id": "bts:Myocarditis" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Reflux Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RiskFactor", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactor", + "rdfs:subClassOf": [ { - "@id": "bts:Myositis" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NailDiscoloration" + "@id": "bts:AlcoholConsumption" }, { - "@id": "bts:NailInfection" + "@id": "bts:AlcoholicLiverDisease" }, { - "@id": "bts:NailLoss" + "@id": "bts:AllergyAnimalNOS" }, { - "@id": "bts:NailRidging" + "@id": "bts:AllergyAnt" }, { - "@id": "bts:NasalCongestion" + "@id": "bts:AllergyBee" }, { - "@id": "bts:Nausea" + "@id": "bts:AllergyCat" }, { - "@id": "bts:NeckEdema" + "@id": "bts:AllergyDairyorLactose" }, { - "@id": "bts:NeckPain" + "@id": "bts:AllergyDog" }, { - "@id": "bts:NeckSoftTissueNecrosis" + "@id": "bts:AllergyEggs" }, { - "@id": "bts:NeoplasmsBenign" + "@id": "bts:AllergyFoodNOS" }, { - "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" + "@id": "bts:AllergyFruit" }, { - "@id": "bts:NervousSystemDisordersOther" + "@id": "bts:AllergyMeat" }, { - "@id": "bts:Neuralgia" + "@id": "bts:AllergyMoldorDust" }, { - 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"@id": "bts:PenileInfection" + "@id": "bts:Hypospadias" }, { - "@id": "bts:PenilePain" + "@id": "bts:IntestinalMetaplasia" }, { - "@id": "bts:PerforationBileDuct" + "@id": "bts:IronOverload" }, { - "@id": "bts:PericardialEffusion" + "@id": "bts:Li-FraumeniSyndrome" }, { - "@id": "bts:PericardialTamponade" + "@id": "bts:LowGradeDysplasia" }, { - "@id": "bts:Pericarditis" + "@id": "bts:LymphocyticThyroiditis" }, { - "@id": "bts:PerinealPain" + "@id": "bts:LynchSyndrome" }, { - "@id": "bts:PeriodontalDisease" + "@id": "bts:MyastheniaGravis" }, { - "@id": "bts:PeriorbitalEdema" + "@id": "bts:NonalcoholicFattyLiverDisease" }, { - "@id": "bts:PeriorbitalInfection" + "@id": "bts:NonalcoholicSteatohepatitis" }, { - "@id": "bts:PeripheralIschemia" + "@id": "bts:Obesity" }, { - "@id": "bts:PeripheralMotorNeuropathy" + "@id": "bts:OralContraceptives" }, { - "@id": "bts:PeripheralNerveInfection" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:PeripheralSensoryNeuropathy" + "@id": "bts:ParasiticDiseaseofBiliaryTract" }, { - 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoImaging", + "rdfs:subClassOf": [ { - "@id": "bts:Respiratory" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Imaging", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:EvidenceofRecurrenceType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", + "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:subClassOf": [ { - "@id": "bts:ThoracicandMediastinalDisordersOther" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Restlessness" + "@id": "bts:BiopsywithHistologicConfirmation" }, { - "@id": "bts:RestrictiveCardiomyopathy" + "@id": "bts:ConvincingImageSource" }, { - "@id": "bts:RetinalDetachment" - }, + "@id": "bts:PositiveBiomarkers" + } + ], + "sms:displayName": "Evidence of Recurrence Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HAARTTreatmentIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", + "rdfs:label": "HAARTTreatmentIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:RetinalTear" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RetinalVascularDisorder" + "@id": "bts:Yes" }, { - "@id": "bts:RetinoicAcidSyndrome" + "@id": "bts:No" }, { - "@id": "bts:Retinopathy" + "@id": "bts:Unknown" }, { - "@id": "bts:RetroperitonealHemorrhage" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HAART Treatment Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HIVViralLoad", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", + "rdfs:label": "HIVViralLoad", + "rdfs:subClassOf": [ { - 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"@id": "bts:SerumSickness" + "@id": "bts:Notperformed" }, { - "@id": "bts:SickSinusSyndrome" + "@id": "bts:RadicalHysterectomy" }, { - "@id": "bts:SinusBradycardia" + "@id": "bts:SimpleHysterectomy" }, { - "@id": "bts:SinusDisorder" + "@id": "bts:Unknown" }, { - "@id": "bts:SinusPain" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Hysterectomy Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingResult", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", + "rdfs:label": "ImagingResult", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Positive" }, { - "@id": "bts:SinusTachycardia" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Sinusitis" + "@id": "bts:Negative" }, { - "@id": "bts:SkinandSubcutaneousTissueDisordersOther" + "@id": "bts:NotPerformed" }, { - "@id": "bts:SkinAtrophy" + "@id": "bts:Unknown" }, { - "@id": "bts:SkinHyperpigmentation" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Imaging Result", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", + "rdfs:label": "ImagingType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:99mTcBoneScintigraphy" }, { - "@id": "bts:SkinHypopigmentation" + "@id": "bts:CTScan" }, { - "@id": "bts:SkinInduration" + "@id": "bts:MRI" }, { - "@id": "bts:SkinInfection" + "@id": "bts:PET" + } + ], + "sms:displayName": "Imaging Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmunosuppressiveTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of immunosuppresive treatment the patient received.", + "rdfs:label": "ImmunosuppressiveTreatmentType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Anti-TNFTherapy" }, { - "@id": "bts:SkinUlceration" + "@id": "bts:Azathioprine" }, { - "@id": "bts:SleepApnea" + "@id": "bts:Cyclophosphamide" }, { - "@id": "bts:SmallIntestinalAnastomoticLeak" + "@id": "bts:Methotrexate" }, { - "@id": "bts:SmallIntestinalMucositis" + "@id": "bts:None" }, { - "@id": "bts:SmallIntestinalObstruction" + "@id": "bts:Other" }, { - "@id": "bts:SmallIntestinalPerforation" + "@id": "bts:Unknown" }, { - "@id": "bts:SmallIntestinalStenosis" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Immunosuppressive Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NadirCD4Count", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).", + "rdfs:label": "NadirCD4Count", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nadir CD4 Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnancyOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of pregnancy the patient had", + "rdfs:label": "PregnancyOutcome", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:EctopicPregnancy" }, { - "@id": "bts:SmallIntestineInfection" + "@id": "bts:InducedAbortion" }, { - "@id": "bts:SmallIntestineUlcer" + "@id": "bts:LiveBirth" }, { - "@id": "bts:Sneezing" + "@id": "bts:Miscarriage" }, { - "@id": "bts:SocialCircumstancesOther" + "@id": "bts:Stillbirth" }, { - "@id": "bts:SoftTissueInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:SoftTissueNecrosisLowerLimb" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pregnancy Outcome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RecistTargetedRegionsNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria", + "rdfs:label": "RecistTargetedRegionsNumber", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Recist Targeted Regions Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RecistTargetedRegionsSum", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.", + "rdfs:label": "RecistTargetedRegionsSum", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Recist Targeted Regions Sum", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScanTracerUsed", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of tracer used during the imaging or scan of the patient.", + "rdfs:label": "ScanTracerUsed", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Acetate" }, { - "@id": "bts:SoftTissueNecrosisUpperLimb" + "@id": "bts:Axumin" }, { - "@id": "bts:Somnolence" + "@id": "bts:Choline" }, { - "@id": "bts:SoreThroat" + "@id": "bts:PSMA" }, { - "@id": "bts:Spasticity" + "@id": "bts:SodiumFluoride" + } + ], + "sms:displayName": "Scan Tracer Used", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentorTherapy", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.", + "rdfs:label": "TreatmentorTherapy", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SpermaticCordAnastomoticLeak" + "@id": "bts:No" }, { - "@id": "bts:SpermaticCordHemorrhage" + "@id": "bts:Unknown" }, { - "@id": "bts:SpermaticCordObstruction" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment or Therapy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentEffect", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the pathologic effect a treatment(s) had on the tumor.", + "rdfs:label": "TreatmentEffect", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CompleteNecrosis(NoViableTumor)" }, { - 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"@id": "bts:StomalUlcer" + "@id": "bts:PartialResponse" }, { - "@id": "bts:Stridor" + "@id": "bts:PersistentDisease" }, { - "@id": "bts:Stroke" + "@id": "bts:ProgressiveDisease" }, { - "@id": "bts:SuddenDeathNOS" + "@id": "bts:StableDisease" }, { - "@id": "bts:SuicidalIdeation" + "@id": "bts:TreatmentOngoing" }, { - "@id": "bts:SuicideAttempt" + "@id": "bts:TreatmentStoppedDuetoToxicity" }, { - "@id": "bts:SuperficialSoftTissueFibrosis" + "@id": "bts:VeryGoodPartialResponse" }, { - "@id": "bts:SuperficialThrombophlebitis" + "@id": "bts:Unknown" }, { - "@id": "bts:SuperiorVenaCavaSyndrome" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Outcome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoTreatmentEnd", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentEnd", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Treatment End", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:TreatmentAnatomicSite", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment", + "rdfs:label": "TreatmentAnatomicSite", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:SupraventricularTachycardia" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:SurgicalandMedicalProceduresOther" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:Syncope" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:Telangiectasia" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:TesticularDisorder" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:TesticularHemorrhage" + "@id": "bts:Analcanal" }, { - "@id": "bts:TesticularPain" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:ThromboembolicEvent" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:ThromboticThrombocytopenicPurpura" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Tinnitus" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:ToothDevelopmentDisorder" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:ToothDiscoloration" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:ToothInfection" + "@id": "bts:AnusNOS" }, { - "@id": "bts:Toothache" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:ToxicEpidermalNecrolysis" + "@id": "bts:Appendix" }, { - "@id": "bts:TrachealFistula" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:TrachealHemorrhage" + "@id": "bts:AutonomicnervoussystemNOS" }, { - 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"@type": "rdfs:Class", - "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", - "rdfs:label": "BarrettsEsophagusGobletCellsPresent", - "rdfs:subClassOf": [ + "@id": "bts:HematopoieticsystemNOS" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hepaticflexureofcolon" + }, { - "@id": "bts:Yes" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Barretts Esophagus Goblet Cells Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BMI", - "@type": "rdfs:Class", - "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", - "rdfs:label": "BMI", - "rdfs:subClassOf": [ + "@id": "bts:HypopharynxNOS" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "BMI", - "sms:required": "sms:false", - 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"@id": "bts:Diverticulitis" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:DVT/PE" + "@id": "bts:MouthNOS" }, { - "@id": "bts:Dyslipidemia" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:Epilepsy" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:Eczema" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:Myometrium" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:Fibrosis" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:GastroesophagealRefluxDisease" + "@id": "bts:Nipple" }, { - "@id": "bts:GERD" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:Glaucoma" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:GlycogenStorageDisease" + "@id": "bts:Opticnerve" }, { - "@id": "bts:Gout" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:GonadalDysfunction" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:Otherill-definedsites" }, { - 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"@id": "bts:InflammatoryBowelDisease" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:InsulinControlledDiabetes" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:InterstitialPneumontisorARDS" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:IntraductalPapillaryMucinousNeoplasm" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:IronOverload" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:IschemicHeartDisease" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:ITP" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:JointReplacement" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:KidneyDisease" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:LiverCirrhosis(LiverDisease)" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:LiverToxicity(Non-Infectious)" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - 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"@id": "bts:Stroke" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:TransientIschemicAttack" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:Tuberculosis" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:Tyrosinemia" + "@id": "bts:Prepuce" }, { - "@id": "bts:UlcerativeColitis" + "@id": "bts:Prostategland" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:Pylorus" }, { - "@id": "bts:Unknown" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ComorbidityMethodofDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", - "rdfs:label": "ComorbidityMethodofDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:Rectosigmoidjunction" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RectumNOS" + }, { - "@id": "bts:Histology" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:Pathology" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Radiology" + "@id": "bts:Retina" }, { - "@id": "bts:Unknown" + "@id": "bts:Retromolararea" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity Method of Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoAdverseEvent", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoAdverseEvent", - "rdfs:subClassOf": [ + "@id": "bts:Retroperitoneum" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoComorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoComorbidity", - "rdfs:subClassOf": [ + "@id": "bts:Ribsternumclavicleandassociatedjoints" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DiabetesTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", - "rdfs:label": "DiabetesTreatmentType", - "rdfs:subClassOf": [ + "@id": "bts:Roundligament" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ScrotumNOS" + }, { - "@id": "bts:Alpha-GlucosidaseInhibitor" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:Biguanide" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:Diet" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:InjectedInsulin" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:Insulin" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:OralHypoglycemic" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:Sulfonylurea" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:Thiazolidinedione" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:Other" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:Unknown" + "@id": "bts:SkinNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Diabetes Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DiseaseResponse", - "@type": "rdfs:Class", - "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", - "rdfs:label": "DiseaseResponse", - "rdfs:subClassOf": [ + "@id": "bts:SmallintestineNOS" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SoftpalateNOS" + }, { - "@id": "bts:AJ-AdjuvantTherapy" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:BED-BiochemicalEvidenceofDisease" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:CPD-ClinicalProgression" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:CR-CompleteResponse" + "@id": "bts:Spinalcord" }, { - "@id": "bts:CRU-CompleteResponseUnconfirmed" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:DU-DiseaseUnchanged" + "@id": "bts:Spleen" }, { - "@id": "bts:IMR-Immunoresponse" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:IPD-Immunoprogression" + "@id": "bts:StomachNOS" }, { - "@id": "bts:MR-Minimal/Marginalresponse" + "@id": "bts:Subglottis" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:NR-NoResponse" + "@id": "bts:Supraglottis" }, { - "@id": "bts:PA-PalliativeTherapy" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:Temporallobe" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:TestisNOS" }, { - "@id": "bts:PDM-PersistentDistantMetastasis" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:PLD-PersistentLocoregionalDisease" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:Thymus" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:TongueNOS" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:RP-Response" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:Trachea" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:Transversecolon" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:TF-TumorFree" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:Uppergum" }, { - "@id": "bts:WT-WithTumor" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Disease Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DLCORefPredictivePercent", - "@type": "rdfs:Class", - "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", - "rdfs:label": "DLCORefPredictivePercent", - "rdfs:subClassOf": [ + "@id": "bts:UpperrespiratorytractNOS" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DLCO Ref Predictive Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ECOGPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The ECOG functional performance status of the patient/participant.", - "rdfs:label": "ECOGPerformanceStatus", - "rdfs:subClassOf": [ + "@id": "bts:Upperthirdofesophagus" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Upper-innerquadrantofbreast" + }, { - "@id": "bts:\"0\"" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:\"1\"" + "@id": "bts:Urachus" }, { - "@id": "bts:\"2\"" + "@id": "bts:Ureter" }, { - "@id": "bts:\"3\"" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:\"4\"" + "@id": "bts:Urethra" }, { - "@id": "bts:\"5\"" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:\"0.0\"" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:\"1.0\"" + "@id": "bts:UterusNOS" }, { - "@id": "bts:\"2.0\"" + "@id": "bts:Uvula" }, { - "@id": "bts:\"3.0\"" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:\"4.0\"" + "@id": "bts:Vallecula" }, { - "@id": "bts:\"5.0\"" + "@id": "bts:VentralsurfaceoftongueNOS" + }, + { + "@id": "bts:VentricleNOS" + }, + { + "@id": "bts:Vertebralcolumn" + }, + { + "@id": "bts:Vestibuleofmouth" + }, + { + "@id": "bts:VulvaNOS" + }, + { + "@id": "bts:Waldeyerring" + }, + { + "@id": "bts:BiliarytractNOS" + }, + { + "@id": "bts:Cheekmucosa" + }, + { + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" }, { "@id": "bts:Unknown" @@ -23150,103 +22628,108 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "ECOG Performance Status", + "sms:displayName": "Treatment Anatomic Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FEV1FVCPostBronchPercent", + "@id": "bts:DaystoTreatmentStart", "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", - "rdfs:label": "FEV1FVCPostBronchPercent", + "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentStart", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FEV1 FVC Post Bronch Percent", + "sms:displayName": "Days to Treatment Start", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:FEV1FVCPreBronchPercent", + "@id": "bts:InitialDiseaseStatus", "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", - "rdfs:label": "FEV1FVCPreBronchPercent", + "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", + "rdfs:label": "InitialDiseaseStatus", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FEV 1 FVC Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", - "rdfs:label": "FEV1RefPostBronchPercent", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:FollowUp" + "@id": "bts:InitialDiagnosis" + }, + { + "@id": "bts:ProgressiveDisease" + }, + { + "@id": "bts:RecurrentDisease" + }, + { + "@id": "bts:ResidualDisease" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Post Bronch Percent", + "sms:displayName": "Initial Disease Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FEV1RefPreBronchPercent", + "@id": "bts:RegimenorLineofTherapy", "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", - "rdfs:label": "FEV1RefPreBronchPercent", + "rdfs:comment": "The text term used to describe the regimen or line of therapy.", + "rdfs:label": "RegimenorLineofTherapy", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FEV1 Ref Pre Bronch Percent", + "sms:displayName": "Regimen or Line of Therapy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Height", + "@id": "bts:TherapeuticAgents", "@type": "rdfs:Class", - "rdfs:comment": "The height of the patient in centimeters.", - "rdfs:label": "Height", + "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", + "rdfs:label": "TherapeuticAgents", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Height", + "sms:displayName": "Therapeutic Agents", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HepatitisSustainedVirologicalResponse", + "@id": "bts:TreatmentIntentType", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "HepatitisSustainedVirologicalResponse", + "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", + "rdfs:label": "TreatmentIntentType", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -23254,10 +22737,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Adjuvant" }, { - "@id": "bts:No" + "@id": "bts:CancerControl" + }, + { + "@id": "bts:Cure" + }, + { + "@id": "bts:Neoadjuvant" + }, + { + "@id": "bts:Palliative" + }, + { + "@id": "bts:Prevention" }, { "@id": "bts:Unknown" @@ -23266,18 +22761,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hepatitis Sustained Virological Response", + "sms:displayName": "Treatment Intent Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HPVPositiveType", + "@id": "bts:ChemoConcurrenttoRadiation", "@type": "rdfs:Class", - "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", - "rdfs:label": "HPVPositiveType", + "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", + "rdfs:label": "ChemoConcurrenttoRadiation", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -23285,67 +22780,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:\"16\"" - }, - { - "@id": "bts:\"18\"" - }, - { - "@id": "bts:\"26\"" - }, - { - "@id": "bts:\"31\"" - }, - { - "@id": "bts:\"33\"" - }, - { - "@id": "bts:\"35\"" - }, - { - "@id": "bts:\"39\"" - }, - { - "@id": "bts:\"45\"" - }, - { - "@id": "bts:\"51\"" - }, - { - "@id": "bts:\"52\"" - }, - { - "@id": "bts:\"53\"" - }, - { - "@id": "bts:\"56\"" - }, - { - "@id": "bts:\"58\"" - }, - { - "@id": "bts:\"59\"" - }, - { - "@id": "bts:\"63\"" - }, - { - "@id": "bts:\"66\"" - }, - { - "@id": "bts:\"68\"" - }, - { - "@id": "bts:\"70\"" - }, - { - "@id": "bts:\"73\"" - }, - { - "@id": "bts:\"82\"" + "@id": "bts:Yes" }, { - "@id": "bts:Other" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -23354,76 +22792,72 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "HPV Positive Type", + "sms:displayName": "Chemo Concurrent to Radiation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:KarnofskyPerformanceStatus", + "@id": "bts:NumberofCycles", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", - "rdfs:label": "KarnofskyPerformanceStatus", + "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", + "rdfs:label": "NumberofCycles", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:\"0\"" - }, - { - "@id": "bts:\"10\"" - }, - { - "@id": "bts:\"20\"" - }, - { - "@id": "bts:\"30\"" - }, - { - "@id": "bts:\"40\"" - }, - { - "@id": "bts:\"50\"" - }, + "sms:displayName": "Number of Cycles", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ReasonTreatmentEnded", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", + "rdfs:label": "ReasonTreatmentEnded", + "rdfs:subClassOf": [ { - "@id": "bts:\"60\"" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:\"70\"" + "@id": "bts:AdverseTherapyEvent" }, { - "@id": "bts:\"80\"" + "@id": "bts:CourseofTherapyCompleted" }, { - "@id": "bts:\"90\"" + "@id": "bts:Death" }, { - "@id": "bts:\"100\"" + "@id": "bts:DiseaseProgression" }, { - "@id": "bts:Unknown" + "@id": "bts:Other" }, { - "@id": "bts:NotReported" + "@id": "bts:WithdrawalbySubject" } ], - "sms:displayName": "Karnofsky Performance Status", + "sms:displayName": "Reason Treatment Ended", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MenopauseStatus", + "@id": "bts:TreatmentArm", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's menopause status.", - "rdfs:label": "MenopauseStatus", + "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", + "rdfs:label": "TreatmentArm", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -23431,52 +22865,44 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Premenopausal" - }, - { - "@id": "bts:Perimenopausal" - }, - { - "@id": "bts:Postmenopausal" + "@id": "bts:A081105" }, { - "@id": "bts:Unknown" + "@id": "bts:E4512" }, { - "@id": "bts:NotReported" + "@id": "bts:EA5142" } ], - "sms:displayName": "Menopause Status", + "sms:displayName": "Treatment Arm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PancreatitisOnsetYear", + "@id": "bts:TreatmentDose", "@type": "rdfs:Class", - "rdfs:comment": "Date of onset of pancreatitis.", - "rdfs:label": "PancreatitisOnsetYear", + "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", + "rdfs:label": "TreatmentDose", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pancreatitis Onset Year", + "sms:displayName": "Treatment Dose", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:RefluxTreatmentType", + "@id": "bts:TreatmentDoseUnits", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", - "rdfs:label": "RefluxTreatmentType", + "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", + "rdfs:label": "TreatmentDoseUnits", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -23484,45 +22910,55 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Antacids" + "@id": "bts:CGy" }, { - "@id": "bts:H2Blockers" - }, + "@id": "bts:Gy" + } + ], + "sms:displayName": "Treatment Dose Units", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentEffectIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", + "rdfs:label": "TreatmentEffectIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:MedicallyTreated" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NoTreatment" + "@id": "bts:Yes" }, { - "@id": "bts:NotApplicable" + "@id": "bts:No" }, { "@id": "bts:NotReported" }, - { - "@id": "bts:ProtonPumpInhibitors" - }, - { - "@id": "bts:SurgicallyTreated" - }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Reflux Treatment Type", + "sms:displayName": "Treatment Effect Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RiskFactor", + "@id": "bts:TreatmentFrequency", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactor", + "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", + "rdfs:label": "TreatmentFrequency", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -23530,277 +22966,275 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AlcoholConsumption" - }, - { - "@id": "bts:AlcoholicLiverDisease" - }, - { - "@id": "bts:AllergyAnimalNOS" - }, - { - "@id": "bts:AllergyAnt" - }, - { - "@id": "bts:AllergyBee" - }, - { - "@id": "bts:AllergyCat" - }, - { - "@id": "bts:AllergyDairyorLactose" - }, - { - "@id": "bts:AllergyDog" - }, - { - "@id": "bts:AllergyEggs" - }, - { - "@id": "bts:AllergyFoodNOS" - }, - { - "@id": "bts:AllergyFruit" - }, - { - "@id": "bts:AllergyMeat" - }, - { - "@id": "bts:AllergyMoldorDust" - }, - { - "@id": "bts:AllergyNuts" - }, - { - "@id": "bts:AllergyProcessedFoods" - }, - { - "@id": "bts:AllergySeafood" - }, - { - "@id": "bts:AllergyWasp" + "@id": "bts:EveryHour" }, { - "@id": "bts:Alpha-1AntitrypsinDeficiency" + "@id": "bts:FiveTimesDaily" }, { - "@id": "bts:AutoimmuneAtrophicChronicGastritis" + "@id": "bts:FourTimesDaily" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:ThreeTimesDaily" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:TwiceDaily" }, { - "@id": "bts:Behcet'sDisease" + "@id": "bts:Every24Hours" }, { - "@id": "bts:Cancer" + "@id": "bts:EveryOtherDay" }, { - "@id": "bts:Cholelithiasis" + "@id": "bts:TwiceWeekly" }, { - "@id": "bts:ChronicHepatitis" + "@id": "bts:OnceWeekly" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:Unknown" }, { - "@id": "bts:ColonPolyps" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Frequency", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:YearofDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", + "rdfs:label": "YearofDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:Commonvariableimmunedeficiency(CVID)" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Year of Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrecancerousConditionType", + "@type": "rdfs:Class", + "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", + "rdfs:label": "PrecancerousConditionType", + "rdfs:subClassOf": [ { - "@id": "bts:Denys-DrashSyndrome" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DiabetesNOS" + "@id": "bts:DuctalCarcinomaInSitu" }, { - "@id": "bts:DiabetesTypeI" + "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" }, { - "@id": "bts:DiabetesTypeII" + "@id": "bts:AtypicalAdenomatousLungHyperplasia" }, { - "@id": "bts:Diet" + "@id": "bts:Other" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:PancreaticIntraepithelialNeoplasia" }, { - "@id": "bts:Endometriosis" + "@id": "bts:ProstaticIntraepithelialNeoplasia" }, { - "@id": "bts:Endosalpingiosis" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:Eczema" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:Melanomainsitu" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:Superficialspreading" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:Lentigomalignatype" }, { - "@id": "bts:Fibrosis" + "@id": "bts:Acral-lentiginous" }, { - "@id": "bts:GastricPolyp(s)" + "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" }, { - "@id": "bts:Gilbert'sSyndrome" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:Melanomainsitunototherwiseclassified" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:HayFever" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:Headache" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:HelicobacterPylori-AssociatedGastritis" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:HematologicDisorderNOS" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:Hemihypertrophy" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:Hemochromatosis" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:HepaticEncephalopathy" + "@id": "bts:Invasivemelanoma" }, { - "@id": "bts:HepatitisBInfection" + "@id": "bts:NormalWDA" }, { - "@id": "bts:HepatitisCInfection" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:HepatitisNOS" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:HighGradeDysplasia" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:HIV" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:Hypospadias" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:IntestinalMetaplasia" + "@id": "bts:Atypicaladenomatoushyperplasia" }, { - "@id": "bts:IronOverload" + "@id": "bts:Adenocarcinomainsitu-nonmucinous" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:Adenocarcinomainsitu-mucinous" }, { - "@id": "bts:LowGradeDysplasia" + "@id": "bts:BenigntumorNOS" }, { - "@id": "bts:LymphocyticThyroiditis" + "@id": "bts:Hamartoma" }, { - "@id": "bts:LynchSyndrome" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:MyastheniaGravis" + "@id": "bts:Nodiagnosispossible" }, { - "@id": "bts:NonalcoholicFattyLiverDisease" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Precancerous Condition Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MethodofDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", + "rdfs:label": "MethodofDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:NonalcoholicSteatohepatitis" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Obesity" + "@id": "bts:Autopsy" }, { - "@id": "bts:OralContraceptives" + "@id": "bts:Biopsy" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:BloodDraw" }, { - "@id": "bts:ParasiticDiseaseofBiliaryTract" + "@id": "bts:BoneMarrowAspirate" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:CoreBiopsy" }, { - "@id": "bts:RecurrentPyogenicCholangitis" + "@id": "bts:Cytology" }, { - "@id": "bts:RefluxDisease" + "@id": "bts:Cystoscopy" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:Debulking" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:DiagnosticImaging" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:DilationandCurettageProcedure" }, { - "@id": "bts:Seizure" + "@id": "bts:Enucleation" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:ExcisionalBiopsy" }, { - "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + "@id": "bts:FineNeedleAspiration" }, { - "@id": "bts:Steatosis" + "@id": "bts:IncisionalBiopsy" }, { - "@id": "bts:Tattoo" + "@id": "bts:Laparoscopy" }, { - "@id": "bts:ThyroidNodularHyperplasia" + "@id": "bts:Laparotomy" }, { - "@id": "bts:TobaccoNOS" + "@id": "bts:Other" }, { - "@id": "bts:TobaccoSmokeless" + "@id": "bts:PapSmear" }, { - "@id": "bts:TobaccoSmoking" + "@id": "bts:PhysicalExam" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:PathologicReview" }, { - "@id": "bts:UndescendedTestis" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:VisionChanges" + "@id": "bts:Thoracentesis" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:UltrasoundGuidedBiopsy" }, { "@id": "bts:Unknown" @@ -23809,18 +23243,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Risk Factor", + "sms:displayName": "Method of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RiskFactorTreatment", + "@id": "bts:PriorMalignancy", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactorTreatment", + "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", + "rdfs:label": "PriorMalignancy", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23838,20 +23272,23 @@ }, { "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" } ], - "sms:displayName": "Risk Factor Treatment", + "sms:displayName": "Prior Malignancy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ViralHepatitisSerologies", + "@id": "bts:PriorTreatment", "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", - "rdfs:label": "ViralHepatitisSerologies", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", + "rdfs:label": "PriorTreatment", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23859,65 +23296,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HBVCoreAntibody" - }, - { - "@id": "bts:HBVDNA" - }, - { - "@id": "bts:HBVGenotype" - }, - { - "@id": "bts:HBVSurfaceAntibody" - }, - { - "@id": "bts:HCVGenotype" - }, - { - "@id": "bts:HepatitisBSurfaceAntigen" - }, - { - "@id": "bts:HepatitisCAntibody" + "@id": "bts:Yes" }, { - "@id": "bts:HepatitisCVirusRNA" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - } - ], - "sms:displayName": "Viral Hepatitis Serologies", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Weight", - "@type": "rdfs:Class", - "rdfs:comment": "The weight of the patient measured in kilograms.", - "rdfs:label": "Weight", - "rdfs:subClassOf": [ + }, { - "@id": "bts:FollowUp" + "@id": "bts:NotAllowedToCollect" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weight", + "sms:displayName": "Prior Treatment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdverseEventGrade", + "@id": "bts:MetastasisatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "AdverseEventGrade", + "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", + "rdfs:label": "MetastasisatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23925,33 +23330,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Grade1" + "@id": "bts:DistantMetastasis" }, { - "@id": "bts:Grade2" + "@id": "bts:MetastasisNOS" }, { - "@id": "bts:Grade3" + "@id": "bts:NoMetastasis" }, { - "@id": "bts:Grade4" + "@id": "bts:RegionalMetastasis" }, { - "@id": "bts:Grade5" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Adverse Event Grade", + "sms:displayName": "Metastasis at Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AIDSRiskFactors", + "@id": "bts:MetastasisatDiagnosisSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", - "rdfs:label": "AIDSRiskFactors", + "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", + "rdfs:label": "MetastasisatDiagnosisSite", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23959,109 +23367,117 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Candidiasis" + "@id": "bts:Abdomen" }, { - "@id": "bts:Coccidioidomycosis" + "@id": "bts:AdrenalGland" }, { - "@id": "bts:Cryptococcosis" + "@id": "bts:Ascites" }, { - "@id": "bts:Cytomegalovirus" + "@id": "bts:Bone" }, { - "@id": "bts:Encephalopathy" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:HerpesSimplexVirus" + "@id": "bts:Brain" }, { - "@id": "bts:Histoplasmosis" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:Isosporiasis" + "@id": "bts:CentralNervousSystem" }, { - "@id": "bts:MycobacteriumaviumComplex" + "@id": "bts:Colon" }, { - "@id": "bts:Mycobacteriumtuberculosis" + "@id": "bts:DistantNodes" }, { - "@id": "bts:Mycobacterium" + "@id": "bts:DistantOrgan" }, { - "@id": "bts:NOS" + "@id": "bts:Groin" }, { - "@id": "bts:Nocardiosis" + "@id": "bts:Kidney" }, { - "@id": "bts:PneumocystisPneumonia" + "@id": "bts:Liver" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Lung" }, { - "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" + "@id": "bts:LymphNode" }, { - "@id": "bts:SalmonellaSepticemia" + "@id": "bts:Axillary" }, { - "@id": "bts:Toxoplasmosis" + "@id": "bts:Inguinal" }, { - "@id": "bts:WastingSyndrome" + "@id": "bts:LymphNodeNOS" + }, + { + "@id": "bts:Mediastinum" + }, + { + "@id": "bts:Omentum" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Pelvis" + }, + { + "@id": "bts:PeritonealCavity" + }, + { + "@id": "bts:Peritoneum" + }, + { + "@id": "bts:Pleura" + }, + { + "@id": "bts:Scalp" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:SmallIntestine" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:SpinalCord" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "AIDS Risk Factors", + "sms:displayName": "Metastasis at Diagnosis Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BodySurfaceArea", + "@id": "bts:FirstSymptomPriortoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", - "rdfs:label": "BodySurfaceArea", + "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", + "rdfs:label": "FirstSymptomPriortoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Body Surface Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CD4Count", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", - "rdfs:label": "CD4Count", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "CD4 Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CDCHIVRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", - "rdfs:label": "CDCHIVRiskFactors", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24069,22 +23485,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Hemophiliac" + "@id": "bts:AlteredMentalStatus" }, { - "@id": "bts:HeterosexualContact" + "@id": "bts:Headaches" }, { - "@id": "bts:HomosexualContact" + "@id": "bts:MotororMovementChanges" }, { - "@id": "bts:IntravenousDrugUser" + "@id": "bts:Seizures" }, { - "@id": "bts:None" + "@id": "bts:SensoryChanges" }, { - "@id": "bts:TransfusionRecipient" + "@id": "bts:VisualChanges" }, { "@id": "bts:Unknown" @@ -24093,37 +23509,57 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "CDC HIV Risk Factors", + "sms:displayName": "First Symptom Prior to Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoImaging", + "@id": "bts:DaystoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoImaging", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Imaging", + "sms:displayName": "Days to Diagnosis", "sms:required": "sms:false", "sms:validationRules": [ "regex match \\d+$|Not\\sApplicable$|unknown$" ] }, { - "@id": "bts:EvidenceofRecurrenceType", + "@id": "bts:PercentTumorInvasion", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", - "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", + "rdfs:label": "PercentTumorInvasion", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Percent Tumor Invasion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ResidualDisease", + "@type": "rdfs:Class", + "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", + "rdfs:label": "ResidualDisease", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:InitialDiseaseStatus" } ], "schema:isPartOf": { @@ -24131,27 +23567,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BiopsywithHistologicConfirmation" + "@id": "bts:R0" }, { - "@id": "bts:ConvincingImageSource" + "@id": "bts:R1" }, { - "@id": "bts:PositiveBiomarkers" + "@id": "bts:R2" + }, + { + "@id": "bts:RX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Evidence of Recurrence Type", + "sms:displayName": "Residual Disease", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HAARTTreatmentIndicator", + "@id": "bts:SynchronousMalignancy", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", - "rdfs:label": "HAARTTreatmentIndicator", + "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", + "rdfs:label": "SynchronousMalignancy", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24171,35 +23616,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "HAART Treatment Indicator", + "sms:displayName": "Synchronous Malignancy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HIVViralLoad", + "@id": "bts:TumorConfinedtoOrganofOrigin", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", - "rdfs:label": "HIVViralLoad", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", + "rdfs:label": "TumorConfinedtoOrganofOrigin", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HIV Viral Load", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Confined to Organ of Origin", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HormonalContraceptiveUse", + "@id": "bts:TumorFocality", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", - "rdfs:label": "HormonalContraceptiveUse", + "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", + "rdfs:label": "TumorFocality", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24207,13 +23666,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CurrentUser" - }, - { - "@id": "bts:FormerUser" + "@id": "bts:Multifocal" }, { - "@id": "bts:NeverUsed" + "@id": "bts:Unifocal" }, { "@id": "bts:Unknown" @@ -24222,58 +23678,86 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hormonal Contraceptive Use", + "sms:displayName": "Tumor Focality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HysterectomyMarginsInvolved", + "@id": "bts:GrossTumorWeight", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", - "rdfs:label": "HysterectomyMarginsInvolved", + "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", + "rdfs:label": "GrossTumorWeight", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bladder" - }, + "sms:displayName": "Gross Tumor Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreslowThickness", + "@type": "rdfs:Class", + "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", + "rdfs:label": "BreslowThickness", + "rdfs:subClassOf": [ { - "@id": "bts:MacroscopicParametrium" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breslow Thickness", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", + "rdfs:label": "VascularInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:MicroscopicParametrium" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:None" + "@id": "bts:Yes-VascularInvasionPresent" }, { - "@id": "bts:Vagina" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" } ], - "sms:displayName": "Hysterectomy Margins Involved", + "sms:displayName": "Vascular Invasion Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HysterectomyType", + "@id": "bts:VascularInvasionType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", - "rdfs:label": "HysterectomyType", + "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", + "rdfs:label": "VascularInvasionType", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24281,16 +23765,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HysterectomyNOS" + "@id": "bts:Extramural" }, { - "@id": "bts:Notperformed" + "@id": "bts:Intramural" }, { - "@id": "bts:RadicalHysterectomy" + "@id": "bts:Macro" }, { - "@id": "bts:SimpleHysterectomy" + "@id": "bts:Micro" + }, + { + "@id": "bts:NoVascularInvasion" }, { "@id": "bts:Unknown" @@ -24299,18 +23786,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hysterectomy Type", + "sms:displayName": "Vascular Invasion Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingResult", + "@id": "bts:AnaplasiaPresent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", - "rdfs:label": "ImagingResult", + "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", + "rdfs:label": "AnaplasiaPresent", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24318,16 +23805,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Positive" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:Negative" + "@id": "bts:Yes-AnaplasiaPresent" }, { - "@id": "bts:NotPerformed" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -24336,18 +23817,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Imaging Result", + "sms:displayName": "Anaplasia Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingType", + "@id": "bts:AnaplasiaPresentType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", - "rdfs:label": "ImagingType", + "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", + "rdfs:label": "AnaplasiaPresentType", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24355,30 +23836,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:99mTcBoneScintigraphy" + "@id": "bts:Absent" }, { - "@id": "bts:CTScan" + "@id": "bts:Diffuse" }, { - "@id": "bts:MRI" + "@id": "bts:Equivocal" }, { - "@id": "bts:PET" + "@id": "bts:Focal" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Sclerosis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Imaging Type", + "sms:displayName": "Anaplasia Present Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmunosuppressiveTreatmentType", + "@id": "bts:Laterality", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of immunosuppresive treatment the patient received.", - "rdfs:label": "ImmunosuppressiveTreatmentType", + "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", + "rdfs:label": "Laterality", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24386,22 +23879,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Anti-TNFTherapy" - }, - { - "@id": "bts:Azathioprine" + "@id": "bts:Bilateral" }, { - "@id": "bts:Cyclophosphamide" + "@id": "bts:Left" }, { - "@id": "bts:Methotrexate" + "@id": "bts:Midline" }, { - "@id": "bts:None" + "@id": "bts:Right" }, { - "@id": "bts:Other" + "@id": "bts:Unilateral" }, { "@id": "bts:Unknown" @@ -24410,35 +23900,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Immunosuppressive Treatment Type", + "sms:displayName": "Laterality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NadirCD4Count", + "@id": "bts:PerineuralInvasionPresent", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).", - "rdfs:label": "NadirCD4Count", + "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", + "rdfs:label": "PerineuralInvasionPresent", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nadir CD4 Count", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Perineural Invasion Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PregnancyOutcome", + "@id": "bts:LymphaticInvasionPresent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of pregnancy the patient had", - "rdfs:label": "PregnancyOutcome", + "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", + "rdfs:label": "LymphaticInvasionPresent", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24446,19 +23950,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EctopicPregnancy" - }, - { - "@id": "bts:InducedAbortion" - }, - { - "@id": "bts:LiveBirth" - }, - { - "@id": "bts:Miscarriage" + "@id": "bts:Yes" }, { - "@id": "bts:Stillbirth" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -24467,52 +23962,52 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Pregnancy Outcome", + "sms:displayName": "Lymphatic Invasion Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RecistTargetedRegionsNumber", + "@id": "bts:LymphNodesPositive", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria", - "rdfs:label": "RecistTargetedRegionsNumber", + "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", + "rdfs:label": "LymphNodesPositive", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Recist Targeted Regions Number", + "sms:displayName": "Lymph Nodes Positive", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RecistTargetedRegionsSum", + "@id": "bts:LymphNodesTested", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.", - "rdfs:label": "RecistTargetedRegionsSum", + "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", + "rdfs:label": "LymphNodesTested", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Recist Targeted Regions Sum", + "sms:displayName": "Lymph Nodes Tested", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanTracerUsed", + "@id": "bts:PeritonealFluidCytologicalStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of tracer used during the imaging or scan of the patient.", - "rdfs:label": "ScanTracerUsed", + "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", + "rdfs:label": "PeritonealFluidCytologicalStatus", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24520,33 +24015,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Acetate" + "@id": "bts:Atypical" }, { - "@id": "bts:Axumin" + "@id": "bts:Malignant" }, { - "@id": "bts:Choline" + "@id": "bts:Non-Malignant" }, { - "@id": "bts:PSMA" + "@id": "bts:Unsatisfactory" }, { - "@id": "bts:SodiumFluoride" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Scan Tracer Used", + "sms:displayName": "Peritoneal Fluid Cytological Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentorTherapy", + "@id": "bts:ClassificationofTumor", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.", - "rdfs:label": "TreatmentorTherapy", + "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", + "rdfs:label": "ClassificationofTumor", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24554,30 +24052,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Primary" }, { - "@id": "bts:No" + "@id": "bts:Metastasis" + }, + { + "@id": "bts:Recurrence" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" } ], - "sms:displayName": "Treatment or Therapy", + "sms:displayName": "Classification of Tumor", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentEffect", + "@id": "bts:BestOverallResponse", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the pathologic effect a treatment(s) had on the tumor.", - "rdfs:label": "TreatmentEffect", + "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", + "rdfs:label": "BestOverallResponse", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24585,110 +24092,113 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CompleteNecrosis(NoViableTumor)" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:IncompleteNecrosis(ViableTumorPresent)" + "@id": "bts:CPD-ClinicalProgression" }, { - "@id": "bts:NoNecrosis" + "@id": "bts:CR-CompleteResponse" }, { - "@id": "bts:Unknown" + "@id": "bts:CRU-CompleteResponseUnconfirmed" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Treatment Effect", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TreatmentOutcome", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the patient's final outcome after the treatment was administered.", - "rdfs:label": "TreatmentOutcome", - "rdfs:subClassOf": [ + "@id": "bts:DU-DiseaseUnchanged" + }, { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IMR-Immunoresponse" + }, { - "@id": "bts:CompleteResponse" + "@id": "bts:IPD-Immunoprogression" }, { - "@id": "bts:MixedResponse" + "@id": "bts:MR-Minimal/MarginalResponse" }, { - "@id": "bts:NoMeasurableDisease" + "@id": "bts:MX-MixedResponse" }, { - "@id": "bts:NoResponse" + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" }, { - "@id": "bts:PartialResponse" + "@id": "bts:NPB-NoPalliativeBenefit" }, { - "@id": "bts:PersistentDisease" + "@id": "bts:NR-NoResponse" }, { - "@id": "bts:ProgressiveDisease" + "@id": "bts:PA-PalliativeTherapy" }, { - "@id": "bts:StableDisease" + "@id": "bts:PB-PalliativeBenefit" }, { - "@id": "bts:TreatmentOngoing" + "@id": "bts:PD-ProgressiveDisease" }, { - "@id": "bts:TreatmentStoppedDuetoToxicity" + "@id": "bts:PPD-Pseudoprogression" }, { - "@id": "bts:VeryGoodPartialResponse" + "@id": "bts:PR-PartialResponse" }, { - "@id": "bts:Unknown" + "@id": "bts:PSR-Pseudoresponse" }, { - "@id": "bts:NotReported" + "@id": "bts:RD-ResponsiveDisease" + }, + { + "@id": "bts:RP-Response" + }, + { + "@id": "bts:RPD-RadiographicProgressiveDisease" + }, + { + "@id": "bts:SCR-StringentCompleteResponse" + }, + { + "@id": "bts:SD-StableDisease" + }, + { + "@id": "bts:SPD-SurgicalProgression" + }, + { + "@id": "bts:TE-TooEarly" + }, + { + "@id": "bts:VGPR-VeryGoodPartialResponse" } ], - "sms:displayName": "Treatment Outcome", + "sms:displayName": "Best Overall Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoTreatmentEnd", + "@id": "bts:MitoticCount", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoTreatmentEnd", + "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", + "rdfs:label": "MitoticCount", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Treatment End", + "sms:displayName": "Mitotic Count", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:TreatmentAnatomicSite", + "@id": "bts:AJCCClinicalM", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment", - "rdfs:label": "TreatmentAnatomicSite", + "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalM", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24696,994 +24206,1389 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbdomenNOS" + "@id": "bts:M0" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:M1" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:M1a" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:M1b" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:M1c" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:MX" }, { - "@id": "bts:Analcanal" + "@id": "bts:CM0(i+)" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Anteriorfloorofmouth" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Clinical M", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCClinicalN", + "@type": "rdfs:Class", + "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalN", + "rdfs:subClassOf": [ { - 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"@id": "bts:Urachus" + "@id": "bts:Cervical" }, { - "@id": "bts:Ureter" + "@id": "bts:Epitrochlear" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:Femoral" }, { - "@id": "bts:Urethra" + "@id": "bts:Hilar" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:Iliac-common" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:Iliac-external" }, { - "@id": "bts:UterusNOS" + "@id": "bts:Iliac" }, { - "@id": "bts:Uvula" + "@id": "bts:NOS" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:Inguinal" }, { - "@id": "bts:Vallecula" + "@id": "bts:Mediastinal" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:Mesenteric" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:None" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:Occipital" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:Paraaortic" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:Parotid" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:Popliteal" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:Retroperitoneal" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:Splenic" }, { - "@id": "bts:Clitoris" + "@id": "bts:Submandibular" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:Supraclavicular" }, { "@id": "bts:Unknown" @@ -25692,37 +25597,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Anatomic Site", + "sms:displayName": "Lymph Node Involved Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoTreatmentStart", + "@id": "bts:MarginDistance", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoTreatmentStart", + "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", + "rdfs:label": "MarginDistance", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Treatment Start", + "sms:displayName": "Margin Distance", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:InitialDiseaseStatus", + "@id": "bts:MarginsInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", - "rdfs:label": "InitialDiseaseStatus", + "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", + "rdfs:label": "MarginsInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25730,70 +25633,110 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:InitialDiagnosis" + "@id": "bts:GerotaFascia" }, { - "@id": "bts:ProgressiveDisease" + "@id": "bts:Parenchyma" }, { - "@id": "bts:RecurrentDisease" + "@id": "bts:PerinephricFat" }, { - "@id": "bts:ResidualDisease" + "@id": "bts:Renal" }, { - "@id": "bts:Unknown" + "@id": "bts:RenalCapsule" }, { - "@id": "bts:NotReported" + "@id": "bts:RenalSinus" + }, + { + "@id": "bts:RenalVein" + }, + { + "@id": "bts:Ureter" } ], - "sms:displayName": "Initial Disease Status", + "sms:displayName": "Margins Involved Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RegimenorLineofTherapy", + "@id": "bts:MedulloblastomaMolecularClassification", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the regimen or line of therapy.", - "rdfs:label": "RegimenorLineofTherapy", + "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", + "rdfs:label": "MedulloblastomaMolecularClassification", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Regimen or Line of Therapy", + "schema:rangeIncludes": [ + { + "@id": "bts:NotDetermined" + }, + { + "@id": "bts:Non-WNT/non-SHHActivated" + }, + { + "@id": "bts:SHH-Activated" + }, + { + "@id": "bts:WNT-Activated" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Medulloblastoma Molecular Classification", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TherapeuticAgents", + "@id": "bts:MicropapillaryFeatures", "@type": "rdfs:Class", - "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", - "rdfs:label": "TherapeuticAgents", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", + "rdfs:label": "MicropapillaryFeatures", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Therapeutic Agents", + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Micropapillary Features", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentIntentType", + "@id": "bts:MitosisKaryorrhexisIndex", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", - "rdfs:label": "TreatmentIntentType", + "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", + "rdfs:label": "MitosisKaryorrhexisIndex", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25801,22 +25744,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Adjuvant" - }, - { - "@id": "bts:CancerControl" - }, - { - "@id": "bts:Cure" - }, - { - "@id": "bts:Neoadjuvant" + "@id": "bts:High" }, { - "@id": "bts:Palliative" + "@id": "bts:Intermediate" }, { - "@id": "bts:Prevention" + "@id": "bts:Low" }, { "@id": "bts:Unknown" @@ -25825,18 +25759,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Intent Type", + "sms:displayName": "Mitosis Karyorrhexis Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChemoConcurrenttoRadiation", + "@id": "bts:NonNodalRegionalDisease", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", - "rdfs:label": "ChemoConcurrenttoRadiation", + "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", + "rdfs:label": "NonNodalRegionalDisease", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25844,10 +25778,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Absent" }, { - "@id": "bts:No" + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Present" }, { "@id": "bts:Unknown" @@ -25856,35 +25793,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Chemo Concurrent to Radiation", + "sms:displayName": "Non Nodal Regional Disease", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NumberofCycles", + "@id": "bts:NonNodalTumorDeposits", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", - "rdfs:label": "NumberofCycles", + "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", + "rdfs:label": "NonNodalTumorDeposits", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Cycles", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Tumor Deposits", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReasonTreatmentEnded", + "@id": "bts:OvarianSpecimenStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", - "rdfs:label": "ReasonTreatmentEnded", + "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", + "rdfs:label": "OvarianSpecimenStatus", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25892,36 +25843,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AdverseTherapyEvent" - }, - { - "@id": "bts:CourseofTherapyCompleted" + "@id": "bts:OvarianCapsuleIntact" }, { - "@id": "bts:Death" + "@id": "bts:OvarianCapsuleRuptured" }, { - "@id": "bts:DiseaseProgression" + "@id": "bts:OvarianCapsuleFragmented" }, { - "@id": "bts:Other" + "@id": "bts:Unknown" }, { - "@id": "bts:WithdrawalbySubject" + "@id": "bts:NotReported" } ], - "sms:displayName": "Reason Treatment Ended", + "sms:displayName": "Ovarian Specimen Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentArm", + "@id": "bts:OvarianSurfaceInvolvement", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", - "rdfs:label": "TreatmentArm", + "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", + "rdfs:label": "OvarianSurfaceInvolvement", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25929,44 +25877,64 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:A081105" + "@id": "bts:Absent" }, { - "@id": "bts:E4512" + "@id": "bts:Present" }, { - "@id": "bts:EA5142" + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Arm", + "sms:displayName": "Ovarian Surface Involvement", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDose", + "@id": "bts:PregnantatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", - "rdfs:label": "TreatmentDose", + "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", + "rdfs:label": "PregnantatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Treatment Dose", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pregnant at Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDoseUnits", + "@id": "bts:PrimaryGleasonGrade", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", - "rdfs:label": "TreatmentDoseUnits", + "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "PrimaryGleasonGrade", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25974,24 +25942,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CGy" + "@id": "bts:Pattern1" }, { - "@id": "bts:Gy" + "@id": "bts:Pattern2" + }, + { + "@id": "bts:Pattern3" + }, + { + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" } ], - "sms:displayName": "Treatment Dose Units", + "sms:displayName": "Primary Gleason Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentEffectIndicator", + "@id": "bts:SecondaryGleasonGrade", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", - "rdfs:label": "TreatmentEffectIndicator", + "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "SecondaryGleasonGrade", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -25999,30 +25976,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Pattern1" }, { - "@id": "bts:No" + "@id": "bts:Pattern2" }, { - "@id": "bts:NotReported" + "@id": "bts:Pattern3" }, { - "@id": "bts:Unknown" + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" } ], - "sms:displayName": "Treatment Effect Indicator", + "sms:displayName": "Secondary Gleason Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentFrequency", + "@id": "bts:SupratentorialLocalization", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", - "rdfs:label": "TreatmentFrequency", + "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", + "rdfs:label": "SupratentorialLocalization", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26030,31 +26010,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EveryHour" - }, - { - "@id": "bts:FiveTimesDaily" - }, - { - "@id": "bts:FourTimesDaily" - }, - { - "@id": "bts:ThreeTimesDaily" - }, - { - "@id": "bts:TwiceDaily" - }, - { - "@id": "bts:Every24Hours" + "@id": "bts:CerebralCortex" }, { - "@id": "bts:EveryOtherDay" + "@id": "bts:DeepGray" }, { - "@id": "bts:TwiceWeekly" + "@id": "bts:SpinalCord" }, { - "@id": "bts:OnceWeekly" + "@id": "bts:WhiteMatter" }, { "@id": "bts:Unknown" @@ -26063,15 +26028,15 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Frequency", + "sms:displayName": "Supratentorial Localization", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearofDiagnosis", + "@id": "bts:TumorDepth", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", - "rdfs:label": "YearofDiagnosis", + "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", + "rdfs:label": "TumorDepth", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -26080,15 +26045,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year of Diagnosis", + "sms:displayName": "Tumor Depth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrecancerousConditionType", + "@id": "bts:WHOCNSGrade", "@type": "rdfs:Class", - "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", - "rdfs:label": "PrecancerousConditionType", + "rdfs:comment": "WHO CNS Grade", + "rdfs:label": "WHOCNSGrade", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -26099,132 +26064,202 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DuctalCarcinomaInSitu" + "@id": "bts:GradeI" }, { - "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" + "@id": "bts:GradeII" }, { - "@id": "bts:AtypicalAdenomatousLungHyperplasia" + "@id": "bts:GradeIII" }, { - "@id": "bts:Other" + "@id": "bts:GradeIV" }, { - "@id": "bts:PancreaticIntraepithelialNeoplasia" + "@id": "bts:GradeNotAssigned" }, { - "@id": "bts:ProstaticIntraepithelialNeoplasia" + "@id": "bts:Unknown" }, { - "@id": "bts:Melanocytichyperplasia" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO CNS Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHONTEGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO NTE Grade", + "rdfs:label": "WHONTEGrade", + "rdfs:subClassOf": [ { - "@id": "bts:Atypicalmelanocyticproliferation" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Melanomainsitu" + "@id": "bts:G1" }, { - "@id": "bts:Superficialspreading" + "@id": "bts:G2" }, { - "@id": "bts:Lentigomalignatype" + "@id": "bts:G3" }, { - "@id": "bts:Acral-lentiginous" + "@id": "bts:GX" }, { - "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" + "@id": "bts:Unknown" }, { - "@id": "bts:Persistentmelanomainsitu" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO NTE Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AAChange", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "AAChange", + "rdfs:subClassOf": [ { - "@id": "bts:Melanomainsitunototherwiseclassified" + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "AA Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Antigen", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Antigen", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:BCL6" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:CA-125" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:CA19-9" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:CCND1" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:CD10" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:CD117" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:CD138" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:CD14" }, { - "@id": "bts:Invasivemelanoma" + "@id": "bts:CD15" }, { - "@id": "bts:NormalWDA" + "@id": "bts:CD19" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:CD20" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:CD22" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:CD23" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:CD25" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:CD3" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:CD30" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:CD33" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:CD34" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:CD45" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:CD5" }, { - "@id": "bts:Hamartoma" + "@id": "bts:CD56" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:CD7" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:CD79A" }, { - "@id": "bts:NotApplicable" + "@id": "bts:CEA" + }, + { + "@id": "bts:HLA-DR" + }, + { + "@id": "bts:Mesothelin" + }, + { + "@id": "bts:NSE" + }, + { + "@id": "bts:SquamousCellCarcinomaAntigen" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Precancerous Condition Type", + "sms:displayName": "Antigen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofDiagnosis", + "@id": "bts:ClinicalBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", - "rdfs:label": "MethodofDiagnosis", + "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "ClinicalBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -26232,73 +26267,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" + "@id": "bts:Blood" }, { - "@id": "bts:BloodDraw" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:BoneMarrowAspirate" + "@id": "bts:BuccalMucosa" }, { - "@id": "bts:CoreBiopsy" + "@id": "bts:BuffyCoat" }, { - "@id": "bts:Cytology" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:Cystoscopy" + "@id": "bts:ConnectiveTissue" }, { - "@id": "bts:Debulking" + "@id": "bts:EmbryonicFluid" }, { - "@id": "bts:DiagnosticImaging" + "@id": "bts:EmbryonicTissue" }, { - "@id": "bts:DilationandCurettageProcedure" + "@id": "bts:Feces" }, { - "@id": "bts:Enucleation" + "@id": "bts:Granulocyte" }, { - "@id": "bts:ExcisionalBiopsy" + "@id": "bts:MuscleTissue" }, { - "@id": "bts:FineNeedleAspiration" + "@id": "bts:NerveTissue" }, { - "@id": "bts:IncisionalBiopsy" + "@id": "bts:PeritonealFluid" }, { - "@id": "bts:Laparoscopy" + "@id": "bts:Plasma" }, { - "@id": "bts:Laparotomy" + "@id": "bts:PleuralFluid" }, { - "@id": "bts:Other" + "@id": "bts:Saliva" }, { - "@id": "bts:PapSmear" + "@id": "bts:Serum" }, { - "@id": "bts:PhysicalExam" + "@id": "bts:Skin" }, { - "@id": "bts:PathologicReview" + "@id": "bts:SoftTissue" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:TissueNOS" }, { - "@id": "bts:Thoracentesis" + "@id": "bts:UninvolvedTissueNOS" }, { - "@id": "bts:UltrasoundGuidedBiopsy" + "@id": "bts:Urine" }, { "@id": "bts:Unknown" @@ -26307,123 +26339,69 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Method of Diagnosis", + "sms:displayName": "Clinical Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorMalignancy", + "@id": "bts:BloodTestNormalRangeUpper", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", - "rdfs:label": "PriorMalignancy", + "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeUpper", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Malignancy", + "sms:displayName": "Blood Test Normal Range Upper", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorTreatment", + "@id": "bts:BloodTestNormalRangeLower", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", - "rdfs:label": "PriorTreatment", + "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeLower", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Treatment", + "sms:displayName": "Blood Test Normal Range Lower", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MetastasisatDiagnosis", + "@id": "bts:CellCount", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", - "rdfs:label": "MetastasisatDiagnosis", + "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CellCount", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:DistantMetastasis" - }, - { - "@id": "bts:MetastasisNOS" - }, - { - "@id": "bts:NoMetastasis" - }, - { - "@id": "bts:RegionalMetastasis" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Metastasis at Diagnosis", + "sms:displayName": "Cell Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MetastasisatDiagnosisSite", + "@id": "bts:Chromosome", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", - "rdfs:label": "MetastasisatDiagnosisSite", + "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Chromosome", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -26431,97 +26409,82 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Abdomen" - }, - { - "@id": "bts:AdrenalGland" - }, - { - "@id": "bts:Ascites" - }, - { - "@id": "bts:Bone" - }, - { - "@id": "bts:BoneMarrow" - }, - { - "@id": "bts:Brain" + "@id": "bts:Chr1" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:Chr2" }, { - "@id": "bts:CentralNervousSystem" + "@id": "bts:Chr3" }, { - "@id": "bts:Colon" + "@id": "bts:Chr4" }, { - "@id": "bts:DistantNodes" + "@id": "bts:Chr5" }, { - "@id": "bts:DistantOrgan" + "@id": "bts:Chr6" }, { - "@id": "bts:Groin" + "@id": "bts:Chr7" }, { - "@id": "bts:Kidney" + "@id": "bts:Chr8" }, { - "@id": "bts:Liver" + "@id": "bts:Chr9" }, { - "@id": "bts:Lung" + "@id": "bts:Chr10" }, { - "@id": "bts:LymphNode" + "@id": "bts:Chr11" }, { - "@id": "bts:Axillary" + "@id": "bts:Chr12" }, { - "@id": "bts:Inguinal" + "@id": "bts:Chr13" }, { - "@id": "bts:LymphNodeNOS" + "@id": "bts:Chr14" }, { - "@id": "bts:Mediastinum" + "@id": "bts:Chr15" }, { - "@id": "bts:Omentum" + "@id": "bts:Chr16" }, { - "@id": "bts:Ovary" + "@id": "bts:Chr17" }, { - "@id": "bts:Pelvis" + "@id": "bts:Chr18" }, { - "@id": "bts:PeritonealCavity" + "@id": "bts:Chr19" }, { - "@id": "bts:Peritoneum" + "@id": "bts:Chr20" }, { - "@id": "bts:Pleura" + "@id": "bts:Chr21" }, { - "@id": "bts:Scalp" + "@id": "bts:Chr22" }, { - "@id": "bts:Skin" + "@id": "bts:Chr23" }, { - "@id": "bts:SmallIntestine" + "@id": "bts:ChrM" }, { - "@id": "bts:SoftTissue" + "@id": "bts:ChrX" }, { - "@id": "bts:SpinalCord" + "@id": "bts:ChrY" }, { "@id": "bts:Unknown" @@ -26530,18 +26493,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Metastasis at Diagnosis Site", + "sms:displayName": "Chromosome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FirstSymptomPriortoDiagnosis", + "@id": "bts:Clonality", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", - "rdfs:label": "FirstSymptomPriortoDiagnosis", + "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Clonality", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -26549,81 +26512,75 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AlteredMentalStatus" - }, - { - "@id": "bts:Headaches" - }, - { - "@id": "bts:MotororMovementChanges" - }, - { - "@id": "bts:Seizures" - }, - { - "@id": "bts:SensoryChanges" - }, - { - "@id": "bts:VisualChanges" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Clonal" }, { - "@id": "bts:NotReported" + "@id": "bts:Non-clonal" } ], - "sms:displayName": "First Symptom Prior to Diagnosis", + "sms:displayName": "Clonality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoDiagnosis", + "@id": "bts:CopyNumber", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDiagnosis", + "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CopyNumber", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Diagnosis", + "sms:displayName": "Copy Number", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:PercentTumorInvasion", + "@id": "bts:Cytoband", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", + "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Cytoband", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Invasion", + "sms:displayName": "Cytoband", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ResidualDisease", + "@id": "bts:Exon", "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", + "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Exon", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneFamily", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "rdfs:label": "HistoneFamily", + "rdfs:subClassOf": [ { - "@id": "bts:InitialDiseaseStatus" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -26631,16 +26588,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:R0" + "@id": "bts:H1" }, { - "@id": "bts:R1" + "@id": "bts:H2A" }, { - "@id": "bts:R2" + "@id": "bts:H2B" }, { - "@id": "bts:RX" + "@id": "bts:H3" + }, + { + "@id": "bts:H4" }, { "@id": "bts:Unknown" @@ -26649,18 +26609,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Residual Disease", + "sms:displayName": "Histone Family", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SynchronousMalignancy", + "@id": "bts:HistoneVariant", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "HistoneVariant", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -26668,72 +26628,55 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:CENP-A" }, { - "@id": "bts:No" + "@id": "bts:H2A-Bbd" }, { - "@id": "bts:Unknown" + "@id": "bts:H2A.X" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Synchronous Malignancy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorConfinedtoOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", - "rdfs:subClassOf": [ + "@id": "bts:H2A.Z" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:H2A.Z.1" + }, { - "@id": "bts:Yes" + "@id": "bts:H2A.Z.2" }, { - "@id": "bts:No" + "@id": "bts:H2A.Z.2.2" }, { - "@id": "bts:Unknown" + "@id": "bts:H3.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Confined to Organ of Origin", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorFocality", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", - "rdfs:label": "TumorFocality", - "rdfs:subClassOf": [ + "@id": "bts:H3.2" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:H3.3" + }, { - "@id": "bts:Multifocal" + "@id": "bts:H3.5" }, { - "@id": "bts:Unifocal" + "@id": "bts:H3.X" + }, + { + "@id": "bts:H3.Y" + }, + { + "@id": "bts:H3t(H3.4)" + }, + { + "@id": "bts:MH2A" + }, + { + "@id": "bts:MH2A.1" + }, + { + "@id": "bts:MH2A.2" }, { "@id": "bts:Unknown" @@ -26742,52 +26685,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Tumor Focality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GrossTumorWeight", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", - "rdfs:label": "GrossTumorWeight", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gross Tumor Weight", + "sms:displayName": "Histone Variant", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreslowThickness", + "@id": "bts:Intron", "@type": "rdfs:Class", - "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", - "rdfs:label": "BreslowThickness", + "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", + "rdfs:label": "Intron", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breslow Thickness", + "sms:displayName": "Intron", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionPresent", + "@id": "bts:LaboratoryTest", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", - "rdfs:label": "VascularInvasionPresent", + "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", + "rdfs:label": "LaboratoryTest", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -26795,198 +26721,139 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-VascularInvasionPresent" + "@id": "bts:AbsoluteNeutrophil" }, { - "@id": "bts:No" + "@id": "bts:Albumin" }, { - "@id": "bts:Unknown" + "@id": "bts:AlphaFetoprotein" }, { - "@id": "bts:NotReported" + "@id": "bts:B-cellgenotyping" }, { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Vascular Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VascularInvasionType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", - "rdfs:subClassOf": [ + "@id": "bts:Basophil" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Beta2Microglobulin" + }, { - "@id": "bts:Extramural" + "@id": "bts:BloodUreaNitrogen" }, { - "@id": "bts:Intramural" + "@id": "bts:C-ReactiveProtein" }, { - "@id": "bts:Macro" + "@id": "bts:Calcium" }, { - "@id": "bts:Micro" + "@id": "bts:Cellularity" }, { - "@id": "bts:NoVascularInvasion" + "@id": "bts:CirculatingTumorCells" }, { - "@id": "bts:Unknown" + "@id": "bts:Creatinine" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vascular Invasion Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnaplasiaPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", - "rdfs:label": "AnaplasiaPresent", - "rdfs:subClassOf": [ + "@id": "bts:Eosinophil" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Epstein-BarrVirus" + }, { - "@id": "bts:Yes-AnaplasiaPresent" + "@id": "bts:Glucose" }, { - "@id": "bts:No" + "@id": "bts:Hematocrit" }, { - "@id": "bts:Unknown" + "@id": "bts:Hemoglobin" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Anaplasia Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnaplasiaPresentType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", - "rdfs:label": "AnaplasiaPresentType", - "rdfs:subClassOf": [ + "@id": "bts:HPV-E6/E7" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HumanChorionicGonadotropin" + }, { - "@id": "bts:Absent" + "@id": "bts:HumanPapillomavirus" }, { - "@id": "bts:Diffuse" + "@id": "bts:ImmunoglobulinA" }, { - "@id": "bts:Equivocal" + "@id": "bts:ImmunoglobulinG" }, { - "@id": "bts:Focal" + "@id": "bts:ImmunoglobulinM" }, { - "@id": "bts:Present" + "@id": "bts:LactateDehydrogenase" }, { - "@id": "bts:Sclerosis" + "@id": "bts:Leukocytes" }, { - "@id": "bts:Unknown" + "@id": "bts:LuteinizingHormone" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Anaplasia Present Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Laterality", - "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", - "rdfs:label": "Laterality", - "rdfs:subClassOf": [ + "@id": "bts:Lymphoblasts" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lymphocytes" + }, { - "@id": "bts:Bilateral" + "@id": "bts:MProtein" }, { - "@id": "bts:Left" + "@id": "bts:Metamyelocytes" }, { - "@id": "bts:Midline" + "@id": "bts:Myeloblasts" }, { - "@id": "bts:Right" + "@id": "bts:Myelocytes" }, { - "@id": "bts:Unilateral" + "@id": "bts:NeutrophilBands" }, { - "@id": "bts:Unknown" + "@id": "bts:Platelets" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Laterality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerineuralInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", - "rdfs:subClassOf": [ + "@id": "bts:Prolymphocytes" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Promonocytes" + }, { - "@id": "bts:Yes" + "@id": "bts:Promyelocytes" }, { - "@id": "bts:No" + "@id": "bts:SegmentedNeutrophil" + }, + { + "@id": "bts:SerumFreeImmunoglobulinLightChain" + }, + { + "@id": "bts:Kappa" + }, + { + "@id": "bts:Lambda" + }, + { + "@id": "bts:NOS" + }, + { + "@id": "bts:Testosterone" + }, + { + "@id": "bts:TotalBilirubin" + }, + { + "@id": "bts:TotalProtein" }, { "@id": "bts:Unknown" @@ -26995,83 +26862,69 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Perineural Invasion Present", + "sms:displayName": "Laboratory Test", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphaticInvasionPresent", + "@id": "bts:LociAbnormalCount", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", - "rdfs:label": "LymphaticInvasionPresent", + "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", + "rdfs:label": "LociAbnormalCount", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lymphatic Invasion Present", + "sms:displayName": "Loci Abnormal Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesPositive", + "@id": "bts:LociCount", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", - "rdfs:label": "LymphNodesPositive", + "rdfs:comment": "Numeric value used to describe the number of loci tested.", + "rdfs:label": "LociCount", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Positive", + "sms:displayName": "Loci Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesTested", + "@id": "bts:Locus", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", - "rdfs:label": "LymphNodesTested", + "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label": "Locus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Tested", + "sms:displayName": "Locus", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeritonealFluidCytologicalStatus", + "@id": "bts:MismatchRepairMutation", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MismatchRepairMutation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -27079,16 +26932,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Atypical" - }, - { - "@id": "bts:Malignant" - }, - { - "@id": "bts:Non-Malignant" + "@id": "bts:Yes" }, { - "@id": "bts:Unsatisfactory" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -27097,18 +26944,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Peritoneal Fluid Cytological Status", + "sms:displayName": "Mismatch Repair Mutation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClassificationofTumor", + "@id": "bts:MolecularConsequence", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", - "rdfs:label": "ClassificationofTumor", + "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularConsequence", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -27116,153 +26963,157 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Primary" + "@id": "bts:3PrimeUTRVariant" }, { - "@id": "bts:Metastasis" + "@id": "bts:5PrimeUTRVariant" }, { - "@id": "bts:Recurrence" + "@id": "bts:CodingSequenceVariant" }, { - "@id": "bts:Other" + "@id": "bts:DownstreamGeneVariant" }, { - "@id": "bts:Unknown" + "@id": "bts:FeatureElongation" }, { - "@id": "bts:NotReported" + "@id": "bts:FeatureTruncation" }, { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Classification of Tumor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BestOverallResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", - "rdfs:label": "BestOverallResponse", - "rdfs:subClassOf": [ + "@id": "bts:FrameshiftVariant" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IncompleteTerminalCodonVariant" + }, { - "@id": "bts:AJ-AdjuvantTherapy" + "@id": "bts:InframeDeletion" }, { - "@id": "bts:CPD-ClinicalProgression" + "@id": "bts:InframeInsertion" }, { - "@id": "bts:CR-CompleteResponse" + "@id": "bts:IntergenicVariant" }, { - "@id": "bts:CRU-CompleteResponseUnconfirmed" + "@id": "bts:IntronVariant" }, { - "@id": "bts:DU-DiseaseUnchanged" + "@id": "bts:MaturemiRNAVariant" }, { - "@id": "bts:IMR-Immunoresponse" + "@id": "bts:MissenseVariant" }, { - "@id": "bts:IPD-Immunoprogression" + "@id": "bts:NMDTranscriptVariant" }, { - "@id": "bts:MR-Minimal/MarginalResponse" + "@id": "bts:Non-codingTranscriptExonVariant" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:Non-codingTranscriptVariant" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:ProteinAlteringVariant" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:RegulatoryRegionAblation" }, { - "@id": "bts:NR-NoResponse" + "@id": "bts:RegulatoryRegionAmplification" }, { - "@id": "bts:PA-PalliativeTherapy" + "@id": "bts:RegulatoryRegionVariant" }, { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:SpliceAcceptorVariant" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:SpliceDonorVariant" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:SpliceRegionVariant" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:StartLost" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:StopGain" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:StopLost" }, { - "@id": "bts:RP-Response" + "@id": "bts:StopRetainedVariant" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:SynonymousVariant" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:TFBindingSiteVariant" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:TFBSAblation" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:TFBSAmplification" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:TranscriptAblation" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:TranscriptAmplification" + }, + { + "@id": "bts:UpstreamGeneVariant" } ], - "sms:displayName": "Best Overall Response", + "sms:displayName": "Molecular Consequence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitoticCount", + "@id": "bts:Pathogenicity", "@type": "rdfs:Class", - "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", + "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "rdfs:label": "Pathogenicity", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mitotic Count", + "schema:rangeIncludes": [ + { + "@id": "bts:Benign" + }, + { + "@id": "bts:LikelyBenign" + }, + { + "@id": "bts:LikelyPathogenic" + }, + { + "@id": "bts:Pathogenic" + }, + { + "@id": "bts:UncertainSignificance" + } + ], + "sms:displayName": "Pathogenicity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalM", + "@id": "bts:Ploidy", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalM", + "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", + "rdfs:label": "Ploidy", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -27270,25 +27121,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:M0" - }, - { - "@id": "bts:M1" + "@id": "bts:Aneuploid" }, { - "@id": "bts:M1a" + "@id": "bts:Diploid" }, { - "@id": "bts:M1b" + "@id": "bts:Hyperdiploid" }, { - "@id": "bts:M1c" + "@id": "bts:Hypodiploid" }, { - "@id": "bts:MX" + "@id": "bts:NearDiploid" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:Tetraploid" }, { "@id": "bts:Unknown" @@ -27297,115 +27145,188 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "AJCC Clinical M", + "sms:displayName": "Ploidy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalN", + "@id": "bts:SecondExon", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalN", + "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label": "SecondExon", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Second Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondGeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SecondGeneSymbol", + "rdfs:subClassOf": [ { - "@id": "bts:N0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Gene Symbol", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpecializedMolecularTest", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SpecializedMolecularTest", + "rdfs:subClassOf": [ { - "@id": "bts:N0(i+)" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Specialized Molecular Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestAnalyteType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestAnalyteType", + "rdfs:subClassOf": [ { - "@id": "bts:N0(i-)" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:N0(mol+)" + "@id": "bts:DNA" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:MRNA" }, { - "@id": "bts:N1" + "@id": "bts:MiRNA" }, { - "@id": "bts:N1a" + "@id": "bts:ProteinAnalyte" }, { - "@id": "bts:N1b" + "@id": "bts:TotalRNA" }, { - "@id": "bts:N1bI" + "@id": "bts:Unknown" }, { - "@id": "bts:N1bII" - }, - { - "@id": "bts:N1bIII" - }, - { - "@id": "bts:N1bIV" - }, - { - "@id": "bts:N1c" - }, - { - "@id": "bts:N1mi" - }, - { - "@id": "bts:N2" - }, - { - "@id": "bts:N2a" - }, - { - "@id": "bts:N2b" - }, - { - "@id": "bts:N2c" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Test Analyte Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestUnits", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestUnits", + "rdfs:subClassOf": [ { - "@id": "bts:N3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Units", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestValue", + "@type": "rdfs:Class", + "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", + "rdfs:label": "TestValue", + "rdfs:subClassOf": [ { - "@id": "bts:N3a" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Transcript", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Transcript", + "rdfs:subClassOf": [ { - "@id": "bts:N3b" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Transcript", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VariantOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "VariantOrigin", + "rdfs:subClassOf": [ { - "@id": "bts:N3c" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:N4" + "@id": "bts:Germline" }, { - "@id": "bts:NX" + "@id": "bts:Somatic" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" } ], - "sms:displayName": "AJCC Clinical N", + "sms:displayName": "Variant Origin", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalStage", + "@id": "bts:VariantType", "@type": "rdfs:Class", - "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", - "rdfs:label": "AJCCClinicalStage", + "rdfs:comment": "The text term used to describe the type of genetic variation.", + "rdfs:label": "VariantType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -27413,97 +27334,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Stage0" - }, - { - "@id": "bts:Stage0a" - }, - { - "@id": "bts:Stage0is" - }, - { - "@id": "bts:StageI" - }, - { - "@id": "bts:StageIA" - }, - { - "@id": "bts:StageIA1" - }, - { - "@id": "bts:StageIA2" - }, - { - "@id": "bts:StageIB" - }, - { - "@id": "bts:StageIB1" - }, - { - "@id": "bts:StageIB2" + "@id": "bts:Alleles" }, { - "@id": "bts:StageIC" + "@id": "bts:Amplification" }, { - "@id": "bts:StageII" + "@id": "bts:Chrimerism" }, { - "@id": "bts:StageIIA" + "@id": "bts:Conversion" }, { - "@id": "bts:StageIIA1" + "@id": "bts:Deletion" }, { - "@id": "bts:StageIIA2" + "@id": "bts:Deletion-Insertion" }, { - "@id": "bts:StageIIB" + "@id": "bts:Duplication" }, { - "@id": "bts:StageIIC" + "@id": "bts:Extension" }, { - "@id": "bts:StageIIC1" + "@id": "bts:Gain" }, { - "@id": "bts:StageIII" + "@id": "bts:Hypermethylation" }, { - "@id": "bts:StageIIIA" + "@id": "bts:Insertion" }, { - "@id": "bts:StageIIIB" + "@id": "bts:Inversion" }, { - "@id": "bts:StageIIIC" + "@id": "bts:Loss" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:Methylation" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:Mosaicism" }, { - "@id": "bts:StageIS" + "@id": "bts:Other" }, { - "@id": "bts:StageIV" + "@id": "bts:PartialMethylation" }, { - "@id": "bts:StageIVA" + "@id": "bts:Rearrangement" }, { - "@id": "bts:StageIVB" + "@id": "bts:RepeatedSequences" }, { - "@id": "bts:StageIVC" + "@id": "bts:Splice" }, { - "@id": "bts:StageTis" + "@id": "bts:Substitution" }, { - "@id": "bts:StageX" + "@id": "bts:Translocation" }, { "@id": "bts:Unknown" @@ -27512,18 +27406,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "AJCC Clinical Stage", + "sms:displayName": "Variant Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalT", + "@id": "bts:Zygosity", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalT", + "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", + "rdfs:label": "Zygosity", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -27531,172 +27425,223 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:T0" - }, - { - "@id": "bts:T1" + "@id": "bts:Heterozygous" }, { - "@id": "bts:T1a" + "@id": "bts:Hemizygous" }, { - "@id": "bts:T1a1" + "@id": "bts:Homozygous" }, { - "@id": "bts:T1a2" + "@id": "bts:Nullizygous" }, { - "@id": "bts:T1b" + "@id": "bts:Unknown" }, { - "@id": "bts:T1b1" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Zygosity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SourceHTANBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", + "rdfs:label": "SourceHTANBiospecimenID", + "rdfs:subClassOf": [ { - "@id": "bts:T1b2" - }, + "@id": "bts:Biosample" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Source HTAN Biospecimen ID", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CollectionDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", + "rdfs:label": "CollectionDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:T1c" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Collection Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:AdjacentBiospecimenIDs", + "@type": "rdfs:Class", + "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", + "rdfs:label": "AdjacentBiospecimenIDs", + "rdfs:subClassOf": [ { - "@id": "bts:T1mi" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adjacent Biospecimen IDs", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "Biospecimen Type", + "rdfs:label": "BiospecimenType", + "rdfs:subClassOf": [ { - "@id": "bts:T2" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:T2a" + "@id": "bts:TissueBiospecimenType" }, { - "@id": "bts:T2a1" + "@id": "bts:BloodBiospecimenType" }, { - "@id": "bts:T2a2" + "@id": "bts:AnalyteBiospecimenType" }, { - "@id": "bts:T2b" + "@id": "bts:MouthRinseBiospecimenType" }, { - "@id": "bts:T2c" + "@id": "bts:StoolBiospecimenType" }, { - "@id": "bts:T2d" + "@id": "bts:UrineBiospecimenType" }, { - "@id": "bts:T3" + "@id": "bts:AscitesBiospecimenType" }, { - "@id": "bts:T3a" + "@id": "bts:SputumBiospecimenType" }, { - "@id": "bts:T3b" + "@id": "bts:FluidsBiospecimenType" }, { - "@id": "bts:T3c" + "@id": "bts:BoneMarrowBiospecimenType" }, { - "@id": "bts:T3d" - }, + "@id": "bts:CellsBiospecimenType" + } + ], + "sms:displayName": "Biospecimen Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AcquisitionMethodType", + "@type": "rdfs:Class", + "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", + "rdfs:label": "AcquisitionMethodType", + "rdfs:subClassOf": [ { - "@id": "bts:T4" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:T4a" + "@id": "bts:Autopsy" }, { - "@id": "bts:T4b" + "@id": "bts:Biopsy" }, { - "@id": "bts:T4c" + "@id": "bts:FineNeedleAspirate" }, { - "@id": "bts:T4d" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:T4e" + "@id": "bts:PunchBiopsy" }, { - "@id": "bts:TX" + "@id": "bts:ShaveBiopsy" }, { - "@id": "bts:Ta" + "@id": "bts:Excision" }, { - "@id": "bts:Tis" + "@id": "bts:Re-excision" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:SentinelNodeBiopsy" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:Lymphadenectomy-RegionalNodes" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:OtherAcquisitionMethod" }, { - "@id": "bts:Unknown" + "@id": "bts:Noninducedsputum" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical T", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicM", - "@type": "rdfs:Class", - "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicM", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:M0" + "@id": "bts:Inducedsputum" }, { - "@id": "bts:M1" + "@id": "bts:BAL(bronchialalveolarlavage)" }, { - "@id": "bts:M1a" + "@id": "bts:Cytobrush" }, { - "@id": "bts:M1b" + "@id": "bts:Blooddraw" }, { - "@id": "bts:M1c" + "@id": "bts:Fluidcollection" }, { - "@id": "bts:MX" + "@id": "bts:Forcepsbiopsy" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:Coreneedlebiopsy" }, { - "@id": "bts:Unknown" + "@id": "bts:Endoscopicbiopsy" }, { - "@id": "bts:NotReported" + "@id": "bts:Notspecified" } ], - "sms:displayName": "AJCC Pathologic M", - "sms:required": "sms:false", + "sms:displayName": "Acquisition Method Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicN", + "@id": "bts:FixativeType", "@type": "rdfs:Class", - "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", - "rdfs:label": "AJCCPathologicN", + "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", + "rdfs:label": "FixativeType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -27704,96 +27649,87 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:N0" - }, - { - "@id": "bts:N0(i+)" - }, - { - "@id": "bts:N0(i-)" - }, - { - "@id": "bts:N0(mol+)" + "@id": "bts:Acetone" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:Alcohol" }, { - "@id": "bts:N1" + "@id": "bts:Formalin" }, { - "@id": "bts:N1a" + "@id": "bts:Glutaraldehyde" }, { - "@id": "bts:N1b" + "@id": "bts:OCTmedia" }, { - "@id": "bts:N1bI" + "@id": "bts:RNAlater" }, { - "@id": "bts:N1bII" + "@id": "bts:Saline" }, { - "@id": "bts:N1bIII" + "@id": "bts:95%Ethanol" }, { - "@id": "bts:N1bIV" + "@id": "bts:Dimidoester" }, { - "@id": "bts:N1c" + "@id": "bts:Carbodiimide" }, { - "@id": "bts:N1mi" + "@id": "bts:Dimethylacetamide" }, { - "@id": "bts:N2" + "@id": "bts:Para-benzoquinone" }, { - "@id": "bts:N2a" + "@id": "bts:PAXgenetissue" }, { - "@id": "bts:N2b" + "@id": "bts:TCLlysisbuffer" }, { - "@id": "bts:N2c" + "@id": "bts:NP40lysisbuffer" }, { - "@id": "bts:N3" + "@id": "bts:Methacarn" }, { - "@id": "bts:N3a" + "@id": "bts:Cryo-store" }, { - "@id": "bts:N3b" + "@id": "bts:Carnoy'sFixative" }, { - "@id": "bts:N3c" + "@id": "bts:Polaxamer" }, { - "@id": "bts:N4" + "@id": "bts:Other" }, { - "@id": "bts:NX" + "@id": "bts:None" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Unfixed" } ], - "sms:displayName": "AJCC Pathologic N", - "sms:required": "sms:false", + "sms:displayName": "Fixative Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicStage", + "@id": "bts:StorageMethod", "@type": "rdfs:Class", - "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", - "rdfs:label": "AJCCPathologicStage", + "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", + "rdfs:label": "StorageMethod", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -27801,97 +27737,194 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Stage0" + "@id": "bts:Ambienttemperature" }, { - "@id": "bts:Stage0a" + "@id": "bts:Cutslide" }, { - "@id": "bts:Stage0is" + "@id": "bts:Fresh" }, { - "@id": "bts:StageI" + "@id": "bts:Frozenat-20C" }, { - "@id": "bts:StageIA" + "@id": "bts:Frozenat-70C" }, { - "@id": "bts:StageIA1" + "@id": "bts:Frozenat-80C" }, { - "@id": "bts:StageIA2" + "@id": "bts:Frozenat-150C" }, { - "@id": "bts:StageIB" + "@id": "bts:Frozeninliquidnitrogen" }, { - "@id": "bts:StageIB1" + "@id": "bts:Frozeninvaporphase" }, { - "@id": "bts:StageIB2" + "@id": "bts:Paraffinblock" }, { - "@id": "bts:StageIC" + "@id": "bts:RNAlaterat4C" }, { - "@id": "bts:StageII" + "@id": "bts:RNAlaterat25C" }, { - "@id": "bts:StageIIA" + "@id": "bts:RNAlaterat-20C" }, { - "@id": "bts:StageIIA1" + "@id": "bts:Refrigeratedat4degrees" }, { - "@id": "bts:StageIIA2" + "@id": "bts:Refrigeratedvacuumchamber" }, { - "@id": "bts:StageIIB" + "@id": "bts:4Cinvacuumchamber" }, { - "@id": "bts:StageIIC" + "@id": "bts:Desiccantat4C" }, { - "@id": "bts:StageIIC1" + "@id": "bts:NotApplicable" }, { - "@id": "bts:StageIII" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Storage Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProcessingDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", + "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:ProtocolLink", + "@type": "rdfs:Class", + "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label": "ProtocolLink", + "rdfs:subClassOf": [ + { + "@id": "bts:InformationContentEntity" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Protocol Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SiteDataSource", + "@type": "rdfs:Class", + "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", + "rdfs:label": "SiteDataSource", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Site Data Source", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CollectionMedia", + "@type": "rdfs:Class", + "rdfs:comment": "Material Specimen is collected into post procedure", + "rdfs:label": "CollectionMedia", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DMEM" }, { - "@id": "bts:StageIIIA" + "@id": "bts:DMEM+Serum" }, { - "@id": "bts:StageIIIB" + "@id": "bts:RPMI" }, { - "@id": "bts:StageIIIC" + "@id": "bts:RPMI+Serum" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:PBS" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:PBS+Serum" }, { - "@id": "bts:StageIS" + "@id": "bts:None" + } + ], + "sms:displayName": "Collection Media", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MountingMedium", + "@type": "rdfs:Class", + "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", + "rdfs:label": "MountingMedium", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Aqueouswaterbased" }, { - "@id": "bts:StageIV" + "@id": "bts:Non-AqueousSolventbased" }, { - "@id": "bts:StageIVA" + "@id": "bts:Xylene" }, { - "@id": "bts:StageIVB" + "@id": "bts:Toluene" }, { - "@id": "bts:StageIVC" + "@id": "bts:AntifadewithDAPI" }, { - "@id": "bts:StageTis" + "@id": "bts:AntifadewithoutDAPI" }, { - "@id": "bts:StageX" + "@id": "bts:PBS" }, { "@id": "bts:Unknown" @@ -27900,18 +27933,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "AJCC Pathologic Stage", + "sms:displayName": "Mounting Medium", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicT", + "@id": "bts:ProcessingLocation", "@type": "rdfs:Class", - "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicT", + "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", + "rdfs:label": "ProcessingLocation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistologyAssessmentBy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", + "rdfs:label": "HistologyAssessmentBy", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -27919,175 +27969,190 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:T0" + "@id": "bts:Pathologist" }, { - "@id": "bts:T1" + "@id": "bts:ResearchScientist" }, { - "@id": "bts:T1a" + "@id": "bts:Other" }, { - "@id": "bts:T1a1" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Histology Assessment By", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistologyAssessmentMedium", + "@type": "rdfs:Class", + "rdfs:comment": "The method of assessment used to characterize histology", + "rdfs:label": "HistologyAssessmentMedium", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Digital" }, { - "@id": "bts:T1a2" + "@id": "bts:Microscopy" }, { - "@id": "bts:T1b" + "@id": "bts:Other" }, { - "@id": "bts:T1b1" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Histology Assessment Medium", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PreinvasiveMorphology", + "@type": "rdfs:Class", + "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", + "rdfs:label": "PreinvasiveMorphology", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:T1b2" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:T1c" + "@id": "bts:Melanomainsitu-superficialspreading" }, { - "@id": "bts:T1mi" + "@id": "bts:Melanomainsitu-lentigomalignatype" }, { - "@id": "bts:T2" + "@id": "bts:Melanomainsitu-acral-lentiginous" }, { - "@id": "bts:T2a" + "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" }, { - "@id": "bts:T2a1" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:T2a2" + "@id": "bts:Melanomainsitu-nototherwiseclassified" }, { - "@id": "bts:T2b" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:T2c" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:T2d" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:T3" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:T3a" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:T3b" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:T3c" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:T3d" + "@id": "bts:Invasivemelanoma-other" }, { - "@id": "bts:T4" + "@id": "bts:NormalWDA" }, { - "@id": "bts:T4a" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:T4b" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:T4c" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:T4d" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:T4e" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:TX" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:Ta" + "@id": "bts:SquamousCarcinomainsitu" }, { - "@id": "bts:Tis" + "@id": "bts:Atypicaladenomatoushyperplasia" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:Adenocarcinomainsitu-nonmucinous" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:Adenocarcinomainsitu-mucinous" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:BenigntumorNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Hamartoma" }, { - "@id": "bts:NotReported" + "@id": "bts:CarcinomaNOS" + }, + { + "@id": "bts:Nodiagnosispossible" } ], - "sms:displayName": "AJCC Pathologic T", + "sms:displayName": "Preinvasive Morphology", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCStagingSystemEdition", + "@id": "bts:TumorInfiltratingLymphocytes", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", - "rdfs:label": "AJCCStagingSystemEdition", + "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", + "rdfs:label": "TumorInfiltratingLymphocytes", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:1st" - }, - { - "@id": "bts:2nd" - }, - { - "@id": "bts:3rd" - }, - { - "@id": "bts:4th" - }, - { - "@id": "bts:5th" - }, - { - "@id": "bts:6th" - }, - { - "@id": "bts:7th" - }, - { - "@id": "bts:8th" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Staging System Edition", + "sms:displayName": "Tumor Infiltrating Lymphocytes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CogNeuroblastomaRiskGroup", + "@id": "bts:DegreeofDysplasia", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.", - "rdfs:label": "CogNeuroblastomaRiskGroup", + "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", + "rdfs:label": "DegreeofDysplasia", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -28095,370 +28160,257 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HighRisk" + "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" }, { - "@id": "bts:IntermediateRisk" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:LowRisk" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:Unknown" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:NotReported" + "@id": "bts:CarcinomainSitu" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Cog Neuroblastoma Risk Group", + "sms:displayName": "Degree of Dysplasia", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CogRhabdomyosarcomaRiskGroup", + "@id": "bts:DysplasiaFraction", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).", - "rdfs:label": "CogRhabdomyosarcomaRiskGroup", + "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", + "rdfs:label": "DysplasiaFraction", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:HighRisk" - }, - { - "@id": "bts:IntermediateRisk" - }, - { - "@id": "bts:LowRisk" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Cog Rhabdomyosarcoma Risk Group", + "sms:displayName": "Dysplasia Fraction", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GleasonGradeGroup", + "@id": "bts:NumberProliferatingCells", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "GleasonGradeGroup", + "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", + "rdfs:label": "NumberProliferatingCells", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Group1" - }, - { - "@id": "bts:Group2" - }, - { - "@id": "bts:Group3" - }, - { - "@id": "bts:Group4" - }, - { - "@id": "bts:Group5" - } - ], - "sms:displayName": "Gleason Grade Group", + "sms:displayName": "Number Proliferating Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GleasonGradeTertiary", + "@id": "bts:PercentEosinophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", - "rdfs:label": "GleasonGradeTertiary", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", + "rdfs:label": "PercentEosinophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pattern4" - }, - { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Gleason Grade Tertiary", + "sms:displayName": "Percent Eosinophil Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GleasonPatternsPercent", + "@id": "bts:PercentGranulocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", - "rdfs:label": "GleasonPatternsPercent", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", + "rdfs:label": "PercentGranulocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gleason Patterns Percent", + "sms:displayName": "Percent Granulocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GreatestTumorDimension", + "@id": "bts:PercentInflamInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", - "rdfs:label": "GreatestTumorDimension", + "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", + "rdfs:label": "PercentInflamInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Greatest Tumor Dimension", + "sms:displayName": "Percent Inflam Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IGCCCGStage", + "@id": "bts:PercentLymphocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", - "rdfs:label": "IGCCCGStage", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", + "rdfs:label": "PercentLymphocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GoodPrognosis" - }, - { - "@id": "bts:IntermediatePrognosis" - }, - { - "@id": "bts:PoorPrognosis" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "IGCCCG Stage", + "sms:displayName": "Percent Lymphocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:INPCGrade", + "@id": "bts:PercentMonocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", - "rdfs:label": "INPCGrade", + "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", + "rdfs:label": "PercentMonocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Differentiating" - }, - { - "@id": "bts:PoorlyDifferentiated" - }, - { - "@id": "bts:Undifferentiated" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INPC Grade", + "sms:displayName": "Percent Monocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:INPCHistologicGroup", + "@id": "bts:PercentNecrosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", - "rdfs:label": "INPCHistologicGroup", + "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNecrosis", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Favorable" - }, - { - "@id": "bts:Unfavorable" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INPC Histologic Group", + "sms:displayName": "Percent Necrosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:INRGStage", + "@id": "bts:PercentNeutrophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", - "rdfs:label": "INRGStage", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", + "rdfs:label": "PercentNeutrophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:L1" - }, - { - "@id": "bts:L2" - }, - { - "@id": "bts:M" - }, - { - "@id": "bts:Ms" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INRG Stage", + "sms:displayName": "Percent Neutrophil Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:INSSStage", + "@id": "bts:PercentNormalCells", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", - "rdfs:label": "INSSStage", + "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNormalCells", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Stage1" - }, - { - "@id": "bts:Stage2A" - }, - { - "@id": "bts:Stage2B" - }, - { - "@id": "bts:Stage3" - }, - { - "@id": "bts:Stage4" - }, - { - "@id": "bts:Stage4S" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Percent Normal Cells", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PercentStromalCells", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", + "rdfs:label": "PercentStromalCells", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "INSS Stage", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Percent Stromal Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InternationalPrognosticIndex", + "@id": "bts:PercentTumorCells", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.", - "rdfs:label": "InternationalPrognosticIndex", + "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", + "rdfs:label": "PercentTumorCells", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:LowRisk" - }, - { - "@id": "bts:Low-IntermediateRisk" - }, - { - "@id": "bts:High-IntermediateRisk" - }, + "sms:displayName": "Percent Tumor Cells", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PercentTumorNuclei", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", + "rdfs:label": "PercentTumorNuclei", + "rdfs:subClassOf": [ { - "@id": "bts:HighRisk" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "International Prognostic Index", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Percent Tumor Nuclei", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IRSGroup", + "@id": "bts:FiducialMarker", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", - "rdfs:label": "IRSGroup", + "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", + "rdfs:label": "FiducialMarker", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -28466,34 +28418,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GroupI" - }, - { - "@id": "bts:GroupIa" - }, - { - "@id": "bts:GroupIb" - }, - { - "@id": "bts:GroupII" - }, - { - "@id": "bts:GroupIIa" - }, - { - "@id": "bts:GroupIIc" + "@id": "bts:NuclearStain-DAPI" }, { - "@id": "bts:GroupIII" + "@id": "bts:FluorescentBeads" }, { - "@id": "bts:GroupIIIa" + "@id": "bts:GridSlides-Hemocytometer" }, { - "@id": "bts:GroupIIIb" + "@id": "bts:AdhesiveMarkers" }, { - "@id": "bts:GroupIV" + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -28502,18 +28439,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "IRS Group", + "sms:displayName": "Fiducial Marker", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IRSStage", + "@id": "bts:SlicingMethod", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", - "rdfs:label": "IRSStage", + "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", + "rdfs:label": "SlicingMethod", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -28521,16 +28458,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:1" + "@id": "bts:Vibratome" }, { - "@id": "bts:2" + "@id": "bts:Cryosectioning" }, { - "@id": "bts:3" + "@id": "bts:Tissuemolds" }, { - "@id": "bts:4" + "@id": "bts:Slidingmicrotome" + }, + { + "@id": "bts:Sectioning" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -28539,157 +28482,173 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "IRS Stage", + "sms:displayName": "Slicing Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ISSStage", + "@id": "bts:LysisBuffer", "@type": "rdfs:Class", - "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", - "rdfs:label": "ISSStage", + "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", + "rdfs:label": "LysisBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:I" - }, - { - "@id": "bts:II" - }, - { - "@id": "bts:III" - }, - { - "@id": "bts:NotReported" - }, + "sms:displayName": "Lysis Buffer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MethodofNucleicAcidIsolation", + "@type": "rdfs:Class", + "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", + "rdfs:label": "MethodofNucleicAcidIsolation", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "ISS Stage", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Method of Nucleic Acid Isolation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodeInvolvedSite", + "@id": "bts:Biosample", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", - "rdfs:label": "LymphNodeInvolvedSite", + "rdfs:comment": "TBD", + "rdfs:label": "Biosample", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Biosample", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSBiospecimen", + "@type": "rdfs:Class", + "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", + "rdfs:label": "SRRSBiospecimen", + "rdfs:subClassOf": [ { - "@id": "bts:Axillary" - }, + "@id": "bts:Biosample" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Biospecimen", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Cervical" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Epitrochlear" + "@id": "bts:Component" }, { - "@id": "bts:Femoral" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:Hilar" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:Iliac-common" + "@id": "bts:HTANParentID" }, { - "@id": "bts:Iliac-external" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:Iliac" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:NOS" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Inguinal" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:Mediastinal" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:Mesenteric" + "@id": "bts:IschemicTime" }, { - "@id": "bts:None" + "@id": "bts:IschemicTemperature" }, { - "@id": "bts:Occipital" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:Paraaortic" + "@id": "bts:TopographyCode" }, { - "@id": "bts:Parotid" + "@id": "bts:AdditionalTopography" }, { - "@id": "bts:Popliteal" + "@id": "bts:FixativeType" }, { - "@id": "bts:Retroperitoneal" + "@id": "bts:StorageMethod" }, { - "@id": "bts:Splenic" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:Submandibular" + "@id": "bts:HistologicMorphologyCode" }, { - "@id": "bts:Supraclavicular" + "@id": "bts:PreservationMethod" }, { - "@id": "bts:Unknown" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:NotReported" + "@id": "bts:ProtocolLink" } ], - "sms:displayName": "Lymph Node Involved Site", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MarginDistance", + "@id": "bts:IschemicTime", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", - "rdfs:label": "MarginDistance", + "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", + "rdfs:label": "IschemicTime", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Margin Distance", + "sms:displayName": "Ischemic Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MarginsInvolvedSite", + "@id": "bts:IschemicTemperature", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", - "rdfs:label": "MarginsInvolvedSite", + "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", + "rdfs:label": "IschemicTemperature", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -28697,39 +28656,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GerotaFascia" + "@id": "bts:WarmIschemia" }, { - "@id": "bts:Parenchyma" + "@id": "bts:ColdIschemia" }, { - "@id": "bts:PerinephricFat" + "@id": "bts:Ambientair" }, { - "@id": "bts:Renal" + "@id": "bts:4Cwetice" }, { - "@id": "bts:RenalCapsule" + "@id": "bts:Negative-20C" }, { - "@id": "bts:RenalSinus" + "@id": "bts:DryIce" }, { - "@id": "bts:RenalVein" + "@id": "bts:LiquidNitrogen" }, { - "@id": "bts:Ureter" + "@id": "bts:Unknown" } ], - "sms:displayName": "Margins Involved Site", + "sms:displayName": "Ischemic Temperature", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedulloblastomaMolecularClassification", + "@id": "bts:TopographyCode", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", - "rdfs:label": "MedulloblastomaMolecularClassification", + "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", + "rdfs:label": "TopographyCode", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -28740,1467 +28699,973 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NotDetermined" + "@id": "bts:C00.0" }, { - "@id": "bts:Non-WNT/non-SHHActivated" + "@id": "bts:C00.1" }, { - "@id": "bts:SHH-Activated" + "@id": "bts:C00.2" }, { - "@id": "bts:WNT-Activated" + "@id": "bts:C00.3" }, { - "@id": "bts:Unknown" + "@id": "bts:C00.4" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Medulloblastoma Molecular Classification", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MicropapillaryFeatures", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", - "rdfs:label": "MicropapillaryFeatures", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" + "@id": "bts:C00.5" }, { - "@id": "bts:Present" + "@id": "bts:C00.6" }, { - "@id": "bts:Unknown" + "@id": "bts:C00.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Micropapillary Features", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MitosisKaryorrhexisIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", - "rdfs:label": "MitosisKaryorrhexisIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:High" + "@id": "bts:C01.9" }, { - "@id": "bts:Intermediate" + "@id": "bts:C02.0" }, { - "@id": "bts:Low" + "@id": "bts:C02.1" }, { - "@id": "bts:Unknown" + "@id": "bts:C02.2" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mitosis Karyorrhexis Index", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NonNodalRegionalDisease", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", - "rdfs:label": "NonNodalRegionalDisease", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" + "@id": "bts:C02.3" }, { - "@id": "bts:Indeterminate" + "@id": "bts:C02.4" }, { - "@id": "bts:Present" + "@id": "bts:C02.8" }, { - "@id": "bts:Unknown" + "@id": "bts:C02.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Non Nodal Regional Disease", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NonNodalTumorDeposits", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", - "rdfs:label": "NonNodalTumorDeposits", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:C03.0" }, { - "@id": "bts:No" + "@id": "bts:C03.1" }, { - "@id": "bts:Unknown" + "@id": "bts:C03.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Non Nodal Tumor Deposits", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianSpecimenStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", - "rdfs:label": "OvarianSpecimenStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:OvarianCapsuleIntact" + "@id": "bts:C04.0" }, { - "@id": "bts:OvarianCapsuleRuptured" + "@id": "bts:C04.1" }, { - "@id": "bts:OvarianCapsuleFragmented" + "@id": "bts:C04.8" }, { - "@id": "bts:Unknown" + "@id": "bts:C04.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Ovarian Specimen Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianSurfaceInvolvement", - "@type": "rdfs:Class", - "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", - "rdfs:label": "OvarianSurfaceInvolvement", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" + "@id": "bts:C05.0" }, { - "@id": "bts:Present" + "@id": "bts:C05.1" }, { - "@id": "bts:Indeterminate" + "@id": "bts:C05.2" }, { - "@id": "bts:Unknown" + "@id": "bts:C05.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Ovarian Surface Involvement", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PregnantatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", - "rdfs:label": "PregnantatDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:C05.9" }, { - "@id": "bts:No" + "@id": "bts:C06.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C06.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pregnant at Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PrimaryGleasonGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "PrimaryGleasonGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pattern1" + "@id": "bts:C06.2" }, { - "@id": "bts:Pattern2" + "@id": "bts:C06.8" }, { - "@id": "bts:Pattern3" + "@id": "bts:C06.9" }, { - "@id": "bts:Pattern4" + "@id": "bts:C07.9" }, { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Primary Gleason Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondaryGleasonGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "SecondaryGleasonGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C08.0" + }, { - "@id": "bts:Pattern1" + "@id": "bts:C08.1" }, { - "@id": "bts:Pattern2" + "@id": "bts:C08.8" }, { - "@id": "bts:Pattern3" + "@id": "bts:C08.9" }, { - "@id": "bts:Pattern4" + "@id": "bts:C09.0" }, { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Secondary Gleason Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SupratentorialLocalization", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", - "rdfs:label": "SupratentorialLocalization", - "rdfs:subClassOf": [ + "@id": "bts:C09.1" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C09.8" + }, { - "@id": "bts:CerebralCortex" + "@id": "bts:C09.9" }, { - "@id": "bts:DeepGray" + "@id": "bts:C10.0" }, { - "@id": "bts:SpinalCord" + "@id": "bts:C10.1" }, { - "@id": "bts:WhiteMatter" + "@id": "bts:C10.2" }, { - "@id": "bts:Unknown" + "@id": "bts:C10.3" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Supratentorial Localization", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorDepth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", - "rdfs:label": "TumorDepth", - "rdfs:subClassOf": [ + "@id": "bts:C10.4" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Depth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WHOCNSGrade", - "@type": "rdfs:Class", - "rdfs:comment": "WHO CNS Grade", - "rdfs:label": "WHOCNSGrade", - "rdfs:subClassOf": [ + "@id": "bts:C10.8" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C10.9" + }, { - "@id": "bts:GradeI" + "@id": "bts:C11.0" }, { - "@id": "bts:GradeII" + "@id": "bts:C11.1" }, { - "@id": "bts:GradeIII" + "@id": "bts:C11.2" }, { - "@id": "bts:GradeIV" + "@id": "bts:C11.3" }, { - "@id": "bts:GradeNotAssigned" + "@id": "bts:C11.8" }, { - "@id": "bts:Unknown" + "@id": "bts:C11.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "WHO CNS Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WHONTEGrade", - "@type": "rdfs:Class", - "rdfs:comment": "WHO NTE Grade", - "rdfs:label": "WHONTEGrade", - "rdfs:subClassOf": [ + "@id": "bts:C12.9" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C13.0" + }, { - "@id": "bts:G1" + "@id": "bts:C13.1" }, { - "@id": "bts:G2" + "@id": "bts:C13.2" }, { - "@id": "bts:G3" + "@id": "bts:C13.8" }, { - "@id": "bts:GX" + "@id": "bts:C13.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C14.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "WHO NTE Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AAChange", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "AAChange", - "rdfs:subClassOf": [ + "@id": "bts:C14.2" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "AA Change", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Antigen", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Antigen", - "rdfs:subClassOf": [ + "@id": "bts:C14.8" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C15.0" + }, { - "@id": "bts:BCL6" + "@id": "bts:C15.1" }, { - "@id": "bts:CA-125" + "@id": "bts:C15.2" }, { - "@id": "bts:CA19-9" + "@id": "bts:C15.3" }, { - "@id": "bts:CCND1" + "@id": "bts:C15.4" }, { - "@id": "bts:CD10" + "@id": "bts:C15.5" }, { - "@id": "bts:CD117" + "@id": "bts:C15.8" }, { - "@id": "bts:CD138" + "@id": "bts:C15.9" }, { - "@id": "bts:CD14" + "@id": "bts:C16.0" }, { - "@id": "bts:CD15" + "@id": "bts:C16.1" }, { - "@id": "bts:CD19" + "@id": "bts:C16.2" }, { - "@id": "bts:CD20" + "@id": "bts:C16.3" }, { - "@id": "bts:CD22" + "@id": "bts:C16.4" }, { - "@id": "bts:CD23" + "@id": "bts:C16.5" }, { - "@id": "bts:CD25" + "@id": "bts:C16.6" }, { - "@id": "bts:CD3" + "@id": "bts:C16.8" }, { - "@id": "bts:CD30" + "@id": "bts:C16.9" }, { - "@id": "bts:CD33" + "@id": "bts:C17.0" }, { - "@id": "bts:CD34" + "@id": "bts:C17.1" }, { - "@id": "bts:CD45" + "@id": "bts:C17.2" }, { - "@id": "bts:CD5" + "@id": "bts:C17.3" }, { - "@id": "bts:CD56" + "@id": "bts:C17.8" }, { - "@id": "bts:CD7" + "@id": "bts:C17.9" }, { - "@id": "bts:CD79A" + "@id": "bts:C18.0" }, { - "@id": "bts:CEA" + "@id": "bts:C18.1" }, { - "@id": "bts:HLA-DR" + "@id": "bts:C18.2" }, { - "@id": "bts:Mesothelin" + "@id": "bts:C18.3" }, { - "@id": "bts:NSE" + "@id": "bts:C18.4" }, { - "@id": "bts:SquamousCellCarcinomaAntigen" + "@id": "bts:C18.5" }, { - "@id": "bts:Unknown" + "@id": "bts:C18.6" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Antigen", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ClinicalBiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "ClinicalBiospecimenType", - "rdfs:subClassOf": [ + "@id": "bts:C18.7" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C18.8" + }, { - "@id": "bts:Blood" + "@id": "bts:C18.9" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:C19.9" }, { - "@id": "bts:BuccalMucosa" + "@id": "bts:C20.9" }, { - "@id": "bts:BuffyCoat" + "@id": "bts:C21.0" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:C21.1" }, { - "@id": "bts:ConnectiveTissue" + "@id": "bts:C21.2" }, { - "@id": "bts:EmbryonicFluid" + "@id": "bts:C21.8" }, { - "@id": "bts:EmbryonicTissue" + "@id": "bts:C22.0" }, { - "@id": "bts:Feces" + "@id": "bts:C22.1" }, { - "@id": "bts:Granulocyte" + "@id": "bts:C23.9" }, { - "@id": "bts:MuscleTissue" + "@id": "bts:C24.0" }, { - "@id": "bts:NerveTissue" + "@id": "bts:C24.1" }, { - "@id": "bts:PeritonealFluid" + "@id": "bts:C24.8" }, { - "@id": "bts:Plasma" + "@id": "bts:C24.9" }, { - "@id": "bts:PleuralFluid" + "@id": "bts:C25.0" }, { - "@id": "bts:Saliva" + "@id": "bts:C25.1" }, { - "@id": "bts:Serum" + "@id": "bts:C25.2" }, { - "@id": "bts:Skin" + "@id": "bts:C25.3" }, { - "@id": "bts:SoftTissue" + "@id": "bts:C25.4" }, { - "@id": "bts:TissueNOS" + "@id": "bts:C25.7" }, { - "@id": "bts:UninvolvedTissueNOS" + "@id": "bts:C25.8" }, { - "@id": "bts:Urine" + "@id": "bts:C25.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C26.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Clinical Biospecimen Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BloodTestNormalRangeUpper", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeUpper", - "rdfs:subClassOf": [ + "@id": "bts:C26.8" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blood Test Normal Range Upper", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BloodTestNormalRangeLower", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeLower", - "rdfs:subClassOf": [ + "@id": "bts:C26.9" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blood Test Normal Range Lower", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CellCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CellCount", - "rdfs:subClassOf": [ + "@id": "bts:C30.0" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chromosome", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Chromosome", - "rdfs:subClassOf": [ + "@id": "bts:C30.1" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C31.0" + }, { - "@id": "bts:Chr1" + "@id": "bts:C31.1" }, { - "@id": "bts:Chr2" + "@id": "bts:C31.2" }, { - "@id": "bts:Chr3" + "@id": "bts:C31.3" }, { - "@id": "bts:Chr4" + "@id": "bts:C31.8" }, { - "@id": "bts:Chr5" + "@id": "bts:C31.9" }, { - "@id": "bts:Chr6" + "@id": "bts:C32.0" }, { - "@id": "bts:Chr7" + "@id": "bts:C32.1" }, { - "@id": "bts:Chr8" + "@id": "bts:C32.2" }, { - "@id": "bts:Chr9" + "@id": "bts:C32.3" }, { - "@id": "bts:Chr10" + "@id": "bts:C32.8" }, { - "@id": "bts:Chr11" + "@id": "bts:C32.9" }, { - "@id": "bts:Chr12" + "@id": "bts:C33.9" }, { - "@id": "bts:Chr13" + "@id": "bts:C34.0" }, { - "@id": "bts:Chr14" + "@id": "bts:C34.1" }, { - "@id": "bts:Chr15" + "@id": "bts:C34.2" }, { - "@id": "bts:Chr16" + "@id": "bts:C34.3" }, { - "@id": "bts:Chr17" + "@id": "bts:C34.8" }, { - "@id": "bts:Chr18" + "@id": "bts:C34.9" }, { - "@id": "bts:Chr19" + "@id": "bts:C37.9" }, { - "@id": "bts:Chr20" + "@id": "bts:C38.0" }, { - "@id": "bts:Chr21" + "@id": "bts:C38.1" }, { - "@id": "bts:Chr22" + "@id": "bts:C38.2" }, { - "@id": "bts:Chr23" + "@id": "bts:C38.3" }, { - "@id": "bts:ChrM" + "@id": "bts:C38.4" }, { - "@id": "bts:ChrX" + "@id": "bts:C38.8" }, { - "@id": "bts:ChrY" + "@id": "bts:C39.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C39.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Chromosome", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Clonality", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Clonality", - "rdfs:subClassOf": [ + "@id": "bts:C39.9" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C40.0" + }, { - "@id": "bts:Clonal" + "@id": "bts:C40.1" }, { - "@id": "bts:Non-clonal" - } - ], - "sms:displayName": "Clonality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CopyNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CopyNumber", - "rdfs:subClassOf": [ + "@id": "bts:C40.3" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Copy Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Cytoband", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Cytoband", - "rdfs:subClassOf": [ + "@id": "bts:C40.8" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cytoband", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Exon", - "@type": "rdfs:Class", - "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Exon", - "rdfs:subClassOf": [ + "@id": "bts:C40.9" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Exon", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoneFamily", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", - "rdfs:label": "HistoneFamily", - "rdfs:subClassOf": [ + "@id": "bts:C41.0" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C41.1" + }, { - "@id": "bts:H1" + "@id": "bts:C41.2" }, { - "@id": "bts:H2A" + "@id": "bts:C41.3" }, { - "@id": "bts:H2B" + "@id": "bts:C41.4" }, { - "@id": "bts:H3" + "@id": "bts:C41.8" }, { - "@id": "bts:H4" + "@id": "bts:C41.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C42.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Histone Family", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoneVariant", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "HistoneVariant", - "rdfs:subClassOf": [ + "@id": "bts:C42.1" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C42.2" + }, { - "@id": "bts:CENP-A" + "@id": "bts:C42.3" }, { - "@id": "bts:H2A-Bbd" + "@id": "bts:C42.4" }, { - "@id": "bts:H2A.X" + "@id": "bts:C44.0" }, { - "@id": "bts:H2A.Z" + "@id": "bts:C44.1" }, { - "@id": "bts:H2A.Z.1" + "@id": "bts:C44.2" }, { - "@id": "bts:H2A.Z.2" + "@id": "bts:C44.3" }, { - "@id": "bts:H2A.Z.2.2" + "@id": "bts:C44.4" }, { - "@id": "bts:H3.1" + "@id": "bts:C44.5" }, { - "@id": "bts:H3.2" + "@id": "bts:C44.6" }, { - "@id": "bts:H3.3" + "@id": "bts:C44.7" }, { - "@id": "bts:H3.5" + "@id": "bts:C47.0" }, { - "@id": "bts:H3.X" + "@id": "bts:C47.1" }, { - "@id": "bts:H3.Y" + "@id": "bts:C47.2" }, { - "@id": "bts:H3t(H3.4)" + "@id": "bts:C47.3" }, { - "@id": "bts:MH2A" + "@id": "bts:C47.4" }, { - "@id": "bts:MH2A.1" + "@id": "bts:C47.5" }, { - "@id": "bts:MH2A.2" + "@id": "bts:C47.6" }, { - "@id": "bts:Unknown" + "@id": "bts:C47.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Histone Variant", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Intron", - "@type": "rdfs:Class", - "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", - "rdfs:label": "Intron", - "rdfs:subClassOf": [ + "@id": "bts:C47.9" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Intron", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LaboratoryTest", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", - "rdfs:label": "LaboratoryTest", - "rdfs:subClassOf": [ + "@id": "bts:C48.0" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C48.1" + }, { - "@id": "bts:AbsoluteNeutrophil" + "@id": "bts:C48.2" }, { - "@id": "bts:Albumin" + "@id": "bts:C48.8" }, { - "@id": "bts:AlphaFetoprotein" + "@id": "bts:C49.0" }, { - "@id": "bts:B-cellgenotyping" + "@id": "bts:C49.1" }, { - "@id": "bts:Basophil" + "@id": "bts:C49.2" }, { - "@id": "bts:Beta2Microglobulin" + "@id": "bts:C49.3" }, { - "@id": "bts:BloodUreaNitrogen" + "@id": "bts:C49.4" }, { - "@id": "bts:C-ReactiveProtein" + "@id": "bts:C49.5" }, { - "@id": "bts:Calcium" + "@id": "bts:C49.6" }, { - "@id": "bts:Cellularity" + "@id": "bts:C49.8" }, { - "@id": "bts:CirculatingTumorCells" + "@id": "bts:C49.9" }, { - "@id": "bts:Creatinine" + "@id": "bts:C50.0" }, { - "@id": "bts:Eosinophil" + "@id": "bts:C50.1" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:C50.2" }, { - "@id": "bts:Glucose" + "@id": "bts:C50.3" }, { - "@id": "bts:Hematocrit" + "@id": "bts:C50.4" }, { - "@id": "bts:Hemoglobin" + "@id": "bts:C50.5" }, { - "@id": "bts:HPV-E6/E7" + "@id": "bts:C50.6" }, { - "@id": "bts:HumanChorionicGonadotropin" + "@id": "bts:C50.8" }, { - "@id": "bts:HumanPapillomavirus" + "@id": "bts:C50.9" }, { - "@id": "bts:ImmunoglobulinA" + "@id": "bts:C51.0" }, { - "@id": "bts:ImmunoglobulinG" + "@id": "bts:C51.1" }, { - "@id": "bts:ImmunoglobulinM" + "@id": "bts:C51.2" }, { - "@id": "bts:LactateDehydrogenase" + "@id": "bts:C51.8" }, { - "@id": "bts:Leukocytes" + "@id": "bts:C51.9" }, { - "@id": "bts:LuteinizingHormone" + "@id": "bts:C52.9" }, { - "@id": "bts:Lymphoblasts" + "@id": "bts:C53.0" }, { - "@id": "bts:Lymphocytes" + "@id": "bts:C53.1" }, { - "@id": "bts:MProtein" + "@id": "bts:C53.8" }, { - "@id": "bts:Metamyelocytes" + "@id": "bts:C53.9" }, { - "@id": "bts:Myeloblasts" + "@id": "bts:C54.0" }, { - "@id": "bts:Myelocytes" + "@id": "bts:C54.1" }, { - "@id": "bts:NeutrophilBands" + "@id": "bts:C54.2" }, { - "@id": "bts:Platelets" + "@id": "bts:C54.3" }, { - "@id": "bts:Prolymphocytes" + "@id": "bts:C54.8" }, { - "@id": "bts:Promonocytes" + "@id": "bts:C54.9" }, { - "@id": "bts:Promyelocytes" + "@id": "bts:C55.9" }, { - "@id": "bts:SegmentedNeutrophil" + "@id": "bts:C56.9" }, { - "@id": "bts:SerumFreeImmunoglobulinLightChain" + "@id": "bts:C57.0" }, { - "@id": "bts:Kappa" + "@id": "bts:C57.1" }, { - "@id": "bts:Lambda" + "@id": "bts:C57.2" }, { - "@id": "bts:NOS" + "@id": "bts:C57.3" }, { - "@id": "bts:Testosterone" + "@id": "bts:C57.4" }, { - "@id": "bts:TotalBilirubin" + "@id": "bts:C57.7" }, { - "@id": "bts:TotalProtein" + "@id": "bts:C57.8" }, { - "@id": "bts:Unknown" + "@id": "bts:C57.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Laboratory Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LociAbnormalCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", - "rdfs:label": "LociAbnormalCount", - "rdfs:subClassOf": [ + "@id": "bts:C60.0" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loci Abnormal Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LociCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci tested.", - "rdfs:label": "LociCount", - "rdfs:subClassOf": [ + "@id": "bts:C60.1" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loci Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Locus", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", - "rdfs:label": "Locus", - "rdfs:subClassOf": [ + "@id": "bts:C60.2" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Locus", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MismatchRepairMutation", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MismatchRepairMutation", - "rdfs:subClassOf": [ + "@id": "bts:C60.8" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C60.9" + }, { - "@id": "bts:Yes" + "@id": "bts:C61.9" }, { - "@id": "bts:No" + "@id": "bts:C62.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C62.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mismatch Repair Mutation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MolecularConsequence", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularConsequence", - "rdfs:subClassOf": [ + "@id": "bts:C62.9" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C63.0" + }, { - "@id": "bts:3PrimeUTRVariant" + "@id": "bts:C63.1" }, { - "@id": "bts:5PrimeUTRVariant" + "@id": "bts:C63.2" }, { - "@id": "bts:CodingSequenceVariant" + "@id": "bts:C63.7" }, { - "@id": "bts:DownstreamGeneVariant" + "@id": "bts:C63.8" }, { - "@id": "bts:FeatureElongation" + "@id": "bts:C63.9" }, { - "@id": "bts:FeatureTruncation" + "@id": "bts:C64.9" }, { - "@id": "bts:FrameshiftVariant" + "@id": "bts:C65.9" }, { - "@id": "bts:IncompleteTerminalCodonVariant" + "@id": "bts:C66.9" }, { - "@id": "bts:InframeDeletion" + "@id": "bts:C67.0" }, { - "@id": "bts:InframeInsertion" + "@id": "bts:C67.1" }, { - "@id": "bts:IntergenicVariant" + "@id": "bts:C67.2" }, { - "@id": "bts:IntronVariant" + "@id": "bts:C67.4" }, { - "@id": "bts:MaturemiRNAVariant" + "@id": "bts:C67.6" }, { - "@id": "bts:MissenseVariant" + "@id": "bts:C67.7" }, { - "@id": "bts:NMDTranscriptVariant" + "@id": "bts:C67.8" }, { - "@id": "bts:Non-codingTranscriptExonVariant" + "@id": "bts:C67.9" }, { - "@id": "bts:Non-codingTranscriptVariant" + "@id": "bts:C68.0" }, { - "@id": "bts:ProteinAlteringVariant" + "@id": "bts:C68.1" }, { - "@id": "bts:RegulatoryRegionAblation" + "@id": "bts:C68.8" }, { - "@id": "bts:RegulatoryRegionAmplification" + "@id": "bts:C68.9" }, { - "@id": "bts:RegulatoryRegionVariant" + "@id": "bts:C69.0" }, { - "@id": "bts:SpliceAcceptorVariant" + "@id": "bts:C69.1" }, { - "@id": "bts:SpliceDonorVariant" + "@id": "bts:C69.2" }, { - "@id": "bts:SpliceRegionVariant" + "@id": "bts:C69.3" }, { - "@id": "bts:StartLost" + "@id": "bts:C69.4" }, { - "@id": "bts:StopGain" + "@id": "bts:C69.5" }, { - "@id": "bts:StopLost" + "@id": "bts:C69.6" }, { - "@id": "bts:StopRetainedVariant" + "@id": "bts:C69.8" }, { - "@id": "bts:SynonymousVariant" + "@id": "bts:C69.9" }, { - "@id": "bts:TFBindingSiteVariant" + "@id": "bts:C70.0" }, { - "@id": "bts:TFBSAblation" + "@id": "bts:C70.1" }, { - "@id": "bts:TFBSAmplification" + "@id": "bts:C70.9" }, { - "@id": "bts:TranscriptAblation" + "@id": "bts:C71.0" }, { - "@id": "bts:TranscriptAmplification" + "@id": "bts:C71.1" }, { - "@id": "bts:UpstreamGeneVariant" - } - ], - "sms:displayName": "Molecular Consequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pathogenicity", - "@type": "rdfs:Class", - "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", - "rdfs:label": "Pathogenicity", - "rdfs:subClassOf": [ + "@id": "bts:C71.2" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C71.3" + }, { - "@id": "bts:Benign" + "@id": "bts:C71.4" }, { - "@id": "bts:LikelyBenign" + "@id": "bts:C71.5" }, { - "@id": "bts:LikelyPathogenic" + "@id": "bts:C71.6" }, { - "@id": "bts:Pathogenic" + "@id": "bts:C71.7" }, { - "@id": "bts:UncertainSignificance" - } - ], - "sms:displayName": "Pathogenicity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ploidy", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", - "rdfs:label": "Ploidy", - "rdfs:subClassOf": [ + "@id": "bts:C71.8" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C71.9" + }, { - "@id": "bts:Aneuploid" + "@id": "bts:C72.0" }, { - "@id": "bts:Diploid" + "@id": "bts:C72.1" }, { - "@id": "bts:Hyperdiploid" + "@id": "bts:C72.2" }, { - "@id": "bts:Hypodiploid" + "@id": "bts:C72.3" }, { - "@id": "bts:NearDiploid" + "@id": "bts:C72.4" }, { - "@id": "bts:Tetraploid" + "@id": "bts:C72.5" + }, + { + "@id": "bts:C72.8" + }, + { + "@id": "bts:C72.9" + }, + { + "@id": "bts:C73.9" + }, + { + "@id": "bts:C74.0" + }, + { + "@id": "bts:C74.1" + }, + { + "@id": "bts:C74.9" + }, + { + "@id": "bts:C75.0" + }, + { + "@id": "bts:C75.1" + }, + { + "@id": "bts:C75.2" + }, + { + "@id": "bts:C75.3" + }, + { + "@id": "bts:C75.4" + }, + { + "@id": "bts:C75.5" + }, + { + "@id": "bts:C75.8" + }, + { + "@id": "bts:C75.9" + }, + { + "@id": "bts:C76.0" + }, + { + "@id": "bts:C76.1" + }, + { + "@id": "bts:C76.2" + }, + { + "@id": "bts:C76.3" + }, + { + "@id": "bts:C76.4" + }, + { + "@id": "bts:C76.5" + }, + { + "@id": "bts:C76.7" + }, + { + "@id": "bts:C76.8" + }, + { + "@id": "bts:C77.0" + }, + { + "@id": "bts:C77.1" + }, + { + "@id": "bts:C77.2" + }, + { + "@id": "bts:C77.3" + }, + { + "@id": "bts:C77.4" + }, + { + "@id": "bts:C77.5" + }, + { + "@id": "bts:C77.8" + }, + { + "@id": "bts:C77.9" + }, + { + "@id": "bts:C80.9" }, { "@id": "bts:Unknown" @@ -30209,69 +29674,123 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Ploidy", + "sms:displayName": "Topography Code", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SecondExon", + "@id": "bts:AdditionalTopography", "@type": "rdfs:Class", - "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", - "rdfs:label": "SecondExon", + "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", + "rdfs:label": "AdditionalTopography", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Second Exon", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondGeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SecondGeneSymbol", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Skinofscalp" + }, + { + "@id": "bts:Skinofeyelid" + }, + { + "@id": "bts:Skinofnose" + }, + { + "@id": "bts:Skinoflip" + }, + { + "@id": "bts:Skinofear" + }, + { + "@id": "bts:Skinofneck" + }, + { + "@id": "bts:Skinofotherpartsofface" + }, + { + "@id": "bts:Skinofchest" + }, + { + "@id": "bts:Skinofback" + }, + { + "@id": "bts:Skinofabdomen" + }, + { + "@id": "bts:Skinoftrunk" + }, + { + "@id": "bts:Skinofbreast" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:Skinofpalm" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:HilarAirway" + }, + { + "@id": "bts:Peri-tumoralAirway" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second Gene Symbol", + "sms:displayName": "Additional Topography", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpecializedMolecularTest", + "@id": "bts:HistologicMorphologyCode", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SpecializedMolecularTest", + "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:label": "HistologicMorphologyCode", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Specialized Molecular Test", - "sms:required": "sms:false", + "sms:displayName": "Histologic Morphology Code", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TestAnalyteType", + "@id": "bts:PreservationMethod", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestAnalyteType", + "rdfs:comment": "Text term that represents the method used to preserve the sample.", + "rdfs:label": "PreservationMethod", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30279,19 +29798,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DNA" + "@id": "bts:Cryopreserved" }, { - "@id": "bts:MRNA" + "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" }, { - "@id": "bts:MiRNA" + "@id": "bts:Cryopreservationindryice-deadtissue" }, { - "@id": "bts:ProteinAnalyte" + "@id": "bts:Cryopreservationinliquidnitrogen-livecells" }, { - "@id": "bts:TotalRNA" + "@id": "bts:Formalinfixedparaffinembedded-FFPE" + }, + { + "@id": "bts:Formalinfixed-unbuffered" + }, + { + "@id": "bts:Formalinfixed-buffered" + }, + { + "@id": "bts:Fresh" + }, + { + "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + }, + { + "@id": "bts:OCT" + }, + { + "@id": "bts:SnapFrozen" + }, + { + "@id": "bts:Frozen" + }, + { + "@id": "bts:Negative80DegC" + }, + { + "@id": "bts:LiquidNitrogen" + }, + { + "@id": "bts:Freshdissociated" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsorted" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + }, + { + "@id": "bts:Methacarnfixedparaffinembedded-MFPE" }, { "@id": "bts:Unknown" @@ -30300,188 +29858,221 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Test Analyte Type", - "sms:required": "sms:false", + "sms:displayName": "Preservation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TestUnits", + "@id": "bts:OtherAssay", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestUnits", + "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", + "rdfs:label": "OtherAssay", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Assay" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Test Units", + "sms:displayName": "Other Assay", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" + } + ], "sms:validationRules": [] }, { - "@id": "bts:TestValue", + "@id": "bts:AssayType", "@type": "rdfs:Class", - "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", - "rdfs:label": "TestValue", + "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", + "rdfs:label": "AssayType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Test Value", - "sms:required": "sms:false", + "sms:displayName": "Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Transcript", + "@id": "bts:ExSeqMinimal", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Transcript", + "rdfs:comment": "Minimal metadata for the ExSeq assay", + "rdfs:label": "ExSeqMinimal", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcript", + "sms:displayName": "ExSeq Minimal", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VariantOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "VariantOrigin", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Germline" + "@id": "bts:Component" }, { - "@id": "bts:Somatic" + "@id": "bts:Filename" }, { - "@id": "bts:Unknown" + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" } ], - "sms:displayName": "Variant Origin", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VariantType", + "@id": "bts:ScRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of genetic variation.", - "rdfs:label": "VariantType", + "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", + "rdfs:label": "ScRNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scRNA-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Alleles" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Amplification" + "@id": "bts:Filename" }, { - "@id": "bts:Chrimerism" + "@id": "bts:FileFormat" }, { - "@id": "bts:Conversion" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Deletion" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Deletion-Insertion" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:Duplication" + "@id": "bts:CryopreservedCellsinSample" }, { - "@id": "bts:Extension" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:Gain" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:Hypermethylation" + "@id": "bts:LibraryConstructionMethod" }, { - "@id": "bts:Insertion" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:Inversion" + "@id": "bts:Read1" }, { - "@id": "bts:Loss" + "@id": "bts:Read2" }, { - "@id": "bts:Methylation" + "@id": "bts:EndBias" }, { - "@id": "bts:Mosaicism" + "@id": "bts:ReverseTranscriptionPrimer" }, { - "@id": "bts:Other" + "@id": "bts:SpikeIn" }, { - "@id": "bts:PartialMethylation" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:Rearrangement" + "@id": "bts:TotalNumberofInputCells" }, { - "@id": "bts:RepeatedSequences" + "@id": "bts:InputCellsandNuclei" }, { - "@id": "bts:Splice" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:Substitution" + "@id": "bts:SingleCellDissociationDaysfromIndex" }, { - "@id": "bts:Translocation" + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" }, { - "@id": "bts:Unknown" + "@id": "bts:NucleicAcidCaptureDaysfromIndex" }, { - "@id": "bts:NotReported" + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:TechnicalReplicateGroup" } ], - "sms:displayName": "Variant Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zygosity", + "@id": "bts:NucleicAcidSource", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", - "rdfs:label": "Zygosity", + "rdfs:comment": "The source of the input nucleic molecule", + "rdfs:label": "NucleicAcidSource", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30489,89 +30080,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Heterozygous" - }, - { - "@id": "bts:Hemizygous" + "@id": "bts:SingleCell" }, { - "@id": "bts:Homozygous" + "@id": "bts:BulkWholeCell" }, { - "@id": "bts:Nullizygous" + "@id": "bts:SingleNucleus" }, { - "@id": "bts:Unknown" + "@id": "bts:BulkNuclei" }, { - "@id": "bts:NotReported" + "@id": "bts:Micro-region" } ], - "sms:displayName": "Zygosity", - "sms:required": "sms:false", + "sms:displayName": "Nucleic Acid Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SourceHTANBiospecimenID", + "@id": "bts:CryopreservedCellsinSample", "@type": "rdfs:Class", - "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", - "rdfs:label": "SourceHTANBiospecimenID", + "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", + "rdfs:label": "CryopreservedCellsinSample", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Source HTAN Biospecimen ID", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Cryopreserved Cells in Sample", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CollectionDaysfromIndex", + "@id": "bts:SingleCellIsolationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", - "rdfs:label": "CollectionDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:AdjacentBiospecimenIDs", - "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenIDs", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adjacent Biospecimen IDs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Biospecimen Type", - "rdfs:label": "BiospecimenType", + "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", + "rdfs:label": "SingleCellIsolationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -30579,51 +30139,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TissueBiospecimenType" - }, - { - "@id": "bts:BloodBiospecimenType" - }, - { - "@id": "bts:AnalyteBiospecimenType" - }, - { - "@id": "bts:MouthRinseBiospecimenType" - }, - { - "@id": "bts:StoolBiospecimenType" - }, - { - "@id": "bts:UrineBiospecimenType" + "@id": "bts:MicrofluidicsChip" }, { - "@id": "bts:AscitesBiospecimenType" + "@id": "bts:Droplets" }, { - "@id": "bts:SputumBiospecimenType" + "@id": "bts:FACS" }, { - "@id": "bts:FluidsBiospecimenType" + "@id": "bts:Plates" }, { - "@id": "bts:BoneMarrowBiospecimenType" + "@id": "bts:10x" }, { - "@id": "bts:CellsBiospecimenType" + "@id": "bts:NucleiIsolation" } ], - "sms:displayName": "Biospecimen Type", + "sms:displayName": "Single Cell Isolation Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AcquisitionMethodType", + "@id": "bts:DissociationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", + "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", + "rdfs:label": "DissociationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -30631,81 +30176,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" - }, - { - "@id": "bts:FineNeedleAspirate" - }, - { - "@id": "bts:SurgicalResection" - }, - { - "@id": "bts:PunchBiopsy" - }, - { - "@id": "bts:ShaveBiopsy" - }, - { - "@id": "bts:Excision" - }, - { - "@id": "bts:Re-excision" - }, - { - "@id": "bts:SentinelNodeBiopsy" - }, - { - "@id": "bts:Lymphadenectomy-RegionalNodes" - }, - { - "@id": "bts:OtherAcquisitionMethod" - }, - { - "@id": "bts:Noninducedsputum" - }, - { - "@id": "bts:Inducedsputum" - }, - { - "@id": "bts:BAL(bronchialalveolarlavage)" - }, - { - "@id": "bts:Cytobrush" - }, - { - "@id": "bts:Blooddraw" - }, - { - "@id": "bts:Fluidcollection" - }, - { - "@id": "bts:Forcepsbiopsy" + "@id": "bts:GentleMACS" }, { - "@id": "bts:Coreneedlebiopsy" + "@id": "bts:Dounce" }, { - "@id": "bts:Endoscopicbiopsy" + "@id": "bts:EnzymaticDigestion" }, { - "@id": "bts:Notspecified" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Acquisition Method Type", + "sms:displayName": "Dissociation Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FixativeType", + "@id": "bts:LibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "LibraryConstructionMethod", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30713,87 +30207,72 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Acetone" - }, - { - "@id": "bts:Alcohol" - }, - { - "@id": "bts:Formalin" - }, - { - "@id": "bts:Glutaraldehyde" - }, - { - "@id": "bts:OCTmedia" - }, - { - "@id": "bts:RNAlater" + "@id": "bts:Smart-seq2" }, { - "@id": "bts:Saline" + "@id": "bts:Smart-SeqV4" }, { - "@id": "bts:95%Ethanol" + "@id": "bts:10xV1.0" }, { - "@id": "bts:Dimidoester" + "@id": "bts:10xV1.1" }, { - "@id": "bts:Carbodiimide" + "@id": "bts:10xV2" }, { - "@id": "bts:Dimethylacetamide" + "@id": "bts:10xV3" }, { - "@id": "bts:Para-benzoquinone" + "@id": "bts:10xV3.1" }, { - "@id": "bts:PAXgenetissue" + "@id": "bts:CEL-seq2" }, { - "@id": "bts:TCLlysisbuffer" + "@id": "bts:Drop-seq" }, { - "@id": "bts:NP40lysisbuffer" + "@id": "bts:InDropsV2" }, { - "@id": "bts:Methacarn" + "@id": "bts:InDropsV3" }, { - "@id": "bts:Cryo-store" + "@id": "bts:TruDrop" }, { - "@id": "bts:Carnoy'sFixative" + "@id": "bts:Sci-ATAC-seq" }, { - "@id": "bts:Polaxamer" + "@id": "bts:NexteraXT" }, { - "@id": "bts:Other" + "@id": "bts:10xMultiome" }, { - "@id": "bts:None" + "@id": "bts:10xFLEX" }, { - "@id": "bts:Unknown" + "@id": "bts:10xGEM3'" }, { - "@id": "bts:Unfixed" + "@id": "bts:10xGEM5'" } ], - "sms:displayName": "Fixative Type", + "sms:displayName": "Library Construction Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:StorageMethod", + "@id": "bts:ReadIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", + "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", + "rdfs:label": "ReadIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30801,128 +30280,83 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Ambienttemperature" - }, - { - "@id": "bts:Cutslide" - }, - { - "@id": "bts:Fresh" - }, - { - "@id": "bts:Frozenat-20C" - }, - { - "@id": "bts:Frozenat-70C" - }, - { - "@id": "bts:Frozenat-80C" - }, - { - "@id": "bts:Frozenat-150C" - }, - { - "@id": "bts:Frozeninliquidnitrogen" - }, - { - "@id": "bts:Frozeninvaporphase" - }, - { - "@id": "bts:Paraffinblock" - }, - { - "@id": "bts:RNAlaterat4C" - }, - { - "@id": "bts:RNAlaterat25C" - }, - { - "@id": "bts:RNAlaterat-20C" - }, - { - "@id": "bts:Refrigeratedat4degrees" - }, - { - "@id": "bts:Refrigeratedvacuumchamber" + "@id": "bts:R1" }, { - "@id": "bts:4Cinvacuumchamber" + "@id": "bts:R2" }, { - "@id": "bts:Desiccantat4C" + "@id": "bts:R1&R2" }, { - "@id": "bts:NotApplicable" + "@id": "bts:I1" }, { - "@id": "bts:Unknown" + "@id": "bts:Other" } ], - "sms:displayName": "Storage Method", + "sms:displayName": "Read Indicator", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProcessingDaysfromIndex", + "@id": "bts:Read1", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", - "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "Read1", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:ProtocolLink", - "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label": "ProtocolLink", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Protocol Link", + "sms:displayName": "Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SiteDataSource", + "@id": "bts:Read2", "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "Read2", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Site Data Source", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CollectionMedia", + "@id": "bts:EndBias", "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", + "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", + "rdfs:label": "EndBias", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -30930,39 +30364,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DMEM" - }, - { - "@id": "bts:DMEM+Serum" - }, - { - "@id": "bts:RPMI" - }, - { - "@id": "bts:RPMI+Serum" - }, - { - "@id": "bts:PBS" + "@id": "bts:3Prime" }, { - "@id": "bts:PBS+Serum" + "@id": "bts:5Prime" }, { - "@id": "bts:None" + "@id": "bts:FullLengthTranscript" } ], - "sms:displayName": "Collection Media", - "sms:required": "sms:false", + "sms:displayName": "End Bias", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MountingMedium", + "@id": "bts:ReverseTranscriptionPrimer", "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", + "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", + "rdfs:label": "ReverseTranscriptionPrimer", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -30970,62 +30392,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aqueouswaterbased" - }, - { - "@id": "bts:Non-AqueousSolventbased" - }, - { - "@id": "bts:Xylene" - }, - { - "@id": "bts:Toluene" - }, - { - "@id": "bts:AntifadewithDAPI" - }, - { - "@id": "bts:AntifadewithoutDAPI" + "@id": "bts:Oligo-dT" }, { - "@id": "bts:PBS" + "@id": "bts:Poly-dT" }, { - "@id": "bts:Unknown" + "@id": "bts:Featurebarcoding" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mounting Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingLocation", - "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" + "@id": "bts:Random" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Location", - "sms:required": "sms:false", + "sms:displayName": "Reverse Transcription Primer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentBy", + "@id": "bts:SpikeIn", "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", + "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", + "rdfs:label": "SpikeIn", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -31033,30 +30423,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pathologist" + "@id": "bts:ERCC" }, { - "@id": "bts:ResearchScientist" + "@id": "bts:OtherSpikeIn" }, { - "@id": "bts:Other" + "@id": "bts:NoSpikeIn" }, { - "@id": "bts:Unknown" + "@id": "bts:PhiX" } ], - "sms:displayName": "Histology Assessment By", - "sms:required": "sms:false", + "sms:displayName": "Spike In", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentMedium", + "@id": "bts:SequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "SequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Device" } ], "schema:isPartOf": { @@ -31064,561 +30454,565 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Digital" + "@id": "bts:IlluminaNextSeq500" }, { - "@id": "bts:Microscopy" + "@id": "bts:IlluminaNextSeq550" }, { - "@id": "bts:Other" + "@id": "bts:IlluminaNextSeq2500" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PreinvasiveMorphology", - "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", - "rdfs:label": "PreinvasiveMorphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IlluminaNovaSeq6000" + }, { - "@id": "bts:Melanocytichyperplasia" + "@id": "bts:IlluminaMiSeq" }, { - "@id": "bts:Atypicalmelanocyticproliferation" + "@id": "bts:454GSFLXTitanium" }, { - "@id": "bts:Melanomainsitu-superficialspreading" + "@id": "bts:ABSOLiD4" }, { - "@id": "bts:Melanomainsitu-lentigomalignatype" + "@id": "bts:ABSOLiD2" }, { - "@id": "bts:Melanomainsitu-acral-lentiginous" + "@id": "bts:ABSOLiD3" }, { - "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" + "@id": "bts:CompleteGenomics" }, { - "@id": "bts:Persistentmelanomainsitu" + "@id": "bts:IlluminaHiSeqXTen" }, { - "@id": "bts:Melanomainsitu-nototherwiseclassified" + "@id": "bts:IlluminaHiSeqXFive" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:IlluminaGenomeAnalyzerII" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:IlluminaGenomeAnalyzerIIx" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:IlluminaHiSeq2000" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:IlluminaHiSeq2500" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:IlluminaHiSeq4000" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:IlluminaNextSeq" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:IonTorrentPGM" }, { - "@id": "bts:Invasivemelanoma-other" + "@id": "bts:IonTorrentProton" }, { - "@id": "bts:NormalWDA" + "@id": "bts:IonTorrentS5" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:PacBioRS" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:NovaSeq6000" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:NovaSeqS4" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:UltimaGenomicsUG100" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:OxfordNanoporeminION" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:GridION" }, { - "@id": "bts:SquamousCarcinomainsitu" + "@id": "bts:PromethION" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:PacBioSequel2" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:Revio" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:IlluminaNextSeq1000" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:IlluminaNextSeq2000" }, { - "@id": "bts:Hamartoma" + "@id": "bts:Other" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:NotReported" } ], - "sms:displayName": "Preinvasive Morphology", - "sms:required": "sms:false", + "sms:displayName": "Sequencing Platform", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TumorInfiltratingLymphocytes", + "@id": "bts:TotalNumberofInputCells", "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:comment": "Number of cells loaded/placed on plates", + "rdfs:label": "TotalNumberofInputCells", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Input Cells", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DegreeofDysplasia", + "@id": "bts:InputCellsandNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", + "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label": "InputCellsandNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" - }, - { - "@id": "bts:Milddysplasia" - }, - { - "@id": "bts:Moderatedysplasia" - }, - { - "@id": "bts:Severedysplasia" - }, - { - "@id": "bts:CarcinomainSitu" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Degree of Dysplasia", - "sms:required": "sms:false", + "sms:displayName": "Input Cells and Nuclei", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DysplasiaFraction", + "@id": "bts:LibraryPreparationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", + "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "LibraryPreparationDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dysplasia Fraction", + "sms:displayName": "Library Preparation Days from Index", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:NumberProliferatingCells", + "@id": "bts:SingleCellDissociationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SingleCellDissociationDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number Proliferating Cells", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Single Cell Dissociation Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:PercentEosinophilInfiltration", + "@id": "bts:SequencingLibraryConstructionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Eosinophil Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Sequencing Library Construction Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:PercentGranulocyteInfiltration", + "@id": "bts:NucleicAcidCaptureDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "NucleicAcidCaptureDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Granulocyte Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Nucleic Acid Capture Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:PercentInflamInfiltration", + "@id": "bts:TechnicalReplicateGroup", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", + "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", + "rdfs:label": "TechnicalReplicateGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Inflam Infiltration", + "sms:displayName": "Technical Replicate Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentLymphocyteInfiltration", + "@id": "bts:ScRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", + "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", + "rdfs:label": "ScRNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Lymphocyte Infiltration", + "sms:displayName": "scRNA-seq Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentMonocyteInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:GenomicReferenceURL" + }, + { + "@id": "bts:GenomeAnnotationURL" + }, + { + "@id": "bts:Checksum" + }, + { + "@id": "bts:WhitelistCellBarcodeFileLink" + }, + { + "@id": "bts:CellBarcodeTag" + }, + { + "@id": "bts:UMITag" + }, + { + "@id": "bts:AppliedHardTrimming" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Monocyte Infiltration", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNecrosis", + "@id": "bts:ScRNAseqWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScRNAseqWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Necrosis", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CellRanger" + }, + { + "@id": "bts:STARsolo" + }, + { + "@id": "bts:HCAOptimus" + }, + { + "@id": "bts:DropEST" + }, + { + "@id": "bts:SEQC" + }, + { + "@id": "bts:Cufflinks" + }, + { + "@id": "bts:DEXSeq" + }, + { + "@id": "bts:HTSeq-FPKM" + }, + { + "@id": "bts:Cellannotation" + }, + { + "@id": "bts:Differentiationtrajectoryanalysis" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "scRNAseq Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentNeutrophilInfiltration", + "@id": "bts:WorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", + "rdfs:label": "WorkflowVersion", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Neutrophil Infiltration", - "sms:required": "sms:false", + "sms:displayName": "Workflow Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentNormalCells", + "@id": "bts:ScRNAseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", + "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", + "rdfs:label": "ScRNAseqWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Normal Cells", - "sms:required": "sms:false", + "sms:displayName": "scRNAseq Workflow Parameters Description", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentStromalCells", + "@id": "bts:WorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "WorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Stromal Cells", - "sms:required": "sms:false", + "sms:displayName": "Workflow Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorCells", + "@id": "bts:GenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", + "rdfs:label": "GenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Cells", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorNuclei", + "@id": "bts:GenomicReferenceURL", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", + "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", + "rdfs:label": "GenomicReferenceURL", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Nuclei", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FiducialMarker", + "@id": "bts:GenomeAnnotationURL", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", + "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", + "rdfs:label": "GenomeAnnotationURL", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NuclearStain-DAPI" - }, - { - "@id": "bts:FluorescentBeads" - }, - { - "@id": "bts:GridSlides-Hemocytometer" - }, - { - "@id": "bts:AdhesiveMarkers" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Fiducial Marker", - "sms:required": "sms:false", + "sms:displayName": "Genome Annotation URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SlicingMethod", + "@id": "bts:WhitelistCellBarcodeFileLink", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", + "rdfs:comment": "Link to file listing all possible cell barcodes. URL", + "rdfs:label": "WhitelistCellBarcodeFileLink", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Vibratome" - }, - { - "@id": "bts:Cryosectioning" - }, - { - "@id": "bts:Tissuemolds" - }, - { - "@id": "bts:Slidingmicrotome" - }, - { - "@id": "bts:Sectioning" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Slicing Method", - "sms:required": "sms:false", + "sms:displayName": "Whitelist Cell Barcode File Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LysisBuffer", + "@id": "bts:CellBarcodeTag", "@type": "rdfs:Class", - "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", - "rdfs:label": "LysisBuffer", + "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", + "rdfs:label": "CellBarcodeTag", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lysis Buffer", - "sms:required": "sms:false", + "sms:displayName": "Cell Barcode Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MethodofNucleicAcidIsolation", + "@id": "bts:UMITag", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", - "rdfs:label": "MethodofNucleicAcidIsolation", + "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", + "rdfs:label": "UMITag", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Method of Nucleic Acid Isolation", - "sms:required": "sms:false", + "sms:displayName": "UMI Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Biosample", + "@id": "bts:AppliedHardTrimming", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Biosample", + "rdfs:comment": "Was Hard Trimming applied", + "rdfs:label": "AppliedHardTrimming", "rdfs:subClassOf": [ { - "@id": "bts:Thing" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biosample", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AppliedHardTrimming" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Applied Hard Trimming", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SRRSBiospecimen", + "@id": "bts:ScRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", - "rdfs:label": "SRRSBiospecimen", + "rdfs:comment": "Gene and Isoform expression files", + "rdfs:label": "ScRNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Biospecimen", + "sms:displayName": "scRNA-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Patient" + "@id": "bts:ScRNA-seqLevel2" } ], "sms:requiresDependency": [ @@ -31626,1130 +31020,1329 @@ "@id": "bts:Component" }, { - "@id": "bts:HTANBiospecimenID" + "@id": "bts:Filename" }, { - "@id": "bts:SourceHTANBiospecimenID" + "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentID" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:AdjacentBiospecimenIDs" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:BiospecimenType" + "@id": "bts:DataCategory" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:MatrixType" }, { - "@id": "bts:CollectionDaysfromIndex" + "@id": "bts:LinkedMatrices" }, { - "@id": "bts:AcquisitionMethodType" + "@id": "bts:CellMedianNumberReads" }, { - "@id": "bts:IschemicTime" + "@id": "bts:CellMedianNumberGenes" }, { - "@id": "bts:IschemicTemperature" + "@id": "bts:CellTotal" }, { - "@id": "bts:CollectionMedia" + "@id": "bts:ScRNAseqWorkflowType" }, { - "@id": "bts:TopographyCode" + "@id": "bts:ScRNAseqWorkflowParametersDescription" }, { - "@id": "bts:AdditionalTopography" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:FixativeType" + "@id": "bts:WorkflowVersion" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:DataCategory", + "@type": "rdfs:Class", + "rdfs:comment": "Specific content type of the data file.", + "rdfs:label": "DataCategory", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GeneExpression" }, { - "@id": "bts:StorageMethod" + "@id": "bts:TranscriptExpression" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:ExonExpressionQuantification" }, { - "@id": "bts:HistologicMorphologyCode" + "@id": "bts:GeneExpressionQuantification" }, { - "@id": "bts:PreservationMethod" + "@id": "bts:IsoformExpressionQuantification" }, { - "@id": "bts:ProcessingDaysfromIndex" + "@id": "bts:SpliceJunctionQuantification" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Other" } ], + "sms:displayName": "Data Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IschemicTime", + "@id": "bts:MatrixType", "@type": "rdfs:Class", - "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", - "rdfs:label": "IschemicTime", + "rdfs:comment": "Type of data stored in matrix.", + "rdfs:label": "MatrixType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ischemic Time", - "sms:required": "sms:false", - "sms:validationRules": [] - }, + "schema:rangeIncludes": [ + { + "@id": "bts:RawCounts" + }, + { + "@id": "bts:NormalizedCounts" + }, + { + "@id": "bts:ScaledCounts" + }, + { + "@id": "bts:BatchCorrectedCounts" + } + ], + "sms:displayName": "Matrix Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { - "@id": "bts:IschemicTemperature", + "@id": "bts:LinkedMatrices", "@type": "rdfs:Class", - "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", - "rdfs:label": "IschemicTemperature", + "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", + "rdfs:label": "LinkedMatrices", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Linked Matrices", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CellMedianNumberReads", + "@type": "rdfs:Class", + "rdfs:comment": "Median number of reads per cell. Number", + "rdfs:label": "CellMedianNumberReads", + "rdfs:subClassOf": [ { - "@id": "bts:WarmIschemia" + "@id": "bts:ScRNA-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Median Number Reads", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CellMedianNumberGenes", + "@type": "rdfs:Class", + "rdfs:comment": "Median number of genes detected per cell. Number", + "rdfs:label": "CellMedianNumberGenes", + "rdfs:subClassOf": [ + { + "@id": "bts:ScRNA-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Median Number Genes", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CellTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Number of sequenced cells. 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"@id": "bts:SkinNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HilarAirway" + "@id": "bts:RarecytePick-Seq" }, { - "@id": "bts:Peri-tumoralAirway" - }, + "@id": "bts:LaserCaptureMicrodissection" + } + ], + "sms:displayName": "Micro-region Seq Platform", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ROITag", + "@type": "rdfs:Class", + "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", + "rdfs:label": "ROITag", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Additional Topography", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ROI Tag", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologicMorphologyCode", + "@id": "bts:ReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", - "rdfs:label": "HistologicMorphologyCode", + "rdfs:comment": "The length of the sequencing reads. Can be integer, null", + "rdfs:label": "ReadLength", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Histologic Morphology Code", + "sms:displayName": "Read Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PreservationMethod", + "@id": "bts:LibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the method used to preserve the sample.", - "rdfs:label": "PreservationMethod", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "LibrarySelectionMethod", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -32862,134 +32440,90 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Cryopreserved" - }, - { - "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" - }, - { - "@id": "bts:Cryopreservationindryice-deadtissue" - }, - { - "@id": "bts:Cryopreservationinliquidnitrogen-livecells" - }, - { - "@id": "bts:Formalinfixedparaffinembedded-FFPE" - }, - { - "@id": "bts:Formalinfixed-unbuffered" - }, - { - "@id": "bts:Formalinfixed-buffered" - }, - { - "@id": "bts:Fresh" - }, - { - "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" - }, - { - "@id": "bts:OCT" - }, - { - "@id": "bts:SnapFrozen" - }, - { - "@id": "bts:Frozen" - }, - { - "@id": "bts:Negative80DegC" + "@id": "bts:HybridSelection" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:PCR" }, { - "@id": "bts:Freshdissociated" + "@id": "bts:AffinityEnrichment" }, { - "@id": "bts:Freshdissociatedandsinglecellsorted" + "@id": "bts:Poly-TEnrichment" }, { - "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + "@id": "bts:Random" }, { - "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + "@id": "bts:RRNADepletion" }, { - "@id": "bts:Unknown" + "@id": "bts:MiRNASizeFractionation" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" } ], - "sms:displayName": "Preservation Method", + "sms:displayName": "Library Selection Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AssayType", + "@id": "bts:LibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", - "rdfs:label": "AssayType", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitName", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Assay Type", + "sms:displayName": "Library Preparation Kit Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExSeqMinimal", + "@id": "bts:LibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "Minimal metadata for the ExSeq assay", - "rdfs:label": "ExSeqMinimal", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVendor", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq Minimal", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, + "sms:displayName": "Library Preparation Kit Vendor", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LibraryPreparationKitVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVersion", + "rdfs:subClassOf": [ { - "@id": "bts:AssayType" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Library Preparation Kit Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel1", + "@id": "bts:AdapterName", "@type": "rdfs:Class", - "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", - "rdfs:label": "ScRNA-seqLevel1", + "rdfs:comment": "Name of the sequencing adapter. String", + "rdfs:label": "AdapterName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32998,97 +32532,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 1", + "sms:displayName": "Adapter Name", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:CryopreservedCellsinSample" - }, - { - "@id": "bts:SingleCellIsolationMethod" - }, - { - "@id": "bts:DissociationMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:Read1" - }, - { - "@id": "bts:Read2" - }, - { - "@id": "bts:EndBias" - }, - { - "@id": "bts:ReverseTranscriptionPrimer" - }, - { - "@id": "bts:SpikeIn" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:TotalNumberofInputCells" - }, - { - "@id": "bts:InputCellsandNuclei" - }, - { - "@id": "bts:LibraryPreparationDaysfromIndex" - }, - { - "@id": "bts:SingleCellDissociationDaysfromIndex" - }, - { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" - }, - { - "@id": "bts:NucleicAcidCaptureDaysfromIndex" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:TechnicalReplicateGroup" - } - ], "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidSource", + "@id": "bts:AdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "The source of the input nucleic molecule", - "rdfs:label": "NucleicAcidSource", + "rdfs:comment": "Base sequence of the sequencing adapter. String", + "rdfs:label": "AdapterSequence", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33097,125 +32549,117 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:SingleCell" - }, - { - "@id": "bts:BulkWholeCell" - }, - { - "@id": "bts:SingleNucleus" - }, - { - "@id": "bts:BulkNuclei" - }, - { - "@id": "bts:Micro-region" - } - ], - "sms:displayName": "Nucleic Acid Source", - "sms:required": "sms:true", + "sms:displayName": "Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CryopreservedCellsinSample", + "@id": "bts:BaseCallerName", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", - "rdfs:label": "CryopreservedCellsinSample", + "rdfs:comment": "Name of the base caller. String", + "rdfs:label": "BaseCallerName", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, + "sms:displayName": "Base Caller Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BaseCallerVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Version of the base caller. String", + "rdfs:label": "BaseCallerVersion", + "rdfs:subClassOf": [ { - "@id": "bts:No" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Cryopreserved Cells in Sample", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Base Caller Version", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SingleCellIsolationMethod", + "@id": "bts:FlowCellBarcode", "@type": "rdfs:Class", - "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", - "rdfs:label": "SingleCellIsolationMethod", + "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", + "rdfs:label": "FlowCellBarcode", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MicrofluidicsChip" - }, - { - "@id": "bts:Droplets" - }, - { - "@id": "bts:FACS" - }, - { - "@id": "bts:Plates" - }, - { - "@id": "bts:10x" - }, + "sms:displayName": "Flow Cell Barcode", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentMaximumLength", + "@type": "rdfs:Class", + "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMaximumLength", + "rdfs:subClassOf": [ { - "@id": "bts:NucleiIsolation" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Single Cell Isolation Method", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Maximum Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DissociationMethod", + "@id": "bts:FragmentMeanLength", "@type": "rdfs:Class", - "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", - "rdfs:label": "DissociationMethod", + "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentMeanLength", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GentleMACS" - }, - { - "@id": "bts:Dounce" - }, - { - "@id": "bts:EnzymaticDigestion" - }, + "sms:displayName": "Fragment Mean Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentMinimumLength", + "@type": "rdfs:Class", + "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMinimumLength", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Dissociation Method", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Minimum Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryConstructionMethod", + "@id": "bts:FragmentStandardDeviationLength", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "LibraryConstructionMethod", + "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentStandardDeviationLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33224,71 +32668,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Smart-seq2" - }, - { - "@id": "bts:Smart-SeqV4" - }, - { - "@id": "bts:10xV1.0" - }, - { - "@id": "bts:10xV1.1" - }, - { - "@id": "bts:10xV2" - }, - { - "@id": "bts:10xV3" - }, - { - "@id": "bts:10xV3.1" - }, - { - "@id": "bts:CEL-seq2" - }, - { - "@id": "bts:Drop-seq" - }, - { - "@id": "bts:InDropsV2" - }, - { - "@id": "bts:InDropsV3" - }, - { - "@id": "bts:TruDrop" - }, - { - "@id": "bts:Sci-ATAC-seq" - }, - { - "@id": "bts:NexteraXT" - }, - { - "@id": "bts:10xMultiome" - }, - { - "@id": "bts:10xFLEX" - }, - { - "@id": "bts:10xGEM3'" - }, + "sms:displayName": "Fragment Standard Deviation Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LaneNumber", + "@type": "rdfs:Class", + "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label": "LaneNumber", + "rdfs:subClassOf": [ { - "@id": "bts:10xGEM5'" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Library Construction Method", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lane Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReadIndicator", + "@id": "bts:LibraryStrand", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", - "rdfs:label": "ReadIndicator", + "rdfs:comment": "Library stranded-ness.", + "rdfs:label": "LibraryStrand", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33299,83 +32704,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:R1" - }, - { - "@id": "bts:R2" + "@id": "bts:Unstranded" }, { - "@id": "bts:R1&R2" + "@id": "bts:FirstStranded" }, { - "@id": "bts:I1" + "@id": "bts:SecondStranded" }, { - "@id": "bts:Other" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Read Indicator", - "sms:required": "sms:true", + "sms:displayName": "Library Strand", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Read1", + "@id": "bts:MultiplexBarcode", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "Read1", + "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", + "rdfs:label": "MultiplexBarcode", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" - }, - { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "Read1", - "sms:required": "sms:true", + "sms:displayName": "Multiplex Barcode", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Read2", + "@id": "bts:SizeSelectionRange", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "Read2", + "rdfs:comment": "Range of size selection. String", + "rdfs:label": "SizeSelectionRange", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" - }, + "sms:displayName": "Size Selection Range", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TargetDepth", + "@type": "rdfs:Class", + "rdfs:comment": "The targeted read depth prior to sequencing. Integer", + "rdfs:label": "TargetDepth", + "rdfs:subClassOf": [ { - "@id": "bts:CDNA" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Read2", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Target Depth", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EndBias", + "@id": "bts:ToTrimAdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "rdfs:label": "EndBias", + "rdfs:comment": "Does the user suggest adapter trimming?", + "rdfs:label": "ToTrimAdapterSequence", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -33383,58 +32786,75 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:3Prime" - }, - { - "@id": "bts:5Prime" + "@id": "bts:Yes-TrimAdapterSequence" }, { - "@id": "bts:FullLengthTranscript" + "@id": "bts:No" } ], - "sms:displayName": "End Bias", - "sms:required": "sms:true", + "sms:displayName": "To Trim Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReverseTranscriptionPrimer", + "@id": "bts:TranscriptIntegrityNumber", "@type": "rdfs:Class", - "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", - "rdfs:label": "ReverseTranscriptionPrimer", + "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", + "rdfs:label": "TranscriptIntegrityNumber", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Oligo-dT" - }, - { - "@id": "bts:Poly-dT" - }, - { - "@id": "bts:Featurebarcoding" - }, - { - "@id": "bts:Random" - } - ], - "sms:displayName": "Reverse Transcription Primer", - "sms:required": "sms:true", + "sms:displayName": "Transcript Integrity Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpikeIn", + "@id": "bts:RIN", "@type": "rdfs:Class", - "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", - "rdfs:label": "SpikeIn", + "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", + "rdfs:label": "RIN", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "RIN", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DV200", + "@type": "rdfs:Class", + "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", + "rdfs:label": "DV200", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DV200", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdapterContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "AdapterContent", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -33442,30 +32862,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ERCC" + "@id": "bts:FAIL" }, { - "@id": "bts:OtherSpikeIn" + "@id": "bts:PASS" }, { - "@id": "bts:NoSpikeIn" + "@id": "bts:WARN" }, { - "@id": "bts:PhiX" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Spike In", - "sms:required": "sms:true", + "sms:displayName": "Adapter Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SequencingPlatform", + "@id": "bts:BasicStatistics", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "SequencingPlatform", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "BasicStatistics", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -33473,103 +32896,302 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:IlluminaNextSeq500" + "@id": "bts:FAIL" }, { - "@id": "bts:IlluminaNextSeq550" + "@id": "bts:PASS" }, { - "@id": "bts:IlluminaNextSeq2500" + "@id": "bts:WARN" }, { - "@id": "bts:IlluminaNovaSeq6000" + "@id": "bts:Unknown" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Basic Statistics", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Encoding", + "@type": "rdfs:Class", + "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", + "rdfs:label": "Encoding", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Encoding", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KmerContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "KmerContent", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:PASS" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:WARN" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:Unknown" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Kmer Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OverrepresentedSequences", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "OverrepresentedSequences", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:PASS" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:WARN" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:Unknown" }, { - "@id": "bts:IlluminaGenomeAnalyzerII" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Overrepresented Sequences", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseNContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseNContent", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:IlluminaGenomeAnalyzerIIx" + "@id": "bts:PASS" }, { - "@id": "bts:IlluminaHiSeq2000" + "@id": "bts:WARN" }, { - "@id": "bts:IlluminaHiSeq2500" + "@id": "bts:Unknown" }, { - "@id": "bts:IlluminaHiSeq4000" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base N Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseSequenceContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceContent", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:PASS" }, { - "@id": "bts:IonTorrentPGM" + "@id": "bts:WARN" }, { - "@id": "bts:IonTorrentProton" + "@id": "bts:Unknown" }, { - "@id": "bts:IonTorrentS5" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseSequenceQuality", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceQuality", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:PacBioRS" + "@id": "bts:PASS" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:WARN" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:Unknown" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Quality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerSequenceGCContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceGCContent", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:PASS" }, { - "@id": "bts:GridION" + "@id": "bts:WARN" }, { - "@id": "bts:PromethION" + "@id": "bts:Unknown" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence GC Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerSequenceQualityScore", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceQualityScore", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:Revio" + "@id": "bts:PASS" }, { - "@id": "bts:IlluminaNextSeq1000" + "@id": "bts:WARN" }, { - "@id": "bts:IlluminaNextSeq2000" + "@id": "bts:Unknown" }, { - "@id": "bts:Other" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence Quality Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerTileSequenceQuality", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerTileSequenceQuality", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" }, { "@id": "bts:Unknown" @@ -33578,15 +33200,15 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sequencing Platform", - "sms:required": "sms:true", + "sms:displayName": "Per Tile Sequence Quality", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofInputCells", + "@id": "bts:PercentGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells loaded/placed on plates", - "rdfs:label": "TotalNumberofInputCells", + "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", + "rdfs:label": "PercentGCContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33595,32 +33217,49 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Input Cells", - "sms:required": "sms:true", + "sms:displayName": "Percent GC Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InputCellsandNuclei", + "@id": "bts:SequenceDuplicationLevels", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", - "rdfs:label": "InputCellsandNuclei", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceDuplicationLevels", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Input Cells and Nuclei", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Duplication Levels", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationDaysfromIndex", + "@id": "bts:SequenceLengthDistribution", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "LibraryPreparationDaysfromIndex", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceLengthDistribution", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33629,36 +33268,49 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Days from Index", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Length Distribution", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:SingleCellDissociationDaysfromIndex", + "@id": "bts:TotalReads", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SingleCellDissociationDaysfromIndex", + "rdfs:comment": "Total number of reads per sample. Integer", + "rdfs:label": "TotalReads", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell Dissociation Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Total Reads", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex", + "@id": "bts:QCWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", + "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", + "rdfs:label": "QCWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33667,17 +33319,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Library Construction Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "QC Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex", + "@id": "bts:QCWorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "NucleicAcidCaptureDaysfromIndex", + "rdfs:comment": "Major version for a workflow. String", + "rdfs:label": "QCWorkflowVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33686,17 +33336,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleic Acid Capture Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "QC Workflow Version", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:TechnicalReplicateGroup", + "@id": "bts:QCWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", - "rdfs:label": "TechnicalReplicateGroup", + "rdfs:comment": "Link to workflow used. String", + "rdfs:label": "QCWorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33705,15 +33353,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Technical Replicate Group", + "sms:displayName": "QC Workflow Link", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel2", + "@id": "bts:BulkRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", - "rdfs:label": "ScRNA-seqLevel2", + "rdfs:comment": "Bulk RNA-seq alignment protocol description", + "rdfs:label": "BulkRNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33722,11 +33370,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 2", + "sms:displayName": "Bulk RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:BulkRNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -33746,49 +33394,102 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ScRNAseqWorkflowType" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription" + "@id": "bts:GenomicReference" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:GenomicReference" + "@id": "bts:IndexFileName" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:Checksum" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:WhitelistCellBarcodeFileLink" + "@id": "bts:Contamination" }, { - "@id": "bts:CellBarcodeTag" + "@id": "bts:ContaminationError" }, { - "@id": "bts:UMITag" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:MSIWorkflowLink" + }, + { + "@id": "bts:MSIScore" + }, + { + "@id": "bts:MSIStatus" + }, + { + "@id": "bts:PairsOnDiffCHR" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:TotalUniquelyMapped" + }, + { + "@id": "bts:TotalUnmappedreads" + }, + { + "@id": "bts:ProportionReadsDuplicated" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:ProportionTargetsNoCoverage" + }, + { + "@id": "bts:ProportionBaseMismatch" + }, + { + "@id": "bts:ShortReads" + }, + { + "@id": "bts:Islowestlevel" } ], "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowType", + "@id": "bts:AlignmentWorkflowUrl", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", + "rdfs:label": "AlignmentWorkflowUrl", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Alignment Workflow Url", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AlignmentWorkflowType", "@type": "rdfs:Class", "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScRNAseqWorkflowType", + "rdfs:label": "AlignmentWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33799,48 +33500,105 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellRanger" + "@id": "bts:BWA" }, { - "@id": "bts:STARsolo" + "@id": "bts:BWAwithBQSR" }, { - "@id": "bts:HCAOptimus" + "@id": "bts:BWA-aln" }, { - "@id": "bts:DropEST" + "@id": "bts:BWA-mem" }, { - "@id": "bts:SEQC" + "@id": "bts:BWAwithMarkDuplicatesandBQSR" }, { - "@id": "bts:Cufflinks" + "@id": "bts:STAR2-Pass" }, { - "@id": "bts:DEXSeq" + "@id": "bts:STAR2-PassChimeric" }, { - "@id": "bts:HTSeq-FPKM" + "@id": "bts:STAR2-PassGenome" }, { - "@id": "bts:Cellannotation" + "@id": "bts:STAR2-PassTranscriptome" }, { - "@id": "bts:Differentiationtrajectoryanalysis" + "@id": "bts:Bowtie" }, { - "@id": "bts:Other" + "@id": "bts:Bismark" + }, + { + "@id": "bts:GSNAP" + }, + { + "@id": "bts:BSMAP" + }, + { + "@id": "bts:BSmooth" + }, + { + "@id": "bts:BS-Seeker2" + }, + { + "@id": "bts:BS-Seeker" + }, + { + "@id": "bts:RMAP" + }, + { + "@id": "bts:MethylCoder" + }, + { + "@id": "bts:BRAT-BW" + }, + { + "@id": "bts:Pash" + }, + { + "@id": "bts:Segemehl" + }, + { + "@id": "bts:Bisulfighter" + }, + { + "@id": "bts:BatMeth" + }, + { + "@id": "bts:LAST" + }, + { + "@id": "bts:ERNE-BS5" + }, + { + "@id": "bts:B-SOLANA" + }, + { + "@id": "bts:SOCS-B" + }, + { + "@id": "bts:BWA-meth" + }, + { + "@id": "bts:OtherAlignmentWorkflow" + }, + { + "@id": "bts:None" } ], - "sms:displayName": "scRNAseq Workflow Type", + "sms:displayName": "Alignment Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WorkflowVersion", + "@id": "bts:IndexFileName", "@type": "rdfs:Class", - "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", - "rdfs:label": "WorkflowVersion", + "rdfs:comment": "The name (or part of a name) of a file (of any type). String", + "rdfs:label": "IndexFileName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33849,15 +33607,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Version", + "sms:displayName": "Index File Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription", + "@id": "bts:AverageBaseQuality", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", - "rdfs:label": "ScRNAseqWorkflowParametersDescription", + "rdfs:comment": "Average base quality collected from samtools. Number", + "rdfs:label": "AverageBaseQuality", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33866,15 +33624,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNAseq Workflow Parameters Description", - "sms:required": "sms:true", + "sms:displayName": "Average Base Quality", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowLink", + "@id": "bts:AverageInsertSize", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "WorkflowLink", + "rdfs:comment": "Average insert size collected from samtools. Integer", + "rdfs:label": "AverageInsertSize", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33883,15 +33641,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Link", - "sms:required": "sms:true", + "sms:displayName": "Average Insert Size", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReference", + "@id": "bts:AverageReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", - "rdfs:label": "GenomicReference", + "rdfs:comment": "Average read length collected from samtools. Integer", + "rdfs:label": "AverageReadLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33900,15 +33658,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference", - "sms:required": "sms:true", + "sms:displayName": "Average Read Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:Contamination", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", + "rdfs:label": "Contamination", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33917,15 +33675,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", - "sms:required": "sms:true", + "sms:displayName": "Contamination", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomeAnnotationURL", + "@id": "bts:ContaminationError", "@type": "rdfs:Class", - "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", - "rdfs:label": "GenomeAnnotationURL", + "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", + "rdfs:label": "ContaminationError", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33934,15 +33692,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genome Annotation URL", - "sms:required": "sms:true", + "sms:displayName": "Contamination Error", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WhitelistCellBarcodeFileLink", + "@id": "bts:MeanCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible cell barcodes. URL", - "rdfs:label": "WhitelistCellBarcodeFileLink", + "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", + "rdfs:label": "MeanCoverage", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33951,15 +33709,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whitelist Cell Barcode File Link", - "sms:required": "sms:true", + "sms:displayName": "Mean Coverage", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeTag", + "@id": "bts:MSIWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", - "rdfs:label": "CellBarcodeTag", + "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", + "rdfs:label": "MSIWorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33968,15 +33726,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Tag", - "sms:required": "sms:true", + "sms:displayName": "MSI Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UMITag", + "@id": "bts:MSIScore", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", - "rdfs:label": "UMITag", + "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", + "rdfs:label": "MSIScore", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33985,15 +33743,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Tag", - "sms:required": "sms:true", + "sms:displayName": "MSI Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AppliedHardTrimming", + "@id": "bts:MSIStatus", "@type": "rdfs:Class", - "rdfs:comment": "Was Hard Trimming applied", - "rdfs:label": "AppliedHardTrimming", + "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", + "rdfs:label": "MSIStatus", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34004,21 +33762,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AppliedHardTrimming" + "@id": "bts:MSI" }, { - "@id": "bts:No" + "@id": "bts:MSI-low" + }, + { + "@id": "bts:MSI-high" + }, + { + "@id": "bts:MSS" } ], - "sms:displayName": "Applied Hard Trimming", - "sms:required": "sms:true", + "sms:displayName": "MSI Status", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel3", + "@id": "bts:PairsOnDiffCHR", "@type": "rdfs:Class", - "rdfs:comment": "Gene and Isoform expression files", - "rdfs:label": "ScRNA-seqLevel3", + "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", + "rdfs:label": "PairsOnDiffCHR", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34027,67 +33791,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 3", + "sms:displayName": "Pairs On Diff CHR", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScRNA-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:DataCategory" - }, - { - "@id": "bts:MatrixType" - }, - { - "@id": "bts:LinkedMatrices" - }, - { - "@id": "bts:CellMedianNumberReads" - }, - { - "@id": "bts:CellMedianNumberGenes" - }, - { - "@id": "bts:CellTotal" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:WorkflowVersion" - } - ], "sms:validationRules": [] }, { - "@id": "bts:DataCategory", + "@id": "bts:TotalUniquelyMapped", "@type": "rdfs:Class", - "rdfs:comment": "Specific content type of the data file.", - "rdfs:label": "DataCategory", + "rdfs:comment": "Number of reads that map to genome. Integer", + "rdfs:label": "TotalUniquelyMapped", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34096,38 +33808,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GeneExpression" - }, - { - "@id": "bts:TranscriptExpression" - }, - { - "@id": "bts:ExonExpressionQuantification" - }, - { - "@id": "bts:GeneExpressionQuantification" - }, - { - "@id": "bts:IsoformExpressionQuantification" - }, - { - "@id": "bts:SpliceJunctionQuantification" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Data Category", - "sms:required": "sms:true", + "sms:displayName": "Total Uniquely Mapped", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MatrixType", + "@id": "bts:TotalUnmappedreads", "@type": "rdfs:Class", - "rdfs:comment": "Type of data stored in matrix.", - "rdfs:label": "MatrixType", + "rdfs:comment": "Number of reads that did not map to genome. Integer", + "rdfs:label": "TotalUnmappedreads", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34136,29 +33825,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:RawCounts" - }, - { - "@id": "bts:NormalizedCounts" - }, - { - "@id": "bts:ScaledCounts" - }, - { - "@id": "bts:BatchCorrectedCounts" - } - ], - "sms:displayName": "Matrix Type", - "sms:required": "sms:true", + "sms:displayName": "Total Unmapped reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LinkedMatrices", + "@id": "bts:ProportionReadsDuplicated", "@type": "rdfs:Class", - "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", - "rdfs:label": "LinkedMatrices", + "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", + "rdfs:label": "ProportionReadsDuplicated", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34167,66 +33842,66 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Linked Matrices", + "sms:displayName": "Proportion Reads Duplicated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberReads", + "@id": "bts:ProportionReadsMapped", "@type": "rdfs:Class", - "rdfs:comment": "Median number of reads per cell. Number", - "rdfs:label": "CellMedianNumberReads", + "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", + "rdfs:label": "ProportionReadsMapped", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Reads", - "sms:required": "sms:true", + "sms:displayName": "Proportion Reads Mapped", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberGenes", + "@id": "bts:ProportionTargetsNoCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Median number of genes detected per cell. Number", - "rdfs:label": "CellMedianNumberGenes", + "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", + "rdfs:label": "ProportionTargetsNoCoverage", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Genes", - "sms:required": "sms:true", + "sms:displayName": "Proportion Targets No Coverage", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellTotal", + "@id": "bts:ProportionBaseMismatch", "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", - "rdfs:label": "CellTotal", + "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", + "rdfs:label": "ProportionBaseMismatch", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Total", - "sms:required": "sms:true", + "sms:displayName": "Proportion Base Mismatch", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel4", + "@id": "bts:ShortReads", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScRNA-seqLevel4", + "rdfs:comment": "Number of reads that were too short. Integer", + "rdfs:label": "ShortReads", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34235,62 +33910,53 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 4", + "sms:displayName": "Short Reads", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:Islowestlevel", + "@type": "rdfs:Class", + "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", + "rdfs:label": "Islowestlevel", + "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ScRNA-seqLevel2" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:WorkflowVersion" + "@id": "bts:Yes-Islowestlevel" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:No" } ], + "sms:displayName": "Is lowest level", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqLevel1", + "@id": "bts:BulkRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Raw sequencing files for the Slide-seq assay.", - "rdfs:label": "Slide-seqLevel1", + "rdfs:comment": "Bulk RNA-seq gene expression matrices", + "rdfs:label": "BulkRNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Level 1", + "sms:displayName": "Bulk RNA-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BulkRNA-seqLevel2" } ], "sms:requiresDependency": [ @@ -34304,70 +33970,40 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:SpatialRead1" - }, - { - "@id": "bts:SpatialRead2" - }, - { - "@id": "bts:EndBias" - }, - { - "@id": "bts:ReverseTranscriptionPrimer" - }, - { - "@id": "bts:SpatialBarcodeOffset" - }, - { - "@id": "bts:SpatialBarcodeandUMI" - }, - { - "@id": "bts:SpikeIn" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:PseudoAlignmentUsed" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:DataCategory" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:ExpressionUnits" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:MatrixType" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:FusionGeneDetected" }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex" + "@id": "bts:FusionGeneIdentity" } ], "sms:validationRules": [] }, { - "@id": "bts:SpatialRead1", + "@id": "bts:PseudoAlignmentUsed", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "SpatialRead1", + "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", + "rdfs:label": "PseudoAlignmentUsed", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -34375,24 +34011,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CDNA" + "@id": "bts:Yes-PseudoAlignmentUsed" }, { - "@id": "bts:SpatialBarcodeandUMI" + "@id": "bts:No" } ], - "sms:displayName": "Spatial Read1", + "sms:displayName": "Pseudo Alignment Used", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialRead2", + "@id": "bts:ExpressionUnits", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "SpatialRead2", + "rdfs:comment": "How quantities are corrected for gene length", + "rdfs:label": "ExpressionUnits", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -34400,80 +34036,64 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CDNA" + "@id": "bts:TPM" }, { - "@id": "bts:SpatialBarcodeandUMI" - } - ], - "sms:displayName": "Spatial Read2", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialBarcodeOffset", - "@type": "rdfs:Class", - "rdfs:comment": "Offset in sequence for spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeOffset", - "rdfs:subClassOf": [ + "@id": "bts:RPKM" + }, { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:FPKM" + }, + { + "@id": "bts:Counts" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:NA" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Barcode Offset", + "sms:displayName": "Expression Units", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeandUMI", + "@id": "bts:FusionGeneDetected", "@type": "rdfs:Class", - "rdfs:comment": "Spot and transcript identifiers", - "rdfs:label": "SpatialBarcodeandUMI", + "rdfs:comment": "Was a fusion gene identified?", + "rdfs:label": "FusionGeneDetected", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" - }, - { - "@id": "bts:SpatialRead1" - }, - { - "@id": "bts:SpatialRead2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode and UMI", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:SpatialBarcodeOffset" - }, + "schema:rangeIncludes": [ { - "@id": "bts:SpatialBarcodeLength" + "@id": "bts:Yes-FusionGeneDetected" }, { - "@id": "bts:UMIBarcodeOffset" + "@id": "bts:No" }, { - "@id": "bts:UMIBarcodeLength" + "@id": "bts:Unknown" } ], - "sms:validationRules": [ - "num" - ] + "sms:displayName": "Fusion Gene Detected", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SpatialLibraryConstructionMethod", + "@id": "bts:FusionGeneIdentity", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "SpatialLibraryConstructionMethod", + "rdfs:comment": "The gene symbols of fused genes.", + "rdfs:label": "FusionGeneIdentity", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -34481,81 +34101,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" - }, - { - "@id": "bts:Smart-SeqV4" - }, - { - "@id": "bts:10xV1.0" - }, - { - "@id": "bts:10xV1.1" - }, - { - "@id": "bts:10xV2" - }, - { - "@id": "bts:10xV3" - }, - { - "@id": "bts:10xV3.1" + "@id": "bts:EWS-FLI" }, { - "@id": "bts:Drop-seq" + "@id": "bts:EWS-ERG" }, { - "@id": "bts:InDropsV2" + "@id": "bts:SYT-SSX1" }, { - "@id": "bts:InDropsV3" + "@id": "bts:SYT-SSX2" }, { - "@id": "bts:TruDrop" + "@id": "bts:EWS-WT1" }, { - "@id": "bts:NexteraXT" - } - ], - "sms:displayName": "Spatial Library Construction Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialTranscriptomics", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SpatialTranscriptomics", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" + "@id": "bts:OtherFusionGene" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Transcriptomics", + "sms:displayName": "Fusion Gene Identity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:Slide-seqLevel2", + "@id": "bts:BulkWESLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Aligned sequencing files and QC for the Slide-seq assay.", - "rdfs:label": "Slide-seqLevel2", + "rdfs:comment": "Bulk Whole Exome Sequencing raw files", + "rdfs:label": "BulkWESLevel1", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Level 2", + "sms:displayName": "Bulk WES Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Slide-seqLevel1" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -34569,218 +34156,94 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Slide-seqWorkflowType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:Slide-seqWorkflowParameterDescription" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:GenomicReference" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:Checksum" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:SpatialBarcodeTag" + "@id": "bts:ReadLength" }, { - "@id": "bts:MatchedSpatialBarcodeTag" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:UMITag" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:AppliedHardTrimming" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the Slide-seq data set. String", - "rdfs:label": "Slide-seqWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seqWorkflowParameterDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the Slide-seq workflow. String", - "rdfs:label": "Slide-seqWorkflowParameterDescription", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Workflow Parameter Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialBarcodeTag", - "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)", - "rdfs:label": "SpatialBarcodeTag", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Barcode Tag", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MatchedSpatialBarcodeTag", - "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)", - "rdfs:label": "MatchedSpatialBarcodeTag", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matched Spatial Barcode Tag", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seqLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).", - "rdfs:label": "Slide-seqLevel3", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Slide-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:Filename" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:FileFormat" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:AdapterName" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:RunID" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:DataCategory" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:MatrixType" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:Slide-seqWorkflowType" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:Slide-seqWorkflowParameterDescription" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:LaneNumber" }, { - "@id": "bts:BeadsTotal" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:MedianUMICountsperSpot" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:MedianNumberGenesperSpatialSpot" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:Slide-seqBeadFileType" + "@id": "bts:TargetDepth" }, { - "@id": "bts:Slide-seqFragmentSize" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:RunID", - "@type": "rdfs:Class", - "rdfs:comment": "A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.", - "rdfs:label": "RunID", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ToTrimAdapterSequence" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Run ID", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequencingBatchID", + "@id": "bts:TargetCaptureKit", "@type": "rdfs:Class", - "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", - "rdfs:label": "SequencingBatchID", + "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", + "rdfs:label": "TargetCaptureKit", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34789,387 +34252,167 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Batch ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:BeadsTotal", - "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced beads. Applies to raw counts matrix only. Integer", - "rdfs:label": "BeadsTotal", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Beads Total", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedianUMICountsperSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The median number of UMI counts per tissue covered spot.", - "rdfs:label": "MedianUMICountsperSpot", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median UMI Counts per Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MedianNumberGenesperSpatialSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.", - "rdfs:label": "MedianNumberGenesperSpatialSpot", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median Number Genes per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:Slide-seqBeadFileType", - "@type": "rdfs:Class", - "rdfs:comment": "The type of Level 3 file submitted as part of the Slide-seq workflow.", - "rdfs:label": "Slide-seqBeadFileType", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, "schema:rangeIncludes": [ { - "@id": "bts:MatrixFeatures" - }, - { - "@id": "bts:MatrixBarcodes" - }, - { - "@id": "bts:AllBeadLocations" - }, - { - "@id": "bts:AllBeadBarcodes" - }, - { - "@id": "bts:MatchedBeadBarcodes" + "@id": "bts:NotApplicable" }, { - "@id": "bts:MatchedBeadLocations" + "@id": "bts:CustomTargetsFileProvided" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Slide-seq Bead File Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seqFragmentSize", - "@type": "rdfs:Class", - "rdfs:comment": "Average cDNA length associated with the experiemtn. Integer", - "rdfs:label": "Slide-seqFragmentSize", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Fragment Size", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatrixFeatures", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatrixFeatures", - "rdfs:subClassOf": [ - { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matrix Features", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatrixBarcodes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatrixBarcodes", - "rdfs:subClassOf": [ - { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matrix Barcodes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AllBeadLocations", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "AllBeadLocations", - "rdfs:subClassOf": [ - { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "All Bead Locations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AllBeadBarcodes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "AllBeadBarcodes", - "rdfs:subClassOf": [ - { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "All Bead Barcodes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatchedBeadBarcodes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatchedBeadBarcodes", - "rdfs:subClassOf": [ - { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matched Bead Barcodes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatchedBeadLocations", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatchedBeadLocations", - "rdfs:subClassOf": [ - { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matched Bead Locations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NotApplicable", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NotApplicable", - "rdfs:subClassOf": [ - { - "@id": "bts:TargetCaptureKit" + "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" }, { - "@id": "bts:SomaticVariantsSampleType" + "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" }, { - "@id": "bts:ReplicateType" + "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:CustomMSKIMPACTPanel-341Genes" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:CustomMSKIMPACTPanel-410Genes" }, { - "@id": "bts:Immunosuppression" + "@id": "bts:CustomMSKIMPACTPanel-468Genes" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" }, { - "@id": "bts:GliomaSpecificRadiationField" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" }, { - "@id": "bts:RefluxTreatmentType" + "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" }, { - "@id": "bts:COVID19ComplicationsSeverity" + "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" + "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" }, { - "@id": "bts:ColorectalPolypShape" + "@id": "bts:FoundationMedicineT5aPanel-322Genes" }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:FoundationMedicineT7Panel-429Genes" }, { - "@id": "bts:SpecimenLaterality" + "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" }, { - "@id": "bts:LabTestsforMMRStatus" + "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" }, { - "@id": "bts:Slide-seqBeadFileType" + "@id": "bts:NexteraDNAExome" }, { - "@id": "bts:GliomaSpecificMetastasisSites" + "@id": "bts:NexteraRapidCaptureExomev1.2" }, { - "@id": "bts:COVID19AntibodyTesting" + "@id": "bts:SeqCapEZHGSCVCRomev2.1" }, { - "@id": "bts:ColorectalPolypAdenomaType" + "@id": "bts:SeqCapEZHumanExomev2.0" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:SeqCapEZHumanExomev3.0" }, { - "@id": "bts:CutaneousMelanomaAdditionalFindings" + "@id": "bts:SureSelectHumanAllExonv3" }, { - "@id": "bts:CauseofDeath" + "@id": "bts:SureSelectHumanAllExonv4" }, { - "@id": "bts:TumorGrade" + "@id": "bts:SureSelectHumanAllExonv5" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:SureSelectHumanAllExonv5+UTR" }, { - "@id": "bts:ExtentofTumorResection" + "@id": "bts:TruSeqAmpliconCancerPanel" }, { - "@id": "bts:TestResult" + "@id": "bts:TruSeqExomeEnrichment-62Mb" }, { - "@id": "bts:StorageMethod" + "@id": "bts:TruSeqRNAExome" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:TruSightMyeloidSequencingPanel" }, { - "@id": "bts:ConcomitantMedicationReceivedType" + "@id": "bts:XGenExomeResearchPanelv1.0" }, { - "@id": "bts:HereditaryCancerPredispositionSyndrome" + "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" }, { - "@id": "bts:CancerAssociatedGeneMutations" + "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" }, { - "@id": "bts:MutationalSignatures" + "@id": "bts:SureSelectHumanAllExonv6" }, { - "@id": "bts:PrecancerousConditionType" + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Not Applicable", - "sms:required": "sms:false", + "sms:displayName": "Target Capture Kit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel1", + "@id": "bts:BulkWESLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", - "rdfs:label": "BulkRNA-seqLevel1", + "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", + "rdfs:label": "BulkWESLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35178,11 +34421,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 1", + "sms:displayName": "Bulk WES Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BulkWESLevel1" } ], "sms:requiresDependency": [ @@ -35196,169 +34439,142 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:Micro-regionSeqPlatform" - }, - { - "@id": "bts:ROITag" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:SequencingBatchID" - }, - { - "@id": "bts:ReadLength" - }, - { - "@id": "bts:LibrarySelectionMethod" - }, - { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:GenomicReference" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:IndexFileName" }, { - "@id": "bts:SpikeIn" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:AdapterName" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:Contamination" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:ContaminationError" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:AdapterContent" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:Encoding" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:LaneNumber" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:PerSequenceGCContent" }, { - "@id": "bts:TargetDepth" + "@id": "bts:PerSequenceQualityScore" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:PerTileSequenceQuality" }, { - "@id": "bts:TranscriptIntegrityNumber" + "@id": "bts:PercentGCContent" }, { - "@id": "bts:RIN" + "@id": "bts:SequenceDuplicationLevels" }, { - "@id": "bts:DV200" + "@id": "bts:SequenceLengthDistribution" }, { - "@id": "bts:AdapterContent" + "@id": "bts:QCWorkflowType" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:QCWorkflowVersion" }, { - "@id": "bts:Encoding" + "@id": "bts:QCWorkflowLink" }, { - "@id": "bts:KmerContent" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:MSIScore" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:MSIStatus" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:TotalReads" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:TotalReads" + "@id": "bts:ShortReads" }, { - "@id": "bts:QCWorkflowType" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:QCWorkflowVersion" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:QCWorkflowLink" + "@id": "bts:Islowestlevel" } ], "sms:validationRules": [] }, { - "@id": "bts:LibraryLayout", + "@id": "bts:ProportionCoverage10x", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "LibraryLayout", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage10x", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35367,29 +34583,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:PairedEnd" - }, - { - "@id": "bts:SingleRead" - }, - { - "@id": "bts:Mid-length" - }, - { - "@id": "bts:LongRead" - } - ], - "sms:displayName": "Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Proportion Coverage 10x", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Micro-regionSeqPlatform", + "@id": "bts:ProportionCoverage30X", "@type": "rdfs:Class", - "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", - "rdfs:label": "Micro-regionSeqPlatform", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage30X", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35398,23 +34600,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:RarecytePick-Seq" - }, - { - "@id": "bts:LaserCaptureMicrodissection" - } - ], - "sms:displayName": "Micro-region Seq Platform", + "sms:displayName": "Proportion Coverage 30X", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ROITag", + "@id": "bts:BulkWESLevel3", "@type": "rdfs:Class", - "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", - "rdfs:label": "ROITag", + "rdfs:comment": "Bulk Whole Exome Sequencing called variants", + "rdfs:label": "BulkWESLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35423,75 +34617,64 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI Tag", + "sms:displayName": "Bulk WES Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ReadLength", - "@type": "rdfs:Class", - "rdfs:comment": "The length of the sequencing reads. Can be integer, null", - "rdfs:label": "ReadLength", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkWESLevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Read Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibrarySelectionMethod", - "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "LibrarySelectionMethod", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:HybridSelection" + "@id": "bts:Filename" }, { - "@id": "bts:PCR" + "@id": "bts:FileFormat" }, { - "@id": "bts:AffinityEnrichment" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Poly-TEnrichment" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Random" + "@id": "bts:GenomicReference" }, { - "@id": "bts:RRNADepletion" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:MiRNASizeFractionation" + "@id": "bts:GermlineVariantsWorkflowURL" }, { - "@id": "bts:Other" + "@id": "bts:GermlineVariantsWorkflowType" + }, + { + "@id": "bts:SomaticVariantsWorkflowURL" + }, + { + "@id": "bts:SomaticVariantsWorkflowType" + }, + { + "@id": "bts:SomaticVariantsSampleType" + }, + { + "@id": "bts:StructuralVariantWorkflowURL" + }, + { + "@id": "bts:StructuralVariantWorkflowType" } ], - "sms:displayName": "Library Selection Method", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitName", + "@id": "bts:GermlineVariantsWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitName", + "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", + "rdfs:label": "GermlineVariantsWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35500,15 +34683,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Name", + "sms:displayName": "Germline Variants Workflow URL", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitVendor", + "@id": "bts:GermlineVariantsWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVendor", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "GermlineVariantsWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35517,15 +34700,26 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Vendor", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:GATK4" + }, + { + "@id": "bts:OtherGermlineVariantsWorkflowType" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Germline Variants Workflow Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitVersion", + "@id": "bts:SomaticVariantsWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVersion", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35534,15 +34728,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Version", + "sms:displayName": "Somatic Variants Workflow URL", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterName", + "@id": "bts:SomaticVariantsWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Name of the sequencing adapter. String", - "rdfs:label": "AdapterName", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35551,15 +34745,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Name", + "schema:rangeIncludes": [ + { + "@id": "bts:CaVEMan" + }, + { + "@id": "bts:GATK4" + }, + { + "@id": "bts:MuTect2" + }, + { + "@id": "bts:MuSE" + }, + { + "@id": "bts:Pindel" + }, + { + "@id": "bts:SomaticSniper" + }, + { + "@id": "bts:VarScan2" + }, + { + "@id": "bts:OtherSomaticVariantsWorkflowType" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Somatic Variants Workflow Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdapterSequence", + "@id": "bts:SomaticVariantsSampleType", "@type": "rdfs:Class", - "rdfs:comment": "Base sequence of the sequencing adapter. String", - "rdfs:label": "AdapterSequence", + "rdfs:comment": "Is the sample case or control in somatic variant analysis", + "rdfs:label": "SomaticVariantsSampleType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35568,15 +34791,26 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Sequence", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CaseSample" + }, + { + "@id": "bts:ControlSample" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Somatic Variants Sample Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerName", + "@id": "bts:StructuralVariantWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Name of the base caller. String", - "rdfs:label": "BaseCallerName", + "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", + "rdfs:label": "StructuralVariantWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35585,15 +34819,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Name", - "sms:required": "sms:false", + "sms:displayName": "Structural Variant Workflow URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerVersion", + "@id": "bts:StructuralVariantWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Version of the base caller. String", - "rdfs:label": "BaseCallerVersion", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "StructuralVariantWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35602,120 +34836,117 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Version", + "schema:rangeIncludes": [ + { + "@id": "bts:BRASS" + }, + { + "@id": "bts:GATK4" + }, + { + "@id": "bts:CNV" + }, + { + "@id": "bts:CNVkit" + }, + { + "@id": "bts:OtherStructuralVariantWorkflowType" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Structural Variant Workflow Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FlowCellBarcode", + "@id": "bts:MicroarrayLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", - "rdfs:label": "FlowCellBarcode", + "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", + "rdfs:label": "MicroarrayLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Flow Cell Barcode", + "sms:displayName": "Microarray Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMaximumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMaximumLength", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Maximum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMeanLength", - "@type": "rdfs:Class", - "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentMeanLength", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Mean Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMinimumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMinimumLength", - "rdfs:subClassOf": [ + "@id": "bts:Component" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Minimum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentStandardDeviationLength", - "@type": "rdfs:Class", - "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentStandardDeviationLength", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:Sequencing" + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:NucleicAcidSource" + }, + { + "@id": "bts:MicroarrayPlatformID" + }, + { + "@id": "bts:MicroarrayMolecule" + }, + { + "@id": "bts:MicroarrayLabel" + }, + { + "@id": "bts:MicroarrayValueDefinition" + }, + { + "@id": "bts:MicroarrayProtocolAuxiliaryFile" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Standard Deviation Length", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LaneNumber", + "@id": "bts:MicroarrayPlatformID", "@type": "rdfs:Class", - "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", - "rdfs:label": "LaneNumber", + "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", + "rdfs:label": "MicroarrayPlatformID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lane Number", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Microarray Platform ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match GPL\\d+" + ] }, { - "@id": "bts:LibraryStrand", + "@id": "bts:MicroarrayMolecule", "@type": "rdfs:Class", - "rdfs:comment": "Library stranded-ness.", - "rdfs:label": "LibraryStrand", + "rdfs:comment": "Microarray is measuring this kind of molecule", + "rdfs:label": "MicroarrayMolecule", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { @@ -35723,137 +34954,142 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Unstranded" - }, - { - "@id": "bts:FirstStranded" - }, - { - "@id": "bts:SecondStranded" + "@id": "bts:DNA" }, { - "@id": "bts:NotApplicable" + "@id": "bts:RNA" } ], - "sms:displayName": "Library Strand", - "sms:required": "sms:false", + "sms:displayName": "Microarray Molecule", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MultiplexBarcode", + "@id": "bts:MicroarrayLabel", "@type": "rdfs:Class", - "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", - "rdfs:label": "MultiplexBarcode", + "rdfs:comment": "Microarray used this kind of label", + "rdfs:label": "MicroarrayLabel", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Multiplex Barcode", - "sms:required": "sms:false", + "sms:displayName": "Microarray Label", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SizeSelectionRange", + "@id": "bts:MicroarrayValueDefinition", "@type": "rdfs:Class", - "rdfs:comment": "Range of size selection. String", - "rdfs:label": "SizeSelectionRange", + "rdfs:comment": "What the provided value signifies", + "rdfs:label": "MicroarrayValueDefinition", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Size Selection Range", - "sms:required": "sms:false", + "sms:displayName": "Microarray Value Definition", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TargetDepth", + "@id": "bts:MicroarrayProtocolAuxiliaryFile", "@type": "rdfs:Class", - "rdfs:comment": "The targeted read depth prior to sequencing. Integer", - "rdfs:label": "TargetDepth", + "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", + "rdfs:label": "MicroarrayProtocolAuxiliaryFile", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Target Depth", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Microarray Protocol Auxiliary File", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match syn\\d+" + ] }, { - "@id": "bts:ToTrimAdapterSequence", + "@id": "bts:MicroarrayLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Does the user suggest adapter trimming?", - "rdfs:label": "ToTrimAdapterSequence", + "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", + "rdfs:label": "MicroarrayLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-TrimAdapterSequence" - }, + "sms:displayName": "Microarray Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:No" + "@id": "bts:MicroarrayLevel1" } ], - "sms:displayName": "To Trim Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TranscriptIntegrityNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", - "rdfs:label": "TranscriptIntegrityNumber", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:MicroarrayPlatformID" + }, + { + "@id": "bts:NormalizationMethod" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript Integrity Number", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RIN", + "@id": "bts:NormalizationMethod", "@type": "rdfs:Class", - "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", - "rdfs:label": "RIN", + "rdfs:comment": "Description of Normalization Process", + "rdfs:label": "NormalizationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:RPPALevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RIN", + "sms:displayName": "Normalization Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DV200", + "@id": "bts:ScATAC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", - "rdfs:label": "DV200", + "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", + "rdfs:label": "ScATAC-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35862,137 +35098,109 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DV200", + "sms:displayName": "scATAC-seq Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "AdapterContent", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:FAIL" + "@id": "bts:Component" }, { - "@id": "bts:PASS" + "@id": "bts:Filename" }, { - "@id": "bts:WARN" + "@id": "bts:FileFormat" }, { - "@id": "bts:Unknown" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Adapter Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BasicStatistics", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "BasicStatistics", - "rdfs:subClassOf": [ + "@id": "bts:HTANDataFileID" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:NucleicAcidSource" + }, { - "@id": "bts:FAIL" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:PASS" + "@id": "bts:SingleNucleusBuffer" }, { - "@id": "bts:WARN" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:Unknown" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Basic Statistics", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Encoding", - "@type": "rdfs:Class", - "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", - "rdfs:label": "Encoding", - "rdfs:subClassOf": [ + "@id": "bts:ScATACseqLibraryLayout" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Encoding", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KmerContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "KmerContent", - "rdfs:subClassOf": [ + "@id": "bts:NucleusIdentifier" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:NucleiBarcodeLength" + }, { - "@id": "bts:FAIL" + "@id": "bts:NucleiBarcodeRead" }, { - "@id": "bts:PASS" + "@id": "bts:ScATACseqRead1" }, { - "@id": "bts:WARN" + "@id": "bts:ScATACseqRead2" }, { - "@id": "bts:Unknown" + "@id": "bts:ScATACseqRead3" }, { - "@id": "bts:NotReported" + "@id": "bts:LibraryConstructionMethod" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:ThresholdforMinimumPassingReads" + }, + { + "@id": "bts:TotalNumberofPassingNuclei" + }, + { + "@id": "bts:MedianFractionofReadsinPeaks" + }, + { + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" + }, + { + "@id": "bts:MedianPassingReadPercentage" + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:ProtocolLink" } ], - "sms:displayName": "Kmer Content", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OverrepresentedSequences", + "@id": "bts:SingleNucleusBuffer", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "OverrepresentedSequences", + "rdfs:comment": "Nuclei isolation buffer", + "rdfs:label": "SingleNucleusBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -36000,33 +35208,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:NIB" }, { - "@id": "bts:WARN" + "@id": "bts:10x" }, { - "@id": "bts:Unknown" + "@id": "bts:Omni" }, { - "@id": "bts:NotReported" + "@id": "bts:TST" } ], - "sms:displayName": "Overrepresented Sequences", - "sms:required": "sms:false", + "sms:displayName": "Single Nucleus Buffer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseNContent", + "@id": "bts:TranspositionReaction", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseNContent", + "rdfs:comment": "Name of the transposase, transposon sequences", + "rdfs:label": "TranspositionReaction", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -36034,33 +35239,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:Tn5" }, { - "@id": "bts:PASS" + "@id": "bts:EZ-Tn5" }, { - "@id": "bts:WARN" + "@id": "bts:Tn5-059" }, { - "@id": "bts:Unknown" + "@id": "bts:NexteraTn5" }, { - "@id": "bts:NotReported" + "@id": "bts:Diagenode-unloadedApex-Bio" + }, + { + "@id": "bts:Diagenode-loadedApex-Bio" + }, + { + "@id": "bts:In-House" } ], - "sms:displayName": "Per Base N Content", - "sms:required": "sms:false", + "sms:displayName": "Transposition Reaction", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceContent", + "@id": "bts:ScATACseqLibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceContent", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "ScATACseqLibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -36068,33 +35279,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" + "@id": "bts:ScATACseqPairedEnd" } ], - "sms:displayName": "Per Base Sequence Content", - "sms:required": "sms:false", + "sms:displayName": "scATACseq Library Layout", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceQuality", + "@id": "bts:NucleusIdentifier", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceQuality", + "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", + "rdfs:label": "NucleusIdentifier", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -36102,33 +35301,64 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, + "@id": "bts:NucleiBarcode" + } + ], + "sms:displayName": "Nucleus Identifier", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleiBarcodeLength", + "@type": "rdfs:Class", + "rdfs:comment": "Nuclei Barcode Length", + "rdfs:label": "NucleiBarcodeLength", + "rdfs:subClassOf": [ { - "@id": "bts:PASS" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:WARN" - }, + "@id": "bts:NucleiBarcode" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei Barcode Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleiBarcodeRead", + "@type": "rdfs:Class", + "rdfs:comment": "Nuclei Barcode Read", + "rdfs:label": "NucleiBarcodeRead", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:NotReported" + "@id": "bts:NucleiBarcode" } ], - "sms:displayName": "Per Base Sequence Quality", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei Barcode Read", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerSequenceGCContent", + "@id": "bts:ScATACseqRead1", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceGCContent", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScATACseqRead1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:ScATACseqPairedEnd" } ], "schema:isPartOf": { @@ -36136,33 +35366,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:PASS" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:WARN" + "@id": "bts:DNAInsert" }, { - "@id": "bts:Unknown" + "@id": "bts:SampleIndex" }, { - "@id": "bts:NotReported" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Per Sequence GC Content", - "sms:required": "sms:false", + "sms:displayName": "scATACseq Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerSequenceQualityScore", + "@id": "bts:ScATACseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceQualityScore", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScATACseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:ScATACseqPairedEnd" } ], "schema:isPartOf": { @@ -36170,33 +35403,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:PASS" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:WARN" + "@id": "bts:DNAInsert" }, { - "@id": "bts:Unknown" + "@id": "bts:SampleIndex" }, { - "@id": "bts:NotReported" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Per Sequence Quality Score", - "sms:required": "sms:false", + "sms:displayName": "scATACseq Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerTileSequenceQuality", + "@id": "bts:ScATACseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerTileSequenceQuality", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScATACseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -36204,183 +35437,142 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:PASS" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:WARN" + "@id": "bts:DNAInsert" }, { - "@id": "bts:Unknown" + "@id": "bts:SampleIndex" }, { - "@id": "bts:NotReported" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Per Tile Sequence Quality", + "sms:displayName": "scATACseq Read3", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentGCContent", + "@id": "bts:ThresholdforMinimumPassingReads", "@type": "rdfs:Class", - "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", - "rdfs:label": "PercentGCContent", + "rdfs:comment": "Threshold for calling cells", + "rdfs:label": "ThresholdforMinimumPassingReads", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent GC Content", - "sms:required": "sms:false", + "sms:displayName": "Threshold for Minimum Passing Reads", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceDuplicationLevels", + "@id": "bts:TotalNumberofPassingNuclei", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceDuplicationLevels", + "rdfs:comment": "Number of nuclei sequenced", + "rdfs:label": "TotalNumberofPassingNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Duplication Levels", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Passing Nuclei", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceLengthDistribution", + "@id": "bts:MedianFractionofReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceLengthDistribution", + "rdfs:comment": "Median fraction of reads in peaks (FRIP)", + "rdfs:label": "MedianFractionofReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Median Fraction of Reads in Peaks", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:NotReported" + "@id": "bts:PeaksCallingSoftware" } ], - "sms:displayName": "Sequence Length Distribution", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalReads", + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", "@type": "rdfs:Class", - "rdfs:comment": "Total number of reads per sample. Integer", - "rdfs:label": "TotalReads", + "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:QCWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", - "rdfs:label": "QCWorkflowType", - "rdfs:subClassOf": [ + "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" + "@id": "bts:PeaksCallingSoftware" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC Workflow Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:QCWorkflowVersion", + "@id": "bts:MedianPassingReadPercentage", "@type": "rdfs:Class", - "rdfs:comment": "Major version for a workflow. String", - "rdfs:label": "QCWorkflowVersion", + "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", + "rdfs:label": "MedianPassingReadPercentage", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Version", - "sms:required": "sms:false", + "sms:displayName": "Median Passing Read Percentage", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:QCWorkflowLink", + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used. String", - "rdfs:label": "QCWorkflowLink", + "rdfs:comment": "Contamination from mitochondrial sequences", + "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Link", - "sms:required": "sms:false", + "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel2", + "@id": "bts:ScATAC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq alignment protocol description", - "rdfs:label": "BulkRNA-seqLevel2", + "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", + "rdfs:label": "ScATAC-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36389,11 +35581,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 2", + "sms:displayName": "scATAC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "sms:requiresDependency": [ @@ -36436,29 +35628,20 @@ { "@id": "bts:AverageReadLength" }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, { "@id": "bts:MeanCoverage" }, { - "@id": "bts:MSIWorkflowLink" - }, - { - "@id": "bts:MSIScore" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:MSIStatus" + "@id": "bts:TotalReads" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:TotalReads" + "@id": "bts:MapQ30" }, { "@id": "bts:TotalUniquelyMapped" @@ -36470,7 +35653,13 @@ "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:ShortReads" + }, + { + "@id": "bts:ProportionCoverage10x" + }, + { + "@id": "bts:ProportionCoverage30X" }, { "@id": "bts:ProportionTargetsNoCoverage" @@ -36479,36 +35668,42 @@ "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:ShortReads" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" }, { - "@id": "bts:Islowestlevel" + "@id": "bts:Contamination" + }, + { + "@id": "bts:ContaminationError" } ], "sms:validationRules": [] }, { - "@id": "bts:AlignmentWorkflowUrl", + "@id": "bts:MapQ30", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", - "rdfs:label": "AlignmentWorkflowUrl", + "rdfs:comment": "Number of reads with Quality >= 30.", + "rdfs:label": "MapQ30", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Alignment Workflow Url", - "sms:required": "sms:true", + "sms:displayName": "MapQ30", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlignmentWorkflowType", + "@id": "bts:ScATAC-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "AlignmentWorkflowType", + "rdfs:comment": "Processed data files containing peak information for cells", + "rdfs:label": "ScATAC-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36517,452 +35712,797 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scATAC-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:BWA" + "@id": "bts:ScATAC-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:BWAwithBQSR" + "@id": "bts:Filename" }, { - "@id": "bts:BWA-aln" + "@id": "bts:FileFormat" }, { - "@id": "bts:BWA-mem" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:BWAwithMarkDuplicatesandBQSR" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:STAR2-Pass" + "@id": "bts:ScATAC-seqObjectID" }, { - "@id": "bts:STAR2-PassChimeric" + "@id": "bts:NCountPeaks" }, { - "@id": "bts:STAR2-PassGenome" + "@id": "bts:NFeaturePeaks" }, { - "@id": "bts:STAR2-PassTranscriptome" + "@id": "bts:TotalRead-Pairs" }, { - "@id": "bts:Bowtie" + "@id": "bts:DuplicateRead-Pairs" }, { - "@id": "bts:Bismark" + "@id": "bts:ChimericRead-Pairs" }, { - "@id": "bts:GSNAP" + "@id": "bts:UnmappedRead-Pairs" }, { - "@id": "bts:BSMAP" + "@id": "bts:LowMapQ" }, { - "@id": "bts:BSmooth" + "@id": "bts:MitochondrialRead-Pairs" }, { - "@id": "bts:BS-Seeker2" + "@id": "bts:PassedFilters" }, { - "@id": "bts:BS-Seeker" + "@id": "bts:TSSFragments" }, { - "@id": "bts:RMAP" + "@id": "bts:DNaseSensitiveRegionFragments" }, { - "@id": "bts:MethylCoder" + "@id": "bts:EnhancerRegionFragments" }, { - "@id": "bts:BRAT-BW" + "@id": "bts:PromoterRegionFragments" }, { - "@id": "bts:Pash" + "@id": "bts:OnTargetFragments" }, { - "@id": "bts:Segemehl" + "@id": "bts:BlacklistRegionFragments" }, { - "@id": "bts:Bisulfighter" + "@id": "bts:PeakRegionFragments" }, { - "@id": "bts:BatMeth" + "@id": "bts:PeakRegionCutsites" }, { - "@id": "bts:LAST" + "@id": "bts:NucleosomeSignal" }, { - "@id": "bts:ERNE-BS5" + "@id": "bts:NucleosomePercentile" }, { - "@id": "bts:B-SOLANA" + "@id": "bts:TSSEnrichment" }, { - "@id": "bts:SOCS-B" + "@id": "bts:TSSPercentile" }, { - "@id": "bts:BWA-meth" + "@id": "bts:PctReadsinPeaks" }, { - "@id": "bts:OtherAlignmentWorkflow" + "@id": "bts:BlacklistRatio" }, { - "@id": "bts:None" + "@id": "bts:SeuratClusters" + }, + { + "@id": "bts:NCountRNA" + }, + { + "@id": "bts:NFeatureRNA" + }, + { + "@id": "bts:MACS2Seqnames" + }, + { + "@id": "bts:MACS2Start" + }, + { + "@id": "bts:MACS2End" + }, + { + "@id": "bts:MACS2Width" + }, + { + "@id": "bts:MACS2Strand" + }, + { + "@id": "bts:MACS2Name" + }, + { + "@id": "bts:MACS2Score" + }, + { + "@id": "bts:MACS2FoldChange" + }, + { + "@id": "bts:MACS2NegLog10pvalueSummit" + }, + { + "@id": "bts:MACS2NegLog10qvalueSummit" + }, + { + "@id": "bts:MACS2RelativeSummitPosition" } ], - "sms:displayName": "Alignment Workflow Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IndexFileName", + "@id": "bts:ScATAC-seqObjectID", "@type": "rdfs:Class", - "rdfs:comment": "The name (or part of a name) of a file (of any type). String", - "rdfs:label": "IndexFileName", + "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", + "rdfs:label": "ScATAC-seqObjectID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Index File Name", - "sms:required": "sms:true", + "sms:displayName": "scATAC-seq Object ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageBaseQuality", + "@id": "bts:NCountPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Average base quality collected from samtools. Number", - "rdfs:label": "AverageBaseQuality", + "rdfs:comment": "Total number of fragments in peaks", + "rdfs:label": "NCountPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Base Quality", + "sms:displayName": "nCount Peaks", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageInsertSize", + "@id": "bts:NFeaturePeaks", "@type": "rdfs:Class", - "rdfs:comment": "Average insert size collected from samtools. Integer", - "rdfs:label": "AverageInsertSize", + "rdfs:comment": "Number of peaks with at least one read", + "rdfs:label": "NFeaturePeaks", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Insert Size", + "sms:displayName": "nFeature Peaks", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageReadLength", + "@id": "bts:TotalRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Average read length collected from samtools. Integer", - "rdfs:label": "AverageReadLength", + "rdfs:comment": "Total read-pairs", + "rdfs:label": "TotalRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Read Length", + "sms:displayName": "Total Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Contamination", + "@id": "bts:DuplicateRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", - "rdfs:label": "Contamination", + "rdfs:comment": "Number of duplicate read-pairs", + "rdfs:label": "DuplicateRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination", + "sms:displayName": "Duplicate Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ContaminationError", + "@id": "bts:ChimericRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", - "rdfs:label": "ContaminationError", + "rdfs:comment": "Number of chimerically mapped read-pairs", + "rdfs:label": "ChimericRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination Error", + "sms:displayName": "Chimeric Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MeanCoverage", + "@id": "bts:UnmappedRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", - "rdfs:label": "MeanCoverage", + "rdfs:comment": "Number of read-pairs with at least one end not mapped", + "rdfs:label": "UnmappedRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Coverage", + "sms:displayName": "Unmapped Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIWorkflowLink", + "@id": "bts:LowMapQ", "@type": "rdfs:Class", - "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", - "rdfs:label": "MSIWorkflowLink", + "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", + "rdfs:label": "LowMapQ", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Workflow Link", + "sms:displayName": "LowMapQ", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIScore", + "@id": "bts:MitochondrialRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", - "rdfs:label": "MSIScore", + "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", + "rdfs:label": "MitochondrialRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Score", + "sms:displayName": "Mitochondrial Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIStatus", + "@id": "bts:PassedFilters", "@type": "rdfs:Class", - "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", - "rdfs:label": "MSIStatus", + "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", + "rdfs:label": "PassedFilters", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MSI" - }, - { - "@id": "bts:MSI-low" - }, - { - "@id": "bts:MSI-high" - }, - { - "@id": "bts:MSS" - } - ], - "sms:displayName": "MSI Status", + "sms:displayName": "Passed Filters", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PairsOnDiffCHR", + "@id": "bts:TSSFragments", "@type": "rdfs:Class", - "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", - "rdfs:label": "PairsOnDiffCHR", + "rdfs:comment": "Number of fragments overlapping with TSS regions", + "rdfs:label": "TSSFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pairs On Diff CHR", + "sms:displayName": "TSS Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalUniquelyMapped", + "@id": "bts:DNaseSensitiveRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that map to genome. Integer", - "rdfs:label": "TotalUniquelyMapped", + "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", + "rdfs:label": "DNaseSensitiveRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Uniquely Mapped", + "sms:displayName": "DNase Sensitive Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalUnmappedreads", + "@id": "bts:EnhancerRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that did not map to genome. Integer", - "rdfs:label": "TotalUnmappedreads", + "rdfs:comment": "Number of fragments overlapping enhancer regions", + "rdfs:label": "EnhancerRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Unmapped reads", + "sms:displayName": "Enhancer Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsDuplicated", + "@id": "bts:PromoterRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", - "rdfs:label": "ProportionReadsDuplicated", + "rdfs:comment": "Number of fragments overlapping promoter regions", + "rdfs:label": "PromoterRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Duplicated", + "sms:displayName": "Promoter Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMapped", + "@id": "bts:OnTargetFragments", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", - "rdfs:label": "ProportionReadsMapped", + "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", + "rdfs:label": "OnTargetFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped", + "sms:displayName": "On Target Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionTargetsNoCoverage", + "@id": "bts:BlacklistRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", - "rdfs:label": "ProportionTargetsNoCoverage", + "rdfs:comment": "Number of fragments overlapping blacklisted regions", + "rdfs:label": "BlacklistRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Targets No Coverage", + "sms:displayName": "Blacklist Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionBaseMismatch", + "@id": "bts:PeakRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", - "rdfs:label": "ProportionBaseMismatch", + "rdfs:comment": "Number of fragments overlapping peaks", + "rdfs:label": "PeakRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Base Mismatch", + "sms:displayName": "Peak Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ShortReads", + "@id": "bts:PeakRegionCutsites", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that were too short. Integer", - "rdfs:label": "ShortReads", + "rdfs:comment": "Number of ends of fragments in peak regions", + "rdfs:label": "PeakRegionCutsites", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Short Reads", + "sms:displayName": "Peak Region Cutsites", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Islowestlevel", + "@id": "bts:NucleosomeSignal", "@type": "rdfs:Class", - "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", - "rdfs:label": "Islowestlevel", + "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", + "rdfs:label": "NucleosomeSignal", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel2" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Nucleosome Signal", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleosomePercentile", + "@type": "rdfs:Class", + "rdfs:comment": "Percentile rank of nucleosome score", + "rdfs:label": "NucleosomePercentile", + "rdfs:subClassOf": [ { - "@id": "bts:Yes-Islowestlevel" - }, + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nucleosome Percentile", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TSSEnrichment", + "@type": "rdfs:Class", + "rdfs:comment": "Transcription start site (TSS) enrichment score", + "rdfs:label": "TSSEnrichment", + "rdfs:subClassOf": [ { - "@id": "bts:No" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "Is lowest level", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "TSS Enrichment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel3", + "@id": "bts:TSSPercentile", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq gene expression matrices", - "rdfs:label": "BulkRNA-seqLevel3", + "rdfs:comment": "Percentile rank of TSS score", + "rdfs:label": "TSSPercentile", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "TSS Percentile", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PctReadsinPeaks", + "@type": "rdfs:Class", + "rdfs:comment": "Percentage of reads in peaks", + "rdfs:label": "PctReadsinPeaks", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pct Reads in Peaks", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BlacklistRatio", + "@type": "rdfs:Class", + "rdfs:comment": "Ratio of reads in blacklist regions", + "rdfs:label": "BlacklistRatio", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blacklist Ratio", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SeuratClusters", + "@type": "rdfs:Class", + "rdfs:comment": "Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm", + "rdfs:label": "SeuratClusters", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Seurat Clusters", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NCountRNA", + "@type": "rdfs:Class", + "rdfs:comment": "Total number of fragments in genes", + "rdfs:label": "NCountRNA", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "nCount RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NFeatureRNA", + "@type": "rdfs:Class", + "rdfs:comment": "Number of genes detected in cell", + "rdfs:label": "NFeatureRNA", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "nFeature RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Seqnames", + "@type": "rdfs:Class", + "rdfs:comment": "Chromosome id", + "rdfs:label": "MACS2Seqnames", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Seqnames", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Start", + "@type": "rdfs:Class", + "rdfs:comment": "Genomic starting position in MACS2", + "rdfs:label": "MACS2Start", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Start", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2End", + "@type": "rdfs:Class", + "rdfs:comment": "Genomic ending position in MACS2", + "rdfs:label": "MACS2End", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 End", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Width", + "@type": "rdfs:Class", + "rdfs:comment": "Width of the peak in bases in MACS2", + "rdfs:label": "MACS2Width", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Width", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Strand", + "@type": "rdfs:Class", + "rdfs:comment": "DNA stand aligned with in MACS2", + "rdfs:label": "MACS2Strand", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Strand", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Name", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the peak in MACS2", + "rdfs:label": "MACS2Name", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Score", + "@type": "rdfs:Class", + "rdfs:comment": "Peak score (proportional to q-value) in MACS2", + "rdfs:label": "MACS2Score", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2FoldChange", + "@type": "rdfs:Class", + "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", + "rdfs:label": "MACS2FoldChange", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Fold Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2NegLog10pvalueSummit", + "@type": "rdfs:Class", + "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10pvalueSummit", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Neg Log10 pvalue Summit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2NegLog10qvalueSummit", + "@type": "rdfs:Class", + "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10qvalueSummit", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Neg Log10 qvalue Summit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2RelativeSummitPosition", + "@type": "rdfs:Class", + "rdfs:comment": "Position of the peak summit related to the start position in MACS2", + "rdfs:label": "MACS2RelativeSummitPosition", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Relative Summit Position", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScmC-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Files contain raw scmC-seq data.", + "rdfs:label": "ScmC-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36971,11 +36511,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 3", + "sms:displayName": "scmC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -36989,40 +36529,79 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:PseudoAlignmentUsed" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:DataCategory" + "@id": "bts:ScmCseqRead1" }, { - "@id": "bts:ExpressionUnits" + "@id": "bts:ScmCseqRead2" }, { - "@id": "bts:MatrixType" + "@id": "bts:ScmCseqRead3" }, { - "@id": "bts:FusionGeneDetected" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:FusionGeneIdentity" + "@id": "bts:SingleNucleusBuffer" + }, + { + "@id": "bts:SingleNucleusCapture" + }, + { + "@id": "bts:BisulfiteConversion" + }, + { + "@id": "bts:LibraryLayout" + }, + { + "@id": "bts:NucleusIdentifier" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:MedianFractionofReadsinPeaks" + }, + { + "@id": "bts:MedianPassingReadPercentage" + }, + { + "@id": "bts:PeaksCallingSoftware" + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:ThresholdforMinimumPassingReads" + }, + { + "@id": "bts:TotalNumberofPassingNuclei" + }, + { + "@id": "bts:TotalReads" } ], "sms:validationRules": [] }, { - "@id": "bts:PseudoAlignmentUsed", + "@id": "bts:ScmCseqRead1", "@type": "rdfs:Class", - "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", - "rdfs:label": "PseudoAlignmentUsed", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScmCseqRead1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -37030,24 +36609,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-PseudoAlignmentUsed" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:No" + "@id": "bts:CDNA" } ], - "sms:displayName": "Pseudo Alignment Used", + "sms:displayName": "scmCseq Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExpressionUnits", + "@id": "bts:ScmCseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "How quantities are corrected for gene length", - "rdfs:label": "ExpressionUnits", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScmCseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -37055,36 +36634,49 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TPM" - }, - { - "@id": "bts:RPKM" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:FPKM" - }, + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read2", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScmCseqRead3", + "@type": "rdfs:Class", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScmCseqRead3", + "rdfs:subClassOf": [ { - "@id": "bts:Counts" - }, + "@id": "bts:ScmC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Other" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:NA" + "@id": "bts:CDNA" } ], - "sms:displayName": "Expression Units", + "sms:displayName": "scmCseq Read3", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneDetected", + "@id": "bts:SingleNucleusCapture", "@type": "rdfs:Class", - "rdfs:comment": "Was a fusion gene identified?", - "rdfs:label": "FusionGeneDetected", + "rdfs:comment": "Nuclei isolation method", + "rdfs:label": "SingleNucleusCapture", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -37092,27 +36684,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-FusionGeneDetected" + "@id": "bts:Plates" }, { - "@id": "bts:No" + "@id": "bts:10x" }, { - "@id": "bts:Unknown" + "@id": "bts:Droplet" } ], - "sms:displayName": "Fusion Gene Detected", + "sms:displayName": "Single Nucleus Capture", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneIdentity", + "@id": "bts:BisulfiteConversion", "@type": "rdfs:Class", - "rdfs:comment": "The gene symbols of fused genes.", - "rdfs:label": "FusionGeneIdentity", + "rdfs:comment": "Name of the kit used in bisulfite conversion.", + "rdfs:label": "BisulfiteConversion", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel1" } ], "schema:isPartOf": { @@ -37120,35 +36712,47 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EWS-FLI" + "@id": "bts:ZimoEZDNAMethylationKit" }, { - "@id": "bts:EWS-ERG" + "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" }, { - "@id": "bts:SYT-SSX1" + "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" }, { - "@id": "bts:SYT-SSX2" + "@id": "bts:NEBNextEnzymaticMethyl-seqKit" }, { - "@id": "bts:EWS-WT1" - }, + "@id": "bts:AgilentSureSelectXTMethyl-Seq" + } + ], + "sms:displayName": "Bisulfite Conversion", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PeaksCallingSoftware", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name of peaks calling tool", + "rdfs:label": "PeaksCallingSoftware", + "rdfs:subClassOf": [ { - "@id": "bts:OtherFusionGene" + "@id": "bts:ScATAC-seqLevel1" } ], - "sms:displayName": "Fusion Gene Identity", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Peaks Calling Software", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel1", + "@id": "bts:ScmC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing raw files", - "rdfs:label": "BulkWESLevel1", + "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", + "rdfs:label": "ScmC-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37157,11 +36761,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 1", + "sms:displayName": "scmC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScmC-seqLevel1" } ], "sms:requiresDependency": [ @@ -37175,94 +36779,130 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:GenomicReference" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:ReadLength" + "@id": "bts:IndexFileName" }, { - "@id": "bts:TargetCaptureKit" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:Contamination" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:ContaminationError" }, { - "@id": "bts:AdapterName" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:TotalReads" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:LaneNumber" + "@id": "bts:ShortReads" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ScATAC-seqLevel4", + "@type": "rdfs:Class", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScATAC-seqLevel4", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATAC-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScATAC-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:Filename" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:FileFormat" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:TargetDepth" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:ScATACseqWorkflowType" + }, + { + "@id": "bts:ScATACseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:TargetCaptureKit", + "@id": "bts:ScATACseqWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", - "rdfs:label": "TargetCaptureKit", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScATACseqWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37271,167 +36911,194 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NotApplicable" - }, + "sms:displayName": "scATACseq Workflow Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATACseqWorkflowParametersDescription", + "@type": "rdfs:Class", + "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", + "rdfs:label": "ScATACseqWorkflowParametersDescription", + "rdfs:subClassOf": [ { - "@id": "bts:CustomTargetsFileProvided" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATACseq Workflow Parameters Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScDNA-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Single-cell DNA-seq", + "rdfs:label": "ScDNA-seqLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scDNA-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" + "@id": "bts:Component" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" + "@id": "bts:Filename" }, { - "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" + "@id": "bts:FileFormat" }, { - "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:CustomMSKIMPACTPanel-341Genes" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:CustomMSKIMPACTPanel-410Genes" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:CustomMSKIMPACTPanel-468Genes" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + "@id": "bts:ReadLength" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" + "@id": "bts:AdapterName" }, { - "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" + "@id": "bts:LaneNumber" }, { - "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:FoundationMedicineT5aPanel-322Genes" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:FoundationMedicineT7Panel-429Genes" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" + "@id": "bts:TargetDepth" }, { - "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" + "@id": "bts:ToTrimAdapterSequence" }, { - "@id": "bts:NexteraDNAExome" + "@id": "bts:AdapterContent" }, { - "@id": "bts:NexteraRapidCaptureExomev1.2" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:SeqCapEZHGSCVCRomev2.1" + "@id": "bts:Encoding" }, { - "@id": "bts:SeqCapEZHumanExomev2.0" + "@id": "bts:KmerContent" }, { - "@id": "bts:SeqCapEZHumanExomev3.0" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:SureSelectHumanAllExonv3" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:SureSelectHumanAllExonv4" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:SureSelectHumanAllExonv5" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:SureSelectHumanAllExonv5+UTR" + "@id": "bts:PerSequenceGCContent" }, { - "@id": "bts:TruSeqAmpliconCancerPanel" + "@id": "bts:PerSequenceQualityScore" }, { - "@id": "bts:TruSeqExomeEnrichment-62Mb" + "@id": "bts:PerTileSequenceQuality" }, { - "@id": "bts:TruSeqRNAExome" + "@id": "bts:PercentGCContent" }, { - "@id": "bts:TruSightMyeloidSequencingPanel" + "@id": "bts:SequenceDuplicationLevels" }, { - "@id": "bts:XGenExomeResearchPanelv1.0" + "@id": "bts:SequenceLengthDistribution" }, { - "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" + "@id": "bts:TotalReads" }, { - "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" + "@id": "bts:QCWorkflowType" }, { - "@id": "bts:SureSelectHumanAllExonv6" + "@id": "bts:QCWorkflowVersion" }, { - "@id": "bts:Unknown" + "@id": "bts:QCWorkflowLink" } ], - "sms:displayName": "Target Capture Kit", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel2", + "@id": "bts:ScDNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", - "rdfs:label": "BulkWESLevel2", + "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", + "rdfs:label": "ScDNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37440,11 +37107,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 2", + "sms:displayName": "scDNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkWESLevel1" + "@id": "bts:ScDNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -37463,6 +37130,9 @@ { "@id": "bts:HTANDataFileID" }, + { + "@id": "bts:AlignmentWorkflowUrl" + }, { "@id": "bts:AlignmentWorkflowType" }, @@ -37484,77 +37154,20 @@ { "@id": "bts:AverageReadLength" }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, { "@id": "bts:MeanCoverage" }, { - "@id": "bts:AdapterContent" - }, - { - "@id": "bts:BasicStatistics" - }, - { - "@id": "bts:Encoding" - }, - { - "@id": "bts:OverrepresentedSequences" - }, - { - "@id": "bts:PerBaseNContent" - }, - { - "@id": "bts:PerBaseSequenceContent" - }, - { - "@id": "bts:PerBaseSequenceQuality" - }, - { - "@id": "bts:PerSequenceGCContent" - }, - { - "@id": "bts:PerSequenceQualityScore" - }, - { - "@id": "bts:PerTileSequenceQuality" - }, - { - "@id": "bts:PercentGCContent" - }, - { - "@id": "bts:SequenceDuplicationLevels" - }, - { - "@id": "bts:SequenceLengthDistribution" - }, - { - "@id": "bts:QCWorkflowType" - }, - { - "@id": "bts:QCWorkflowVersion" - }, - { - "@id": "bts:QCWorkflowLink" - }, - { - "@id": "bts:MSIWorkflowLink" - }, - { - "@id": "bts:MSIScore" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:MSIStatus" + "@id": "bts:TotalReads" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:TotalReads" + "@id": "bts:MapQ30" }, { "@id": "bts:TotalUniquelyMapped" @@ -37566,51 +37179,37 @@ "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:ShortReads" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:ShortReads" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:ProportionMitochondrialReads" }, { - "@id": "bts:Islowestlevel" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionCoverage10x", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage10x", - "rdfs:subClassOf": [ + "@id": "bts:Contamination" + }, { - "@id": "bts:Sequencing" + "@id": "bts:ContaminationError" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Coverage 10x", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage30X", + "@id": "bts:ProportionMitochondrialReads", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage30X", + "rdfs:comment": "Proportion of reads mapping to mitochondria.", + "rdfs:label": "ProportionMitochondrialReads", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37619,15 +37218,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 30X", + "sms:displayName": "Proportion Mitochondrial Reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel3", + "@id": "bts:BulkMethylation-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing called variants", - "rdfs:label": "BulkWESLevel3", + "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", + "rdfs:label": "BulkMethylation-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37636,11 +37235,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 3", + "sms:displayName": "Bulk Methylation-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkWESLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -37654,46 +37253,37 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:GermlineVariantsWorkflowURL" - }, - { - "@id": "bts:GermlineVariantsWorkflowType" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:SomaticVariantsWorkflowURL" + "@id": "bts:BisulfiteConversion" }, { - "@id": "bts:SomaticVariantsWorkflowType" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:SomaticVariantsSampleType" + "@id": "bts:ReplicateType" }, { - "@id": "bts:StructuralVariantWorkflowURL" + "@id": "bts:BulkMethylationAssayType" }, { - "@id": "bts:StructuralVariantWorkflowType" + "@id": "bts:TotalDNAInput" } ], "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowURL", + "@id": "bts:ReplicateType", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", - "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", + "rdfs:label": "ReplicateType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37702,18 +37292,29 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Germline Variants Workflow URL", + "schema:rangeIncludes": [ + { + "@id": "bts:Technicalreplicate" + }, + { + "@id": "bts:Biologicalreplicate" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Replicate Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowType", + "@id": "bts:BulkMethylationAssayType", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:comment": "Assay types normally determine genomic coverage", + "rdfs:label": "BulkMethylationAssayType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel1" } ], "schema:isPartOf": { @@ -37721,41 +37322,49 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GATK4" + "@id": "bts:Wholegenome" }, { - "@id": "bts:OtherGermlineVariantsWorkflowType" + "@id": "bts:TargetedGenome" }, { - "@id": "bts:None" + "@id": "bts:BeadchipArray" + } + ], + "sms:displayName": "Bulk Methylation Assay Type", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:TargetedGenome" + }, + { + "@id": "bts:BeadchipArray" } ], - "sms:displayName": "Germline Variants Workflow Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowURL", + "@id": "bts:TotalDNAInput", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", + "rdfs:label": "TotalDNAInput", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylationAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Somatic Variants Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Total DNA Input", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowType", + "@id": "bts:BulkMethylation-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", + "rdfs:label": "BulkMethylation-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37764,208 +37373,118 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Bulk Methylation-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:CaVEMan" + "@id": "bts:BulkMethylation-seqLevel1" }, { - "@id": "bts:GATK4" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:MuTect2" + "@id": "bts:Component" }, { - "@id": "bts:MuSE" + "@id": "bts:Filename" }, { - "@id": "bts:Pindel" + "@id": "bts:FileFormat" }, { - "@id": "bts:SomaticSniper" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:VarScan2" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:OtherSomaticVariantsWorkflowType" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Somatic Variants Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SomaticVariantsSampleType", - "@type": "rdfs:Class", - "rdfs:comment": "Is the sample case or control in somatic variant analysis", - "rdfs:label": "SomaticVariantsSampleType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaseSample" + "@id": "bts:Trimmer" }, { - "@id": "bts:ControlSample" + "@id": "bts:BulkMethylationGenomicReference" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Somatic Variants Sample Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StructuralVariantWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", - "rdfs:label": "StructuralVariantWorkflowURL", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Structural Variant Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StructuralVariantWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "StructuralVariantWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:GenomicReferenceURL" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IndexFileName" + }, { - "@id": "bts:BRASS" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:GATK4" + "@id": "bts:DuplicateRemovalSoftware" }, { - "@id": "bts:CNV" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:CNVkit" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:OtherStructuralVariantWorkflowType" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Structural Variant Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MicroarrayLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", - "rdfs:label": "MicroarrayLevel1", - "rdfs:subClassOf": [ + "@id": "bts:AverageInsertSize" + }, { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microarray Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:AverageReadLength" + }, { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Contamination" + }, { - "@id": "bts:Component" + "@id": "bts:ContaminationError" }, { - "@id": "bts:Filename" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:FileFormat" + "@id": "bts:TotalReads" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:MicroarrayMolecule" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:MicroarrayLabel" + "@id": "bts:ShortReads" }, { - "@id": "bts:MicroarrayValueDefinition" + "@id": "bts:ProportionofMinimumCpGCoverage10X" }, { - "@id": "bts:MicroarrayProtocolAuxiliaryFile" + "@id": "bts:ProportionCoverage30X" } ], "sms:validationRules": [] }, { - "@id": "bts:MicroarrayPlatformID", - "@type": "rdfs:Class", - "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", - "rdfs:label": "MicroarrayPlatformID", - "rdfs:subClassOf": [ - { - "@id": "bts:MicroarrayLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microarray Platform ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match GPL\\d+" - ] - }, - { - "@id": "bts:MicroarrayMolecule", + "@id": "bts:Trimmer", "@type": "rdfs:Class", - "rdfs:comment": "Microarray is measuring this kind of molecule", - "rdfs:label": "MicroarrayMolecule", + "rdfs:comment": "Software used for trimming", + "rdfs:label": "Trimmer", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { @@ -37973,142 +37492,118 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DNA" + "@id": "bts:FASTXtoolkit" }, { - "@id": "bts:RNA" - } - ], - "sms:displayName": "Microarray Molecule", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MicroarrayLabel", - "@type": "rdfs:Class", - "rdfs:comment": "Microarray used this kind of label", - "rdfs:label": "MicroarrayLabel", - "rdfs:subClassOf": [ + "@id": "bts:SolexaQA" + }, { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Btrim" + }, + { + "@id": "bts:Cutadapt" + }, + { + "@id": "bts:Kraken" + }, + { + "@id": "bts:PRINSEQ" + }, + { + "@id": "bts:Adapterremoval" + }, + { + "@id": "bts:TrimGalore!" + }, + { + "@id": "bts:ConDeTri" + }, + { + "@id": "bts:ERNE-FILTER" + }, + { + "@id": "bts:Trimmo-matic" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microarray Label", + "sms:displayName": "Trimmer", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayValueDefinition", + "@id": "bts:BulkMethylationGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "What the provided value signifies", - "rdfs:label": "MicroarrayValueDefinition", + "rdfs:comment": "The human genome reference used in the alignment of reads", + "rdfs:label": "BulkMethylationGenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Value Definition", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MicroarrayProtocolAuxiliaryFile", - "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", - "rdfs:label": "MicroarrayProtocolAuxiliaryFile", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:HG19" + }, + { + "@id": "bts:HG38" + }, + { + "@id": "bts:T2TCHM13" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microarray Protocol Auxiliary File", + "sms:displayName": "Bulk Methylation Genomic Reference", "sms:required": "sms:true", - "sms:validationRules": [ - "regex match syn\\d+" - ] + "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLevel2", + "@id": "bts:DuplicateRemovalSoftware", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", - "rdfs:label": "MicroarrayLevel2", + "rdfs:comment": "Software used for remove duplicate reads", + "rdfs:label": "DuplicateRemovalSoftware", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:MicroarrayLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, + "schema:rangeIncludes": [ { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:Samtoolssort" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:PicardMarkDuplicates" } ], + "sms:displayName": "Duplicate Removal Software", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NormalizationMethod", + "@id": "bts:ProportionofMinimumCpGCoverage10X", "@type": "rdfs:Class", - "rdfs:comment": "Description of Normalization Process", - "rdfs:label": "NormalizationMethod", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", + "rdfs:label": "ProportionofMinimumCpGCoverage10X", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Normalization Method", + "sms:displayName": "Proportion of Minimum CpG Coverage 10X", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel1", + "@id": "bts:BulkMethylation-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", - "rdfs:label": "ScATAC-seqLevel1", + "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", + "rdfs:label": "BulkMethylation-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -38117,9 +37612,12 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 1", + "sms:displayName": "Bulk Methylation-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ + { + "@id": "bts:BulkMethylation-seqLevel2" + }, { "@id": "bts:Biospecimen" } @@ -38135,122 +37633,114 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:DissociationMethod" - }, - { - "@id": "bts:SingleNucleusBuffer" - }, - { - "@id": "bts:SingleCellIsolationMethod" - }, - { - "@id": "bts:TranspositionReaction" + "@id": "bts:DMCCallingTool" }, { - "@id": "bts:ScATACseqLibraryLayout" + "@id": "bts:DMCCallingWorkflowURL" }, { - "@id": "bts:NucleusIdentifier" + "@id": "bts:DMRCallingTool" }, { - "@id": "bts:NucleiBarcodeLength" + "@id": "bts:DMRCallingWorkflowURL" }, { - "@id": "bts:NucleiBarcodeRead" + "@id": "bts:PUC19methylationratio" }, { - "@id": "bts:ScATACseqRead1" + "@id": "bts:Lambdamethylationratio" }, { - "@id": "bts:ScATACseqRead2" + "@id": "bts:DMCdatafileformat" }, { - "@id": "bts:ScATACseqRead3" - }, + "@id": "bts:DMRdatafileFormat" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:DMCCallingTool", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMCCallingTool", + "rdfs:subClassOf": [ { - "@id": "bts:LibraryConstructionMethod" - }, + "@id": "bts:BulkMethylation-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SequencingPlatform" + "@id": "bts:MethylKit" }, { - "@id": "bts:ThresholdforMinimumPassingReads" + "@id": "bts:BSmooth" }, { - "@id": "bts:TotalNumberofPassingNuclei" + "@id": "bts:BiSeq" }, { - "@id": "bts:MedianFractionofReadsinPeaks" + "@id": "bts:MethylSig" }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" + "@id": "bts:DSS" }, { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:MOABS" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:DSS-single" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:Metilene" }, { - "@id": "bts:TotalReads" + "@id": "bts:MACAU" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:MethylDackel" } ], + "sms:displayName": "DMC Calling Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SingleNucleusBuffer", + "@id": "bts:DMCCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation buffer", - "rdfs:label": "SingleNucleusBuffer", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMCCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NIB" - }, - { - "@id": "bts:10x" - }, - { - "@id": "bts:Omni" - }, - { - "@id": "bts:TST" - } - ], - "sms:displayName": "Single Nucleus Buffer", + "sms:displayName": "DMC Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:TranspositionReaction", + "@id": "bts:DMRCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "Name of the transposase, transposon sequences", - "rdfs:label": "TranspositionReaction", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMRCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -38258,126 +37748,123 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Tn5" + "@id": "bts:MethylKit" }, { - "@id": "bts:EZ-Tn5" + "@id": "bts:BSmooth" }, { - "@id": "bts:Tn5-059" + "@id": "bts:BiSeq" }, { - "@id": "bts:NexteraTn5" + "@id": "bts:MethylSig" }, { - "@id": "bts:Diagenode-unloadedApex-Bio" + "@id": "bts:DSS" }, { - "@id": "bts:Diagenode-loadedApex-Bio" + "@id": "bts:MOABS" }, { - "@id": "bts:In-House" + "@id": "bts:DSS-single" + }, + { + "@id": "bts:Metilene" + }, + { + "@id": "bts:MACAU" } ], - "sms:displayName": "Transposition Reaction", + "sms:displayName": "DMR Calling Tool", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqLibraryLayout", + "@id": "bts:DMRCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "ScATACseqLibraryLayout", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMRCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:ScATACseqPairedEnd" - } - ], - "sms:displayName": "scATACseq Library Layout", + "sms:displayName": "DMR Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:NucleusIdentifier", + "@id": "bts:PUC19methylationratio", "@type": "rdfs:Class", - "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", - "rdfs:label": "NucleusIdentifier", + "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", + "rdfs:label": "PUC19methylationratio", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NucleiBarcode" - } - ], - "sms:displayName": "Nucleus Identifier", + "sms:displayName": "pUC19 methylation ratio", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleiBarcodeLength", + "@id": "bts:Lambdamethylationratio", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Length", - "rdfs:label": "NucleiBarcodeLength", + "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", + "rdfs:label": "Lambdamethylationratio", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:NucleiBarcode" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei Barcode Length", + "sms:displayName": "Lambda methylation ratio", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleiBarcodeRead", + "@id": "bts:DMCdatafileformat", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Read", - "rdfs:label": "NucleiBarcodeRead", + "rdfs:comment": "Format of the data files", + "rdfs:label": "DMCdatafileformat", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:NucleiBarcode" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei Barcode Read", + "schema:rangeIncludes": [ + { + "@id": "bts:BED" + }, + { + "@id": "bts:BedGraph" + } + ], + "sms:displayName": "DMC data file format", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead1", + "@id": "bts:DMRdatafileFormat", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScATACseqRead1", + "rdfs:comment": "Format of the data files.", + "rdfs:label": "DMRdatafileFormat", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -38385,70 +37872,84 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" - }, - { - "@id": "bts:SampleIndexandDNAInsert" - }, - { - "@id": "bts:DNAInsert" - }, - { - "@id": "bts:SampleIndex" + "@id": "bts:BED" }, { - "@id": "bts:CellBarcode" + "@id": "bts:BedGraph" } ], - "sms:displayName": "scATACseq Read1", + "sms:displayName": "DMR data file Format", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead2", + "@id": "bts:ImagingLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScATACseqRead2", + "rdfs:comment": "Raw imaging data", + "rdfs:label": "ImagingLevel1", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Imaging Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:Filename" }, { - "@id": "bts:DNAInsert" + "@id": "bts:FileFormat" }, { - "@id": "bts:SampleIndex" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CellBarcode" + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:Pre-processingCompleted" + }, + { + "@id": "bts:Pre-processingRequired" + }, + { + "@id": "bts:Comment" } ], - "sms:displayName": "scATACseq Read2", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead3", + "@id": "bts:ImagingAssayType", "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScATACseqRead3", + "rdfs:comment": "Type of imaging assay", + "rdfs:label": "ImagingAssayType", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -38456,286 +37957,198 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:H&E" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:CyCIF" }, { - "@id": "bts:DNAInsert" + "@id": "bts:T-CyCIF" }, { - "@id": "bts:SampleIndex" + "@id": "bts:IHC" }, { - "@id": "bts:CellBarcode" - } - ], - "sms:displayName": "scATACseq Read3", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ThresholdforMinimumPassingReads", - "@type": "rdfs:Class", - "rdfs:comment": "Threshold for calling cells", - "rdfs:label": "ThresholdforMinimumPassingReads", - "rdfs:subClassOf": [ + "@id": "bts:MIHC" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:MxIF" + }, + { + "@id": "bts:SABER" + }, + { + "@id": "bts:IMC" + }, + { + "@id": "bts:CODEX" + }, + { + "@id": "bts:GeoMX-DSP" + }, + { + "@id": "bts:MIBI" + }, + { + "@id": "bts:MERFISH" + }, + { + "@id": "bts:ExSeq" + }, + { + "@id": "bts:RareCyteOrion" + }, + { + "@id": "bts:NotApplicable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Threshold for Minimum Passing Reads", + "sms:displayName": "Imaging Assay Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofPassingNuclei", + "@id": "bts:SoftwareandVersion", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei sequenced", - "rdfs:label": "TotalNumberofPassingNuclei", + "rdfs:comment": "Name of software used to generate expression values. String", + "rdfs:label": "SoftwareandVersion", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Passing Nuclei", + "sms:displayName": "Software and Version", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinPeaks", + "@id": "bts:CommitSHA", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in peaks (FRIP)", - "rdfs:label": "MedianFractionofReadsinPeaks", + "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", + "rdfs:label": "CommitSHA", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Peaks", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PeaksCallingSoftware" - } - ], + "sms:displayName": "Commit SHA", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", + "@id": "bts:Pre-processingCompleted", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", - "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", + "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingCompleted", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:PeaksCallingSoftware" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MedianPassingReadPercentage", - "@type": "rdfs:Class", - "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", - "rdfs:label": "MedianPassingReadPercentage", - "rdfs:subClassOf": [ + "@id": "bts:Illuminationcorrection" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median Passing Read Percentage", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", - "@type": "rdfs:Class", - "rdfs:comment": "Contamination from mitochondrial sequences", - "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", - "rdfs:subClassOf": [ + "@id": "bts:TileStitching" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Channel/CycleRegistration" + }, + { + "@id": "bts:TMAde-arraying" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", + "sms:displayName": "Pre-processing Completed", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel2", + "@id": "bts:Pre-processingRequired", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", - "rdfs:label": "ScATAC-seqLevel2", + "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingRequired", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:PairsOnDiffCHR" - }, - { - "@id": "bts:TotalReads" - }, - { - "@id": "bts:ProportionReadsMapped" - }, - { - "@id": "bts:MapQ30" - }, - { - "@id": "bts:TotalUniquelyMapped" - }, - { - "@id": "bts:TotalUnmappedreads" - }, - { - "@id": "bts:ProportionReadsDuplicated" - }, - { - "@id": "bts:ShortReads" - }, - { - "@id": "bts:ProportionCoverage10x" - }, + "schema:rangeIncludes": [ { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:Illuminationcorrection" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:TileStitching" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:Channel/CycleRegistration" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:TMAde-arraying" }, { - "@id": "bts:Contamination" + "@id": "bts:None" }, { - "@id": "bts:ContaminationError" + "@id": "bts:Other" } ], + "sms:displayName": "Pre-processing Required", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MapQ30", + "@id": "bts:Comment", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads with Quality >= 30.", - "rdfs:label": "MapQ30", + "rdfs:comment": "Free text field (generally for QC comment)", + "rdfs:label": "Comment", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MapQ30", + "sms:displayName": "Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel3", + "@id": "bts:ImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files containing peak information for cells", - "rdfs:label": "ScATAC-seqLevel3", + "rdfs:comment": "Raw and pre-processed image data", + "rdfs:label": "ImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 3", + "sms:displayName": "Imaging Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:ImagingLevel1" } ], "sms:requiresDependency": [ @@ -38749,792 +38162,1022 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ScATAC-seqObjectID" + "@id": "bts:ChannelMetadataFilename" }, { - "@id": "bts:NCountPeaks" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:NFeaturePeaks" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:TotalRead-Pairs" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:DuplicateRead-Pairs" + "@id": "bts:Microscope" }, { - "@id": "bts:ChimericRead-Pairs" + "@id": "bts:Objective" }, { - "@id": "bts:UnmappedRead-Pairs" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:LowMapQ" + "@id": "bts:LensNA" }, { - "@id": "bts:MitochondrialRead-Pairs" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:PassedFilters" + "@id": "bts:WorkingDistanceUnit" }, { - "@id": "bts:TSSFragments" + "@id": "bts:Immersion" }, { - "@id": "bts:DNaseSensitiveRegionFragments" + "@id": "bts:Pyramid" }, { - "@id": "bts:EnhancerRegionFragments" + "@id": "bts:Zstack" }, { - "@id": "bts:PromoterRegionFragments" + "@id": "bts:Tseries" }, { - "@id": "bts:OnTargetFragments" + "@id": "bts:PassedQC" }, { - "@id": "bts:BlacklistRegionFragments" + "@id": "bts:Comment" }, { - "@id": "bts:PeakRegionFragments" + "@id": "bts:FOVnumber" }, { - "@id": "bts:PeakRegionCutsites" + "@id": "bts:FOVX" }, { - "@id": "bts:NucleosomeSignal" + "@id": "bts:FOVXUnit" }, { - "@id": "bts:NucleosomePercentile" + "@id": "bts:FOVY" }, { - "@id": "bts:TSSEnrichment" + "@id": "bts:FOVYUnit" }, { - "@id": "bts:TSSPercentile" + "@id": "bts:FrameAveraging" }, { - "@id": "bts:PctReadsinPeaks" + "@id": "bts:ImageID" }, { - "@id": "bts:BlacklistRatio" + "@id": "bts:DimensionOrder" }, { - "@id": "bts:SeuratClusters" + "@id": "bts:PhysicalSizeX" }, { - "@id": "bts:NCountRNA" + "@id": "bts:PhysicalSizeXUnit" }, { - "@id": "bts:NFeatureRNA" + "@id": "bts:PhysicalSizeY" }, { - "@id": "bts:MACS2Seqnames" + "@id": "bts:PhysicalSizeYUnit" }, { - "@id": "bts:MACS2Start" + "@id": "bts:PhysicalSizeZ" }, { - "@id": "bts:MACS2End" + "@id": "bts:PhysicalSizeZUnit" }, { - "@id": "bts:MACS2Width" + "@id": "bts:PixelsBigEndian" }, { - "@id": "bts:MACS2Strand" + "@id": "bts:PlaneCount" }, { - "@id": "bts:MACS2Name" + "@id": "bts:SizeC" }, { - "@id": "bts:MACS2Score" + "@id": "bts:SizeT" }, { - "@id": "bts:MACS2FoldChange" + "@id": "bts:SizeX" }, { - "@id": "bts:MACS2NegLog10pvalueSummit" + "@id": "bts:SizeY" }, { - "@id": "bts:MACS2NegLog10qvalueSummit" + "@id": "bts:SizeZ" }, { - "@id": "bts:MACS2RelativeSummitPosition" + "@id": "bts:PixelType" + }, + { + "@id": "bts:MERFISHPositionsFile" + }, + { + "@id": "bts:MERFISHCodebookFile" } ], "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqObjectID", + "@id": "bts:ChannelMetadataFilename", "@type": "rdfs:Class", - "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", - "rdfs:label": "ScATAC-seqObjectID", + "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label": "ChannelMetadataFilename", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel3" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Object ID", - "sms:required": "sms:false", + "sms:displayName": "Channel Metadata Filename", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NCountPeaks", + "@id": "bts:Microscope", "@type": "rdfs:Class", - "rdfs:comment": "Total number of fragments in peaks", - "rdfs:label": "NCountPeaks", + "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", + "rdfs:label": "Microscope", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nCount Peaks", - "sms:required": "sms:false", + "sms:displayName": "Microscope", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NFeaturePeaks", + "@id": "bts:Objective", "@type": "rdfs:Class", - "rdfs:comment": "Number of peaks with at least one read", - "rdfs:label": "NFeaturePeaks", + "rdfs:comment": "Objective", + "rdfs:label": "Objective", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nFeature Peaks", + "sms:displayName": "Objective", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalRead-Pairs", + "@id": "bts:NominalMagnification", "@type": "rdfs:Class", - "rdfs:comment": "Total read-pairs", - "rdfs:label": "TotalRead-Pairs", + "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", + "rdfs:label": "NominalMagnification", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Read-Pairs", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "NominalMagnification", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:DuplicateRead-Pairs", + "@id": "bts:LensNA", "@type": "rdfs:Class", - "rdfs:comment": "Number of duplicate read-pairs", - "rdfs:label": "DuplicateRead-Pairs", + "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label": "LensNA", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Duplicate Read-Pairs", + "sms:displayName": "LensNA", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:ChimericRead-Pairs", + "@id": "bts:WorkingDistance", "@type": "rdfs:Class", - "rdfs:comment": "Number of chimerically mapped read-pairs", - "rdfs:label": "ChimericRead-Pairs", + "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", + "rdfs:label": "WorkingDistance", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Chimeric Read-Pairs", + "sms:displayName": "WorkingDistance", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:UnmappedRead-Pairs", - "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs with at least one end not mapped", - "rdfs:label": "UnmappedRead-Pairs", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:WorkingDistanceUnit" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Unmapped Read-Pairs", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LowMapQ", + "@id": "bts:WorkingDistanceUnit", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", - "rdfs:label": "LowMapQ", + "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LowMapQ", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MitochondrialRead-Pairs", - "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", - "rdfs:label": "MitochondrialRead-Pairs", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mitochondrial Read-Pairs", + "sms:displayName": "WorkingDistanceUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PassedFilters", + "@id": "bts:Immersion", "@type": "rdfs:Class", - "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", - "rdfs:label": "PassedFilters", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Passed Filters", + "schema:rangeIncludes": [ + { + "@id": "bts:Air" + }, + { + "@id": "bts:Oil" + }, + { + "@id": "bts:Water" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Immersion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TSSFragments", + "@id": "bts:Pyramid", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping with TSS regions", - "rdfs:label": "TSSFragments", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Fragments", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Pyramid", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DNaseSensitiveRegionFragments", + "@id": "bts:Zstack", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", - "rdfs:label": "DNaseSensitiveRegionFragments", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DNase Sensitive Region Fragments", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Zstack", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:EnhancerRegionFragments", + "@id": "bts:Tseries", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping enhancer regions", - "rdfs:label": "EnhancerRegionFragments", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Enhancer Region Fragments", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Tseries", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PromoterRegionFragments", + "@id": "bts:PassedQC", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping promoter regions", - "rdfs:label": "PromoterRegionFragments", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Promoter Region Fragments", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelsQC" + } + ], + "sms:displayName": "Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OnTargetFragments", + "@id": "bts:FOVnumber", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", - "rdfs:label": "OnTargetFragments", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "On Target Fragments", + "sms:displayName": "FOV number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:BlacklistRegionFragments", + "@id": "bts:FOVX", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping blacklisted regions", - "rdfs:label": "BlacklistRegionFragments", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blacklist Region Fragments", + "sms:displayName": "FOVX", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:requiresDependency": [ + { + "@id": "bts:FOVXUnit" + } + ], + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:PeakRegionFragments", + "@id": "bts:FOVXUnit", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping peaks", - "rdfs:label": "PeakRegionFragments", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peak Region Fragments", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVXUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeakRegionCutsites", + "@id": "bts:FOVY", "@type": "rdfs:Class", - "rdfs:comment": "Number of ends of fragments in peak regions", - "rdfs:label": "PeakRegionCutsites", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peak Region Cutsites", + "sms:displayName": "FOVY", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:requiresDependency": [ + { + "@id": "bts:FOVYUnit" + } + ], + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:NucleosomeSignal", + "@id": "bts:FOVYUnit", "@type": "rdfs:Class", - "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", - "rdfs:label": "NucleosomeSignal", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleosome Signal", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVYUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleosomePercentile", + "@id": "bts:FrameAveraging", "@type": "rdfs:Class", - "rdfs:comment": "Percentile rank of nucleosome score", - "rdfs:label": "NucleosomePercentile", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleosome Percentile", + "sms:displayName": "Frame Averaging", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TSSEnrichment", + "@id": "bts:ImageID", "@type": "rdfs:Class", - "rdfs:comment": "Transcription start site (TSS) enrichment score", - "rdfs:label": "TSSEnrichment", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Enrichment", - "sms:required": "sms:false", + "sms:displayName": "Image ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TSSPercentile", + "@id": "bts:DimensionOrder", "@type": "rdfs:Class", - "rdfs:comment": "Percentile rank of TSS score", - "rdfs:label": "TSSPercentile", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Percentile", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:XYZCT" + }, + { + "@id": "bts:XYZTC" + }, + { + "@id": "bts:XYCTZ" + }, + { + "@id": "bts:XYCZT" + }, + { + "@id": "bts:XYTZC" + }, + { + "@id": "bts:ZYX" + } + ], + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PctReadsinPeaks", + "@id": "bts:PhysicalSizeX", "@type": "rdfs:Class", - "rdfs:comment": "Percentage of reads in peaks", - "rdfs:label": "PctReadsinPeaks", + "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeX", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pct Reads in Peaks", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeXUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:BlacklistRatio", + "@id": "bts:PhysicalSizeXUnit", "@type": "rdfs:Class", - "rdfs:comment": "Ratio of reads in blacklist regions", - "rdfs:label": "BlacklistRatio", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blacklist Ratio", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeXUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SeuratClusters", + "@id": "bts:PhysicalSizeY", "@type": "rdfs:Class", - "rdfs:comment": "Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm", - "rdfs:label": "SeuratClusters", + "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeY", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Seurat Clusters", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeYUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:NCountRNA", + "@id": "bts:PhysicalSizeYUnit", "@type": "rdfs:Class", - "rdfs:comment": "Total number of fragments in genes", - "rdfs:label": "NCountRNA", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nCount RNA", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NFeatureRNA", + "@id": "bts:PhysicalSizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Number of genes detected in cell", - "rdfs:label": "NFeatureRNA", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeZ", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nFeature RNA", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeZ", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeZUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:MACS2Seqnames", + "@id": "bts:PhysicalSizeZUnit", "@type": "rdfs:Class", - "rdfs:comment": "Chromosome id", - "rdfs:label": "MACS2Seqnames", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeZUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Seqnames", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeZUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2Start", + "@id": "bts:PixelsBigEndian", "@type": "rdfs:Class", - "rdfs:comment": "Genomic starting position in MACS2", - "rdfs:label": "MACS2Start", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Start", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:True" + }, + { + "@id": "bts:False" + } + ], + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2End", + "@id": "bts:PlaneCount", "@type": "rdfs:Class", - "rdfs:comment": "Genomic ending position in MACS2", - "rdfs:label": "MACS2End", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 End", - "sms:required": "sms:false", + "sms:displayName": "PlaneCount", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2Width", + "@id": "bts:SizeC", "@type": "rdfs:Class", - "rdfs:comment": "Width of the peak in bases in MACS2", - "rdfs:label": "MACS2Width", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Width", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeC", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:MACS2Strand", + "@id": "bts:SizeT", "@type": "rdfs:Class", - "rdfs:comment": "DNA stand aligned with in MACS2", - "rdfs:label": "MACS2Strand", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Strand", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeT", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:MACS2Name", + "@id": "bts:SizeX", "@type": "rdfs:Class", - "rdfs:comment": "Name of the peak in MACS2", - "rdfs:label": "MACS2Name", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Name", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeX", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:MACS2Score", + "@id": "bts:SizeY", "@type": "rdfs:Class", - "rdfs:comment": "Peak score (proportional to q-value) in MACS2", - "rdfs:label": "MACS2Score", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Score", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeY", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:MACS2FoldChange", + "@id": "bts:SizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", - "rdfs:label": "MACS2FoldChange", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Fold Change", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeZ", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:MACS2NegLog10pvalueSummit", + "@id": "bts:PixelType", "@type": "rdfs:Class", - "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", - "rdfs:label": "MACS2NegLog10pvalueSummit", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Neg Log10 pvalue Summit", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Int8" + }, + { + "@id": "bts:Int16" + }, + { + "@id": "bts:Int32" + }, + { + "@id": "bts:Uint8" + }, + { + "@id": "bts:Uint16" + }, + { + "@id": "bts:Uint32" + }, + { + "@id": "bts:Float" + }, + { + "@id": "bts:Double" + }, + { + "@id": "bts:Bit" + } + ], + "sms:displayName": "PixelType", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2NegLog10qvalueSummit", + "@id": "bts:MERFISHPositionsFile", "@type": "rdfs:Class", - "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", - "rdfs:label": "MACS2NegLog10qvalueSummit", + "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", + "rdfs:label": "MERFISHPositionsFile", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Neg Log10 qvalue Summit", + "sms:displayName": "MERFISH Positions File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MACS2RelativeSummitPosition", + "@id": "bts:MERFISHCodebookFile", "@type": "rdfs:Class", - "rdfs:comment": "Position of the peak summit related to the start position in MACS2", - "rdfs:label": "MACS2RelativeSummitPosition", + "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", + "rdfs:label": "MERFISHCodebookFile", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Relative Summit Position", + "sms:displayName": "MERFISH Codebook File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScmC-seqLevel1", + "@id": "bts:ImagingLevel3Segmentation", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw scmC-seq data.", - "rdfs:label": "ScmC-seqLevel1", + "rdfs:comment": "Object segmentations", + "rdfs:label": "ImagingLevel3Segmentation", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scmC-seq Level 1", + "sms:displayName": "Imaging Level 3 Segmentation", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ImagingLevel2" } ], "sms:requiresDependency": [ @@ -39548,79 +39191,40 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:ScmCseqRead1" - }, - { - "@id": "bts:ScmCseqRead2" - }, - { - "@id": "bts:ScmCseqRead3" - }, - { - "@id": "bts:SingleCellIsolationMethod" - }, - { - "@id": "bts:SingleNucleusBuffer" - }, - { - "@id": "bts:SingleNucleusCapture" - }, - { - "@id": "bts:BisulfiteConversion" - }, - { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:NucleusIdentifier" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:TechnicalReplicateGroup" - }, - { - "@id": "bts:MedianFractionofReadsinPeaks" - }, - { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:ImagingSegmentationDataType" }, { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:Parameterfile" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:ThresholdforMinimumPassingReads" + "@id": "bts:CommitSHA" }, { - "@id": "bts:TotalNumberofPassingNuclei" + "@id": "bts:ImagingObjectClass" }, { - "@id": "bts:TotalReads" + "@id": "bts:NumberofObjects" } ], "sms:validationRules": [] }, { - "@id": "bts:ScmCseqRead1", + "@id": "bts:ImagingSegmentationDataType", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScmCseqRead1", + "rdfs:comment": "Specifies how the segmentation is stored", + "rdfs:label": "ImagingSegmentationDataType", "rdfs:subClassOf": [ { - "@id": "bts:ScmC-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -39628,102 +39232,50 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:Mask" }, { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "scmCseq Read1", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScmCseqRead2", - "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScmCseqRead2", - "rdfs:subClassOf": [ - { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:Outline" }, { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "scmCseq Read2", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScmCseqRead3", - "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScmCseqRead3", - "rdfs:subClassOf": [ - { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Polygon" + }, { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:ProbabilityMap" }, { - "@id": "bts:CDNA" + "@id": "bts:Point" } ], - "sms:displayName": "scmCseq Read3", + "sms:displayName": "Imaging Segmentation Data Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SingleNucleusCapture", + "@id": "bts:Parameterfile", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation method", - "rdfs:label": "SingleNucleusCapture", + "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", + "rdfs:label": "Parameterfile", "rdfs:subClassOf": [ { - "@id": "bts:ScmC-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Plates" - }, - { - "@id": "bts:10x" - }, - { - "@id": "bts:Droplet" - } - ], - "sms:displayName": "Single Nucleus Capture", + "sms:displayName": "Parameter file", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BisulfiteConversion", + "@id": "bts:ImagingObjectClass", "@type": "rdfs:Class", - "rdfs:comment": "Name of the kit used in bisulfite conversion.", - "rdfs:label": "BisulfiteConversion", + "rdfs:comment": "Defines the structure that the mask delineates", + "rdfs:label": "ImagingObjectClass", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -39731,60 +39283,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ZimoEZDNAMethylationKit" + "@id": "bts:Nucleus" }, { - "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" + "@id": "bts:Cytoplasm" }, { - "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" + "@id": "bts:Plasmamembrane" }, { - "@id": "bts:NEBNextEnzymaticMethyl-seqKit" + "@id": "bts:Wholecell" }, { - "@id": "bts:AgilentSureSelectXTMethyl-Seq" + "@id": "bts:Spot" + }, + { + "@id": "bts:ImagingObjectClassOther" } ], - "sms:displayName": "Bisulfite Conversion", + "sms:displayName": "Imaging Object Class", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:PeaksCallingSoftware", + "@id": "bts:NumberofObjects", "@type": "rdfs:Class", - "rdfs:comment": "Generic name of peaks calling tool", - "rdfs:label": "PeaksCallingSoftware", + "rdfs:comment": "The number of objects (eg cells) described", + "rdfs:label": "NumberofObjects", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peaks Calling Software", + "sms:displayName": "Number of Objects", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:ScmC-seqLevel2", + "@id": "bts:ImagingLevel3Image", "@type": "rdfs:Class", - "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", - "rdfs:label": "ScmC-seqLevel2", + "rdfs:comment": "Quality controlled imaging data", + "rdfs:label": "ImagingLevel3Image", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scmC-seq Level 2", + "sms:displayName": "Imaging Level 3 Image", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScmC-seqLevel1" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ImagingLevel2" } ], "sms:requiresDependency": [ @@ -39798,339 +39360,203 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Contamination" + "@id": "bts:HTANParentChannelMetadataID" }, { - "@id": "bts:ContaminationError" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:TotalReads" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:Microscope" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:Objective" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:LensNA" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:Immersion" }, { - "@id": "bts:ShortReads" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScATAC-seqLevel4", - "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScATAC-seqLevel4", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATAC-seq Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScATAC-seqLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:Pyramid" }, { - "@id": "bts:Filename" + "@id": "bts:Zstack" }, { - "@id": "bts:FileFormat" + "@id": "bts:Tseries" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:PassedQC" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Comment" }, { - "@id": "bts:ScATACseqWorkflowType" + "@id": "bts:FOVnumber" }, { - "@id": "bts:ScATACseqWorkflowParametersDescription" + "@id": "bts:FOVX" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:FOVY" }, { - "@id": "bts:WorkflowLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScATACseqWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:FrameAveraging" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqWorkflowParametersDescription", + "@id": "bts:HTANParentChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", - "rdfs:label": "ScATACseqWorkflowParametersDescription", + "rdfs:comment": "HTAN ID for a level 3 channels table.", + "rdfs:label": "HTANParentChannelMetadataID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel4" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATACseq Workflow Parameters Description", + "sms:displayName": "HTAN Parent Channel Metadata ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScDNA-seqLevel1", + "@id": "bts:ImagingLevel3Channels", "@type": "rdfs:Class", - "rdfs:comment": "Single-cell DNA-seq", - "rdfs:label": "ScDNA-seqLevel1", + "rdfs:comment": "Channel-level Metadata Attributes", + "rdfs:label": "ImagingLevel3Channels", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scDNA-seq Level 1", + "sms:displayName": "Imaging Level 3 Channels", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], "sms:requiresDependency": [ { - "@id": "bts:Component" + "@id": "bts:HTANChannelMetadataID" }, { - "@id": "bts:Filename" + "@id": "bts:ChannelID" }, { - "@id": "bts:FileFormat" + "@id": "bts:ChannelName" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:CycleNumber" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:SubCycleNumber" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:AntibodyRole" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:TargetName" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:AntibodyName" }, { - "@id": "bts:ReadLength" + "@id": "bts:RRIDidentifier" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:Fluorophore" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:Clone" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:Lot" }, { - "@id": "bts:AdapterName" + "@id": "bts:Vendor" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:BaseCallerName" - }, - { - "@id": "bts:BaseCallerVersion" - }, - { - "@id": "bts:FlowCellBarcode" - }, - { - "@id": "bts:FragmentMaximumLength" - }, - { - "@id": "bts:FragmentMeanLength" - }, - { - "@id": "bts:FragmentMinimumLength" - }, - { - "@id": "bts:FragmentStandardDeviationLength" - }, - { - "@id": "bts:LaneNumber" - }, - { - "@id": "bts:LibraryStrand" - }, - { - "@id": "bts:MultiplexBarcode" - }, - { - "@id": "bts:SizeSelectionRange" - }, - { - "@id": "bts:TargetDepth" - }, - { - "@id": "bts:ToTrimAdapterSequence" - }, - { - "@id": "bts:AdapterContent" - }, - { - "@id": "bts:BasicStatistics" - }, - { - "@id": "bts:Encoding" - }, - { - "@id": "bts:KmerContent" - }, - { - "@id": "bts:OverrepresentedSequences" - }, - { - "@id": "bts:PerBaseNContent" - }, - { - "@id": "bts:PerBaseSequenceContent" - }, - { - "@id": "bts:PerBaseSequenceQuality" - }, - { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:ExcitationWavelength" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:EmissionWavelength" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:ExcitationBandwidth" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:EmissionBandwidth" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:MetalIsotopeElement" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:MetalIsotopeMass" }, { - "@id": "bts:TotalReads" + "@id": "bts:OligoBarcodeUpperStrand" }, { - "@id": "bts:QCWorkflowType" + "@id": "bts:OligoBarcodeLowerStrand" }, { - "@id": "bts:QCWorkflowVersion" + "@id": "bts:Dilution" }, { - "@id": "bts:QCWorkflowLink" + "@id": "bts:Concentration" } ], "sms:validationRules": [] }, { - "@id": "bts:ScDNA-seqLevel2", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", - "rdfs:label": "ScDNA-seqLevel2", + "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scDNA-seq Level 2", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScDNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -40141,171 +39567,122 @@ "@id": "bts:Filename" }, { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:RunID" }, { - "@id": "bts:IndexFileName" + "@id": "bts:FileFormat" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:SpatialRead1" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:SpatialRead2" }, { - "@id": "bts:TotalReads" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:MapQ30" + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:EndBias" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:ReverseTranscriptionPrimer" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:ShortReads" + "@id": "bts:CaptureArea" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:SlideVersion" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:SlideID" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:ImageRe-orientation" }, { - "@id": "bts:ProportionMitochondrialReads" + "@id": "bts:PermeabilizationTime" }, { - "@id": "bts:Contamination" + "@id": "bts:RIN" }, { - "@id": "bts:ContaminationError" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionMitochondrialReads", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of reads mapping to mitochondria.", - "rdfs:label": "ProportionMitochondrialReads", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:DV200" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Mitochondrial Reads", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel1", + "@id": "bts:CaptureArea", "@type": "rdfs:Class", - "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", - "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", + "rdfs:label": "CaptureArea", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:A" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:B" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:C" }, { - "@id": "bts:BisulfiteConversion" + "@id": "bts:D" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:A1" }, { - "@id": "bts:ReplicateType" + "@id": "bts:B1" }, { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:C1" }, { - "@id": "bts:TotalDNAInput" + "@id": "bts:D1" } ], + "sms:displayName": "Capture Area", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReplicateType", + "@id": "bts:SlideVersion", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", - "rdfs:label": "ReplicateType", + "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "rdfs:label": "SlideVersion", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -40313,93 +39690,99 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Technicalreplicate" + "@id": "bts:V1" }, { - "@id": "bts:Biologicalreplicate" + "@id": "bts:V2" }, { - "@id": "bts:NotApplicable" + "@id": "bts:V3" + }, + { + "@id": "bts:V4" } ], - "sms:displayName": "Replicate Type", - "sms:required": "sms:true", + "sms:displayName": "Slide Version", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationAssayType", + "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "Assay types normally determine genomic coverage", - "rdfs:label": "BulkMethylationAssayType", + "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", + "rdfs:label": "SlideID", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Wholegenome" - }, - { - "@id": "bts:TargetedGenome" - }, + "sms:displayName": "Slide ID", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImageRe-orientation", + "@type": "rdfs:Class", + "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", + "rdfs:label": "ImageRe-orientation", + "rdfs:subClassOf": [ { - "@id": "bts:BeadchipArray" + "@id": "bts:SpatialTranscriptomics" } ], - "sms:displayName": "Bulk Methylation Assay Type", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:TargetedGenome" + "@id": "bts:TRUE" }, { - "@id": "bts:BeadchipArray" + "@id": "bts:FALSE" } ], + "sms:displayName": "Image Re-orientation", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalDNAInput", + "@id": "bts:PermeabilizationTime", "@type": "rdfs:Class", - "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", - "rdfs:label": "TotalDNAInput", + "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", + "rdfs:label": "PermeabilizationTime", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total DNA Input", + "sms:displayName": "Permeabilization Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel2", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", - "rdfs:label": "BulkMethylation-seqLevel2", + "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 2", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkMethylation-seqLevel1" - }, - { - "@id": "bts:Biospecimen" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -40412,6 +39795,9 @@ { "@id": "bts:FileFormat" }, + { + "@id": "bts:Checksum" + }, { "@id": "bts:HTANParentDataFileID" }, @@ -40419,91 +39805,132 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowUrl" + "@id": "bts:UMITag" }, { - "@id": "bts:Trimmer" + "@id": "bts:WhitelistSpatialBarcodeFileLink" }, { - "@id": "bts:BulkMethylationGenomicReference" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:AppliedHardTrimming" }, { - "@id": "bts:IndexFileName" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:DuplicateRemovalSoftware" + "@id": "bts:GenomicReference" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:RunID" }, { - "@id": "bts:AverageReadLength" - }, + "@id": "bts:CaptureArea" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:WhitelistSpatialBarcodeFileLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", + "rdfs:label": "WhitelistSpatialBarcodeFileLink", + "rdfs:subClassOf": [ { - "@id": "bts:Contamination" + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Whitelist Spatial Barcode File Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "@type": "rdfs:Class", + "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" }, { - "@id": "bts:ContaminationError" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:Filename" }, { - "@id": "bts:TotalReads" + "@id": "bts:FileFormat" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:RunID" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:VisiumFileType" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:SlideID" }, { - "@id": "bts:ShortReads" + "@id": "bts:CaptureArea" }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:WorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:Trimmer", + "@id": "bts:VisiumFileType", "@type": "rdfs:Class", - "rdfs:comment": "Software used for trimming", - "rdfs:label": "Trimmer", + "rdfs:comment": "The file type generated for the visium experiment.", + "rdfs:label": "VisiumFileType", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -40511,134 +39938,79 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FASTXtoolkit" + "@id": "bts:Referencepng" }, { - "@id": "bts:SolexaQA" + "@id": "bts:Referencejpg" }, { - "@id": "bts:Btrim" + "@id": "bts:Jsonscalefactors" }, { - "@id": "bts:Cutadapt" + "@id": "bts:Probedatasetcsv" }, { - "@id": "bts:Kraken" + "@id": "bts:Qcresulthtml" }, { - "@id": "bts:PRINSEQ" + "@id": "bts:Filteredmex" }, { - "@id": "bts:Adapterremoval" + "@id": "bts:Unfilteredmex" }, { - "@id": "bts:TrimGalore!" + "@id": "bts:TissuePositions" }, { - "@id": "bts:ConDeTri" + "@id": "bts:Barcodes" }, { - "@id": "bts:ERNE-FILTER" + "@id": "bts:Features" }, { - "@id": "bts:Trimmo-matic" - } - ], - "sms:displayName": "Trimmer", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkMethylationGenomicReference", - "@type": "rdfs:Class", - "rdfs:comment": "The human genome reference used in the alignment of reads", - "rdfs:label": "BulkMethylationGenomicReference", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:HG19" + "@id": "bts:Fiducialimagepng" }, { - "@id": "bts:HG38" + "@id": "bts:Fiducialimagejpg" }, { - "@id": "bts:T2TCHM13" - } - ], - "sms:displayName": "Bulk Methylation Genomic Reference", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DuplicateRemovalSoftware", - "@type": "rdfs:Class", - "rdfs:comment": "Software used for remove duplicate reads", - "rdfs:label": "DuplicateRemovalSoftware", - "rdfs:subClassOf": [ + "@id": "bts:Detectedimagepng" + }, { - "@id": "bts:BulkMethylation-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Detectedjpg" + }, { - "@id": "bts:Samtoolssort" + "@id": "bts:Highresimage" }, { - "@id": "bts:PicardMarkDuplicates" + "@id": "bts:Lowresimage" } ], - "sms:displayName": "Duplicate Removal Software", + "sms:displayName": "Visium File Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", - "rdfs:label": "ProportionofMinimumCpGCoverage10X", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion of Minimum CpG Coverage 10X", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkMethylation-seqLevel3", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", - "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 3", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" }, { - "@id": "bts:Biospecimen" + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" } ], "sms:requiresDependency": [ @@ -40651,6 +40023,9 @@ { "@id": "bts:FileFormat" }, + { + "@id": "bts:HTANParentBiospecimenID" + }, { "@id": "bts:HTANParentDataFileID" }, @@ -40658,1532 +40033,1259 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:DMCCallingTool" + "@id": "bts:RunID" }, { - "@id": "bts:DMCCallingWorkflowURL" + "@id": "bts:VisiumFileType" }, { - "@id": "bts:DMRCallingTool" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:DMRCallingWorkflowURL" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:PUC19methylationratio" + "@id": "bts:CaptureArea" }, { - "@id": "bts:Lambdamethylationratio" + "@id": "bts:Spotsundertissue" }, { - "@id": "bts:DMCdatafileformat" + "@id": "bts:MeanReadsperSpatialSpot" }, { - "@id": "bts:DMRdatafileFormat" + "@id": "bts:MedianNumberGenesperSpatialSpot" + }, + { + "@id": "bts:SequencingSaturation" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:ProportionReadsMappedtoTranscriptome" + }, + { + "@id": "bts:MedianUMICountsperSpot" } ], "sms:validationRules": [] }, { - "@id": "bts:DMCCallingTool", + "@id": "bts:Spotsundertissue", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMCCallingTool", + "rdfs:comment": "The number of barcodes associated with a spot under tissue.", + "rdfs:label": "Spotsundertissue", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" - }, - { - "@id": "bts:MethylSig" - }, - { - "@id": "bts:DSS" - }, - { - "@id": "bts:MOABS" - }, - { - "@id": "bts:DSS-single" - }, - { - "@id": "bts:Metilene" - }, + "sms:displayName": "Spots under tissue", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:MeanReadsperSpatialSpot", + "@type": "rdfs:Class", + "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", + "rdfs:label": "MeanReadsperSpatialSpot", + "rdfs:subClassOf": [ { - "@id": "bts:MACAU" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mean Reads per Spatial Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:SequencingSaturation", + "@type": "rdfs:Class", + "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", + "rdfs:label": "SequencingSaturation", + "rdfs:subClassOf": [ { - "@id": "bts:MethylDackel" + "@id": "bts:SpatialTranscriptomics" } ], - "sms:displayName": "DMC Calling Tool", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sequencing Saturation", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMCCallingWorkflowURL", + "@id": "bts:ProportionReadsMappedtoTranscriptome", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMCCallingWorkflowURL", + "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", + "rdfs:label": "ProportionReadsMappedtoTranscriptome", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DMC Calling Workflow URL", + "sms:displayName": "Proportion Reads Mapped to Transcriptome", "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] + "sms:validationRules": [] }, { - "@id": "bts:DMRCallingTool", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMRCallingTool", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:MethylKit" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:BSmooth" + "@id": "bts:Filename" }, { - "@id": "bts:BiSeq" + "@id": "bts:FileFormat" }, { - "@id": "bts:MethylSig" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:DSS" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:MOABS" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:DSS-single" + "@id": "bts:RunID" }, { - "@id": "bts:Metilene" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:MACAU" + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:VisiumWorkflowType" + }, + { + "@id": "bts:VisiumWorkflowParametersDescription" } ], - "sms:displayName": "DMR Calling Tool", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMRCallingWorkflowURL", + "@id": "bts:VisiumWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMRCallingWorkflowURL", + "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", + "rdfs:label": "VisiumWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DMR Calling Workflow URL", + "sms:displayName": "Visium Workflow Type", "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] + "sms:validationRules": [] }, { - "@id": "bts:PUC19methylationratio", + "@id": "bts:VisiumWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", - "rdfs:label": "PUC19methylationratio", + "rdfs:comment": "Parameters used to run the workflow..", + "rdfs:label": "VisiumWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "pUC19 methylation ratio", + "sms:displayName": "Visium Workflow Parameters Description", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Lambdamethylationratio", + "@id": "bts:Referencepng", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", - "rdfs:label": "Lambdamethylationratio", + "rdfs:comment": "TBD", + "rdfs:label": "Referencepng", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lambda methylation ratio", - "sms:required": "sms:true", + "sms:displayName": "reference png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMCdatafileformat", + "@id": "bts:Referencejpg", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files", - "rdfs:label": "DMCdatafileformat", + "rdfs:comment": "TBD", + "rdfs:label": "Referencejpg", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, - { - "@id": "bts:BedGraph" - } - ], - "sms:displayName": "DMC data file format", - "sms:required": "sms:true", + "sms:displayName": "reference jpg", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMRdatafileFormat", + "@id": "bts:Jsonscalefactors", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files.", - "rdfs:label": "DMRdatafileFormat", + "rdfs:comment": "TBD", + "rdfs:label": "Jsonscalefactors", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, - { - "@id": "bts:BedGraph" - } - ], - "sms:displayName": "DMR data file Format", - "sms:required": "sms:true", + "sms:displayName": "json scale factors", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel1", + "@id": "bts:Probedatasetcsv", "@type": "rdfs:Class", - "rdfs:comment": "Raw imaging data", - "rdfs:label": "ImagingLevel1", + "rdfs:comment": "TBD", + "rdfs:label": "Probedatasetcsv", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 1", + "sms:displayName": "probe dataset csv", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:CommitSHA" - }, - { - "@id": "bts:Pre-processingCompleted" - }, - { - "@id": "bts:Pre-processingRequired" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:Qcresulthtml", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Qcresulthtml", + "rdfs:subClassOf": [ { - "@id": "bts:Comment" + "@id": "bts:VisiumFileType" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "qc result html", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingAssayType", + "@id": "bts:Filteredmex", "@type": "rdfs:Class", - "rdfs:comment": "Type of imaging assay", - "rdfs:label": "ImagingAssayType", + "rdfs:comment": "TBD", + "rdfs:label": "Filteredmex", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:H&E" - }, - { - "@id": "bts:CyCIF" - }, - { - "@id": "bts:T-CyCIF" - }, - { - "@id": "bts:IHC" - }, - { - "@id": "bts:MIHC" - }, - { - "@id": "bts:MxIF" - }, - { - "@id": "bts:SABER" - }, - { - "@id": "bts:IMC" - }, - { - "@id": "bts:CODEX" - }, - { - "@id": "bts:GeoMX-DSP" - }, - { - "@id": "bts:MIBI" - }, - { - "@id": "bts:MERFISH" - }, - { - "@id": "bts:ExSeq" - }, - { - "@id": "bts:RareCyteOrion" - }, + "sms:displayName": "filtered mex", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Unfilteredmex", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Unfilteredmex", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:VisiumFileType" } ], - "sms:displayName": "Imaging Assay Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "unfiltered mex", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SoftwareandVersion", + "@id": "bts:TissuePositions", "@type": "rdfs:Class", - "rdfs:comment": "Name of software used to generate expression values. String", - "rdfs:label": "SoftwareandVersion", + "rdfs:comment": "TBD", + "rdfs:label": "TissuePositions", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Software and Version", - "sms:required": "sms:true", + "sms:displayName": "tissue_positions", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CommitSHA", + "@id": "bts:Barcodes", "@type": "rdfs:Class", - "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", - "rdfs:label": "CommitSHA", + "rdfs:comment": "TBD", + "rdfs:label": "Barcodes", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Commit SHA", + "sms:displayName": "barcodes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingCompleted", + "@id": "bts:Features", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingCompleted", + "rdfs:comment": "TBD", + "rdfs:label": "Features", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, + "sms:displayName": "features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Fiducialimagepng", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Fiducialimagepng", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:VisiumFileType" } ], - "sms:displayName": "Pre-processing Completed", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "fiducial image png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingRequired", + "@id": "bts:Fiducialimagejpg", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingRequired", + "rdfs:comment": "TBD", + "rdfs:label": "Fiducialimagejpg", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, + "sms:displayName": "fiducial image jpg", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Detectedimagepng", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Detectedimagepng", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:VisiumFileType" } ], - "sms:displayName": "Pre-processing Required", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "detected image png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Comment", + "@id": "bts:Detectedjpg", "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", + "rdfs:comment": "TBD", + "rdfs:label": "Detectedjpg", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Comment", + "sms:displayName": "detected jpg", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel2", + "@id": "bts:Highresimage", "@type": "rdfs:Class", - "rdfs:comment": "Raw and pre-processed image data", - "rdfs:label": "ImagingLevel2", + "rdfs:comment": "TBD", + "rdfs:label": "Highresimage", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 2", + "sms:displayName": "high res image", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:Lowresimage", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Lowresimage", + "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:Microscope" - }, - { - "@id": "bts:Objective" - }, - { - "@id": "bts:NominalMagnification" - }, - { - "@id": "bts:LensNA" - }, - { - "@id": "bts:WorkingDistance" - }, - { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:Immersion" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:Comment" - }, - { - "@id": "bts:FOVnumber" - }, - { - "@id": "bts:FOVX" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVY" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:FrameAveraging" - }, - { - "@id": "bts:ImageID" - }, - { - "@id": "bts:DimensionOrder" - }, - { - "@id": "bts:PhysicalSizeX" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeY" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZ" - }, - { - "@id": "bts:PhysicalSizeZUnit" - }, - { - "@id": "bts:PixelsBigEndian" - }, - { - "@id": "bts:PlaneCount" - }, - { - "@id": "bts:SizeC" - }, - { - "@id": "bts:SizeT" - }, - { - "@id": "bts:SizeX" - }, - { - "@id": "bts:SizeY" - }, - { - "@id": "bts:SizeZ" - }, - { - "@id": "bts:PixelType" - }, - { - "@id": "bts:MERFISHPositionsFile" - }, - { - "@id": "bts:MERFISHCodebookFile" + "@id": "bts:VisiumFileType" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "low res image", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChannelMetadataFilename", + "@id": "bts:A", "@type": "rdfs:Class", - "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label": "ChannelMetadataFilename", + "rdfs:comment": "TBD", + "rdfs:label": "A", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Metadata Filename", - "sms:required": "sms:true", + "sms:displayName": "A", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Microscope", + "@id": "bts:B", "@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", + "rdfs:comment": "TBD", + "rdfs:label": "B", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", + "sms:displayName": "B", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Objective", + "@id": "bts:C", "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", + "rdfs:comment": "TBD", + "rdfs:label": "C", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Objective", + "sms:displayName": "C", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NominalMagnification", + "@id": "bts:D", "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", + "rdfs:comment": "TBD", + "rdfs:label": "D", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "D", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:LensNA", + "@id": "bts:A1", "@type": "rdfs:Class", - "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", - "rdfs:label": "LensNA", + "rdfs:comment": "TBD", + "rdfs:label": "A1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LensNA", + "sms:displayName": "A1", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:WorkingDistance", + "@id": "bts:B1", "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", + "rdfs:comment": "TBD", + "rdfs:label": "B1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "WorkingDistance", + "sms:displayName": "B1", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:WorkingDistanceUnit" - } - ], "sms:validationRules": [] }, { - "@id": "bts:WorkingDistanceUnit", + "@id": "bts:C1", "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", + "rdfs:comment": "TBD", + "rdfs:label": "C1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", + "sms:displayName": "C1", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Immersion", + "@id": "bts:D1", "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", + "rdfs:comment": "TBD", + "rdfs:label": "D1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CaptureArea" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Air" - }, - { - "@id": "bts:Oil" - }, - { - "@id": "bts:Water" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", + "sms:displayName": "D1", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pyramid", + "@id": "bts:V1", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", + "rdfs:comment": "TBD", + "rdfs:label": "V1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SlideVersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", + "sms:displayName": "V1", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zstack", + "@id": "bts:V2", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", + "rdfs:comment": "TBD", + "rdfs:label": "V2", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SlideVersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Zstack", - "sms:required": "sms:true", + "sms:displayName": "V2", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tseries", + "@id": "bts:V3", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", + "rdfs:comment": "TBD", + "rdfs:label": "V3", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SlideVersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Tseries", - "sms:required": "sms:true", + "sms:displayName": "V3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PassedQC", + "@id": "bts:V4", "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", + "rdfs:comment": "TBD", + "rdfs:label": "V4", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SlideVersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", + "sms:displayName": "V4", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVnumber", + "@id": "bts:TRUE", "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", + "rdfs:comment": "TBD", + "rdfs:label": "TRUE", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ImageRe-orientation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOV number", + "sms:displayName": "TRUE", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVX", + "@id": "bts:FALSE", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", + "rdfs:comment": "TBD", + "rdfs:label": "FALSE", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ImageRe-orientation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVX", + "sms:displayName": "FALSE", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVXUnit", + "@id": "bts:SpatialBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", + "rdfs:comment": "Length of spot barcode read (in bp): number", + "rdfs:label": "SpatialBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Spatial Barcode Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CDNA", + "@type": "rdfs:Class", + "rdfs:comment": "Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase", + "rdfs:label": "CDNA", + "rdfs:subClassOf": [ { - "@id": "bts:Cm" + "@id": "bts:Sequencing" }, { - "@id": "bts:Mm" + "@id": "bts:SpatialRead1" }, { - "@id": "bts:Μm" + "@id": "bts:SpatialRead2" }, { - "@id": "bts:Nm" + "@id": "bts:ScmCseqRead1" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVY", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", - "rdfs:subClassOf": [ + "@id": "bts:ScmCseqRead2" + }, { - "@id": "bts:Imaging" + "@id": "bts:ScmCseqRead3" + }, + { + "@id": "bts:Read1" + }, + { + "@id": "bts:Read2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVY", + "sms:displayName": "cDNA", "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:FOVYUnit" + "@id": "bts:CDNAOffset" + }, + { + "@id": "bts:CDNALength" } ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVYUnit", + "@id": "bts:Smart-seq2", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", + "rdfs:comment": "TBD", + "rdfs:label": "Smart-seq2", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVYUnit", + "sms:displayName": "Smart-seq2", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FrameAveraging", + "@id": "bts:Smart-SeqV4", "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label": "FrameAveraging", + "rdfs:comment": "TBD", + "rdfs:label": "Smart-SeqV4", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Frame Averaging", + "sms:displayName": "Smart-SeqV4", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageID", + "@id": "bts:10xV1.0", "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", + "rdfs:comment": "TBD", + "rdfs:label": "10xV1.0", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", + "sms:displayName": "10xV1.0", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DimensionOrder", + "@id": "bts:10xV1.1", "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", + "rdfs:comment": "TBD", + "rdfs:label": "10xV1.1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:XYZCT" - }, - { - "@id": "bts:XYZTC" - }, - { - "@id": "bts:XYCTZ" - }, - { - "@id": "bts:XYCZT" - }, - { - "@id": "bts:XYTZC" - }, - { - "@id": "bts:ZYX" - } - ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", + "sms:displayName": "10xV1.1", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeX", + "@id": "bts:10xV2", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeX", + "rdfs:comment": "TBD", + "rdfs:label": "10xV2", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeXUnit" - } - ], + "sms:displayName": "10xV2", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeXUnit", + "@id": "bts:10xV3", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", + "rdfs:comment": "TBD", + "rdfs:label": "10xV3", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", + "sms:displayName": "10xV3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeY", + "@id": "bts:10xV3.1", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeY", + "rdfs:comment": "TBD", + "rdfs:label": "10xV3.1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeYUnit" - } - ], + "sms:displayName": "10xV3.1", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:Drop-seq", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "TBD", + "rdfs:label": "Drop-seq", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, + "sms:displayName": "Drop-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InDropsV2", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "InDropsV2", + "rdfs:subClassOf": [ { - "@id": "bts:Nm" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:Å" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "inDropsV2", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZ", + "@id": "bts:InDropsV3", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeZ", + "rdfs:comment": "TBD", + "rdfs:label": "InDropsV3", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeZ", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeZUnit" - } - ], + "sms:displayName": "inDropsV3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZUnit", + "@id": "bts:TruDrop", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeZUnit", + "rdfs:comment": "TBD", + "rdfs:label": "TruDrop", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, + "sms:displayName": "TruDrop", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NexteraXT", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NexteraXT", + "rdfs:subClassOf": [ { - "@id": "bts:Nm" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:Å" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:displayName": "PhysicalSizeZUnit", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nextera XT", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PixelsBigEndian", + "@id": "bts:UMIBarcodeOffset", "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", + "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", + "rdfs:label": "UMIBarcodeOffset", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Pixels BigEndian", + "sms:displayName": "UMI Barcode Offset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PlaneCount", + "@id": "bts:UMIBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", - "rdfs:label": "PlaneCount", + "rdfs:comment": "Length of UMI barcode read (in bp): number", + "rdfs:label": "UMIBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PlaneCount", + "sms:displayName": "UMI Barcode Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SizeC", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", + "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeC", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:SynapseIDofGeoMxDSPPKCFile" + }, + { + "@id": "bts:GeoMxDSPNGSSequencingPlatform" + }, + { + "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod" + }, + { + "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName" + }, + { + "@id": "bts:GeoMxDSPLibraryPreparationKitVendor" + }, + { + "@id": "bts:GeoMxDSPLibraryPreparationKitVersion" + }, + { + "@id": "bts:SynapseIDofGeoMxLabWorksheetFile" + }, + { + "@id": "bts:SoftwareandVersion" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:SizeT", + "@id": "bts:SynapseIDofGeoMxDSPPKCFile", "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", + "rdfs:comment": "The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.", + "rdfs:label": "SynapseIDofGeoMxDSPPKCFile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeT", + "sms:displayName": "Synapse ID of GeoMx DSP PKC File", "sms:required": "sms:true", "sms:validationRules": [ - "int" + "list", + "regex match syn\\d+" ] }, { - "@id": "bts:SizeX", + "@id": "bts:GeoMxDSPNGSSequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "GeoMxDSPNGSSequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeX", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "GeoMx DSP NGS Sequencing Platform", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeY", + "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeY", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "GeoMxDSPNGSLibrarySelectionMethod", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeY", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "GeoMx DSP NGS Library Selection Method", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeZ", + "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeZ", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "GeoMxDSPNGSLibraryPreparationKitName", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeZ", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "GeoMx DSP NGS Library Preparation Kit Name", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:PixelType", + "@id": "bts:GeoMxDSPLibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", - "rdfs:label": "PixelType", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "GeoMxDSPLibraryPreparationKitVendor", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Int8" - }, - { - "@id": "bts:Int16" - }, - { - "@id": "bts:Int32" - }, - { - "@id": "bts:Uint8" - }, - { - "@id": "bts:Uint16" - }, - { - "@id": "bts:Uint32" - }, - { - "@id": "bts:Float" - }, - { - "@id": "bts:Double" - }, - { - "@id": "bts:Bit" - } - ], - "sms:displayName": "PixelType", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Library Preparation Kit Vendor", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHPositionsFile", + "@id": "bts:GeoMxDSPLibraryPreparationKitVersion", "@type": "rdfs:Class", - "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", - "rdfs:label": "MERFISHPositionsFile", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "GeoMxDSPLibraryPreparationKitVersion", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Positions File", + "sms:displayName": "GeoMx DSP Library Preparation Kit Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHCodebookFile", + "@id": "bts:SynapseIDofGeoMxLabWorksheetFile", "@type": "rdfs:Class", - "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", - "rdfs:label": "MERFISHCodebookFile", + "rdfs:comment": "Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.", + "rdfs:label": "SynapseIDofGeoMxLabWorksheetFile", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Codebook File", + "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list", + "regex match syn\\d+" + ] }, { - "@id": "bts:ImagingLevel3Segmentation", + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", "@type": "rdfs:Class", - "rdfs:comment": "Object segmentations", - "rdfs:label": "ImagingLevel3Segmentation", + "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", + "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -42192,470 +41294,153 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Segmentation", + "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ImagingLevel2" - } - ], "sms:requiresDependency": [ { - "@id": "bts:Component" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Filename" + "@id": "bts:Scanname" }, { - "@id": "bts:FileFormat" + "@id": "bts:ROIname" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:Segmentname" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:ROIXCoordinate" }, { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:ROIYCoordinate" }, { - "@id": "bts:Parameterfile" + "@id": "bts:Tags" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:QCstatus" }, { - "@id": "bts:CommitSHA" + "@id": "bts:ScanHeight" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:ScanWidth" }, { - "@id": "bts:NumberofObjects" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingSegmentationDataType", - "@type": "rdfs:Class", - "rdfs:comment": "Specifies how the segmentation is stored", - "rdfs:label": "ImagingSegmentationDataType", - "rdfs:subClassOf": [ + "@id": "bts:ScanOffsetX" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ScanOffsetY" + }, { - "@id": "bts:Mask" + "@id": "bts:BindingDensity" }, { - "@id": "bts:Outline" + "@id": "bts:Positivenormfactor" }, { - "@id": "bts:Polygon" + "@id": "bts:Surfacearea" }, { - "@id": "bts:ProbabilityMap" + "@id": "bts:Nucleicount" }, { - "@id": "bts:Point" + "@id": "bts:TissueStain" } ], - "sms:displayName": "Imaging Segmentation Data Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Parameterfile", + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", "@type": "rdfs:Class", - "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", - "rdfs:label": "Parameterfile", + "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", + "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Parameter file", + "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingObjectClass", - "@type": "rdfs:Class", - "rdfs:comment": "Defines the structure that the mask delineates", - "rdfs:label": "ImagingObjectClass", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Nucleus" - }, - { - "@id": "bts:Cytoplasm" - }, - { - "@id": "bts:Plasmamembrane" - }, - { - "@id": "bts:Wholecell" - }, - { - "@id": "bts:Spot" - }, - { - "@id": "bts:ImagingObjectClassOther" - } - ], - "sms:displayName": "Imaging Object Class", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] - }, - { - "@id": "bts:NumberofObjects", - "@type": "rdfs:Class", - "rdfs:comment": "The number of objects (eg cells) described", - "rdfs:label": "NumberofObjects", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number of Objects", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:ImagingLevel3Image", - "@type": "rdfs:Class", - "rdfs:comment": "Quality controlled imaging data", - "rdfs:label": "ImagingLevel3Image", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 3 Image", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ImagingLevel2" - } - ], "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, { "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANParentChannelMetadataID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:Microscope" - }, - { - "@id": "bts:Objective" - }, - { - "@id": "bts:NominalMagnification" - }, - { - "@id": "bts:LensNA" - }, - { - "@id": "bts:WorkingDistance" - }, - { - "@id": "bts:Immersion" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:Comment" - }, - { - "@id": "bts:FOVnumber" - }, - { - "@id": "bts:FOVX" - }, - { - "@id": "bts:FOVY" - }, - { - "@id": "bts:FrameAveraging" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentChannelMetadataID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID for a level 3 channels table.", - "rdfs:label": "HTANParentChannelMetadataID", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel4" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Channel Metadata ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingLevel3Channels", - "@type": "rdfs:Class", - "rdfs:comment": "Channel-level Metadata Attributes", - "rdfs:label": "ImagingLevel3Channels", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 3 Channels", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:HTANChannelMetadataID" - }, - { - "@id": "bts:ChannelID" - }, - { - "@id": "bts:ChannelName" - }, - { - "@id": "bts:ChannelPassedQC" - }, - { - "@id": "bts:CycleNumber" - }, - { - "@id": "bts:SubCycleNumber" - }, - { - "@id": "bts:AntibodyRole" - }, - { - "@id": "bts:TargetName" - }, - { - "@id": "bts:AntibodyName" - }, - { - "@id": "bts:RRIDidentifier" - }, - { - "@id": "bts:Fluorophore" - }, - { - "@id": "bts:Clone" - }, - { - "@id": "bts:Lot" - }, - { - "@id": "bts:Vendor" - }, - { - "@id": "bts:CatalogNumber" - }, - { - "@id": "bts:ExcitationWavelength" - }, - { - "@id": "bts:EmissionWavelength" - }, - { - "@id": "bts:ExcitationBandwidth" - }, - { - "@id": "bts:EmissionBandwidth" - }, - { - "@id": "bts:MetalIsotopeElement" - }, - { - "@id": "bts:MetalIsotopeMass" - }, - { - "@id": "bts:OligoBarcodeUpperStrand" - }, - { - "@id": "bts:OligoBarcodeLowerStrand" - }, - { - "@id": "bts:Dilution" - }, - { - "@id": "bts:Concentration" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:RunID" + "@id": "bts:Scanname" }, { - "@id": "bts:FileFormat" + "@id": "bts:Slidename" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:ROIname" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Segmentname" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:ROIXCoordinate" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:ROIYCoordinate" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:Tags" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:ScanHeight" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:ScanWidth" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:ScanOffsetX" }, { - "@id": "bts:EndBias" + "@id": "bts:ScanOffsetY" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:Surfacearea" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:Nucleicount" }, { - "@id": "bts:CaptureArea" + "@id": "bts:SequencingSaturation" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:MapQ30" }, { - "@id": "bts:SlideVersion" + "@id": "bts:Rawreads" }, { - "@id": "bts:SlideID" + "@id": "bts:Stitchedreads" }, { - "@id": "bts:ImageRe-orientation" + "@id": "bts:Alignedreads" }, { - "@id": "bts:PermeabilizationTime" + "@id": "bts:Deduplicatedreads" }, { - "@id": "bts:RIN" + "@id": "bts:InSituNegativemedian" }, { - "@id": "bts:DV200" + "@id": "bts:Biologicalprobemedian" } ], "sms:validationRules": [] }, { - "@id": "bts:CaptureArea", + "@id": "bts:GeoMxDSPAssayType", "@type": "rdfs:Class", - "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", - "rdfs:label": "CaptureArea", + "rdfs:comment": "The assay type which was used for the GeoMx DSP pipeline.", + "rdfs:label": "GeoMxDSPAssayType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -42666,129 +41451,95 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:A" - }, - { - "@id": "bts:B" - }, - { - "@id": "bts:C" - }, - { - "@id": "bts:D" - }, - { - "@id": "bts:A1" + "@id": "bts:RNAnCounter" }, { - "@id": "bts:B1" + "@id": "bts:ProteinnCounter" }, { - "@id": "bts:C1" + "@id": "bts:ProteinNGS" }, { - "@id": "bts:D1" + "@id": "bts:RNANGS" } ], - "sms:displayName": "Capture Area", - "sms:required": "sms:false", + "sms:displayName": "GeoMx DSP Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SlideVersion", + "@id": "bts:RNAnCounter", "@type": "rdfs:Class", - "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "rdfs:label": "SlideVersion", + "rdfs:comment": "TBD", + "rdfs:label": "RNAnCounter", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:V1" - }, - { - "@id": "bts:V2" - }, - { - "@id": "bts:V3" - }, - { - "@id": "bts:V4" - } - ], - "sms:displayName": "Slide Version", + "sms:displayName": "RNA nCounter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlideID", + "@id": "bts:ProteinnCounter", "@type": "rdfs:Class", - "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", - "rdfs:label": "SlideID", + "rdfs:comment": "TBD", + "rdfs:label": "ProteinnCounter", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide ID", + "sms:displayName": "Protein nCounter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageRe-orientation", + "@id": "bts:ProteinNGS", "@type": "rdfs:Class", - "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", - "rdfs:label": "ImageRe-orientation", + "rdfs:comment": "TBD", + "rdfs:label": "ProteinNGS", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:TRUE" - }, - { - "@id": "bts:FALSE" - } - ], - "sms:displayName": "Image Re-orientation", + "sms:displayName": "Protein NGS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PermeabilizationTime", + "@id": "bts:RNANGS", "@type": "rdfs:Class", - "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", - "rdfs:label": "PermeabilizationTime", + "rdfs:comment": "TBD", + "rdfs:label": "RNANGS", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Permeabilization Time", + "sms:displayName": "RNA NGS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -42797,11 +41548,20 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" + }, + { + "@id": "bts:ImagingLevel2" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "sms:requiresDependency": [ @@ -42815,58 +41575,46 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:Checksum" - }, - { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:UMITag" - }, - { - "@id": "bts:WhitelistSpatialBarcodeFileLink" - }, - { - "@id": "bts:SpatialBarcodeTag" - }, - { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:GeoMxDSPAssayType" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:GeoMxDSPUniqueProbeCount" }, { - "@id": "bts:GenomicReference" + "@id": "bts:GeoMxDSPUniqueTargetCount" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:GeoMxDSPGenomicReference" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:MatrixType" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:GeoMxDSPWorkflowType" }, { - "@id": "bts:RunID" + "@id": "bts:GeoMxDSPWorkflowParameterDescription" }, { - "@id": "bts:CaptureArea" + "@id": "bts:GeoMxDSPWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:WhitelistSpatialBarcodeFileLink", + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", - "rdfs:label": "WhitelistSpatialBarcodeFileLink", + "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", + "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -42875,15 +41623,18 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whitelist Spatial Barcode File Link", + "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list", + "regex match syn\\d+" + ] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "@id": "bts:GeoMxDSPUniqueProbeCount", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "rdfs:comment": "Total number of unique probes reported.", + "rdfs:label": "GeoMxDSPUniqueProbeCount", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -42892,61 +41643,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", + "sms:displayName": "GeoMx DSP Unique Probe Count", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:RunID" - }, - { - "@id": "bts:VisiumFileType" - }, - { - "@id": "bts:SlideID" - }, - { - "@id": "bts:CaptureArea" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:WorkflowLink" - } - ], - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:VisiumFileType", + "@id": "bts:GeoMxDSPUniqueTargetCount", "@type": "rdfs:Class", - "rdfs:comment": "The file type generated for the visium experiment.", - "rdfs:label": "VisiumFileType", + "rdfs:comment": "Total number of unique genes reported.", + "rdfs:label": "GeoMxDSPUniqueTargetCount", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -42955,65 +41662,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Referencepng" - }, - { - "@id": "bts:Referencejpg" - }, - { - "@id": "bts:Jsonscalefactors" - }, - { - "@id": "bts:Probedatasetcsv" - }, - { - "@id": "bts:Qcresulthtml" - }, - { - "@id": "bts:Filteredmex" - }, - { - "@id": "bts:Unfilteredmex" - }, - { - "@id": "bts:TissuePositions" - }, - { - "@id": "bts:Barcodes" - }, - { - "@id": "bts:Features" - }, - { - "@id": "bts:Fiducialimagepng" - }, - { - "@id": "bts:Fiducialimagejpg" - }, - { - "@id": "bts:Detectedimagepng" - }, - { - "@id": "bts:Detectedjpg" - }, - { - "@id": "bts:Highresimage" - }, - { - "@id": "bts:Lowresimage" - } - ], - "sms:displayName": "Visium File Type", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "GeoMx DSP Unique Target Count", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "@id": "bts:GeoMxDSPGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", + "rdfs:label": "GeoMxDSPGenomicReference", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43022,79 +41681,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", + "sms:displayName": "GeoMx DSP Genomic Reference", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:RunID" - }, - { - "@id": "bts:VisiumFileType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:CaptureArea" - }, - { - "@id": "bts:Spotsundertissue" - }, - { - "@id": "bts:MeanReadsperSpatialSpot" - }, - { - "@id": "bts:MedianNumberGenesperSpatialSpot" - }, - { - "@id": "bts:SequencingSaturation" - }, - { - "@id": "bts:ProportionReadsMapped" - }, - { - "@id": "bts:ProportionReadsMappedtoTranscriptome" - }, - { - "@id": "bts:MedianUMICountsperSpot" - } - ], - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Spotsundertissue", + "@id": "bts:GeoMxDSPWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "The number of barcodes associated with a spot under tissue.", - "rdfs:label": "Spotsundertissue", + "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", + "rdfs:label": "GeoMxDSPWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43103,17 +41700,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spots under tissue", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "GeoMx DSP Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:MeanReadsperSpatialSpot", + "@id": "bts:GeoMxDSPWorkflowParameterDescription", "@type": "rdfs:Class", - "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", - "rdfs:label": "MeanReadsperSpatialSpot", + "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", + "rdfs:label": "GeoMxDSPWorkflowParameterDescription", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43122,17 +41717,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Reads per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "GeoMx DSP Workflow Parameter Description", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SequencingSaturation", + "@id": "bts:GeoMxDSPWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", - "rdfs:label": "SequencingSaturation", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "GeoMxDSPWorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43141,995 +41734,746 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Saturation", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome", + "@id": "bts:Scanname", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", - "rdfs:label": "ProportionReadsMappedtoTranscriptome", + "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", + "rdfs:label": "Scanname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped to Transcriptome", + "sms:displayName": "Scan name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "@id": "bts:ROIname", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", + "rdfs:label": "ROIname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:RunID" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:WorkflowLink" - }, + "sms:displayName": "ROI name", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Segmentname", + "@type": "rdfs:Class", + "rdfs:comment": "Name given to segment at time of generation", + "rdfs:label": "Segmentname", + "rdfs:subClassOf": [ { - "@id": "bts:VisiumWorkflowType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" }, { - "@id": "bts:VisiumWorkflowParametersDescription" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Segment name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:VisiumWorkflowType", + "@id": "bts:ROIXCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", - "rdfs:label": "VisiumWorkflowType", + "rdfs:comment": "X location within the image", + "rdfs:label": "ROIXCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Visium Workflow Type", + "sms:displayName": "ROI X Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:VisiumWorkflowParametersDescription", + "@id": "bts:ROIYCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow..", - "rdfs:label": "VisiumWorkflowParametersDescription", + "rdfs:comment": "Y location within the image", + "rdfs:label": "ROIYCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Visium Workflow Parameters Description", + "sms:displayName": "ROI Y Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Referencepng", + "@id": "bts:Tags", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencepng", + "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", + "rdfs:label": "Tags", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "reference png", - "sms:required": "sms:false", + "sms:displayName": "Tags", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Referencejpg", + "@id": "bts:QCstatus", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencejpg", + "rdfs:comment": "ROI quality control flag as reported by the application", + "rdfs:label": "QCstatus", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "reference jpg", + "sms:displayName": "QC status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Jsonscalefactors", + "@id": "bts:ScanHeight", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Jsonscalefactors", + "rdfs:comment": "Height of the scan for GeoMx Analysis", + "rdfs:label": "ScanHeight", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "json scale factors", - "sms:required": "sms:false", + "sms:displayName": "Scan Height", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Probedatasetcsv", + "@id": "bts:ScanWidth", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Probedatasetcsv", + "rdfs:comment": "Width of the scan for GeoMx Analysis", + "rdfs:label": "ScanWidth", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "probe dataset csv", - "sms:required": "sms:false", + "sms:displayName": "Scan Width", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Qcresulthtml", + "@id": "bts:ScanOffsetX", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Qcresulthtml", + "rdfs:comment": "Offset X of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetX", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "qc result html", - "sms:required": "sms:false", + "sms:displayName": "Scan Offset X", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Filteredmex", + "@id": "bts:ScanOffsetY", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Filteredmex", + "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetY", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "filtered mex", - "sms:required": "sms:false", + "sms:displayName": "Scan Offset Y", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Unfilteredmex", + "@id": "bts:BindingDensity", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Unfilteredmex", + "rdfs:comment": "The binding density as reported by the application", + "rdfs:label": "BindingDensity", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "unfiltered mex", + "sms:displayName": "Binding Density", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TissuePositions", + "@id": "bts:Positivenormfactor", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TissuePositions", + "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", + "rdfs:label": "Positivenormfactor", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tissue_positions", + "sms:displayName": "Positive norm factor", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Barcodes", + "@id": "bts:Surfacearea", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Barcodes", + "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", + "rdfs:label": "Surfacearea", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "barcodes", - "sms:required": "sms:false", + "sms:displayName": "Surface area", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Features", + "@id": "bts:Nucleicount", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Features", + "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", + "rdfs:label": "Nucleicount", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "features", - "sms:required": "sms:false", + "sms:displayName": "Nuclei count", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Fiducialimagepng", + "@id": "bts:TissueStain", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fiducialimagepng", + "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", + "rdfs:label": "TissueStain", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "fiducial image png", + "sms:displayName": "Tissue Stain", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fiducialimagejpg", + "@id": "bts:Slidename", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fiducialimagejpg", + "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", + "rdfs:label": "Slidename", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "fiducial image jpg", + "sms:displayName": "Slide name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Detectedimagepng", + "@id": "bts:Rawreads", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Detectedimagepng", + "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", + "rdfs:label": "Rawreads", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "detected image png", + "sms:displayName": "Raw reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Detectedjpg", + "@id": "bts:Stitchedreads", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Detectedjpg", + "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", + "rdfs:label": "Stitchedreads", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "detected jpg", + "sms:displayName": "Stitched reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Highresimage", + "@id": "bts:Alignedreads", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Highresimage", + "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", + "rdfs:label": "Alignedreads", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "high res image", + "sms:displayName": "Aligned reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lowresimage", + "@id": "bts:Deduplicatedreads", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Lowresimage", + "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", + "rdfs:label": "Deduplicatedreads", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "low res image", + "sms:displayName": "Deduplicated reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:A", + "@id": "bts:InSituNegativemedian", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "A", + "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", + "rdfs:label": "InSituNegativemedian", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "A", + "sms:displayName": "In Situ Negative median", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:B", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "B", - "rdfs:subClassOf": [ - { - "@id": "bts:CaptureArea" - }, - { - "@id": "bts:MetalIsotopeElement" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "B", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:C", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "C", - "rdfs:subClassOf": [ - { - "@id": "bts:CaptureArea" - }, - { - "@id": "bts:MetalIsotopeElement" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "C", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:D", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "D", - "rdfs:subClassOf": [ - { - "@id": "bts:CaptureArea" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "D", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:A1", + "@id": "bts:Biologicalprobemedian", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "A1", + "rdfs:comment": "Is the median count from all probes except the negative control probes. 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A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase", - "rdfs:label": "CDNA", - "rdfs:subClassOf": [ + "@id": "bts:NucleicAcidSource" + }, { - "@id": "bts:Sequencing" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:CrosslinkingCondtion" }, { - "@id": "bts:ScmCseqRead1" + "@id": "bts:DNADigestionCondition" }, { - "@id": "bts:ScmCseqRead2" + "@id": "bts:NucleiPermeabilizationMethod" }, { - "@id": "bts:ScmCseqRead3" + "@id": "bts:LigationCondition" }, { - "@id": "bts:Read1" + "@id": "bts:BiotinEnrichment" }, { - "@id": "bts:Read2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "cDNA", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:DNAInputAmount" + }, { - "@id": "bts:CDNAOffset" + "@id": "bts:TotalReads" }, { - "@id": "bts:CDNALength" + "@id": "bts:ProtocolLink" } ], "sms:validationRules": [] }, { - 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"@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV1.1", - "sms:required": "sms:false", + "sms:displayName": "Ligation Condition", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xV2", + "@id": "bts:BiotinEnrichment", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV2", + "rdfs:comment": "Whether biotin is used for enriching ligation product", + "rdfs:label": "BiotinEnrichment", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV2", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV3", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Yes" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV3", - "sms:required": "sms:false", + "sms:displayName": "Biotin Enrichment", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xV3.1", + "@id": "bts:DNAInputAmount", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3.1", + "rdfs:comment": "Amount of DNA for library construction, in nanograms.", + "rdfs:label": "DNAInputAmount", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV3.1", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "DNA Input Amount", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:Drop-seq", + "@id": "bts:HI-C-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Drop-seq", + "rdfs:comment": "Aligned read pairs, contact matrix", + "rdfs:label": "HI-C-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Drop-seq", + "sms:displayName": "HI-C-seq Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InDropsV2", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV2", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialLibraryConstructionMethod" - }, + "sms:requiresComponent": [ { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:HI-C-seqLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "inDropsV2", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InDropsV3", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV3", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Component" }, { - "@id": "bts:LibraryConstructionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "inDropsV3", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TruDrop", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TruDrop", - "rdfs:subClassOf": [ + "@id": "bts:HTANDataFileID" + }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:AlignedReadLength" + }, + { + "@id": "bts:Tool" + }, + { + "@id": "bts:Resolution" + }, + { + "@id": "bts:NormalizationMethod" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "TruDrop", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NexteraXT", + "@id": "bts:AlignedReadLength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NexteraXT", + "rdfs:comment": "Read length used for alignment if hard trimming was applied", + "rdfs:label": "AlignedReadLength", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nextera XT", - "sms:required": "sms:false", + "sms:displayName": "Aligned Read Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UMIBarcodeOffset", + "@id": "bts:Tool", "@type": "rdfs:Class", - "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", - "rdfs:label": "UMIBarcodeOffset", + "rdfs:comment": "Were any software or computational tools generated for this content", + "rdfs:label": "Tool", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Offset", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Tool", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UMIBarcodeLength", + "@id": "bts:Resolution", "@type": "rdfs:Class", - "rdfs:comment": "Length of UMI barcode read (in bp): number", - "rdfs:label": "UMIBarcodeLength", + "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", + "rdfs:label": "Resolution", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Length", + "sms:displayName": "Resolution", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "@id": "bts:HI-C-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "rdfs:comment": "Summary data for the HI-C-seq assay.", + "rdfs:label": "HI-C-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 1", + "sms:displayName": "HI-C-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:HI-C-seqLevel2" } ], "sms:requiresDependency": [ @@ -44137,1055 +42481,1277 @@ "@id": "bts:Component" }, { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile" - }, - { - "@id": "bts:GeoMxDSPNGSSequencingPlatform" + "@id": "bts:Filename" }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod" + "@id": "bts:FileFormat" }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName" + "@id": "bts:GenomicReference" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor" + "@id": "bts:StripeCalling" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion" + "@id": "bts:LoopWindow" }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile" + "@id": "bts:StripeWindow" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:LoopCalling" } ], "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile", + "@id": "bts:StripeCalling", "@type": "rdfs:Class", - "rdfs:comment": "The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxDSPPKCFile", + "rdfs:comment": "Tool used for identifying architectural stripe-forming, interaction hotspots.", + "rdfs:label": "StripeCalling", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP PKC File", + "schema:rangeIncludes": [ + { + "@id": "bts:MACS2" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Stripe Calling", "sms:required": "sms:true", "sms:validationRules": [ "list", - "regex match syn\\d+" + "-?\\d+" ] }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform", + "@id": "bts:LoopWindow", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "GeoMxDSPNGSSequencingPlatform", + "rdfs:comment": "Binning size used for calling significant dot interactions (loops)", + "rdfs:label": "LoopWindow", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Sequencing Platform", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Loop Window", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like ", + " regex search -?\\d+" + ] }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", + "@id": "bts:StripeWindow", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "GeoMxDSPNGSLibrarySelectionMethod", + "rdfs:comment": "Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.", + "rdfs:label": "StripeWindow", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Selection Method", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Stripe Window", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like ", + " regex search -?\\d+" + ] }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName", + "@id": "bts:LoopCalling", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. 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"sms:displayName": "GeoMx DSP Workflow Parameter Description", + "sms:displayName": "other", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowLink", + "@id": "bts:HiCCUPS", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "GeoMxDSPWorkflowLink", + "rdfs:comment": "TBD", + "rdfs:label": "HiCCUPS", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:LoopCalling" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Link", + "sms:displayName": "HiCCUPS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Scanname", + "@id": "bts:Cooltools", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", - "rdfs:label": "Scanname", + "rdfs:comment": "TBD", + "rdfs:label": "Cooltools", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:LoopCalling" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan name", - "sms:required": "sms:true", + "sms:displayName": "Cooltools", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ROIname", + "@id": "bts:ImagingLevel4", "@type": "rdfs:Class", - "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", - "rdfs:label": "ROIname", + "rdfs:comment": "Derived imaging data: Object-by-feature array", + "rdfs:label": "ImagingLevel4", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Segmentname", - "@type": "rdfs:Class", - "rdfs:comment": "Name given to segment at time of generation", - "rdfs:label": "Segmentname", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, + "sms:displayName": "Imaging Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:ImagingLevel3Channels" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Segment name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIXCoordinate", - "@type": "rdfs:Class", - "rdfs:comment": "X location within the image", - "rdfs:label": "ROIXCoordinate", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Component" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI X Coordinate", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIYCoordinate", - "@type": "rdfs:Class", - "rdfs:comment": "Y location within the image", - "rdfs:label": "ROIYCoordinate", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:FileFormat" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANParentChannelMetadataID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:Parameterfile" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:NumberofObjects" + }, + { + "@id": "bts:NumberofFeatures" + }, + { + "@id": "bts:ImagingObjectClass" + }, + { + "@id": "bts:ImagingSummaryStatistic" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI Y Coordinate", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Tags", + "@id": "bts:NumberofFeatures", "@type": "rdfs:Class", - "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", - "rdfs:label": "Tags", + "rdfs:comment": "The number of features (eg channels) described", + "rdfs:label": "NumberofFeatures", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tags", + "sms:displayName": "Number of Features", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:QCstatus", + "@id": "bts:ImagingSummaryStatistic", "@type": "rdfs:Class", - "rdfs:comment": "ROI quality control flag as reported by the application", - "rdfs:label": "QCstatus", + "rdfs:comment": "Function used to summarize object/feature intensity", + "rdfs:label": "ImagingSummaryStatistic", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanHeight", - "@type": "rdfs:Class", - "rdfs:comment": "Height of the scan for GeoMx Analysis", - "rdfs:label": "ScanHeight", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Mean" + }, + { + "@id": "bts:Median" + }, + { + "@id": "bts:NotSpecified" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Height", - "sms:required": "sms:true", + "sms:displayName": "Imaging Summary Statistic", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanWidth", + "@id": "bts:SRRSImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Width of the scan for GeoMx Analysis", - "rdfs:label": "ScanWidth", + "rdfs:comment": "SRRS-specific HTAN raw and pre-processed image data", + "rdfs:label": "SRRSImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Width", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanOffsetX", - "@type": "rdfs:Class", - "rdfs:comment": "Offset X of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetX", - "rdfs:subClassOf": [ + "sms:displayName": "SRRS Imaging Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Offset X", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanOffsetY", - "@type": "rdfs:Class", - "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetY", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ChannelMetadataFilename" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:Microscope" + }, + { + "@id": "bts:Objective" + }, + { + "@id": "bts:NominalMagnification" + }, + { + "@id": "bts:Pyramid" + }, + { + "@id": "bts:Zstack" + }, + { + "@id": "bts:Tseries" + }, + { + "@id": "bts:PassedQC" + }, + { + "@id": "bts:FrameAveraging" + }, + { + "@id": "bts:ImageID" + }, + { + "@id": "bts:DimensionOrder" + }, + { + "@id": "bts:PhysicalSizeX" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeY" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PixelsBigEndian" + }, + { + "@id": "bts:PlaneCount" + }, + { + "@id": "bts:SizeC" + }, + { + "@id": "bts:SizeT" + }, + { + "@id": "bts:SizeX" + }, + { + "@id": "bts:SizeY" + }, + { + "@id": "bts:SizeZ" + }, + { + "@id": "bts:PixelType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Offset Y", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BindingDensity", + "@id": "bts:10XGenomicsXeniumISSExperiment", "@type": "rdfs:Class", - "rdfs:comment": "The binding density as reported by the application", - "rdfs:label": "BindingDensity", + "rdfs:comment": "All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment", + "rdfs:label": "10XGenomicsXeniumISSExperiment", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Binding Density", + "sms:displayName": "10X Genomics Xenium ISS Experiment", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Positivenormfactor", - "@type": "rdfs:Class", - "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", - "rdfs:label": "Positivenormfactor", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:XeniumBundleContents" + }, + { + "@id": "bts:SlideID" + }, + { + "@id": "bts:ROIname" + }, + { + "@id": "bts:PanelName" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:TotalNumberofCells" + }, + { + "@id": "bts:TotalNumberofTargets" + }, + { + "@id": "bts:Surfacearea" + }, + { + "@id": "bts:ExperimentIFChannels" + }, + { + "@id": "bts:TranscriptsperCell" + }, + { + "@id": "bts:PercentofTranscriptswithinCells" + }, + { + "@id": "bts:DecodedTranscripts" + }, + { + "@id": "bts:XeniumIFimageHTANFileID" + }, + { + "@id": "bts:XeniumHEimageHTANFileID" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Positive norm factor", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Surfacearea", + "@id": "bts:XeniumBundleContents", "@type": "rdfs:Class", - "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", - "rdfs:label": "Surfacearea", + "rdfs:comment": "A comma separated list of filenames within the Xenium bundle zip file", + "rdfs:label": "XeniumBundleContents", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Surface area", + "sms:displayName": "Xenium Bundle Contents", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Nucleicount", + "@id": "bts:PanelName", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", - "rdfs:label": "Nucleicount", + "rdfs:comment": "The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))", + "rdfs:label": "PanelName", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei count", + "sms:displayName": "Panel Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TissueStain", + "@id": "bts:TotalNumberofCells", "@type": "rdfs:Class", - "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", - "rdfs:label": "TissueStain", + "rdfs:comment": "The total number of cells analyzed on the flow cell", + "rdfs:label": "TotalNumberofCells", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tissue Stain", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Cells", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Slidename", + "@id": "bts:TotalNumberofTargets", "@type": "rdfs:Class", - "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", - "rdfs:label": "Slidename", + "rdfs:comment": "Refers to the target of an assay. Can be genes/transcripts or probes", + "rdfs:label": "TotalNumberofTargets", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide name", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Targets", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Rawreads", + "@id": "bts:ExperimentIFChannels", "@type": "rdfs:Class", - "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", - "rdfs:label": "Rawreads", + "rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)", + "rdfs:label": "ExperimentIFChannels", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Raw reads", - "sms:required": "sms:false", + "sms:displayName": "Experiment IF Channels", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Stitchedreads", + "@id": "bts:TranscriptsperCell", "@type": "rdfs:Class", - "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", - "rdfs:label": "Stitchedreads", + "rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide", + "rdfs:label": "TranscriptsperCell", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stitched reads", - "sms:required": "sms:false", + "sms:displayName": "Transcripts per Cell", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Alignedreads", + "@id": "bts:PercentofTranscriptswithinCells", "@type": "rdfs:Class", - "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", - "rdfs:label": "Alignedreads", + "rdfs:comment": "The percentage of transcripts assigned to assayed cells", + "rdfs:label": "PercentofTranscriptswithinCells", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Aligned reads", - "sms:required": "sms:false", + "sms:displayName": "Percent of Transcripts within Cells", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Deduplicatedreads", + "@id": "bts:DecodedTranscripts", "@type": "rdfs:Class", - "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", - "rdfs:label": "Deduplicatedreads", + "rdfs:comment": "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).", + "rdfs:label": "DecodedTranscripts", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Deduplicated reads", - "sms:required": "sms:false", + "sms:displayName": "Decoded Transcripts", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InSituNegativemedian", + "@id": "bts:XeniumIFimageHTANFileID", "@type": "rdfs:Class", - "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", - "rdfs:label": "InSituNegativemedian", + "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", + "rdfs:label": "XeniumIFimageHTANFileID", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "In Situ Negative median", + "sms:displayName": "Xenium IF image HTAN File ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Biologicalprobemedian", + "@id": "bts:XeniumHEimageHTANFileID", "@type": "rdfs:Class", - "rdfs:comment": "Is the median count from all probes except the negative control probes. A measure of signal to background for each segment", - "rdfs:label": "Biologicalprobemedian", + "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", + "rdfs:label": "XeniumHEimageHTANFileID", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biological probe median", + "sms:displayName": "Xenium HE image HTAN File ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HI-C-seqLevel1", + "@id": "bts:RPPALevel2", "@type": "rdfs:Class", - "rdfs:comment": "Unaligned sequence data", - "rdfs:label": "HI-C-seqLevel1", + "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", + "rdfs:label": "RPPALevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq Level 1", + "sms:displayName": "RPPA Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -45196,12 +43762,58 @@ { "@id": "bts:Component" }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, { "@id": "bts:HTANParentBiospecimenID" }, + { + "@id": "bts:HTANParentDataFileID" + }, { "@id": "bts:HTANDataFileID" }, + { + "@id": "bts:HTANRPPAAntibodyTable" + }, + { + "@id": "bts:AssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:HTANRPPAAntibodyTable", + "@type": "rdfs:Class", + "rdfs:comment": "A table containing antibody level metadata for RPPA", + "rdfs:label": "HTANRPPAAntibodyTable", + "rdfs:subClassOf": [ + { + "@id": "bts:RPPALevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN RPPA Antibody Table", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:HTANRPPAAntibodyTableID" + }, { "@id": "bts:Filename" }, @@ -45209,123 +43821,126 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:GenomicReference" + "@id": "bts:AbNameReportedonDataset" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:GENCODEGeneSymbolTarget" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:UNIPROTProteinIDTarget" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:PhosphoproteinFlag" }, { - "@id": "bts:TranspositionReaction" + "@id": "bts:Vendor" }, { - "@id": "bts:CrosslinkingCondtion" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:DNADigestionCondition" + "@id": "bts:InternalAbID" }, { - "@id": "bts:NucleiPermeabilizationMethod" + "@id": "bts:Species" }, { - "@id": "bts:LigationCondition" + "@id": "bts:RPPADilution" }, { - "@id": "bts:BiotinEnrichment" + "@id": "bts:PhosphoSite" }, { - "@id": "bts:DNAInputAmount" + "@id": "bts:RPPAValidationStatus" }, { - "@id": "bts:TotalReads" + "@id": "bts:Clone" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Clonality" + }, + { + "@id": "bts:AntibodyNotes" } ], "sms:validationRules": [] }, { - "@id": "bts:CrosslinkingCondtion", + "@id": "bts:HTANRPPAAntibodyTableID", "@type": "rdfs:Class", - "rdfs:comment": "Detailed condition for DNA crosslinking", - "rdfs:label": "CrosslinkingCondtion", + "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", + "rdfs:label": "HTANRPPAAntibodyTableID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Crosslinking Condtion", + "sms:displayName": "HTAN RPPA Antibody Table ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DNADigestionCondition", + "@id": "bts:AbNameReportedonDataset", "@type": "rdfs:Class", - "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", - "rdfs:label": "DNADigestionCondition", + "rdfs:comment": "The antibody name.", + "rdfs:label": "AbNameReportedonDataset", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DNA Digestion Condition", + "sms:displayName": "Ab Name Reported on Dataset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleiPermeabilizationMethod", + "@id": "bts:GENCODEGeneSymbolTarget", "@type": "rdfs:Class", - "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", - "rdfs:label": "NucleiPermeabilizationMethod", + "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", + "rdfs:label": "GENCODEGeneSymbolTarget", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei Permeabilization Method", + "sms:displayName": "GENCODE Gene Symbol Target", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LigationCondition", + "@id": "bts:UNIPROTProteinIDTarget", "@type": "rdfs:Class", - "rdfs:comment": "Name of ligase and condition for proximity ligation", - "rdfs:label": "LigationCondition", + "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", + "rdfs:label": "UNIPROTProteinIDTarget", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ligation Condition", + "sms:displayName": "UNIPROT Protein ID Target", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BiotinEnrichment", + "@id": "bts:PhosphoproteinFlag", "@type": "rdfs:Class", - "rdfs:comment": "Whether biotin is used for enriching ligation product", - "rdfs:label": "BiotinEnrichment", + "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", + "rdfs:label": "PhosphoproteinFlag", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -45333,114 +43948,75 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:True" }, { - "@id": "bts:No" + "@id": "bts:False" } ], - "sms:displayName": "Biotin Enrichment", + "sms:displayName": "Phosphoprotein Flag", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DNAInputAmount", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "Amount of DNA for library construction, in nanograms.", - "rdfs:label": "DNAInputAmount", - "rdfs:subClassOf": [ + "rdfs:comment": "Vendor", + "rdfs:label": "Vendor", + "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DNA Input Amount", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "Vendor", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HI-C-seqLevel2", + "@id": "bts:CatalogNumber", "@type": "rdfs:Class", - "rdfs:comment": "Aligned read pairs, contact matrix", - "rdfs:label": "HI-C-seqLevel2", + "rdfs:comment": "Catalog Number", + "rdfs:label": "CatalogNumber", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq Level 2", + "sms:displayName": "Catalog Number", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:HI-C-seqLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:AlignedReadLength" - }, - { - "@id": "bts:Tool" - }, - { - "@id": "bts:Resolution" - }, - { - "@id": "bts:NormalizationMethod" - } - ], "sms:validationRules": [] }, { - "@id": "bts:AlignedReadLength", + "@id": "bts:InternalAbID", "@type": "rdfs:Class", - "rdfs:comment": "Read length used for alignment if hard trimming was applied", - "rdfs:label": "AlignedReadLength", + "rdfs:comment": "Internal lab ID for an antibody.", + "rdfs:label": "InternalAbID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Aligned Read Length", + "sms:displayName": "Internal Ab ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Tool", + "@id": "bts:Species", "@type": "rdfs:Class", - "rdfs:comment": "Were any software or computational tools generated for this content", - "rdfs:label": "Tool", + "rdfs:comment": "Host animal.", + "rdfs:label": "Species", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -45448,95 +44024,66 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Mouse" }, { - "@id": "bts:No" + "@id": "bts:Rabbit" + }, + { + "@id": "bts:Goat" } ], - "sms:displayName": "Tool", + "sms:displayName": "Species", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Resolution", + "@id": "bts:RPPADilution", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", - "rdfs:label": "Resolution", + "rdfs:comment": "The dilution ratio.", + "rdfs:label": "RPPADilution", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Resolution", - "sms:required": "sms:true", + "sms:displayName": "RPPA Dilution", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HI-C-seqLevel3", + "@id": "bts:PhosphoSite", "@type": "rdfs:Class", - "rdfs:comment": "Summary data for the HI-C-seq assay.", - "rdfs:label": "HI-C-seqLevel3", + "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", + "rdfs:label": "PhosphoSite", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq Level 3", + "sms:displayName": "Phospho Site", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:HI-C-seqLevel2" - } - ], "sms:requiresDependency": [ { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:StripeCalling" - }, - { - "@id": "bts:LoopWindow" - }, - { - "@id": "bts:StripeWindow" - }, - { - "@id": "bts:LoopCalling" + "@id": "bts:PhosphoproteinFlag" } ], "sms:validationRules": [] }, { - "@id": "bts:StripeCalling", + "@id": "bts:RPPAValidationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Tool used for identifying architectural stripe-forming, interaction hotspots.", - "rdfs:label": "StripeCalling", + "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", + "rdfs:label": "RPPAValidationStatus", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -45544,623 +44091,420 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MACS2" + "@id": "bts:Valid" }, { - "@id": "bts:Other" + "@id": "bts:UsewithCaution" + }, + { + "@id": "bts:UnderEvaluation" + }, + { + "@id": "bts:UsedforQC" } ], - "sms:displayName": "Stripe Calling", - "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "-?\\d+" - ] + "sms:displayName": "RPPA Validation Status", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:LoopWindow", + "@id": "bts:Clone", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant dot interactions (loops)", - "rdfs:label": "LoopWindow", + "rdfs:comment": "Clone", + "rdfs:label": "Clone", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loop Window", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like ", - " regex search -?\\d+" - ] + "sms:displayName": "Clone", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:StripeWindow", + "@id": "bts:AntibodyNotes", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.", - "rdfs:label": "StripeWindow", + "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", + "rdfs:label": "AntibodyNotes", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stripe Window", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like ", - " regex search -?\\d+" - ] + "sms:displayName": "Antibody Notes", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:LoopCalling", + "@id": "bts:RPPALevel3", "@type": "rdfs:Class", - "rdfs:comment": "Tool used for identifying loop interactions", - "rdfs:label": "LoopCalling", + "rdfs:comment": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", + "rdfs:label": "RPPALevel3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:HiCCUPS" - }, - { - "@id": "bts:Cooltools" - }, + "sms:displayName": "RPPA Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Other" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Loop Calling", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Yes", - "rdfs:subClassOf": [ - { - "@id": "bts:BiotinEnrichment" - }, - { - "@id": "bts:ChannelPassedQC" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:WellIndex" - }, - { - "@id": "bts:CryopreservedCellsinSample" - }, - { - "@id": "bts:PrematureAtBirth" - }, - { - "@id": "bts:AlcoholHistory" - }, - { - "@id": "bts:AsbestosExposure" - }, - { - "@id": "bts:CoalDustExposure" - }, - { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" - }, - { - "@id": "bts:RadonExposure" - }, - { - "@id": "bts:RespirableCrystallineSilicaExposure" - }, - { - "@id": "bts:SecondhandSmokeasChild" - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse" - }, - { - "@id": "bts:HAARTTreatmentIndicator" - }, - { - "@id": "bts:RiskFactorTreatment" - }, - { - "@id": "bts:ChemoConcurrenttoRadiation" - }, - { - "@id": "bts:TreatmentEffectIndicator" - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:COVID19OccurrenceIndicator" - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator" - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup" - }, - { - "@id": "bts:KnownGeneticPredispositionMutation" - }, - { - "@id": "bts:MismatchRepairMutation" - }, - { - "@id": "bts:NonNodalTumorDeposits" - }, - { - "@id": "bts:PregnantatDiagnosis" - }, + "sms:requiresDependency": [ { - "@id": "bts:PriorMalignancy" + "@id": "bts:Component" }, { - "@id": "bts:PriorTreatment" + "@id": "bts:Filename" }, { - "@id": "bts:LymphaticInvasionPresent" + "@id": "bts:FileFormat" }, { - "@id": "bts:PerineuralInvasionPresent" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:SynchronousMalignancy" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:TumorConfinedtoOrganofOrigin" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:AssayType" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" - }, + "@id": "bts:NormalizationMethod" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:RPPALevel4", + "@type": "rdfs:Class", + "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", + "rdfs:label": "RPPALevel4", + "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerKRASIndicator" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "RPPA Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:ColonPolypOccurenceIndicator" - }, + "@id": "bts:RPPALevel2" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:Component" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:Filename" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:FileFormat" }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:HistoryofBlisteringSunburn" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Tool" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:PublicationcontainsHTANID" + "@id": "bts:AssayType" }, { - "@id": "bts:BarrettsEsophagusGobletCellsPresent" - }, + "@id": "bts:BatchCorrectionMethod" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:BatchCorrectionMethod", + "@type": "rdfs:Class", + "rdfs:comment": "Method that was used to batch correct Level 3 data", + "rdfs:label": "BatchCorrectionMethod", + "rdfs:subClassOf": [ { - "@id": "bts:TreatmentorTherapy" + "@id": "bts:RPPALevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "yes", + "sms:displayName": "Batch Correction Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:No", + "@id": "bts:NanostringCosMxSMIExperiment", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "No", + "rdfs:comment": "RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)", + "rdfs:label": "NanostringCosMxSMIExperiment", "rdfs:subClassOf": [ { - "@id": "bts:BiotinEnrichment" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:WellIndex" - }, - { - "@id": "bts:CryopreservedCellsinSample" - }, - { - "@id": "bts:ToTrimAdapterSequence" - }, - { - "@id": "bts:AppliedHardTrimming" - }, - { - "@id": "bts:PseudoAlignmentUsed" - }, - { - "@id": "bts:FusionGeneDetected" - }, - { - "@id": "bts:PrematureAtBirth" - }, - { - "@id": "bts:AlcoholHistory" - }, - { - "@id": "bts:AsbestosExposure" - }, - { - "@id": "bts:CoalDustExposure" - }, - { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" - }, - { - "@id": "bts:RadonExposure" - }, - { - "@id": "bts:RespirableCrystallineSilicaExposure" - }, - { - "@id": "bts:SecondhandSmokeasChild" - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse" - }, - { - "@id": "bts:HAARTTreatmentIndicator" - }, - { - "@id": "bts:ProgressionorRecurrence" - }, - { - "@id": "bts:RiskFactorTreatment" - }, - { - "@id": "bts:ChemoConcurrenttoRadiation" - }, - { - "@id": "bts:TreatmentEffectIndicator" - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:COVID19OccurrenceIndicator" - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator" - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup" - }, - { - "@id": "bts:KnownGeneticPredispositionMutation" - }, - { - "@id": "bts:MismatchRepairMutation" - }, - { - "@id": "bts:NonNodalTumorDeposits" - }, - { - "@id": "bts:PregnantatDiagnosis" - }, - { - "@id": "bts:PriorMalignancy" - }, - { - "@id": "bts:PriorTreatment" - }, - { - "@id": "bts:AnaplasiaPresent" - }, - { - "@id": "bts:LymphaticInvasionPresent" - }, - { - "@id": "bts:PerineuralInvasionPresent" - }, - { - "@id": "bts:SynchronousMalignancy" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nanostring CosMx SMI Experiment", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:TumorConfinedtoOrganofOrigin" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:VascularInvasionPresent" + "@id": "bts:Component" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:Filename" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:FileFormat" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:CosMxBundleContents" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:SlideID" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:CosMxAssayType" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:PanelName" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + "@id": "bts:TotalNumberofCells" }, { - "@id": "bts:HistoryofBlisteringSunburn" + "@id": "bts:TotalNumberofTargets" }, { - "@id": "bts:Tool" + "@id": "bts:NumberofFOVs" }, { - "@id": "bts:Islowestlevel" + "@id": "bts:Surfacearea" }, { - "@id": "bts:PublicationcontainsHTANID" + "@id": "bts:ExperimentIFChannels" }, { - "@id": "bts:BarrettsEsophagusGobletCellsPresent" + "@id": "bts:TranscriptsperCell" }, { - "@id": "bts:PrecancerCase" + "@id": "bts:PercentofTranscriptswithinCells" }, { - "@id": "bts:TreatmentorTherapy" + "@id": "bts:MeanTotalTranscriptsperArea" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:UniqueGenes" }, { - "@id": "bts:HistoryofAtypicalNevi" - }, + "@id": "bts:TotalNegativeProbeCounts" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CosMxBundleContents", + "@type": "rdfs:Class", + "rdfs:comment": "A comma separated list of filenames within the CosMx bundle zip file", + "rdfs:label": "CosMxBundleContents", + "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "no", - "sms:required": "sms:false", + "sms:displayName": "CosMx Bundle Contents", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2", + "@id": "bts:CosMxAssayType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MACS2", + "rdfs:comment": "The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay", + "rdfs:label": "CosMxAssayType", "rdfs:subClassOf": [ { - "@id": "bts:StripeCalling" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:RNA" + }, + { + "@id": "bts:Protein" + } + ], + "sms:displayName": "CosMx Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HiCCUPS", + "@id": "bts:NumberofFOVs", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HiCCUPS", + "rdfs:comment": "The total number of FOVs recorded for the sample on a single flow cell", + "rdfs:label": "NumberofFOVs", "rdfs:subClassOf": [ { - "@id": "bts:LoopCalling" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiCCUPS", - "sms:required": "sms:false", + "sms:displayName": "Number of FOVs", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Cooltools", + "@id": "bts:MeanTotalTranscriptsperArea", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cooltools", + "rdfs:comment": "The mean total transcripts per um3", + "rdfs:label": "MeanTotalTranscriptsperArea", "rdfs:subClassOf": [ { - "@id": "bts:LoopCalling" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cooltools", - "sms:required": "sms:false", + "sms:displayName": "Mean Total Transcripts per Area", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel4", + "@id": "bts:UniqueGenes", "@type": "rdfs:Class", - "rdfs:comment": "Derived imaging data: Object-by-feature array", - "rdfs:label": "ImagingLevel4", + "rdfs:comment": "The total unique genes detected above background", + "rdfs:label": "UniqueGenes", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 4", + "sms:displayName": "Unique Genes", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANParentChannelMetadataID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:Parameterfile" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:CommitSHA" - }, - { - "@id": "bts:NumberofObjects" - }, - { - "@id": "bts:NumberofFeatures" - }, - { - "@id": "bts:ImagingObjectClass" - }, - { - "@id": "bts:ImagingSummaryStatistic" - } - ], "sms:validationRules": [] }, { - "@id": "bts:NumberofFeatures", + "@id": "bts:TotalNegativeProbeCounts", "@type": "rdfs:Class", - "rdfs:comment": "The number of features (eg channels) described", - "rdfs:label": "NumberofFeatures", + "rdfs:comment": "Mean Total Negative probe counts/cell", + "rdfs:label": "TotalNegativeProbeCounts", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Features", + "sms:displayName": "Total Negative Probe Counts", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:ImagingSummaryStatistic", + "@id": "bts:RNA", "@type": "rdfs:Class", - "rdfs:comment": "Function used to summarize object/feature intensity", - "rdfs:label": "ImagingSummaryStatistic", + "rdfs:comment": "TBD", + "rdfs:label": "RNA", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:CosMxAssayType" + }, + { + "@id": "bts:MicroarrayMolecule" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Mean" - }, + "sms:displayName": "RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Protein", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Protein", + "rdfs:subClassOf": [ { - "@id": "bts:Median" + "@id": "bts:CosMxAssayType" }, { - "@id": "bts:NotSpecified" + "@id": "bts:AnalyteType" } ], - "sms:displayName": "Imaging Summary Statistic", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "protein", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SRRSImagingLevel2", + "@id": "bts:MassSpectrometryLevel1", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN raw and pre-processed image data", - "rdfs:label": "SRRSImagingLevel2", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1", + "rdfs:label": "MassSpectrometryLevel1", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -46169,7 +44513,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Imaging Level 2", + "sms:displayName": "Mass Spectrometry Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -46186,9 +44530,6 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:HTANParticipantID" - }, { "@id": "bts:HTANParentBiospecimenID" }, @@ -46196,748 +44537,700 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" + "@id": "bts:MSBatchID" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:MS-basedAssayType" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:AnalyteType" }, { - "@id": "bts:Microscope" + "@id": "bts:MS-basedTargeted" }, { - "@id": "bts:Objective" + "@id": "bts:MSInstrumentVendorandModel" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:MSSource" }, { - "@id": "bts:Pyramid" + "@id": "bts:Polarity" }, { - "@id": "bts:Zstack" + "@id": "bts:MassRangeLowValue" }, { - "@id": "bts:Tseries" + "@id": "bts:MassRangeHighValue" }, { - "@id": "bts:PassedQC" + "@id": "bts:DataCollectionMode" }, { - "@id": "bts:FrameAveraging" + "@id": "bts:MSScanMode" }, { - "@id": "bts:ImageID" + "@id": "bts:MSLabeling" }, { - "@id": "bts:DimensionOrder" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:PhysicalSizeX" + "@id": "bts:LCInstrumentVendorandModel" }, { - "@id": "bts:PhysicalSizeXUnit" + "@id": "bts:LCColumnVendorandModel" }, { - "@id": "bts:PhysicalSizeY" + "@id": "bts:LCResin" }, { - "@id": "bts:PhysicalSizeYUnit" + "@id": "bts:LCLengthValue" }, { - "@id": "bts:PixelsBigEndian" + "@id": "bts:LCTempValue" }, { - "@id": "bts:PlaneCount" + "@id": "bts:LCIDValue" }, { - "@id": "bts:SizeC" + "@id": "bts:LCFlowRate" }, { - "@id": "bts:SizeT" + "@id": "bts:LCGradient" }, { - "@id": "bts:SizeX" + "@id": "bts:LCMobilePhaseA" }, { - "@id": "bts:SizeY" + "@id": "bts:LCMobilePhaseB" }, { - "@id": "bts:SizeZ" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:PixelType" + "@id": "bts:MSInstrumentMetadataFile" } ], "sms:validationRules": [] }, { - "@id": "bts:10XGenomicsXeniumISSExperiment", + "@id": "bts:MSBatchID", "@type": "rdfs:Class", - "rdfs:comment": "All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment", - "rdfs:label": "10XGenomicsXeniumISSExperiment", + "rdfs:comment": "Batch ID indicating a set of samples that were run together.", + "rdfs:label": "MSBatchID", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10X Genomics Xenium ISS Experiment", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "MS Batch ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MS-basedAssayType", + "@type": "rdfs:Class", + "rdfs:comment": "Analytes are the target molecules being measured with the assay.", + "rdfs:label": "MS-basedAssayType", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MassSpectrometryLevel1" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Filename" + "@id": "bts:LC-MS" }, { - "@id": "bts:FileFormat" + "@id": "bts:MS" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:TMT" }, { - "@id": "bts:HTANDataFileID" - }, + "@id": "bts:LC-MS/MS" + } + ], + "sms:displayName": "MS-based Assay Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AnalyteType", + "@type": "rdfs:Class", + "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteType", + "rdfs:subClassOf": [ { - "@id": "bts:XeniumBundleContents" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SlideID" + "@id": "bts:CfDNAAnalyte" }, { - "@id": "bts:ROIname" + "@id": "bts:DNAAnalyte" }, { - "@id": "bts:PanelName" + "@id": "bts:RNAAnalyte" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:TotalRNAAnalyte" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:TissueBlockAnalyte" }, { - "@id": "bts:TotalNumberofCells" + "@id": "bts:TissueSectionAnalyte" }, { - "@id": "bts:TotalNumberofTargets" + "@id": "bts:PBMCsorPlasmaorSerumAnalyte" }, { - "@id": "bts:Surfacearea" + "@id": "bts:CDNALibrariesAnalyte" }, { - "@id": "bts:ExperimentIFChannels" + "@id": "bts:PBMCs" }, { - "@id": "bts:TranscriptsperCell" + "@id": "bts:Plasma" }, { - "@id": "bts:PercentofTranscriptswithinCells" + "@id": "bts:SerumAnalyte" }, { - "@id": "bts:DecodedTranscripts" + "@id": "bts:Lipid" }, { - "@id": "bts:XeniumIFimageHTANFileID" + "@id": "bts:Protein" }, { - "@id": "bts:XeniumHEimageHTANFileID" + "@id": "bts:Metabolite" } ], + "sms:displayName": "Analyte Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:XeniumBundleContents", + "@id": "bts:MS-basedTargeted", "@type": "rdfs:Class", - "rdfs:comment": "A comma separated list of filenames within the Xenium bundle zip file", - "rdfs:label": "XeniumBundleContents", + "rdfs:comment": "Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.", + "rdfs:label": "MS-basedTargeted", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium Bundle Contents", + "schema:rangeIncludes": [ + { + "@id": "bts:Targeted" + }, + { + "@id": "bts:Untargeted" + } + ], + "sms:displayName": "MS-based Targeted", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PanelName", + "@id": "bts:MSInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))", - "rdfs:label": "PanelName", + "rdfs:comment": "An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.", + "rdfs:label": "MSInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Panel Name", + "sms:displayName": "MS Instrument Vendor and Model", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofCells", + "@id": "bts:MSSource", "@type": "rdfs:Class", - "rdfs:comment": "The total number of cells analyzed on the flow cell", - "rdfs:label": "TotalNumberofCells", + "rdfs:comment": "The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)", + "rdfs:label": "MSSource", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:MALDI" + }, + { + "@id": "bts:MALDI-2" + }, + { + "@id": "bts:DESI" + }, + { + "@id": "bts:SIMS" + }, + { + "@id": "bts:NESI" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "MS Source", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofTargets", + "@id": "bts:Polarity", "@type": "rdfs:Class", - "rdfs:comment": "Refers to the target of an assay. Can be genes/transcripts or probes", - "rdfs:label": "TotalNumberofTargets", + "rdfs:comment": "The polarity of the mass analysis (positive or negative ion modes)", + "rdfs:label": "Polarity", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Targets", + "schema:rangeIncludes": [ + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Negative" + } + ], + "sms:displayName": "Polarity", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExperimentIFChannels", + "@id": "bts:MassRangeLowValue", "@type": "rdfs:Class", - "rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)", - "rdfs:label": "ExperimentIFChannels", + "rdfs:comment": "The low value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeLowValue", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Experiment IF Channels", + "sms:displayName": "Mass Range Low Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TranscriptsperCell", + "@id": "bts:MassRangeHighValue", "@type": "rdfs:Class", - "rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide", - "rdfs:label": "TranscriptsperCell", + "rdfs:comment": "The high value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeHighValue", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcripts per Cell", + "sms:displayName": "Mass Range High Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentofTranscriptswithinCells", + "@id": "bts:DataCollectionMode", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of transcripts assigned to assayed cells", - "rdfs:label": "PercentofTranscriptswithinCells", + "rdfs:comment": "Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", + "rdfs:label": "DataCollectionMode", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent of Transcripts within Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:DDA" + }, + { + "@id": "bts:DIA" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Data Collection Mode", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DecodedTranscripts", + "@id": "bts:MSScanMode", "@type": "rdfs:Class", - "rdfs:comment": "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).", - "rdfs:label": "DecodedTranscripts", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Decoded Transcripts", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:XeniumIFimageHTANFileID", - "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumIFimageHTANFileID", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Xenium IF image HTAN File ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:XeniumHEimageHTANFileID", - "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumHEimageHTANFileID", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Xenium HE image HTAN File ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RPPALevel2", - "@type": "rdfs:Class", - "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", - "rdfs:label": "RPPALevel2", + "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", + "rdfs:label": "MSScanMode", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MS" }, { - "@id": "bts:AssayType" + "@id": "bts:MS/MS" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:MS3" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Other" } ], + "sms:displayName": "MS Scan Mode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HTANRPPAAntibodyTable", + "@id": "bts:MSLabeling", "@type": "rdfs:Class", - "rdfs:comment": "A table containing antibody level metadata for RPPA", - "rdfs:label": "HTANRPPAAntibodyTable", + "rdfs:comment": "Indicates whether samples were labeled prior to MS analysis (e.g., TMT)", + "rdfs:label": "MSLabeling", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table", + "sms:displayName": "MS Labeling", "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:HTANRPPAAntibodyTableID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:AbNameReportedonDataset" - }, - { - "@id": "bts:GENCODEGeneSymbolTarget" - }, - { - "@id": "bts:UNIPROTProteinIDTarget" - }, - { - "@id": "bts:PhosphoproteinFlag" - }, - { - "@id": "bts:Vendor" - }, - { - "@id": "bts:CatalogNumber" - }, - { - "@id": "bts:InternalAbID" - }, - { - "@id": "bts:Species" - }, - { - "@id": "bts:RPPADilution" - }, - { - "@id": "bts:PhosphoSite" - }, - { - "@id": "bts:RPPAValidationStatus" - }, - { - "@id": "bts:Clone" - }, - { - "@id": "bts:Clonality" - }, - { - "@id": "bts:AntibodyNotes" - } - ], "sms:validationRules": [] }, { - "@id": "bts:HTANRPPAAntibodyTableID", + "@id": "bts:LCInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", - "rdfs:label": "HTANRPPAAntibodyTableID", + "rdfs:comment": "The manufacturer of the instrument used for LC.", + "rdfs:label": "LCInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table ID", + "sms:displayName": "LC Instrument Vendor and Model", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AbNameReportedonDataset", + "@id": "bts:LCColumnVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "The antibody name.", - "rdfs:label": "AbNameReportedonDataset", + "rdfs:comment": "The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'", + "rdfs:label": "LCColumnVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ab Name Reported on Dataset", + "sms:displayName": "LC Column Vendor and Model", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GENCODEGeneSymbolTarget", + "@id": "bts:LCResin", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", - "rdfs:label": "GENCODEGeneSymbolTarget", + "rdfs:comment": "Details of the resin used for lc, including vendor, particle size, pore size", + "rdfs:label": "LCResin", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GENCODE Gene Symbol Target", + "sms:displayName": "LC Resin", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UNIPROTProteinIDTarget", + "@id": "bts:LCLengthValue", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", - "rdfs:label": "UNIPROTProteinIDTarget", + "rdfs:comment": "LC column length in cm.", + "rdfs:label": "LCLengthValue", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UNIPROT Protein ID Target", + "sms:displayName": "LC Length Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PhosphoproteinFlag", + "@id": "bts:LCTempValue", "@type": "rdfs:Class", - "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", - "rdfs:label": "PhosphoproteinFlag", + "rdfs:comment": "LC temperature in C.", + "rdfs:label": "LCTempValue", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Phosphoprotein Flag", + "sms:displayName": "LC Temp Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Vendor", + "@id": "bts:LCIDValue", "@type": "rdfs:Class", - "rdfs:comment": "Vendor", - "rdfs:label": "Vendor", + "rdfs:comment": "LC column inner diameter in microns.", + "rdfs:label": "LCIDValue", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Vendor", - "sms:required": "sms:false", + "sms:displayName": "LC ID Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CatalogNumber", + "@id": "bts:LCFlowRate", "@type": "rdfs:Class", - "rdfs:comment": "Catalog Number", - "rdfs:label": "CatalogNumber", + "rdfs:comment": "LC flow rate in nL/min.", + "rdfs:label": "LCFlowRate", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Catalog Number", - "sms:required": "sms:false", + "sms:displayName": "LC Flow Rate", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InternalAbID", + "@id": "bts:LCGradient", "@type": "rdfs:Class", - "rdfs:comment": "Internal lab ID for an antibody.", - "rdfs:label": "InternalAbID", + "rdfs:comment": "The program dictates the mobile phase solvent composition over the course of the chromatographic run.", + "rdfs:label": "LCGradient", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Internal Ab ID", + "sms:displayName": "LC Gradient", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Species", + "@id": "bts:LCMobilePhaseA", "@type": "rdfs:Class", - "rdfs:comment": "Host animal.", - "rdfs:label": "Species", + "rdfs:comment": "Composition of mobile phase A", + "rdfs:label": "LCMobilePhaseA", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Mouse" - }, - { - "@id": "bts:Rabbit" - }, - { - "@id": "bts:Goat" - } - ], - "sms:displayName": "Species", + "sms:displayName": "LC Mobile Phase A", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RPPADilution", + "@id": "bts:LCMobilePhaseB", "@type": "rdfs:Class", - "rdfs:comment": "The dilution ratio.", - "rdfs:label": "RPPADilution", + "rdfs:comment": "Composition of mobile phase B", + "rdfs:label": "LCMobilePhaseB", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Dilution", - "sms:required": "sms:false", + "sms:displayName": "LC Mobile Phase B", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PhosphoSite", + "@id": "bts:MSInstrumentMetadataFile", "@type": "rdfs:Class", - "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", - "rdfs:label": "PhosphoSite", + "rdfs:comment": "Additional file containing instrument metadata details. Use either synapse_path or entity_Id", + "rdfs:label": "MSInstrumentMetadataFile", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Phospho Site", + "sms:displayName": "MS Instrument Metadata File", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:PhosphoproteinFlag" - } - ], "sms:validationRules": [] }, { - "@id": "bts:RPPAValidationStatus", + "@id": "bts:MassSpectrometryLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", - "rdfs:label": "RPPAValidationStatus", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2", + "rdfs:label": "MassSpectrometryLevel2", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Mass Spectrometry Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Valid" + "@id": "bts:MassSpectrometryLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:UsewithCaution" + "@id": "bts:Filename" }, { - "@id": "bts:UnderEvaluation" + "@id": "bts:FileFormat" }, { - "@id": "bts:UsedforQC" + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:MSAssayCategory" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:MassSpectrometryAuxiliaryFile" } ], - "sms:displayName": "RPPA Validation Status", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clone", + "@id": "bts:MSAssayCategory", "@type": "rdfs:Class", - "rdfs:comment": "Clone", - "rdfs:label": "Clone", + "rdfs:comment": "Type of Mass Spectrometry performed.", + "rdfs:label": "MSAssayCategory", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Clone", - "sms:required": "sms:false", + "sms:displayName": "MS Assay Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AntibodyNotes", + "@id": "bts:MassSpectrometryAuxiliaryFile", "@type": "rdfs:Class", - "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", - "rdfs:label": "AntibodyNotes", + "rdfs:comment": "Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).", + "rdfs:label": "MassSpectrometryAuxiliaryFile", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody Notes", + "sms:displayName": "Mass Spectrometry Auxiliary File", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + } + ], "sms:validationRules": [] }, { - "@id": "bts:RPPALevel3", + "@id": "bts:MassSpectrometryLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", - "rdfs:label": "RPPALevel3", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3", + "rdfs:label": "MassSpectrometryLevel3", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -46946,11 +45239,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 3", + "sms:displayName": "Mass Spectrometry Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MassSpectrometryLevel2" } ], "sms:requiresDependency": [ @@ -46964,7 +45257,7 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:HTANDataFileID" }, { "@id": "bts:HTANParentBiospecimenID" @@ -46973,25 +45266,22 @@ "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AssayType" + "@id": "bts:MSAssayCategory" }, { "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:MassSpectrometryAuxiliaryFile" } ], "sms:validationRules": [] }, { - "@id": "bts:RPPALevel4", + "@id": "bts:MassSpectrometryLevel4", "@type": "rdfs:Class", - "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", - "rdfs:label": "RPPALevel4", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4", + "rdfs:label": "MassSpectrometryLevel4", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -47000,11 +45290,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 4", + "sms:displayName": "Mass Spectrometry Level 4", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:MassSpectrometryLevel3" } ], "sms:requiresDependency": [ @@ -47018,7 +45308,7 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:HTANDataFileID" }, { "@id": "bts:HTANParentBiospecimenID" @@ -47027,146 +45317,139 @@ "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:MSAssayCategory" }, { - "@id": "bts:AssayType" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:BatchCorrectionMethod" + "@id": "bts:MassSpectrometryAuxiliaryFile" } ], "sms:validationRules": [] }, { - "@id": "bts:BatchCorrectionMethod", + "@id": "bts:HTANChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "Method that was used to batch correct Level 3 data", - "rdfs:label": "BatchCorrectionMethod", + "rdfs:comment": "HTAN ID for this channel metadata table (same for all rows)", + "rdfs:label": "HTANChannelMetadataID", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Batch Correction Method", - "sms:required": "sms:false", + "sms:displayName": "HTAN Channel Metadata ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NanostringCosMxSMIExperiment", + "@id": "bts:ChannelID", "@type": "rdfs:Class", - "rdfs:comment": "RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)", - "rdfs:label": "NanostringCosMxSMIExperiment", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')", + "rdfs:label": "ChannelID", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nanostring CosMx SMI Experiment", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "Channel ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ChannelName", + "@type": "rdfs:Class", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", + "rdfs:label": "ChannelName", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:CosMxBundleContents" - }, - { - "@id": "bts:SlideID" - }, - { - "@id": "bts:CosMxAssayType" - }, - { - "@id": "bts:PanelName" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:TotalNumberofCells" - }, - { - "@id": "bts:TotalNumberofTargets" - }, - { - "@id": "bts:NumberofFOVs" - }, - { - "@id": "bts:Surfacearea" - }, - { - "@id": "bts:ExperimentIFChannels" - }, - { - "@id": "bts:TranscriptsperCell" - }, - { - "@id": "bts:PercentofTranscriptswithinCells" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Channel Name", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ChannelPassedQC", + "@type": "rdfs:Class", + "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", + "rdfs:label": "ChannelPassedQC", + "rdfs:subClassOf": [ { - "@id": "bts:MeanTotalTranscriptsperArea" - }, + "@id": "bts:ImagingLevel3Channels" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:UniqueGenes" + "@id": "bts:Yes" }, { - "@id": "bts:TotalNegativeProbeCounts" + "@id": "bts:No-ChannelFailedQC" } ], + "sms:displayName": "Channel Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CosMxBundleContents", + "@id": "bts:CycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "A comma separated list of filenames within the CosMx bundle zip file", - "rdfs:label": "CosMxBundleContents", + "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", + "rdfs:label": "CycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CosMx Bundle Contents", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "Cycle Number", + "sms:required": "sms:false", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:CosMxAssayType", + "@id": "bts:SubCycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay", - "rdfs:label": "CosMxAssayType", + "rdfs:comment": "Sub cycle number", + "rdfs:label": "SubCycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sub Cycle Number", + "sms:required": "sms:false", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:AntibodyRole", + "@type": "rdfs:Class", + "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", + "rdfs:label": "AntibodyRole", + "rdfs:subClassOf": [ + { + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -47174,1466 +45457,391 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RNA" + "@id": "bts:Primary" }, { - "@id": "bts:Protein" + "@id": "bts:Secondary" } ], - "sms:displayName": "CosMx Assay Type", + "sms:displayName": "Antibody Role", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NumberofFOVs", + "@id": "bts:TargetName", "@type": "rdfs:Class", - "rdfs:comment": "The total number of FOVs recorded for the sample on a single flow cell", - "rdfs:label": "NumberofFOVs", + "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", + "rdfs:label": "TargetName", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of FOVs", + "sms:displayName": "Target Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MeanTotalTranscriptsperArea", + "@id": "bts:AntibodyName", "@type": "rdfs:Class", - "rdfs:comment": "The mean total transcripts per um3", - "rdfs:label": "MeanTotalTranscriptsperArea", + "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", + "rdfs:label": "AntibodyName", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Total Transcripts per Area", + "sms:displayName": "Antibody Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UniqueGenes", + "@id": "bts:RRIDidentifier", "@type": "rdfs:Class", - "rdfs:comment": "The total unique genes detected above background", - "rdfs:label": "UniqueGenes", + "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", + "rdfs:label": "RRIDidentifier", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Unique Genes", + "sms:displayName": "RRID identifier", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match AB_\\d+" + ] + }, + { + "@id": "bts:Fluorophore", + "@type": "rdfs:Class", + "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", + "rdfs:label": "Fluorophore", + "rdfs:subClassOf": [ + { + "@id": "bts:ImagingLevel3Channels" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fluorophore", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNegativeProbeCounts", + "@id": "bts:Lot", "@type": "rdfs:Class", - "rdfs:comment": "Mean Total Negative probe counts/cell", - "rdfs:label": "TotalNegativeProbeCounts", + "rdfs:comment": "Lot number from vendor", + "rdfs:label": "Lot", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Negative Probe Counts", - "sms:required": "sms:true", + "sms:displayName": "Lot", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RNA", + "@id": "bts:ExcitationWavelength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNA", + "rdfs:comment": "Center/peak of the excitation spectrum (nm)", + "rdfs:label": "ExcitationWavelength", "rdfs:subClassOf": [ { - "@id": "bts:CosMxAssayType" - }, - { - "@id": "bts:MicroarrayMolecule" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RNA", + "sms:displayName": "Excitation Wavelength", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Protein", + "@id": "bts:EmissionWavelength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Protein", + "rdfs:comment": "Center/peak of the emission spectrum (nm)", + "rdfs:label": "EmissionWavelength", "rdfs:subClassOf": [ { - "@id": "bts:CosMxAssayType" - }, + "@id": "bts:ImagingLevel3Channels" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Emission Wavelength", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:ExcitationBandwidth", + "@type": "rdfs:Class", + "rdfs:comment": "Nominal width of excitation spectrum (nm)", + "rdfs:label": "ExcitationBandwidth", + "rdfs:subClassOf": [ { - "@id": "bts:AnalyteType" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "protein", + "sms:displayName": "Excitation Bandwidth", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:MassSpectrometryLevel1", + "@id": "bts:EmissionBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1", - "rdfs:label": "MassSpectrometryLevel1", + "rdfs:comment": "Nominal width of emission spectrum (nm)", + "rdfs:label": "EmissionBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Level 1", + "sms:displayName": "Emission Bandwidth", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:MetalIsotopeElement", + "@type": "rdfs:Class", + "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", + "rdfs:label": "MetalIsotopeElement", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:H" }, { - "@id": "bts:Filename" + "@id": "bts:He" }, { - "@id": "bts:FileFormat" + "@id": "bts:Li" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Be" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:B" }, { - "@id": "bts:MSBatchID" + "@id": "bts:C" }, { - "@id": "bts:MS-basedAssayType" + "@id": "bts:N" }, { - "@id": "bts:AnalyteType" + "@id": "bts:O" }, { - "@id": "bts:MS-basedTargeted" + "@id": "bts:F" }, { - "@id": "bts:MSInstrumentVendorandModel" + "@id": "bts:Ne" }, { - "@id": "bts:MSSource" + "@id": "bts:Na" }, { - "@id": "bts:Polarity" + "@id": "bts:Mg" }, { - "@id": "bts:MassRangeLowValue" + "@id": "bts:Al" }, { - "@id": "bts:MassRangeHighValue" + "@id": "bts:Si" }, { - "@id": "bts:DataCollectionMode" + "@id": "bts:P" }, { - "@id": "bts:MSScanMode" + "@id": "bts:S" }, { - "@id": "bts:MSLabeling" + "@id": "bts:Cl" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Ar" }, { - "@id": "bts:LCInstrumentVendorandModel" + "@id": "bts:K" }, { - "@id": "bts:LCColumnVendorandModel" + "@id": "bts:Ca" }, { - "@id": "bts:LCResin" + "@id": "bts:Sc" }, { - "@id": "bts:LCLengthValue" + "@id": "bts:Ti" }, { - "@id": "bts:LCTempValue" + "@id": "bts:V" }, { - "@id": "bts:LCIDValue" + "@id": "bts:Cr" }, { - "@id": "bts:LCFlowRate" + "@id": "bts:Mn" }, { - "@id": "bts:LCGradient" + "@id": "bts:Fe" }, { - "@id": "bts:LCMobilePhaseA" + "@id": "bts:Co" }, { - "@id": "bts:LCMobilePhaseB" + "@id": "bts:Ni" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Cu" }, { - "@id": "bts:MSInstrumentMetadataFile" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MSBatchID", - "@type": "rdfs:Class", - "rdfs:comment": "Batch ID indicating a set of samples that were run together.", - "rdfs:label": "MSBatchID", - "rdfs:subClassOf": [ + "@id": "bts:Zn" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MS Batch ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MS-basedAssayType", - "@type": "rdfs:Class", - "rdfs:comment": "Analytes are the target molecules being measured with the assay.", - "rdfs:label": "MS-basedAssayType", - "rdfs:subClassOf": [ + "@id": "bts:Ga" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ge" + }, { - "@id": "bts:LC-MS" + "@id": "bts:As" }, { - "@id": "bts:MS" + "@id": "bts:Se" }, { - "@id": "bts:TMT" + "@id": "bts:Br" }, { - "@id": "bts:LC-MS/MS" - } - ], - "sms:displayName": "MS-based Assay Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AnalyteType", - "@type": "rdfs:Class", - "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", - "rdfs:label": "AnalyteType", - "rdfs:subClassOf": [ + "@id": "bts:Kr" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Rb" + }, { - "@id": "bts:CfDNAAnalyte" + "@id": "bts:Sr" }, { - "@id": "bts:DNAAnalyte" + "@id": "bts:Y" }, { - "@id": "bts:RNAAnalyte" + "@id": "bts:Zr" }, { - "@id": "bts:TotalRNAAnalyte" + "@id": "bts:Nb" }, { - "@id": "bts:TissueBlockAnalyte" + "@id": "bts:Mo" }, { - "@id": "bts:TissueSectionAnalyte" + "@id": "bts:Tc" }, { - "@id": "bts:PBMCsorPlasmaorSerumAnalyte" + "@id": "bts:Ru" }, { - "@id": "bts:CDNALibrariesAnalyte" + "@id": "bts:Rh" }, { - "@id": "bts:PBMCs" + "@id": "bts:Pd" }, { - "@id": "bts:Plasma" + "@id": "bts:Ag" }, { - "@id": "bts:SerumAnalyte" + "@id": "bts:Cd" }, { - "@id": "bts:Lipid" + "@id": "bts:In" }, { - "@id": "bts:Protein" + "@id": "bts:Sn" }, { - "@id": "bts:Metabolite" - } - ], - "sms:displayName": "Analyte Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MS-basedTargeted", - "@type": "rdfs:Class", - "rdfs:comment": "Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.", - "rdfs:label": "MS-basedTargeted", - "rdfs:subClassOf": [ + "@id": "bts:Sb" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Te" + }, { - "@id": "bts:Targeted" + "@id": "bts:I" }, { - "@id": "bts:Untargeted" - } - ], - "sms:displayName": "MS-based Targeted", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MSInstrumentVendorandModel", - "@type": "rdfs:Class", - "rdfs:comment": "An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.", - "rdfs:label": "MSInstrumentVendorandModel", - "rdfs:subClassOf": [ + "@id": "bts:Xe" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MS Instrument Vendor and Model", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MSSource", - "@type": "rdfs:Class", - "rdfs:comment": "The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)", - "rdfs:label": "MSSource", - "rdfs:subClassOf": [ + "@id": "bts:Cs" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ba" + }, { - "@id": "bts:MALDI" + "@id": "bts:La" }, { - "@id": "bts:MALDI-2" + "@id": "bts:Ce" }, { - "@id": "bts:DESI" + "@id": "bts:Pr" }, { - "@id": "bts:SIMS" + "@id": "bts:Nd" }, { - "@id": "bts:NESI" + "@id": "bts:Pm" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "MS Source", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Polarity", - "@type": "rdfs:Class", - "rdfs:comment": "The polarity of the mass analysis (positive or negative ion modes)", - "rdfs:label": "Polarity", - "rdfs:subClassOf": [ + "@id": "bts:Sm" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Eu" + }, { - "@id": "bts:Positive" + "@id": "bts:Gd" }, { - "@id": "bts:Negative" - } - ], - "sms:displayName": "Polarity", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MassRangeLowValue", - "@type": "rdfs:Class", - "rdfs:comment": "The low value of the scanned mass range for MS1 in m/z.", - "rdfs:label": "MassRangeLowValue", - "rdfs:subClassOf": [ + "@id": "bts:Tb" + }, { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Range Low Value", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MassRangeHighValue", - "@type": "rdfs:Class", - "rdfs:comment": "The high value of the scanned mass range for MS1 in m/z.", - "rdfs:label": "MassRangeHighValue", - "rdfs:subClassOf": [ - { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Range High Value", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DataCollectionMode", - "@type": "rdfs:Class", - "rdfs:comment": "Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", - "rdfs:label": "DataCollectionMode", - "rdfs:subClassOf": [ - { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:DDA" - }, - { - "@id": "bts:DIA" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Data Collection Mode", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MSScanMode", - "@type": "rdfs:Class", - "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", - "rdfs:label": "MSScanMode", - "rdfs:subClassOf": [ - { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:MS" - }, - { - "@id": "bts:MS/MS" - }, - { - "@id": "bts:MS3" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "MS Scan Mode", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MSLabeling", - "@type": "rdfs:Class", - "rdfs:comment": "Indicates whether samples were labeled prior to MS analysis (e.g., TMT)", - "rdfs:label": "MSLabeling", - "rdfs:subClassOf": [ - { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MS Labeling", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LCInstrumentVendorandModel", - "@type": "rdfs:Class", - "rdfs:comment": "The manufacturer of the instrument used for LC.", - "rdfs:label": "LCInstrumentVendorandModel", - "rdfs:subClassOf": [ - { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "LC Instrument Vendor and Model", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LCColumnVendorandModel", - "@type": "rdfs:Class", - "rdfs:comment": "The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - 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(eg 'Blue' or 'CD45' or 'E-cadherin')", - "rdfs:label": "ChannelName", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Channel Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ChannelPassedQC", - "@type": "rdfs:Class", - "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", - "rdfs:label": "ChannelPassedQC", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelFailedQC" - } - ], - "sms:displayName": "Channel Passed QC", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CycleNumber", - "@type": "rdfs:Class", - "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", - "rdfs:label": "CycleNumber", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cycle Number", - "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:SubCycleNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Sub cycle number", - "rdfs:label": "SubCycleNumber", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sub Cycle Number", - "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:AntibodyRole", - "@type": "rdfs:Class", - "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", - "rdfs:label": "AntibodyRole", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Primary" - }, - { - "@id": "bts:Secondary" - } - ], - "sms:displayName": "Antibody Role", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TargetName", - "@type": "rdfs:Class", - "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", - "rdfs:label": "TargetName", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Target Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AntibodyName", - "@type": "rdfs:Class", - "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", - "rdfs:label": "AntibodyName", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Antibody Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:RRIDidentifier", - "@type": "rdfs:Class", - "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", - "rdfs:label": "RRIDidentifier", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RRID identifier", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match AB_\\d+" - ] - }, - { - "@id": "bts:Fluorophore", - "@type": "rdfs:Class", - "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", - "rdfs:label": "Fluorophore", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fluorophore", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Lot", - "@type": "rdfs:Class", - "rdfs:comment": "Lot number from vendor", - "rdfs:label": 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"rdfs:Class", - "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", - "rdfs:label": "MetalIsotopeElement", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:H" - }, - { - "@id": "bts:He" - }, - { - "@id": "bts:Li" - }, - { - "@id": "bts:Be" - }, - { - "@id": "bts:B" - }, - { - "@id": "bts:C" - }, - { - "@id": "bts:N" - }, - { - "@id": "bts:O" - }, - { - "@id": "bts:F" - }, - { - "@id": "bts:Ne" - }, - { - "@id": "bts:Na" - }, - { - "@id": "bts:Mg" - }, - { - "@id": "bts:Al" - }, - { - "@id": "bts:Si" - }, - { - "@id": "bts:P" - }, - { - "@id": "bts:S" - }, - { - "@id": "bts:Cl" - }, - { - "@id": "bts:Ar" - }, - { - "@id": "bts:K" - }, - { - "@id": "bts:Ca" - }, - { - "@id": "bts:Sc" - }, - { - "@id": "bts:Ti" - }, - { - "@id": "bts:V" - }, - { - "@id": "bts:Cr" - }, - { - "@id": "bts:Mn" - }, - { - "@id": "bts:Fe" - }, - { - "@id": "bts:Co" - }, - { - "@id": "bts:Ni" - }, - { - "@id": "bts:Cu" - }, - { - "@id": "bts:Zn" - }, - { - "@id": "bts:Ga" - }, - { - "@id": "bts:Ge" - }, - { - "@id": "bts:As" - }, - { - "@id": "bts:Se" - }, - { - "@id": "bts:Br" - }, - { - "@id": "bts:Kr" - }, - { - "@id": "bts:Rb" - }, - { - "@id": "bts:Sr" - }, - { - "@id": "bts:Y" - }, - { - "@id": "bts:Zr" - }, - { - "@id": "bts:Nb" - }, - { - "@id": "bts:Mo" - }, - { - "@id": "bts:Tc" - }, - { - "@id": "bts:Ru" - }, - { - "@id": "bts:Rh" - }, - { - "@id": "bts:Pd" - }, - { - "@id": "bts:Ag" - }, - { - "@id": "bts:Cd" - }, - { - "@id": "bts:In" - }, - { - "@id": "bts:Sn" - }, - { - "@id": "bts:Sb" - }, - { - "@id": "bts:Te" - }, - { - "@id": "bts:I" - }, - { - "@id": "bts:Xe" - }, - { - "@id": "bts:Cs" - }, - { - "@id": "bts:Ba" - }, - { - "@id": "bts:La" - }, - { - "@id": "bts:Ce" - }, - { - "@id": "bts:Pr" - }, - { - "@id": "bts:Nd" - }, - { - "@id": "bts:Pm" - }, - { - "@id": "bts:Sm" - }, - { - "@id": "bts:Eu" - }, - { - "@id": "bts:Gd" - }, - { - "@id": "bts:Tb" - }, - { - "@id": "bts:Dy" - }, + "@id": "bts:Dy" + }, { "@id": "bts:Ho" }, @@ -51222,6 +48430,26 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:ExSeq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ExSeq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + }, + { + "@id": "bts:ImagingAssayType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ExSeq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:RareCyteOrion", "@type": "rdfs:Class", @@ -51239,6 +48467,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Imaging", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Imaging", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Imaging", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Cm", "@type": "rdfs:Class", @@ -52174,964 +49419,2868 @@ "rdfs:label": "MicrofluidicsChip", "rdfs:subClassOf": [ { - "@id": "bts:SingleCellIsolationMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microfluidics Chip", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Droplets", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Droplets", - "rdfs:subClassOf": [ + "@id": "bts:SingleCellIsolationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microfluidics Chip", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Droplets", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Droplets", + "rdfs:subClassOf": [ + { + "@id": "bts:SingleCellIsolationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Droplets", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FACS", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FACS", + "rdfs:subClassOf": [ + { + "@id": "bts:SingleCellIsolationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FACS", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Plates", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Plates", + "rdfs:subClassOf": [ + { + "@id": "bts:SingleNucleusCapture" + }, + { + "@id": "bts:SingleCellIsolationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Plates", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:10x", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10x", + "rdfs:subClassOf": [ + { + "@id": "bts:SingleNucleusBuffer" + }, + { + "@id": "bts:SingleNucleusCapture" + }, + { + "@id": "bts:SingleCellIsolationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleiIsolation", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NucleiIsolation", + "rdfs:subClassOf": [ + { + "@id": "bts:SingleCellIsolationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei Isolation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GentleMACS", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "GentleMACS", + "rdfs:subClassOf": [ + { + "@id": "bts:DissociationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "gentleMACS", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Dounce", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Dounce", + "rdfs:subClassOf": [ + { + "@id": "bts:DissociationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Dounce", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:EnzymaticDigestion", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "EnzymaticDigestion", + "rdfs:subClassOf": [ + { + "@id": "bts:DissociationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Enzymatic Digestion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PairedEnd", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "PairedEnd", + "rdfs:subClassOf": [ + { + "@id": "bts:LibraryLayout" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Paired End", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SingleRead", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SingleRead", + "rdfs:subClassOf": [ + { + "@id": "bts:LibraryLayout" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Single Read", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Mid-length", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Mid-length", + "rdfs:subClassOf": [ + { + "@id": "bts:LibraryLayout" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mid-length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LongRead", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "LongRead", + "rdfs:subClassOf": [ + { + "@id": "bts:LibraryLayout" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Long Read", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": 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"bts:RiskFactor" + }, { - "@id": "bts:SpikeInConcentration" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:OtherSpikeIn", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "OtherSpikeIn", - "rdfs:subClassOf": [ + "@id": "bts:RelationshipType" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Spike In", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NoSpikeIn", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NoSpikeIn", - "rdfs:subClassOf": [ + "@id": "bts:Comorbidity" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "No Spike In", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PhiX", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "PhiX", - "rdfs:subClassOf": [ + "@id": "bts:PriorSitesofRadiation" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhiX", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SpikeInConcentration", - "@type": "rdfs:Class", - "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", - "rdfs:label": "SpikeInConcentration", - "rdfs:subClassOf": [ + "@id": "bts:TopographyCode" + }, { - "@id": "bts:ERCC" + "@id": "bts:ProgressionorRecurrenceAnatomicSite" + }, + { + "@id": "bts:TreatmentAnatomicSite" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:TissueorOrganofOrigin" + }, + { + "@id": "bts:PrimaryDiagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spike In Concentration", - "sms:required": "sms:true", + "sms:displayName": "Not Reported", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -54188,6 +53337,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:RRNADepletion", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RRNADepletion", + "rdfs:subClassOf": [ + { + "@id": "bts:LibrarySelectionMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "rRNA Depletion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:MiRNASizeFractionation", "@type": "rdfs:Class", @@ -142430,6 +141596,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Publication", + "@type": "rdfs:Class", + "rdfs:comment": "An empty parent attribute for publications", + "rdfs:label": "Publication", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Publication", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:PublicationManifest", "@type": "rdfs:Class", @@ -149789,6 +148972,312 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10xVisiumSpatialTranscriptomics", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BulkMethylation-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkRNA-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BulkRNA-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk RNA-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkWES", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BulkWES", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk WES", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ElectronMicroscopy", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ElectronMicroscopy", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Electron Microscopy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HI-C-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "HI-C-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HI-C-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RPPA", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RPPA", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "RPPA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MassSpectrometry", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MassSpectrometry", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mass Spectrometry", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomics", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSImaging", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SRRSImaging", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Imaging", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Slide-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATAC-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ScATAC-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATAC-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScDNA-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ScDNA-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scDNA-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScRNA-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ScRNA-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scRNA-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AccessoryManifest", + "@type": "rdfs:Class", + "rdfs:comment": "Accessory specific attributes", + "rdfs:label": "AccessoryManifest", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + }, + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory Manifest", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:DatasetName" + }, + { + "@id": "bts:AccessorySynapseID" + }, + { + "@id": "bts:AccessoryDescription" + }, + { + "@id": "bts:DataType" + }, + { + "@id": "bts:HTANCenterID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:Accessory-associatedHTANParentDataFileID" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:OtherDataTypeSpecified", + "@type": "rdfs:Class", + "rdfs:comment": "Other types of data associated with the content.", + "rdfs:label": "OtherDataTypeSpecified", + "rdfs:subClassOf": [ + { + "@id": "bts:Publication" + }, + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Other Data Type Specified", + "sms:required": "sms:false", + "sms:validationRules": [ + "list like" + ] + }, { "@id": "bts:Accessory", "@type": "rdfs:Class", From 0055906480c861c887154f3a34b9d32de2e20e49 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 12:14:55 -0400 Subject: [PATCH 08/14] Update HTAN.model.csv --- HTAN.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index d7545331..b7f4244a 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -7,7 +7,7 @@ Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organis File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, -CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,,,TRUE,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS Genomic Reference, CDS Library Layout, CDS Data Type, CDS Sequencing Platform, CDS Library Selection Method",, +CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS Genomic Reference, CDS Library Layout, CDS Data Type, CDS Sequencing Platform, CDS Library Selection Method",,TRUE,,,, CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,https://dataservice.datacommons.cancer.gov/#/resources,list like @@ -923,7 +923,7 @@ Publication Abstract,The abstract or short description of the content presented/ License,The type of license applicable to the content.,"0BSD, AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement, Proprietary, Other, Not licensed, Freeware",,,FALSE,Publication,,,list like PMID,The PubMed identifier associated with the publication (applicable to published manuscripts). Provide as a URL of the form https://pubmed.ncbi.nlm.nih.gov/{pmid},,,,FALSE,Publication,,,url Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like -Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,CDS Data Type,,list like +Other Data Type Specified,Other types of data associated with the content.,,CDS Data Type,,FALSE,Publication,,,list like Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url warning Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,, From 1c7a71a839a90c489f229e1401606c7fe0085cb8 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Mon, 3 Jun 2024 12:16:33 -0400 Subject: [PATCH 09/14] whitespace fix --- HTAN.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index b7f4244a..1470ec53 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -8,7 +8,7 @@ File,A type of Information Content Entity specific to OS,,,,FALSE,Information Co Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS Genomic Reference, CDS Library Layout, CDS Data Type, CDS Sequencing Platform, CDS Library Selection Method",,TRUE,,,, -CDS Genomic Reference ,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS Genomic Reference,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,https://dataservice.datacommons.cancer.gov/#/resources,list like CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://dataservice.datacommons.cancer.gov/#/resources, From aa986f361df36451b7640c60a5754dbef21d30c6 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 16:17:21 +0000 Subject: [PATCH 10/14] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 48325 ++++++++++++++++++++++---------------------- 1 file changed, 24414 insertions(+), 23911 deletions(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index f73558f7..af28a7e0 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -2877,20 +2877,52 @@ "sms:validationRules": [] }, { - "@id": "bts:Checksum", + "@id": "bts:CDSSequencingTemplate", "@type": "rdfs:Class", - "rdfs:comment": "MD5 checksum of the BAM file", - "rdfs:label": "Checksum", + "rdfs:comment": "CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method", + "rdfs:label": "CDSSequencingTemplate", "rdfs:subClassOf": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Checksum", + "sms:displayName": "CDS Sequencing Template", "sms:required": "sms:true", + "sms:requiresComponent": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:CDSGenomicReference" + }, + { + "@id": "bts:CDSLibraryLayout" + }, + { + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:CDSSequencingPlatform" + }, + { + "@id": "bts:CDSLibrarySelectionMethod" + } + ], "sms:validationRules": [] }, { @@ -2913,10 +2945,10 @@ ] }, { - "@id": "bts:HTANBiospecimenID", + "@id": "bts:HTANParentBiospecimenID", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANBiospecimenID", + "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", + "rdfs:label": "HTANParentBiospecimenID", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -2925,7922 +2957,8554 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Biospecimen ID", + "sms:displayName": "HTAN Parent Biospecimen ID", "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:validationRules": [] }, { - "@id": "bts:Biospecimen", + "@id": "bts:CDSGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", - "rdfs:label": "Biospecimen", + "rdfs:comment": "TBD", + "rdfs:label": "CDSGenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen", + "sms:displayName": "CDS Genomic Reference", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:CDSLibraryLayout", + "@type": "rdfs:Class", + "rdfs:comment": "The read strategy or method that was used for sequencing and analysis of a nucleotide library.", + "rdfs:label": "CDSLibraryLayout", + "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANBiospecimenID" - }, - { - "@id": "bts:SourceHTANBiospecimenID" - }, - { - "@id": "bts:HTANParentID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:CollectionDaysfromIndex" - }, - { - "@id": "bts:AdjacentBiospecimenIDs" - }, - { - "@id": "bts:BiospecimenType" - }, - { - "@id": "bts:AcquisitionMethodType" - }, - { - "@id": "bts:FixativeType" - }, - { - "@id": "bts:StorageMethod" - }, - { - "@id": "bts:ProcessingDaysfromIndex" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SiteDataSource" - }, - { - "@id": "bts:CollectionMedia" - }, - { - "@id": "bts:MountingMedium" - }, - { - "@id": "bts:ProcessingLocation" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HistologyAssessmentBy" + "@id": "bts:PairedEnd" }, { - "@id": "bts:HistologyAssessmentMedium" - }, + "@id": "bts:SingleRead" + } + ], + "sms:displayName": "CDS Library Layout", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CDSDataType", + "@type": "rdfs:Class", + "rdfs:comment": "Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.", + "rdfs:label": "CDSDataType", + "rdfs:subClassOf": [ { - "@id": "bts:PreinvasiveMorphology" - }, + "@id": "bts:Publication" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:TumorInfiltratingLymphocytes" + "@id": "bts:10xVisiumSpatialTranscriptomics" }, { - "@id": "bts:DegreeofDysplasia" + "@id": "bts:BulkMethylation-seq" }, { - "@id": "bts:DysplasiaFraction" + "@id": "bts:BulkRNA-seq" }, { - "@id": "bts:NumberProliferatingCells" + "@id": "bts:BulkWES" }, { - "@id": "bts:PercentEosinophilInfiltration" + "@id": "bts:ElectronMicroscopy" }, { - "@id": "bts:PercentGranulocyteInfiltration" + "@id": "bts:ExSeq" }, { - "@id": "bts:PercentInflamInfiltration" + "@id": "bts:HI-C-seq" }, { - "@id": "bts:PercentLymphocyteInfiltration" + "@id": "bts:RPPA" }, { - "@id": "bts:PercentMonocyteInfiltration" + "@id": "bts:Imaging" }, { - "@id": "bts:PercentNecrosis" + "@id": "bts:MassSpectrometry" }, { - "@id": "bts:PercentNeutrophilInfiltration" + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics" }, { - "@id": "bts:PercentNormalCells" + "@id": "bts:OtherAssay" }, { - "@id": "bts:PercentStromalCells" + "@id": "bts:SRRSImaging" }, { - "@id": "bts:PercentTumorCells" + "@id": "bts:Slide-seq" }, { - "@id": "bts:PercentTumorNuclei" + "@id": "bts:ScATAC-seq" }, { - "@id": "bts:FiducialMarker" + "@id": "bts:ScDNA-seq" }, { - "@id": "bts:SlicingMethod" + "@id": "bts:ScRNA-seq" }, { - "@id": "bts:LysisBuffer" + "@id": "bts:AccessoryManifest" }, { - "@id": "bts:MethodofNucleicAcidIsolation" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", - "rdfs:label": "HTANParentID", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentBiospecimenID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", - "rdfs:label": "HTANParentBiospecimenID", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Biospecimen ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentDataFileID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", - "rdfs:label": "HTANParentDataFileID", - "rdfs:subClassOf": [ - { - "@id": "bts:File" + "@id": "bts:OtherDataTypeSpecified" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Data File ID", + "sms:displayName": "CDS Data Type", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:ClinicalDataTier2", + "@id": "bts:CDSSequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "Tier 2 Cancer Data", - "rdfs:label": "ClinicalDataTier2", + "rdfs:comment": "The words used to describe the instrument used to carry out a high-throughput sequencing experiment.", + "rdfs:label": "CDSSequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Device" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANParticipantID" + "@id": "bts:IlluminaNextSeq500" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:IlluminaNextSeq550" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:IlluminaNextSeq2500" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:IlluminaNovaSeq6000" }, { - "@id": "bts:SentinelLymphNodeCount" + "@id": "bts:IlluminaMiSeq" }, { - "@id": "bts:SentinelNodePositiveAssessmentCount" + "@id": "bts:454GSFLXTitanium" }, { - "@id": "bts:TumorExtranodalExtensionIndicator" + "@id": "bts:ABSOLiD4" }, { - "@id": "bts:SatelliteMetastasisPresentIndicator" + "@id": "bts:ABSOLiD2" }, { - "@id": "bts:OtherBiopsyResectionSite" + "@id": "bts:ABSOLiD3" }, { - "@id": "bts:ExtentofTumorResection" + "@id": "bts:CompleteGenomics" }, { - "@id": "bts:PriorSitesofRadiation" + "@id": "bts:IlluminaHiSeqXTen" }, { - "@id": "bts:Immunosuppression" + "@id": "bts:IlluminaHiSeqXFive" }, { - "@id": "bts:ConcomitantMedicationReceivedType" + "@id": "bts:IlluminaGenomeAnalyzerII" }, { - "@id": "bts:FamilyMemberVitalStatusIndicator" + "@id": "bts:IlluminaGenomeAnalyzerIIx" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:IlluminaHiSeq2000" }, { - "@id": "bts:COVID19CurrentStatus" + "@id": "bts:IlluminaHiSeq2500" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:IlluminaHiSeq4000" }, { - "@id": "bts:COVID19AntibodyTesting" + "@id": "bts:IlluminaNextSeq" }, { - "@id": "bts:COVID19ComplicationsSeverity" + "@id": "bts:IonTorrentPGM" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:IonTorrentProton" }, { - "@id": "bts:Ecigvapeuse" + "@id": "bts:IonTorrentS5" }, { - "@id": "bts:Ecigvape30dayusenum" + "@id": "bts:PacBioRS" }, { - "@id": "bts:Ecigvapetimesperday" + "@id": "bts:NovaSeq6000" }, { - "@id": "bts:Typeofsmokeexposurecumulativeyears" + "@id": "bts:NovaSeqS4" }, { - "@id": "bts:Chewingtobaccodailyusecount" + "@id": "bts:UltimaGenomicsUG100" }, { - "@id": "bts:Secondhandsmokeexposureyears" + "@id": "bts:OxfordNanoporeminION" }, { - "@id": "bts:KnownGeneticPredispositionMutation" + "@id": "bts:GridION" }, { - "@id": "bts:HereditaryCancerPredispositionSyndrome" + "@id": "bts:PromethION" }, { - "@id": "bts:CancerAssociatedGeneMutations" + "@id": "bts:PacBioSequel2" }, { - "@id": "bts:MutationalSignatures" + "@id": "bts:Revio" }, { - "@id": "bts:MismatchRepairSystemStatus" + "@id": "bts:IlluminaNextSeq1000" }, { - "@id": "bts:LabTestsforMMRStatus" + "@id": "bts:IlluminaNextSeq2000" }, { - "@id": "bts:ModeofCancerDetection" + "@id": "bts:Other" }, { - "@id": "bts:EducationLevel" + "@id": "bts:Unknown" }, { - "@id": "bts:CountryofBirth" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "CDS Sequencing Platform", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CDSLibrarySelectionMethod", + "@type": "rdfs:Class", + "rdfs:comment": "The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.", + "rdfs:label": "CDSLibrarySelectionMethod", + "rdfs:subClassOf": [ { - "@id": "bts:MedicallyUnderservedArea" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RuralvsUrban" + "@id": "bts:Random" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:RRNADepletion" }, { - "@id": "bts:CancerIncidenceLocation" + "@id": "bts:Other" } ], + "sms:displayName": "CDS Library Selection Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TimepointLabel", + "@id": "bts:PairedEnd", "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", + "rdfs:comment": "TBD", + "rdfs:label": "PairedEnd", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:CDSLibraryLayout" + }, + { + "@id": "bts:LibraryLayout" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", + "sms:displayName": "Paired End", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StartDaysfromIndex", + "@id": "bts:SingleRead", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", - "rdfs:label": "StartDaysfromIndex", + "rdfs:comment": "TBD", + "rdfs:label": "SingleRead", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:CDSLibraryLayout" + }, + { + "@id": "bts:LibraryLayout" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Start Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Single Read", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:StopDaysfromIndex", + "@id": "bts:10xVisiumSpatialTranscriptomics", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", - "rdfs:label": "StopDaysfromIndex", + "rdfs:comment": "TBD", + "rdfs:label": "10xVisiumSpatialTranscriptomics", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stop Days from Index", + "sms:displayName": "10x Visium Spatial Transcriptomics", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:SentinelLymphNodeCount", + "@id": "bts:BulkMethylation-seq", "@type": "rdfs:Class", - "rdfs:comment": "Numeric count of sentinel lymph nodes.", - "rdfs:label": "SentinelLymphNodeCount", + "rdfs:comment": "TBD", + "rdfs:label": "BulkMethylation-seq", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSDataType" + }, + { + "@id": "bts:DataType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - 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(Extension to GDC attributes in Family History Tier 1)", - "rdfs:label": "FamilyMemberVitalStatusIndicator", - "rdfs:subClassOf": [ + "@id": "bts:HistoneVariant" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PreservationMethod" + }, { - "@id": "bts:VitalStatusAlive" + "@id": "bts:StorageMethod" }, { - "@id": "bts:VitalStatusDead" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Unknown" + "@id": "bts:LocationExtentExtraprostaticExtension" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Family Member Vital Status Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19OccurrenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", - "rdfs:label": "COVID19OccurrenceIndicator", - "rdfs:subClassOf": [ + "@id": "bts:FixativeType" + }, { - 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"@id": "bts:MLH1 promotermethylationanalysis" + "@id": "bts:ProgressionorRecurrenceAnatomicSite" }, { - "@id": "bts:BRAF sequencing" + "@id": "bts:TreatmentAnatomicSite" }, { - "@id": "bts:Other" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:NotApplicable" + "@id": "bts:TissueorOrganofOrigin" }, { - "@id": "bts:Unknown" + "@id": "bts:PrimaryDiagnosis" } ], - "sms:displayName": "Lab Tests for MMR Status", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Not Reported", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ModeofCancerDetection", + "@id": "bts:Random", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the mode of cancer detection, like standard of care screening or random detection", - "rdfs:label": "ModeofCancerDetection", + "rdfs:comment": "TBD", + "rdfs:label": "Random", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CDSLibrarySelectionMethod" + }, + { + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:LibrarySelectionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:StandardofCareScreening" - }, - { - "@id": "bts:ClinicalExaminationofunrelatedcancersymptoms" - }, - { - "@id": "bts:Incidentaloma" - }, + "sms:displayName": "Random", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RRNADepletion", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RRNADepletion", + "rdfs:subClassOf": [ { - "@id": "bts:IntervalCancer" + "@id": "bts:CDSLibrarySelectionMethod" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:LibrarySelectionMethod" } ], - "sms:displayName": "Mode of Cancer Detection", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "rRNA Depletion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EducationLevel", + "@id": "bts:Checksum", "@type": "rdfs:Class", - "rdfs:comment": "Highest level of education that the patient completed (direct patient-derived information)", - "rdfs:label": "EducationLevel", + "rdfs:comment": "MD5 checksum of the BAM file", + "rdfs:label": "Checksum", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:InformationContentEntity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bachelor'sdegree" - }, - { - "@id": "bts:Doctoraldegreeorprofessionaldegree" - }, - { - "@id": "bts:Gradeschool" - }, - { - "@id": "bts:Graduateorprofessionaldegree" - }, - { - "@id": "bts:Highschoolgraduate(includingequivalency)" - }, - { - "@id": "bts:Master'sdegree" - }, - { - "@id": "bts:Noformaleducation" - }, - { - "@id": "bts:Nothighschoolgraduate" - }, - { - "@id": "bts:Somecollegeorassociatedegree" - }, + "sms:displayName": "Checksum", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", + "rdfs:label": "HTANBiospecimenID", + "rdfs:subClassOf": [ { - "@id": "bts:Datanotavailable" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Education Level", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Biospecimen ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" + ] }, { - "@id": "bts:CountryofBirth", + "@id": "bts:Biospecimen", "@type": "rdfs:Class", - "rdfs:comment": "Country where the patient was born.", - "rdfs:label": "CountryofBirth", + "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", + "rdfs:label": "Biospecimen", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Biospecimen", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Afghanistan" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Albania" + "@id": "bts:Component" }, { - "@id": "bts:Algeria" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:Andorra" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:Angola" + "@id": "bts:HTANParentID" }, { - "@id": "bts:Anguilla" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:Argentina" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:Armenia" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:Aruba" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:Australia" + "@id": "bts:FixativeType" }, { - "@id": "bts:Austria" + "@id": "bts:StorageMethod" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:Bahamas" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Bahrain" + "@id": "bts:SiteDataSource" }, { - "@id": "bts:Bangladesh" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:Barbados" + "@id": "bts:MountingMedium" }, { - "@id": "bts:Belarus" + "@id": "bts:ProcessingLocation" }, { - "@id": "bts:Belgium" + "@id": "bts:HistologyAssessmentBy" }, { - "@id": "bts:Belize" + "@id": "bts:HistologyAssessmentMedium" }, { - "@id": "bts:Benin" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:Bermuda" + "@id": "bts:TumorInfiltratingLymphocytes" }, { - "@id": "bts:Bhutan" + "@id": "bts:DegreeofDysplasia" }, { - "@id": "bts:Bolivia" + "@id": "bts:DysplasiaFraction" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:NumberProliferatingCells" }, { - "@id": "bts:Botswana" + "@id": "bts:PercentEosinophilInfiltration" }, { - "@id": "bts:Brazil" + "@id": "bts:PercentGranulocyteInfiltration" }, { - "@id": "bts:Brunei" + "@id": "bts:PercentInflamInfiltration" }, { - "@id": "bts:Bulgaria" + "@id": "bts:PercentLymphocyteInfiltration" }, { - "@id": "bts:BurkinaFaso" + "@id": "bts:PercentMonocyteInfiltration" }, { - "@id": "bts:Burundi" + "@id": "bts:PercentNecrosis" }, { - "@id": "bts:Cambodia" + "@id": "bts:PercentNeutrophilInfiltration" }, { - "@id": "bts:Cameroon" + "@id": "bts:PercentNormalCells" }, { - "@id": "bts:Canada" + "@id": "bts:PercentStromalCells" }, { - "@id": "bts:CapeVerde" + "@id": "bts:PercentTumorCells" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:PercentTumorNuclei" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:FiducialMarker" }, { - "@id": "bts:Chad" + "@id": "bts:SlicingMethod" }, { - "@id": "bts:Chile" + "@id": "bts:LysisBuffer" }, { - "@id": "bts:China" - }, + "@id": "bts:MethodofNucleicAcidIsolation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", + "rdfs:label": "HTANParentID", + "rdfs:subClassOf": [ { - "@id": "bts:Colombia" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentDataFileID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", + "rdfs:label": "HTANParentDataFileID", + "rdfs:subClassOf": [ { - "@id": "bts:Comoros" - }, + "@id": "bts:File" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Data File ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Tier 2 Cancer Data", + "rdfs:label": "ClinicalDataTier2", + "rdfs:subClassOf": [ { - "@id": "bts:Congo" + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:CookIslands" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:CostaRica" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Croatia" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Cuba" + "@id": "bts:SentinelLymphNodeCount" }, { - "@id": "bts:Curacao" + "@id": "bts:SentinelNodePositiveAssessmentCount" }, { - "@id": "bts:Cyprus" + "@id": "bts:TumorExtranodalExtensionIndicator" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:SatelliteMetastasisPresentIndicator" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:OtherBiopsyResectionSite" }, { - "@id": "bts:Denmark" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:Djibouti" + "@id": "bts:PriorSitesofRadiation" }, { - "@id": "bts:Dominica" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:DominicanRepublic" + "@id": "bts:ConcomitantMedicationReceivedType" }, { - "@id": "bts:Ecuador" + "@id": "bts:FamilyMemberVitalStatusIndicator" }, { - "@id": "bts:Egypt" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:ElSalvador" + "@id": "bts:COVID19CurrentStatus" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:Eritrea" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:Estonia" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:Eswatini" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:Ethiopia" + "@id": "bts:Ecigvapeuse" }, { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:Ecigvape30dayusenum" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:Ecigvapetimesperday" }, { - "@id": "bts:FederatedStatesofMicronesia" + "@id": "bts:Typeofsmokeexposurecumulativeyears" }, { - "@id": "bts:Fiji" + "@id": "bts:Chewingtobaccodailyusecount" }, { - "@id": "bts:Finland" + "@id": "bts:Secondhandsmokeexposureyears" }, { - "@id": "bts:France" + "@id": "bts:KnownGeneticPredispositionMutation" }, { - "@id": "bts:FrenchGuiana" + "@id": "bts:HereditaryCancerPredispositionSyndrome" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:CancerAssociatedGeneMutations" }, { - "@id": "bts:Gabon" + "@id": "bts:MutationalSignatures" }, { - "@id": "bts:Gambia" + "@id": "bts:MismatchRepairSystemStatus" }, { - "@id": "bts:Georgia" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:Germany" + "@id": "bts:ModeofCancerDetection" }, { - "@id": "bts:Ghana" + "@id": "bts:EducationLevel" }, { - "@id": "bts:Gibraltar" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:Greece" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:Greenland" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:Grenada" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:Guadeloupe" - }, + "@id": "bts:CancerIncidenceLocation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:TimepointLabel", + "@type": "rdfs:Class", + "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label": "TimepointLabel", + "rdfs:subClassOf": [ { - "@id": "bts:Guam" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Timepoint Label", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:StartDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label": "StartDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:Guatemala" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:StopDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:Guernsey" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stop Days from Index", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SentinelLymphNodeCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric count of sentinel lymph nodes.", + "rdfs:label": "SentinelLymphNodeCount", + "rdfs:subClassOf": [ { - "@id": "bts:Guinea" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Lymph Node Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount", + "@type": "rdfs:Class", + "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", + "rdfs:label": "SentinelNodePositiveAssessmentCount", + "rdfs:subClassOf": [ { - "@id": "bts:Guinea-Bissau" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Node Positive Assessment Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorExtranodalExtensionIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", + "rdfs:label": "TumorExtranodalExtensionIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Guyana" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Haiti" + "@id": "bts:Absent" }, { - "@id": "bts:HolySee" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Honduras" + "@id": "bts:NO" }, { - "@id": "bts:HongKong" + "@id": "bts:YES" }, { - "@id": "bts:Hungary" + "@id": "bts:Nosourcedocumentation" }, { - "@id": "bts:Iceland" + "@id": "bts:Notapplicable" }, { - "@id": "bts:India" + "@id": "bts:Notsampledordissected" }, { - "@id": "bts:Indonesia" + "@id": "bts:Present" }, { - "@id": "bts:Iran" + "@id": "bts:Present-extensive" }, { - "@id": "bts:Iraq" + "@id": "bts:Present-minimal" }, { - "@id": "bts:Ireland" + "@id": "bts:UNKNOWN" }, { - "@id": "bts:IsleofMan" - }, + "@id": "bts:Unspecified" + } + ], + "sms:displayName": "Tumor Extranodal Extension Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SatelliteMetastasisPresentIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", + "rdfs:label": "SatelliteMetastasisPresentIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Israel" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Italy" + "@id": "bts:Yes" }, { - "@id": "bts:Jamaica" + "@id": "bts:No" }, { - "@id": "bts:Japan" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Satellite Metastasis Present Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OtherBiopsyResectionSite", + "@type": "rdfs:Class", + "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", + "rdfs:label": "OtherBiopsyResectionSite", + "rdfs:subClassOf": [ { - "@id": "bts:Jersey" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Other Biopsy Resection Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ExtentofTumorResection", + "@type": "rdfs:Class", + "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", + "rdfs:label": "ExtentofTumorResection", + "rdfs:subClassOf": [ { - "@id": "bts:Jordan" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Kazakhstan" + "@id": "bts:GrossTotalResection" }, { - "@id": "bts:Kenya" + "@id": "bts:OpenBiopsy" }, { - "@id": "bts:Kiribati" + "@id": "bts:SubtotalResection" }, { - "@id": "bts:Kosovo" + "@id": "bts:ExtensiveSubtotal" }, { - "@id": "bts:Kuwait" + "@id": "bts:Minor" }, { - "@id": "bts:Kyrgyzstan" + "@id": "bts:Optimaldebulking" }, { - "@id": "bts:Laos" + "@id": "bts:Other" }, { - "@id": "bts:Latvia" + "@id": "bts:Partialdebulking" }, { - "@id": "bts:Lebanon" + "@id": "bts:Segmental" }, { - "@id": "bts:Lesotho" + "@id": "bts:Suboptimal" }, { - "@id": "bts:Liberia" + "@id": "bts:Suboptimaldebulking" }, { - "@id": "bts:Libya" + "@id": "bts:NTR" }, { - "@id": "bts:Liechtenstein" + "@id": "bts:Unknown" }, { - "@id": "bts:Lithuania" + "@id": "bts:NotReported" }, { - "@id": "bts:Luxembourg" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Extent of Tumor Resection", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorSitesofRadiation", + "@type": "rdfs:Class", + "rdfs:comment": "The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.", + "rdfs:label": "PriorSitesofRadiation", + "rdfs:subClassOf": [ { - "@id": "bts:Macau" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Madagascar" + "@id": "bts:Abdomentotal" }, { - "@id": "bts:Malawi" + "@id": "bts:AbdominalWall" }, { - "@id": "bts:Malaysia" + "@id": "bts:Acetabulum" }, { - "@id": "bts:Maldives" + "@id": "bts:Adenoid" }, { - "@id": "bts:Mali" + "@id": "bts:Adipose" }, { - "@id": "bts:Malta" + "@id": "bts:Adrenal" }, { - "@id": "bts:MarshallIslands" + "@id": "bts:AlveolarRidge" }, { - "@id": "bts:Martinique" + "@id": "bts:AmnioticFluid" }, { - "@id": "bts:Mauritania" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Mauritius" + "@id": "bts:AnalSphincter" }, { - "@id": "bts:Mayotte" + "@id": "bts:Ankle" }, { - "@id": "bts:Mexico" + "@id": "bts:Anorectum" }, { - "@id": "bts:Moldova" + "@id": "bts:AntecubitalFossa" }, { - "@id": "bts:Monaco" + "@id": "bts:Antrum" }, { - "@id": "bts:Mongolia" + "@id": "bts:Anus" }, { - "@id": "bts:Montenegro" + "@id": "bts:Aorta" }, { - "@id": "bts:Montserrat" + "@id": "bts:AorticBody" }, { - "@id": "bts:Morocco" + "@id": "bts:Appendix" }, { - "@id": "bts:Mozambique" + "@id": "bts:AqueousFluid" }, { - "@id": "bts:Myanmar" + "@id": "bts:Arm" }, { - "@id": "bts:Namibia" + "@id": "bts:Artery" }, { - "@id": "bts:Nauru" + "@id": "bts:AscendingColon" }, { - "@id": "bts:Nepal" + "@id": "bts:AscendingColonHepaticFlexure" }, { - "@id": "bts:Netherlands" + "@id": "bts:Ascites" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:AuditoryCanal" }, { - "@id": "bts:NewZealand" + "@id": "bts:AutonomicNervousSystem" }, { - "@id": "bts:Nicaragua" + "@id": "bts:Axilla" }, { - "@id": "bts:Niger" + "@id": "bts:Back" }, { - "@id": "bts:Nigeria" + "@id": "bts:BileDuct" }, { - "@id": "bts:Niue" + "@id": "bts:Bladder" }, { - "@id": "bts:NorthKorea" + "@id": "bts:Blood" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:BloodVessel" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:Bodytotal" }, { - "@id": "bts:Norway" + "@id": "bts:Bone" }, { - "@id": "bts:Oman" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:Pakistan" + "@id": "bts:Bonenon-spine" }, { - "@id": "bts:Palau" + "@id": "bts:Bowel" }, { - "@id": "bts:Panama" + "@id": "bts:Brain" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:BrainStem" }, { - "@id": "bts:Paraguay" + "@id": "bts:Breast" }, { - "@id": "bts:Peru" + "@id": "bts:BroadLigament" }, { - "@id": "bts:Philippines" + "@id": "bts:Bronchiole" }, { - "@id": "bts:Poland" + "@id": "bts:Bronchus" }, { - "@id": "bts:Portugal" + "@id": "bts:Brow" }, { - "@id": "bts:PuertoRico" + "@id": "bts:BuccalCavity" }, { - "@id": "bts:Qatar" + "@id": "bts:BuccalMucosa" }, { - "@id": "bts:Reunion" + "@id": "bts:Buttock" }, { - "@id": "bts:Romania" + "@id": "bts:Calf" }, { - "@id": "bts:Russia" + "@id": "bts:Capillary" }, { - "@id": "bts:Rwanda" + "@id": "bts:Cardia" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Carina" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:CarotidArtery" }, { - "@id": "bts:SaintLucia" + "@id": "bts:CarotidBody" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:Cartilage" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:Cecum" }, { - "@id": "bts:Samoa" + "@id": "bts:Cell-Line" }, { - "@id": "bts:SanMarino" + "@id": "bts:CentralNervousSystem" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:Cerebellum" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:CerebralCortex" }, { - "@id": "bts:Senegal" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:Serbia" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Seychelles" + "@id": "bts:CervicalSpine" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Cervix" }, { - "@id": "bts:Singapore" + "@id": "bts:Chest" }, { - "@id": "bts:Slovakia" + "@id": "bts:ChestWall" }, { - "@id": "bts:Slovenia" + "@id": "bts:Chin" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:Clavicle" }, { - "@id": "bts:Somalia" + "@id": "bts:Clitoris" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:Colon" }, { - "@id": "bts:SouthKorea" + "@id": "bts:ColonMucosaOnly" }, { - "@id": "bts:SouthSudan" + "@id": "bts:CommonDuct" }, { - "@id": "bts:Spain" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:SriLanka" + "@id": "bts:ConnectiveTissue" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:Dermal" }, { - "@id": "bts:Sudan" + "@id": "bts:DescendingColon" }, { - "@id": "bts:Suriname" + "@id": "bts:Diaphragm" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:DistantSite" }, { - "@id": "bts:Sweden" + "@id": "bts:Duodenum" }, { - "@id": "bts:Switzerland" + "@id": "bts:Ear" }, { - "@id": "bts:Syria" + "@id": "bts:EarCanal" }, { - "@id": "bts:Taiwan" + "@id": "bts:EarPinna(External)" }, { - "@id": "bts:Tajikistan" + "@id": "bts:Elbow" }, { - "@id": "bts:Tanzania" + "@id": "bts:EndocrineGland" }, { - "@id": "bts:Thailand" + "@id": "bts:Epididymis" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:EpiduralSpace" }, { - "@id": "bts:Togo" + "@id": "bts:Epitrochlear" }, { - "@id": "bts:Tokelau" + "@id": "bts:EsophagogastricJunction" }, { - "@id": "bts:Tonga" + "@id": "bts:Esophagus" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:EsophagusMucosaOnly" }, { - "@id": "bts:Tunisia" + "@id": "bts:Eye" }, { - "@id": "bts:Turkey" + "@id": "bts:FallopianTube" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:FemoralArtery" }, { - "@id": "bts:Tuvalu" + "@id": "bts:FemoralVein" }, { - "@id": "bts:Uganda" + "@id": "bts:Femur" }, { - "@id": "bts:Ukraine" + "@id": "bts:Fibroblasts" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:Fibula" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:Finger" }, { - "@id": "bts:UnitedStates" + "@id": "bts:FloorofMouth" }, { - "@id": "bts:Uruguay" + "@id": "bts:Fluid" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:Foot" }, { - "@id": "bts:Vanuatu" + "@id": "bts:Forearm" }, { - "@id": "bts:Venezuela" + "@id": "bts:Forehead" }, { - "@id": "bts:Vietnam" + "@id": "bts:Foreskin" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:FrontalCortex" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:FrontalLobe" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:FundusofStomach" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Gallbladder" }, { - "@id": "bts:Yemen" + "@id": "bts:Ganglia" }, { - "@id": "bts:Zambia" + "@id": "bts:GastroesophagealJunction" }, { - "@id": "bts:Zimbabwe" + "@id": "bts:GastrointestinalTract" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Country of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedArea", - "@type": "rdfs:Class", - "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", - "rdfs:label": "MedicallyUnderservedArea", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:MedicallyUnderservedArea-Yes" + "@id": "bts:GastrointestinalIntestine" }, { - "@id": "bts:MedicallyUnderservedArea-No" + "@id": "bts:GenitourinaryNOS" }, { - "@id": "bts:MedicallyUnderservedArea-Unknown" - } - ], - "sms:displayName": "Medically Underserved Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RuralvsUrban", - "@type": "rdfs:Class", - "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", - "rdfs:label": "RuralvsUrban", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:UrbanPopulation(population>50000)" + "@id": "bts:Groin" }, { - "@id": "bts:UrbanCluster(population2500-50000)" + "@id": "bts:Gum" }, { - "@id": "bts:RuralPopulation(population<2500)" - } - ], - "sms:displayName": "Rural vs Urban", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidence", - "@type": "rdfs:Class", - "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", - "rdfs:label": "CancerIncidence", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidenceLocation", - "@type": "rdfs:Class", - "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", - "rdfs:label": "CancerIncidenceLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Cancer related clinical data specific to SRRS", - "rdfs:label": "SRRSClinicalDataTier2", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:Hand" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:HardPalate" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:HeadFaceOrNeckNos" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:HeadandNeck" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Heart" }, { - "@id": "bts:EducationLevel" + "@id": "bts:Hepatic" }, { - "@id": "bts:CountryofBirth" + "@id": "bts:HepaticDuct" }, { - "@id": "bts:MedicallyUnderservedArea" + "@id": "bts:HepaticVein" }, { - "@id": "bts:RuralvsUrban" + "@id": "bts:Hilar" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:Hip" }, { - "@id": "bts:CancerIncidenceLocation" + "@id": "bts:Hippocampus" }, { - "@id": "bts:Ethnicity" + "@id": "bts:Humerus" }, { - "@id": "bts:Gender" + "@id": "bts:Hypopharynx" }, { - "@id": "bts:Race" + "@id": "bts:IleocecalValve" }, { - "@id": "bts:VitalStatus" + "@id": "bts:Ileum" }, { - "@id": "bts:AgeatDiagnosis" + "@id": "bts:Ilium" }, { - "@id": "bts:DaystoLastFollowup" + "@id": "bts:IndexFinger" }, { - "@id": "bts:DaystoLastKnownDiseaseStatus" + "@id": "bts:Ischium" }, { - "@id": "bts:DaystoRecurrence" + "@id": "bts:IsletCells" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:Jaw" }, { - "@id": "bts:Morphology" + "@id": "bts:Jejunum" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:Joint" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:Kidney" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:Knee" }, { - "@id": "bts:TissueorOrganofOrigin" + "@id": "bts:LacrimalGland" }, { - "@id": "bts:NCIAtlasCancerSite" + "@id": "bts:LargeBowel" }, { - "@id": "bts:TumorGrade" + "@id": "bts:Laryngopharynx" }, { - "@id": "bts:PackYearsSmoked" + "@id": "bts:Larynx" }, { - "@id": "bts:YearsSmoked" + "@id": "bts:Leg" }, { - "@id": "bts:DaystoFollowUp" + "@id": "bts:Leptomeninges" }, { - "@id": "bts:GeneSymbol" + "@id": "bts:Ligament" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:Lip" }, { - "@id": "bts:TestResult" + "@id": "bts:Liver" }, { - "@id": "bts:TreatmentType" + "@id": "bts:LumbarSpine" }, { - "@id": "bts:TumorLargestDimensionDiameter" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Ethnicity", - "@type": "rdfs:Class", - "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", - "rdfs:label": "Ethnicity", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Hispanicorlatino" + "@id": "bts:Lung" }, { - "@id": "bts:Nothispanicorlatino" + "@id": "bts:LymphNode" }, { - "@id": "bts:Unknown" + "@id": "bts:LymphNode(s)Axilla" }, { - "@id": "bts:NotReported" + "@id": "bts:LymphNode(s)Cervical" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Ethnicity", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Gender", - "@type": "rdfs:Class", - "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", - "rdfs:label": "Gender", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Female" + "@id": "bts:LymphNode(s)Distant" }, { - "@id": "bts:Male" + "@id": "bts:LymphNode(s)Epitrochlear" }, { - "@id": "bts:Unknown" + "@id": "bts:LymphNode(s)Femoral" }, { - "@id": "bts:Unspecified" + "@id": "bts:LymphNode(s)Hilar" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Gender", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Race", - "@type": "rdfs:Class", - "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", - "rdfs:label": "Race", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:White" + "@id": "bts:LymphNode(s)Iliac-Common" }, { - "@id": "bts:Americanindianoralaskanative" + "@id": "bts:LymphNode(s)Iliac-External" }, { - "@id": "bts:Blackorafricanamerican" + "@id": "bts:LymphNode(s)Inguinal" }, { - "@id": "bts:Asian" + "@id": "bts:LymphNode(s)InternalMammary" }, { - "@id": "bts:Nativehawaiianorotherpacificislander" + "@id": "bts:LymphNode(s)Mammary" }, { - "@id": "bts:Other" + "@id": "bts:LymphNode(s)Mediastinal" }, { - "@id": "bts:Unknown" + "@id": "bts:LymphNode(s)Mesenteric" }, { - "@id": "bts:NotReported" + "@id": "bts:LymphNode(s)Occipital" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Race", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VitalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alive" + "@id": "bts:LymphNode(s)Paraaortic" }, { - "@id": "bts:Dead" + "@id": "bts:LymphNode(s)Parotid" }, { - "@id": "bts:Unknown" + "@id": "bts:LymphNode(s)Pelvic" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vital Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", - "rdfs:label": "AgeatDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Age at Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoLastFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastFollowup", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Follow up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoLastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastKnownDiseaseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoRecurrence", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:LastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", - "rdfs:label": "LastKnownDiseaseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Distantmetrecurrence/progression" + "@id": "bts:LymphNode(s)Popliteal" }, { - "@id": "bts:Loco-regionalrecurrence/progression" + "@id": "bts:LymphNode(s)Regional" }, { - "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" + "@id": "bts:LymphNode(s)Retroperitoneal" }, { - "@id": "bts:Tumorfree" + "@id": "bts:LymphNode(s)Scalene" }, { - "@id": "bts:Unknowntumorstatus" + "@id": "bts:LymphNode(s)Splenic" }, { - "@id": "bts:Withtumor" + "@id": "bts:LymphNode(s)Subclavicular" }, { - "@id": "bts:NotReported" + "@id": "bts:LymphNode(s)Submandibular" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:LymphNode(s)Supraclavicular" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Morphology", - "@type": "rdfs:Class", - "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", - "rdfs:label": "Morphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Morphology", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PrimaryDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "PrimaryDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Mandible" + }, { - "@id": "bts:Acinarcellcarcinoma" + "@id": "bts:Mantle" }, { - "@id": "bts:Acutebasophilicleukaemia" + "@id": "bts:Maxilla" }, { - "@id": "bts:AcuteleukemiaBurkitttype" + "@id": "bts:MediastinalSoftTissue" }, { - "@id": "bts:AcuteleukemiaNOS" + "@id": "bts:Mediastinum" }, { - "@id": "bts:Acutelymphaticleukemia" + "@id": "bts:Mesentery" }, { - "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" + "@id": "bts:Mesothelium" }, { - "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" + "@id": "bts:MiddleFinger" }, { - "@id": "bts:AcutelymphoblasticleukemiaNOS" + "@id": "bts:Mitochondria" }, { - "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" + "@id": "bts:Muscle" }, { - "@id": "bts:Acutelymphocyticleukemia" + "@id": "bts:Nails" }, { - "@id": "bts:Acutelymphoidleukemia" + "@id": "bts:NasalCavity" }, { - "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" + "@id": "bts:NasalSoftTissue" }, { - "@id": "bts:AcutemyeloidleukemiaMLL" + "@id": "bts:Nasopharynx" }, { - "@id": "bts:AcutemyeloidleukemiaNOS" + "@id": "bts:Neck" }, { - "@id": "bts:Acutemyelomonocyticleukemia" + "@id": "bts:Nerve" }, { - "@id": "bts:AcutepromyelocyticleukemiaNOS" + "@id": "bts:Nerve(s)Cranial" }, { - "@id": "bts:Adenocarcinoidtumor" + "@id": "bts:OccipitalCortex" }, { - "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" + "@id": "bts:OcularOrbits" }, { - "@id": "bts:AdenocarcinomainapolypNOS" + "@id": "bts:Omentum" }, { - "@id": "bts:Adenocarcinomainadenomatouspolyp" + "@id": "bts:OralCavity" }, { - "@id": "bts:Adenocarcinomainpolypoidadenoma" + "@id": "bts:OralCavityMucosaOnly" }, { - "@id": "bts:AdenocarcinomainsituinapolypNOS" + "@id": "bts:Oropharynx" }, { - "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" + "@id": "bts:Other" }, { - "@id": "bts:Adenocarcinomainsituintubularadenoma" + "@id": "bts:Ovary" }, { - "@id": "bts:Adenocarcinomainsitumucinous" + "@id": "bts:Palate" }, { - "@id": "bts:Adenocarcinomainsitunon-mucinous" + "@id": "bts:Pancreas" }, { - "@id": "bts:AdenocarcinomainsituNOS" + "@id": "bts:Parametrium" }, { - "@id": "bts:Adenocarcinomaintubularadenoma" + "@id": "bts:ParaspinalGanglion" }, { - "@id": "bts:Adenocarcinomainvillousadenoma" + "@id": "bts:Parathyroid" }, { - "@id": "bts:Adenocarcinomaofanalducts" + "@id": "bts:ParotidGland" }, { - "@id": "bts:Adenocarcinomaofanalglands" + "@id": "bts:Patella" }, { - "@id": "bts:Adenocarcinomadiffusetype" + "@id": "bts:Pelvis" }, { - "@id": "bts:Adenocarcinomaendocervicaltype" + "@id": "bts:Penis" }, { - "@id": "bts:Adenocarcinomaintestinaltype" + "@id": "bts:Pericardium" }, { - "@id": "bts:AdenocarcinomametastaticNOS" + "@id": "bts:PeriorbitalSoftTissue" }, { - "@id": "bts:AdenocarcinomaNOS" + "@id": "bts:PeritonealCavity" }, { - "@id": "bts:Adenocarcinomapancreatobiliarytype" + "@id": "bts:Peritoneum" }, { - "@id": "bts:Adultrhabdomyoma" + "@id": "bts:Pharynx" }, { - "@id": "bts:AdultT-celllymphoma" + "@id": "bts:Pineal" }, { - "@id": "bts:AdultT-celllymphoma/leukemia" + "@id": "bts:PinealGland" }, { - "@id": "bts:Astrocytomaanaplastic" + "@id": "bts:PituitaryGland" }, { - "@id": "bts:Astrocytomalowgrade" + "@id": "bts:Placenta" }, { - "@id": "bts:AstrocytomaNOS" + "@id": "bts:Pleura" }, { - "@id": "bts:BcelllymphomaNOS" + "@id": "bts:PoplitealFossa" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + "@id": "bts:Pouch" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + "@id": "bts:PrimaryTumorField" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" + "@id": "bts:Primarytumorsite" }, { - "@id": "bts:B-ALL" + "@id": "bts:Prostate" }, { - "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" + "@id": "bts:ProstateBed" }, { - "@id": "bts:Basalcelladenocarcinoma" + "@id": "bts:ProstateSeminalVesiclesandLymphNodes" }, { - "@id": "bts:Basalcelladenoma" + "@id": "bts:Pylorus" }, { - "@id": "bts:BasalcellcarcinomaNOS" + "@id": "bts:RectosigmoidJunction" }, { - "@id": "bts:Basalcellepithelioma" + "@id": "bts:Rectum" }, { - "@id": "bts:Basalcelltumor" + "@id": "bts:RegionalSite" }, { - "@id": "bts:Basophiladenocarcinoma" + "@id": "bts:Retina" }, { - "@id": "bts:Basophiladenoma" + "@id": "bts:Retro-OrbitalRegion" }, { - "@id": "bts:Basophilcarcinoma" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:Bileductadenocarcinoma" + "@id": "bts:Rib" }, { - "@id": "bts:Bileductadenoma" + "@id": "bts:RingFinger" }, { - "@id": "bts:Bileductcarcinoma" + "@id": "bts:RoundLigament" }, { - "@id": "bts:Bileductcystadenocarcinoma" + "@id": "bts:Sacrum" }, { - "@id": "bts:Bileductcystadenoma" + "@id": "bts:SalivaryGland" }, { - "@id": "bts:Bronchialadenomacarcinoid" + "@id": "bts:Scalp" }, { - "@id": "bts:Bronchialadenomacylindroid" + "@id": "bts:Scapula" }, { - "@id": "bts:BronchialadenomaNOS" + "@id": "bts:SciaticNerve" }, { - "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" + "@id": "bts:Scrotum" }, { - "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + "@id": "bts:SeminalVesicle" }, { - "@id": "bts:Bronchio-alveolarcarcinomamucinous" + "@id": "bts:Shoulder" }, { - "@id": "bts:Bronchiolaradenocarcinoma" + "@id": "bts:SigmoidColon" }, { - "@id": "bts:Bronchiolarcarcinoma" + "@id": "bts:Sinus" }, { - "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" + "@id": "bts:Sinus(es)Maxillary" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" + "@id": "bts:SkeletalMuscle" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + "@id": "bts:Skin" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" + "@id": "bts:Skinlowerextremitylocal" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + "@id": "bts:Skintotal" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + "@id": "bts:Skintrunklocal" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" + "@id": "bts:Skinupperextremitylocal" }, { - "@id": "bts:Burkittcellleukemia" + "@id": "bts:Skull" }, { - "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" + "@id": "bts:SmallBowel" }, { - "@id": "bts:Burkitttumor" + "@id": "bts:SmallBowelMucosaOnly" }, { - "@id": "bts:Burkitt-likelymphoma" + "@id": "bts:SmallFinger" }, { - "@id": "bts:C-ALL" + "@id": "bts:SoftTissue" }, { - "@id": "bts:Cancer" + "@id": "bts:SpinalColumn" }, { - "@id": "bts:Capillaryhemangioma" + "@id": "bts:SpinalCord" }, { - "@id": "bts:Capillarylymphangioma" + "@id": "bts:Spine" }, { - "@id": "bts:CarcinomainapolypNOS" + "@id": "bts:Spleen" }, { - "@id": "bts:Carcinomainadenomatouspolyp" + "@id": "bts:SplenicFlexure" }, { - "@id": "bts:Carcinomainpleomorphicadenoma" + "@id": "bts:Sternum" }, { - "@id": "bts:CarcinomainsituinapolypNOS" + "@id": "bts:Stomach" }, { - "@id": "bts:Carcinomainsituinadenomatouspolyp" + "@id": "bts:StomachMucosaOnly" }, { - "@id": "bts:CarcinomainsituNOS" + "@id": "bts:SubcutaneousTissue" }, { - "@id": "bts:CarcinomaanaplasticNOS" + "@id": "bts:Synovium" }, { - "@id": "bts:Carcinomadiffusetype" + "@id": "bts:TemporalCortex" }, { - "@id": "bts:Carcinomaintestinaltype" + "@id": "bts:Tendon" }, { - "@id": "bts:CarcinomametastaticNOS" + "@id": "bts:Testis" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Thigh" }, { - "@id": "bts:CarcinosarcomaNOS" + "@id": "bts:ThoracicSpine" }, { - "@id": "bts:CarcinomaundifferentiatedNOS" + "@id": "bts:Thorax" }, { - "@id": "bts:CementomaNOS" + "@id": "bts:Throat" }, { - "@id": "bts:Centralneuroblastoma" + "@id": "bts:Thumb" }, { - "@id": "bts:Centralneurocytoma" + "@id": "bts:Thymus" }, { - "@id": "bts:Cerebellarliponeurocytoma" + "@id": "bts:Thyroid" }, { - "@id": "bts:CerebellarsarcomaNOS" + "@id": "bts:Tibia" }, { - "@id": "bts:CervicalintraepithelialneoplasiagradeIII" + "@id": "bts:Tongue" }, { - "@id": "bts:Cervicalintraepithelialneoplasialowgrade" + "@id": "bts:Tonsil" }, { - "@id": "bts:ChondromaNOS" + "@id": "bts:Tonsil(Pharyngeal)" }, { - "@id": "bts:Chondrosarcomagrade2/3" + "@id": "bts:Trachea/MajorBronchi" }, { - "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" + "@id": "bts:TransverseColon" }, { - "@id": "bts:ChronicgranulocyticleukemiaNOS" + "@id": "bts:Trunk" }, { - "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:UmbilicalCord" }, { - "@id": "bts:ChronicleukemiaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Chroniclymphaticleukemia" + "@id": "bts:Ureter" }, { - "@id": "bts:Chroniclymphocyticleukemia" + "@id": "bts:Urethra" }, { - "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" + "@id": "bts:UrinaryTract" }, { - "@id": "bts:Chroniclymphoidleukemia" + "@id": "bts:Uterus" }, { - "@id": "bts:Chronicmonocyticleukemia" + "@id": "bts:Uvula" }, { - "@id": "bts:ChronicmyelocyticleukemiaNOS" + "@id": "bts:Vagina" }, { - "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" + "@id": "bts:VasDeferens" }, { - "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:Vein" }, { - "@id": "bts:ChronicmyeloidleukemiaNOS" + "@id": "bts:Venous" }, { - "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" + "@id": "bts:Vertebra" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaNOS" + "@id": "bts:Vulva" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaType1" + "@id": "bts:WhiteBloodCells" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" + "@id": "bts:Wrist" }, { - "@id": "bts:ChronicmyeloproliferativediseaseNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Prior Sites of Radiation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Immunosuppression", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not immunosuppressive therapy was administered.", + "rdfs:label": "Immunosuppression", + "rdfs:subClassOf": [ { - 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}, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" + "@id": "bts:Anticoagulantagents" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + "@id": "bts:Anticonvulsant" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + "@id": "bts:Antifungal" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + "@id": "bts:Antiplateletagents" }, { - "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" + "@id": "bts:Antidepressants-ModerateCYP2D6inhibitors" }, { - "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" + "@id": "bts:Antidepressants-StrongCYP2D6inhibitors" }, { - "@id": "bts:Combinedsmallcellcarcinoma" + "@id": "bts:Antidepressants-weakCYP2D2inhibitorsornon-inhibitors" }, { - "@id": "bts:Combinedsmallcell-adenocarcinoma" + "@id": "bts:Anxiolyticsorsedatives" }, { - "@id": "bts:Combinedsmallcell-largecarcinoma" + "@id": "bts:Aspirin" }, { - "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" + "@id": "bts:Bisphosphonatesfortreatment/preventionofboneloss" }, { - "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" + "@id": "bts:Corticosteroid" }, { - "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" + "@id": "bts:COX-2inhibitor" }, { - "@id": "bts:Dermalnevus" + "@id": "bts:Decadron" }, { - "@id": "bts:DermatofibromaNOS" + "@id": "bts:Diabetes-Insulin" }, { - "@id": "bts:DiffuseastrocytomaIDH-mutant" + "@id": "bts:Diabetes-Metformincontainingagents" }, { - "@id": "bts:DiffuseastrocytomaIDH-wildtype" + "@id": "bts:Growthfactor" }, { - "@id": "bts:Diffuseastrocytomalowgrade" + "@id": "bts:Intravaginalestrogenpreparations" }, { - "@id": "bts:DiffuselargeB-celllymphomaNOS" + "@id": "bts:Lipid-loweringdrugs" }, { - "@id": "bts:Diffusemelanocytosis" + "@id": "bts:Non-prescriptionsupplementsformemory" }, { - "@id": "bts:DuctadenocarcinomaNOS" + "@id": "bts:Non-prescriptionsupplementsforreliefofhotflashes" }, { - "@id": "bts:DuctadenomaNOS" + "@id": "bts:Non-steroidalanti-inflammatoryagents" }, { - "@id": "bts:Ductcarcinomadesmoplastictype" + "@id": "bts:Opioids" }, { - "@id": "bts:DuctcarcinomaNOS" + "@id": "bts:Other" }, { - "@id": "bts:Ductcellcarcinoma" + "@id": "bts:Prescriptionmedicationsformemory" }, { - "@id": "bts:DuctalcarcinomainsituNOS" + "@id": "bts:Prescriptionmedicationsforreliefofhotflashes" }, { - "@id": "bts:DuctalcarcinomaNOS" + "@id": "bts:Prophylacticantiplatelettherapy" }, { - "@id": "bts:Dysplasticnevus" + "@id": "bts:Tricyclicantidepressants" }, { - "@id": "bts:EndometrialsarcomaNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:EndometrioidadenocarcinomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:EndometrioidadenofibromaNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Concomitant Medication Received Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyMemberVitalStatusIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", + "rdfs:label": "FamilyMemberVitalStatusIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:EndometrioidadenomaNOS" - }, + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:EndometrioidcarcinomaNOS" + "@id": "bts:VitalStatusAlive" }, { - "@id": "bts:Eosinophiladenocarcinoma" + "@id": "bts:VitalStatusDead" }, { - "@id": "bts:Eosinophiladenoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Eosinophilcarcinoma" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Family Member Vital Status Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19OccurrenceIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", + "rdfs:label": "COVID19OccurrenceIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Eosinophilicgranuloma" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Eosinophilicleukemia" + "@id": "bts:Yes" }, { - "@id": "bts:EpendymomaNOS" + "@id": "bts:No" }, { - "@id": "bts:EpidermoidcarcinomainsituNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:EpidermoidcarcinomaNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Epithelialtumorbenign" - }, + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Occurrence Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CurrentStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", + "rdfs:label": "COVID19CurrentStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Epithelialtumormalignant" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" + "@id": "bts:Patientcurrentlyhassymptoms" }, { - "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" + "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" }, { - "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" + "@id": "bts:PatientneverhadanysymptomsofCOVID-19" }, { - "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" + "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" }, { - "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" + "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" }, { - "@id": "bts:Ewingsarcoma" - }, + "@id": "bts:Statusunknownduetootherreasons" + } + ], + "sms:displayName": "COVID19 Current Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19PositiveLabTestIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", + "rdfs:label": "COVID19PositiveLabTestIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:GangliogliomaNOS" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Familialadenomatouspolyposis" + "@id": "bts:Yes" }, { - "@id": "bts:Gastrincelltumor" + "@id": "bts:No" }, { - "@id": "bts:Gastrincelltumormalignant" + "@id": "bts:Unknown" }, { - "@id": "bts:Gastrinomamalignant" + "@id": "bts:NotApplicable" }, { - "@id": "bts:GastrinomaNOS" - }, + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Positive Lab Test Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19AntibodyTesting", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", + "rdfs:label": "COVID19AntibodyTesting", + "rdfs:subClassOf": [ { - "@id": "bts:Gastrointestinalstromaltumormalignant" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Glioblastoma" + "@id": "bts:SARS-CoV-2IgMantibodypositive" }, { - "@id": "bts:Gliomamalignant" + "@id": "bts:SARS-CoV-2IgGantibodypositive" }, { - "@id": "bts:GliomaNOS" + "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" }, { - "@id": "bts:Haemangioblastoma" + "@id": "bts:SARS-CoV-2IgMantibodynegative" }, { - "@id": "bts:Haemangiosarcoma" + "@id": "bts:SARS-CoV-2IgGantibodynegative" }, { - "@id": "bts:Hepatocarcinoma" + "@id": "bts:SARS-CoV-2IgG/IgMantibodynegative" }, { - "@id": "bts:Hepatocellularadenoma" + "@id": "bts:Unknown" }, { - "@id": "bts:HepatocellularcarcinomaNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Hepatocholangiocarcinoma" - }, + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Antibody Testing", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19ComplicationsSeverity", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.", + "rdfs:label": "COVID19ComplicationsSeverity", + "rdfs:subClassOf": [ { - "@id": "bts:Hepatoidadenocarcinoma" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Hepatoidcarcinoma" + "@id": "bts:Cardiaccomplications" }, { - "@id": "bts:HodgkindiseaseNOS" + "@id": "bts:Pulmonarycomplications" }, { - "@id": "bts:Hodgkingranuloma" + "@id": "bts:Systemiccomplications" }, { - "@id": "bts:HodgkinlymphomamixedcellularityNOS" + "@id": "bts:Other" }, { - "@id": "bts:HodgkinlymphomanodularsclerosisNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:HodgkinlymphomaNOS" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "COVID19 Complications Severity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CancerTreatmentFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder", + "rdfs:label": "COVID19CancerTreatmentFollowup", + "rdfs:subClassOf": [ { - "@id": "bts:HodgkinparagranulomaNOS" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Hodgkinsarcoma" + "@id": "bts:Yes" }, { - "@id": "bts:InfiltratingbasalcellcarcinomaNOS" + "@id": "bts:No" }, { - "@id": "bts:InfiltratingductcarcinomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Infiltratingductandcolloidcarcinoma" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "COVID19 Cancer Treatment Followup", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ecigvapeuse", + "@type": "rdfs:Class", + "rdfs:comment": "Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)", + "rdfs:label": "Ecigvapeuse", + "rdfs:subClassOf": [ { - "@id": "bts:Infiltratingductandcribriformcarcinoma" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - 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"@id": "bts:Intracysticpapilloma" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ecig vape times per day", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Typeofsmokeexposurecumulativeyears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", + "rdfs:label": "Typeofsmokeexposurecumulativeyears", + "rdfs:subClassOf": [ { - "@id": "bts:Intradermalnevus" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Type of smoke exposure cumulative years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Chewingtobaccodailyusecount", + "@type": "rdfs:Class", + "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", + "rdfs:label": "Chewingtobaccodailyusecount", + "rdfs:subClassOf": [ { - "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Chewing tobacco daily use count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Secondhandsmokeexposureyears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of cumulative years of the patient's exposure to second-hand cigarette smoke", + "rdfs:label": "Secondhandsmokeexposureyears", + "rdfs:subClassOf": [ { - "@id": "bts:Intraductalandlobularcarcinoma" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second hand smoke exposure years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KnownGeneticPredispositionMutation", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", + "rdfs:label": "KnownGeneticPredispositionMutation", + "rdfs:subClassOf": [ { - "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" - }, + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Intraductalcarcinomaclinging" + "@id": "bts:Yes" }, { - "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" + "@id": "bts:No" }, { - "@id": "bts:IntraductalcarcinomaNOS" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Known Genetic Predisposition Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome", + "@type": "rdfs:Class", + "rdfs:comment": "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", + "rdfs:label": "HereditaryCancerPredispositionSyndrome", + "rdfs:subClassOf": [ { - "@id": "bts:Intraductalcarcinomasolidtype" - }, + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Intraductalmicropapillarycarcinoma" + "@id": "bts:Alpha-1antitrypsin" }, { - "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" + "@id": "bts:Attenuatedfamilialadenomatouspolyposis" }, { - "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" + "@id": "bts:BAP1mutantdisease" }, { - "@id": "bts:Intraductalpapillarycarcinoma" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" + "@id": "bts:Biliarydisorder" }, { - "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" + "@id": "bts:Birt-Hogg-Dubesyndrome" }, { - "@id": "bts:Intraductaltubulopapillaryneoplasm" + "@id": "bts:Carneycomplex" }, { - "@id": "bts:IntraepidermalcarcinomaNOS" + "@id": "bts:Cirrhosisunknownetiology" }, { - "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" + "@id": "bts:Constitutionalmismatchrepairdeficiency" }, { - "@id": "bts:IntravascularB-celllymphoma" + "@id": "bts:Familialadenomatouspolyposis" }, { - "@id": "bts:Juvenilemyelomonocyticleukemia" + "@id": "bts:Familialgastrointestinalstromaltumor" }, { - "@id": "bts:Kaposisarcoma" + "@id": "bts:Familialpancreaticcancer" }, { - "@id": "bts:LargecellcarcinomaNOS" + "@id": "bts:Familialprostatecancer" }, { - "@id": "bts:Liposarcomadifferentiated" + "@id": "bts:Familialrenalcancer" }, { - "@id": "bts:LiposarcomaNOS" + "@id": "bts:Fanconianemia" }, { - "@id": "bts:Liposarcomawelldifferentiated" + "@id": "bts:GlycogenStorageDisease" }, { - "@id": "bts:Livercelladenoma" + "@id": "bts:Gorlinsyndrome" }, { - "@id": "bts:Livercellcarcinoma" + "@id": "bts:Hereditarybreast–ovariancancersyndrome" }, { - "@id": "bts:Lobularadenocarcinoma" + "@id": "bts:Hereditarydiffusegastriccancer" }, { - "@id": "bts:Lobularandductalcarcinoma" + "@id": "bts:Hereditaryleiomyoma-renalcellcarcinoma" }, { - "@id": "bts:LobularcarcinomainsituNOS" + "@id": "bts:Hereditarymelanoma" }, { - "@id": "bts:Lobularcarcinomanoninfiltrating" + "@id": "bts:Hereditarymixedpolyposissyndrome" }, { - "@id": "bts:LobularcarcinomaNOS" + "@id": "bts:HereditarypapillaryRCC" }, { - "@id": "bts:LymphaticleukemicNOS" + "@id": "bts:Hereditarypapillaryrenalcellcarcinoma" }, { - "@id": "bts:LymphoblasticleukemiaNOS" + "@id": "bts:Hereditaryparaganglioma–pheochromocytomasyndrome" }, { - "@id": "bts:Lymphoblastoma" + "@id": "bts:Hereditaryrenaloncocytoma" }, { - "@id": "bts:LymphocyticleukemiaNOS" + "@id": "bts:Hereditaryretinoblastoma" }, { - "@id": "bts:LymphomaNOS" + "@id": "bts:Juvenilepolyposissyndrome" }, { - "@id": "bts:Malignancy" + "@id": "bts:Li-Fraumenisyndrome" }, { - "@id": "bts:MalignantlymphomadiffuseNOS" + "@id": "bts:Lynchsyndrome" }, { - "@id": "bts:MalignantlymphomaHodgkin" + "@id": "bts:Melanoma–astrocytomasyndrome" }, { - "@id": "bts:MalignantlymphomaimmunoblasticNOS" + "@id": "bts:MultipleendocrineneoplasiatypeI" }, { - "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" + "@id": "bts:MultipleendocrineneoplasiatypeII" }, { - "@id": "bts:MalignantlymphomalargeB-cellNOS" + "@id": "bts:MUTYH-associatedpolyposis" }, { - "@id": "bts:MalignantlymphomalargecellNOS" + "@id": "bts:Nevoidbasalcellcarcinomasyndrome" }, { - "@id": "bts:MalignantlymphomalymphoblasticNOS" + "@id": "bts:NotApplicable" }, { - 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"@id": "bts:Tubulocysticrenalcellcarcinoma" + "@id": "bts:Egypt" }, { - "@id": "bts:Tubulolobularcarcinoma" + "@id": "bts:ElSalvador" }, { - "@id": "bts:Tubulopapillaryadenocarcinoma" + "@id": "bts:EquatorialGuinea" }, { - "@id": "bts:TubulovillousadenomaNOS" + "@id": "bts:Eritrea" }, { - "@id": "bts:Tumorcellsbenign" + "@id": "bts:Estonia" }, { - "@id": "bts:Tumorcellsmalignant" + "@id": "bts:Eswatini" }, { - "@id": "bts:TumorcellsNOS" + "@id": "bts:Ethiopia" }, { - "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" + "@id": "bts:FalklandIslands(Malvinas)" }, { - "@id": "bts:Tumorembolus" + "@id": "bts:FaroeIslands" }, { - "@id": "bts:Tumorbenign" + "@id": "bts:FederatedStatesofMicronesia" }, { - "@id": "bts:TumormalignantNOS" + "@id": "bts:Fiji" }, { - "@id": "bts:Tumormetastatic" + "@id": "bts:Finland" }, { - "@id": "bts:TumorNOS" + "@id": "bts:France" }, { - "@id": "bts:Tumorsecondary" + "@id": "bts:FrenchGuiana" }, { - "@id": "bts:Tumorletbenign" + "@id": "bts:FrenchPolynesia" }, { - "@id": "bts:Typicalcarcinoid" + "@id": "bts:Gabon" }, { - "@id": "bts:Unclassifiedtumorbenign" + "@id": "bts:Gambia" }, { - "@id": "bts:Unclassifiedtumorborderlinemalignancy" + "@id": "bts:Georgia" }, { - "@id": "bts:Unclassifiedtumormalignant" + "@id": "bts:Germany" }, { - "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" + "@id": "bts:Ghana" }, { - "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" + "@id": "bts:Gibraltar" }, { - "@id": "bts:Undifferentiatedepithelioidsarcoma" + "@id": "bts:Greece" }, { - "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" + "@id": "bts:Greenland" }, { - "@id": "bts:Undifferentiatedleukaemia" + "@id": "bts:Grenada" }, { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" + "@id": "bts:Guadeloupe" }, { - "@id": "bts:Undifferentiatedroundcellsarcoma" + "@id": "bts:Guam" }, { - "@id": "bts:Undifferentiatedsarcoma" + "@id": "bts:Guatemala" }, { - "@id": "bts:Undifferentiatedspindlecellsarcoma" + "@id": "bts:Guernsey" }, { - "@id": "bts:Undifferentiateduterinesarcoma" + "@id": "bts:Guinea" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Primary Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProgressionorRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", - "rdfs:label": "ProgressionorRecurrence", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-ProgressionorRecurrence" + "@id": "bts:Guinea-Bissau" }, { - "@id": "bts:No" + "@id": "bts:Guyana" }, { - "@id": "bts:Unknown" + "@id": "bts:Haiti" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Progression or Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteofResectionorBiopsy", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "SiteofResectionorBiopsy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" + "@id": "bts:HolySee" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:Honduras" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:HongKong" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:Hungary" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:Iceland" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:India" }, { - "@id": "bts:Analcanal" + "@id": "bts:Indonesia" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:Iran" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:Iraq" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:Ireland" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:IsleofMan" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:Israel" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:Italy" }, { - "@id": "bts:AnusNOS" + "@id": "bts:Jamaica" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:Japan" }, { - "@id": "bts:Appendix" + "@id": "bts:Jersey" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:Jordan" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:Kazakhstan" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:Kenya" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:Kiribati" }, { - "@id": "bts:Bladderneck" + "@id": "bts:Kosovo" }, { - "@id": "bts:BladderNOS" + "@id": "bts:Kuwait" }, { - "@id": "bts:Blood" + "@id": "bts:Kyrgyzstan" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:Laos" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:Latvia" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:Lebanon" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:Lesotho" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:Liberia" }, { - "@id": "bts:BoneNOS" + "@id": "bts:Libya" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:Liechtenstein" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:Lithuania" }, { - "@id": "bts:Brainstem" + "@id": "bts:Luxembourg" }, { - "@id": "bts:BrainNOS" + "@id": "bts:Macau" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:Madagascar" }, { - "@id": "bts:BreastNOS" + "@id": "bts:Malawi" }, { - "@id": "bts:Broadligament" + "@id": "bts:Malaysia" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:Maldives" }, { - "@id": "bts:Carotidbody" + "@id": "bts:Mali" }, { - "@id": "bts:Caudaequina" + "@id": "bts:Malta" }, { - "@id": "bts:Cecum" + "@id": "bts:MarshallIslands" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:Martinique" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:Mauritania" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:Mauritius" }, { - "@id": "bts:Cerebrum" + "@id": "bts:Mayotte" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:Mexico" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:Moldova" }, { - "@id": "bts:Choroid" + "@id": "bts:Monaco" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:Mongolia" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:Montenegro" }, { - "@id": "bts:ColonNOS" + "@id": "bts:Montserrat" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:Morocco" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:Mozambique" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:Myanmar" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:Namibia" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:Nauru" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:Nepal" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:Netherlands" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:NewCaledonia" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:NewZealand" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:Nicaragua" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:Niger" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:Nigeria" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:Niue" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:NorthKorea" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:NorthMacedonia" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:NorthernMarianaIslands" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:Norway" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:Oman" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Pakistan" }, { - "@id": "bts:Duodenum" + "@id": "bts:Palau" }, { - "@id": "bts:Endocervix" + "@id": "bts:Panama" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:PapuaNewGuinea" }, { - "@id": "bts:Endometrium" + "@id": "bts:Paraguay" }, { - "@id": "bts:Epididymis" + "@id": "bts:Peru" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:Philippines" }, { - "@id": "bts:Ethmoidsinus" + "@id": "bts:Poland" }, { - "@id": "bts:Exocervix" + "@id": "bts:Portugal" }, { - "@id": "bts:Externalear" + "@id": "bts:PuertoRico" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:Qatar" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:Reunion" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:Romania" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:Russia" }, { - "@id": "bts:EyeNOS" + "@id": "bts:Rwanda" }, { - "@id": "bts:Eyelid" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:FemalegenitaltractNOS" + "@id": "bts:SaintLucia" }, { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:Frontallobe" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:Samoa" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:SanMarino" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:Gallbladder" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:Senegal" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:Serbia" }, { - "@id": "bts:Glanspenis" + "@id": "bts:Seychelles" }, { - "@id": "bts:Glottis" + "@id": "bts:SierraLeone" }, { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:Singapore" }, { - "@id": "bts:GumNOS" + "@id": "bts:Slovakia" }, { - "@id": "bts:Hardpalate" + "@id": "bts:Slovenia" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:HeadfaceorneckNOS" + "@id": "bts:Somalia" }, { - "@id": "bts:Heart" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:SouthKorea" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:SouthSudan" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:Spain" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:SriLanka" }, { - "@id": "bts:Ileum" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:Sudan" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:Suriname" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:Sweden" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:Switzerland" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:Syria" }, { - "@id": "bts:Isthmusuteri" + "@id": "bts:Taiwan" }, { - "@id": "bts:Jejunum" + "@id": "bts:Tajikistan" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:Tanzania" }, { - "@id": "bts:Labiummajus" + "@id": "bts:Thailand" }, { - "@id": "bts:Labiumminus" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:Lacrimalgland" + "@id": "bts:Togo" }, { - "@id": "bts:Laryngealcartilage" + "@id": "bts:Tokelau" }, { - "@id": "bts:LarynxNOS" + "@id": "bts:Tonga" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:Tunisia" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:Turkey" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:Tuvalu" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:Uganda" }, { - "@id": "bts:LipNOS" + "@id": "bts:Ukraine" }, { - "@id": "bts:Liver" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + "@id": "bts:UnitedStates" }, { - "@id": "bts:Lowergum" + "@id": "bts:Uruguay" }, { - "@id": "bts:LowerlimbNOS" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:Vanuatu" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:Venezuela" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:Vietnam" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:LungNOS" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:LymphnodeNOS" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:Lymphnodesofaxillaorarm" + "@id": "bts:WesternSahara" }, { - "@id": "bts:Lymphnodesofheadfaceandneck" + "@id": "bts:Yemen" }, { - "@id": "bts:Lymphnodesofinguinalregionorleg" + "@id": "bts:Zambia" }, { - "@id": "bts:Lymphnodesofmultipleregions" + "@id": "bts:Zimbabwe" }, { - "@id": "bts:Mainbronchus" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Country of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea", + "@type": "rdfs:Class", + "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", + "rdfs:label": "MedicallyUnderservedArea", + "rdfs:subClassOf": [ { - "@id": "bts:MajorsalivaryglandNOS" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MalegenitalorgansNOS" + "@id": "bts:MedicallyUnderservedArea-Yes" }, { - "@id": "bts:Mandible" + "@id": "bts:MedicallyUnderservedArea-No" }, { - "@id": "bts:Maxillarysinus" - }, + "@id": "bts:MedicallyUnderservedArea-Unknown" + } + ], + "sms:displayName": "Medically Underserved Area", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RuralvsUrban", + "@type": "rdfs:Class", + "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", + "rdfs:label": "RuralvsUrban", + "rdfs:subClassOf": [ { - "@id": "bts:Meckeldiverticulum" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MediastinumNOS" + "@id": "bts:UrbanPopulation(population>50000)" }, { - "@id": "bts:Medullaofadrenalgland" + "@id": "bts:UrbanCluster(population2500-50000)" }, { - "@id": "bts:MeningesNOS" - }, + "@id": "bts:RuralPopulation(population<2500)" + } + ], + "sms:displayName": "Rural vs Urban", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidence", + "@type": "rdfs:Class", + "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", + "rdfs:label": "CancerIncidence", + "rdfs:subClassOf": [ { - "@id": "bts:Middleear" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidenceLocation", + "@type": "rdfs:Class", + "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", + "rdfs:label": "CancerIncidenceLocation", + "rdfs:subClassOf": [ { - "@id": "bts:Middlelobelung" - }, + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Cancer related clinical data specific to SRRS", + "rdfs:label": "SRRSClinicalDataTier2", + "rdfs:subClassOf": [ { - "@id": "bts:Middlethirdofesophagus" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:MouthNOS" + "@id": "bts:Component" }, { - "@id": "bts:MucosaoflipNOS" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Mucosaoflowerlip" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Mucosaofupperlip" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Myometrium" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Nasalcavity" + "@id": "bts:EducationLevel" }, { - "@id": "bts:NasopharynxNOS" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:NervoussystemNOS" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:Nipple" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:Olfactorynerve" + "@id": "bts:CancerIncidenceLocation" }, { - "@id": "bts:Opticnerve" + "@id": "bts:Ethnicity" }, { - "@id": "bts:OrbitNOS" + "@id": "bts:Gender" }, { - "@id": "bts:OropharynxNOS" + "@id": "bts:Race" }, { - "@id": "bts:Otherill-definedsites" + "@id": "bts:VitalStatus" }, { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + "@id": "bts:DaystoLastFollowup" }, { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:DaystoLastKnownDiseaseStatus" }, { - "@id": "bts:Ovary" + "@id": "bts:DaystoRecurrence" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:Morphology" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:PrimaryDiagnosis" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:Overlappinglesionofbrain" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + "@id": "bts:TissueorOrganofOrigin" }, { - "@id": "bts:Overlappinglesionofbreast" + "@id": "bts:NCIAtlasCancerSite" }, { - "@id": "bts:Overlappinglesionofcervixuteri" + "@id": "bts:TumorGrade" }, { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:PackYearsSmoked" }, { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + "@id": "bts:YearsSmoked" }, { - "@id": "bts:Overlappinglesionofcorpusuteri" + "@id": "bts:DaystoFollowUp" }, { - "@id": "bts:Overlappinglesionofdigestivesystem" + "@id": "bts:GeneSymbol" }, { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Overlappinglesionofesophagus" + "@id": "bts:TestResult" }, { - "@id": "bts:Overlappinglesionofeyeandadnexa" + "@id": "bts:TreatmentType" }, { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" - }, + "@id": "bts:TumorLargestDimensionDiameter" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Ethnicity", + "@type": "rdfs:Class", + "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "rdfs:label": "Ethnicity", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionoffloorofmouth" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + "@id": "bts:Hispanicorlatino" }, { - "@id": "bts:Overlappinglesionofhypopharynx" + "@id": "bts:Nothispanicorlatino" }, { - "@id": "bts:Overlappinglesionofill-definedsites" + "@id": "bts:Unknown" }, { - "@id": "bts:Overlappinglesionoflarynx" + "@id": "bts:NotReported" }, { - "@id": "bts:Overlappinglesionoflip" - }, + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Ethnicity", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Gender", + "@type": "rdfs:Class", + "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "rdfs:label": "Gender", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionoflung" + "@id": "bts:Female" }, { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" + "@id": "bts:Male" }, { - "@id": "bts:Overlappinglesionofmalegenitalorgans" + "@id": "bts:Unknown" }, { - "@id": "bts:Overlappinglesionofnasopharynx" + "@id": "bts:Unspecified" }, { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Gender", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Race", + "@type": "rdfs:Class", + "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "rdfs:label": "Race", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofpalate" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionofpancreas" + "@id": "bts:White" }, { - "@id": "bts:Overlappinglesionofpenis" + "@id": "bts:Americanindianoralaskanative" }, { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + "@id": "bts:Blackorafricanamerican" }, { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + "@id": "bts:Asian" }, { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + "@id": "bts:Nativehawaiianorotherpacificislander" }, { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + "@id": "bts:Other" }, { - "@id": "bts:Overlappinglesionofskin" + "@id": "bts:Unknown" }, { - "@id": "bts:Overlappinglesionofsmallintestine" + "@id": "bts:NotReported" }, { - "@id": "bts:Overlappinglesionofstomach" - }, + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Race", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:VitalStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionoftongue" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionoftonsil" + "@id": "bts:Alive" }, { - "@id": "bts:Overlappinglesionofurinaryorgans" + "@id": "bts:Dead" }, { - "@id": "bts:Overlappinglesionofvulva" + "@id": "bts:Unknown" }, { - "@id": "bts:Overlappinglesionsoforopharynx" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Vital Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label": "AgeatDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:PalateNOS" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Age at Diagnosis", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoLastFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastFollowup", + "rdfs:subClassOf": [ { - "@id": "bts:PancreasNOS" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Follow up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Pancreaticduct" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoRecurrence", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoRecurrence", + "rdfs:subClassOf": [ { - "@id": "bts:Parametrium" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:LastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", + "rdfs:label": "LastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Paraspinal" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Parathyroidgland" + "@id": "bts:Distantmetrecurrence/progression" }, { - "@id": "bts:Paraurethralgland" + "@id": "bts:Loco-regionalrecurrence/progression" }, { - "@id": "bts:Parietallobe" + "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" }, { - "@id": "bts:Parotidgland" + "@id": "bts:Tumorfree" }, { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + "@id": "bts:Unknowntumorstatus" }, { - "@id": "bts:Pelviclymphnodes" + "@id": "bts:Withtumor" }, { - "@id": "bts:PelvisNOS" + "@id": "bts:NotReported" }, { - "@id": "bts:PenisNOS" + "@id": "bts:NotAllowedToCollect" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Morphology", + "@type": "rdfs:Class", + "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", + "rdfs:label": "Morphology", + "rdfs:subClassOf": [ { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Morphology", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "PrimaryDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + "@id": "bts:Acinarcellcarcinoma" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + "@id": "bts:Acutebasophilicleukaemia" }, { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + "@id": "bts:AcuteleukemiaBurkitttype" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + "@id": "bts:AcuteleukemiaNOS" }, { - "@id": "bts:PeritoneumNOS" + "@id": "bts:Acutelymphaticleukemia" }, { - "@id": "bts:PharynxNOS" + "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" }, { - "@id": "bts:Pinealgland" + "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" }, { - "@id": "bts:Pituitarygland" + "@id": "bts:AcutelymphoblasticleukemiaNOS" }, { - "@id": "bts:Placenta" + "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" }, { - "@id": "bts:PleuraNOS" + "@id": "bts:Acutelymphocyticleukemia" }, { - "@id": "bts:Postcricoidregion" + "@id": "bts:Acutelymphoidleukemia" }, { - "@id": "bts:Posteriormediastinum" + "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" }, { - "@id": "bts:Posteriorwallofbladder" + "@id": "bts:AcutemyeloidleukemiaMLL" }, { - "@id": "bts:Posteriorwallofhypopharynx" + "@id": "bts:AcutemyeloidleukemiaNOS" }, { - "@id": "bts:Posteriorwallofnasopharynx" + "@id": "bts:Acutemyelomonocyticleukemia" }, { - "@id": "bts:Posteriorwalloforopharynx" + "@id": "bts:AcutepromyelocyticleukemiaNOS" }, { - "@id": "bts:Prepuce" + "@id": "bts:Adenocarcinoidtumor" }, { - "@id": "bts:Prostategland" + "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" }, { - "@id": "bts:Pylorus" + "@id": "bts:AdenocarcinomainapolypNOS" }, { - "@id": "bts:Pyriformsinus" + "@id": "bts:Adenocarcinomainadenomatouspolyp" }, { - "@id": "bts:Rectosigmoidjunction" + "@id": "bts:Adenocarcinomainpolypoidadenoma" }, { - "@id": "bts:RectumNOS" + "@id": "bts:AdenocarcinomainsituinapolypNOS" }, { - "@id": "bts:Renalpelvis" + "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" }, { - "@id": "bts:ReticuloendothelialsystemNOS" + "@id": "bts:Adenocarcinomainsituintubularadenoma" }, { - "@id": "bts:Retina" + "@id": "bts:Adenocarcinomainsitumucinous" }, { - "@id": "bts:Retromolararea" + "@id": "bts:Adenocarcinomainsitunon-mucinous" }, { - "@id": "bts:Retroperitoneum" + "@id": "bts:AdenocarcinomainsituNOS" }, { - "@id": "bts:Ribsternumclavicleandassociatedjoints" + "@id": "bts:Adenocarcinomaintubularadenoma" }, { - "@id": "bts:Roundligament" + "@id": "bts:Adenocarcinomainvillousadenoma" }, { - "@id": "bts:ScrotumNOS" + "@id": "bts:Adenocarcinomaofanalducts" }, { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + "@id": "bts:Adenocarcinomaofanalglands" }, { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:Adenocarcinomadiffusetype" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:Adenocarcinomaendocervicaltype" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:Adenocarcinomaintestinaltype" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:AdenocarcinomametastaticNOS" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:AdenocarcinomaNOS" }, { - "@id": "bts:Skinofscalpandneck" + "@id": "bts:Adenocarcinomapancreatobiliarytype" }, { - "@id": "bts:Skinoftrunk" + "@id": "bts:Adultrhabdomyoma" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:AdultT-celllymphoma" }, { - "@id": "bts:SkinNOS" + "@id": "bts:AdultT-celllymphoma/leukemia" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:Astrocytomaanaplastic" }, { - "@id": "bts:SoftpalateNOS" + "@id": "bts:Astrocytomalowgrade" }, { - "@id": "bts:Specifiedpartsofperitoneum" + "@id": "bts:AstrocytomaNOS" }, { - "@id": "bts:Spermaticcord" + "@id": "bts:BcelllymphomaNOS" }, { - "@id": "bts:Sphenoidsinus" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" }, { - "@id": "bts:Spinalcord" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" }, { - "@id": "bts:Spleen" + "@id": "bts:B-ALL" }, { - "@id": "bts:Splenicflexureofcolon" + "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" }, { - "@id": "bts:StomachNOS" + "@id": "bts:Basalcelladenocarcinoma" }, { - "@id": "bts:Subglottis" + "@id": "bts:Basalcelladenoma" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:BasalcellcarcinomaNOS" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:Basalcellepithelioma" }, { - "@id": "bts:Superiorwallofnasopharynx" + "@id": "bts:Basalcelltumor" }, { - "@id": "bts:Supraglottis" + "@id": "bts:Basophiladenocarcinoma" }, { - "@id": "bts:Tailofpancreas" + "@id": "bts:Basophiladenoma" }, { - "@id": "bts:Temporallobe" + "@id": "bts:Basophilcarcinoma" }, { - "@id": "bts:TestisNOS" + "@id": "bts:Bileductadenocarcinoma" }, { - "@id": "bts:Thoracicesophagus" + "@id": "bts:Bileductadenoma" }, { - "@id": "bts:ThoraxNOS" + "@id": "bts:Bileductcarcinoma" }, { - "@id": "bts:Thymus" + "@id": "bts:Bileductcystadenocarcinoma" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:Bileductcystadenoma" }, { - "@id": "bts:TongueNOS" + "@id": "bts:Bronchialadenomacarcinoid" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:Bronchialadenomacylindroid" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:BronchialadenomaNOS" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:Trachea" + "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" }, { - "@id": "bts:Transversecolon" + "@id": "bts:Bronchio-alveolarcarcinomamucinous" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:Bronchiolaradenocarcinoma" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:Bronchiolarcarcinoma" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" }, { - "@id": "bts:Uppergum" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:Burkittcellleukemia" }, { - "@id": "bts:Urachus" + "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" }, { - "@id": "bts:Ureter" + "@id": "bts:Burkitttumor" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:Burkitt-likelymphoma" }, { - "@id": "bts:Urethra" + "@id": "bts:C-ALL" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:Cancer" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:Capillaryhemangioma" }, { - "@id": "bts:UterusNOS" + "@id": "bts:Capillarylymphangioma" }, { - "@id": "bts:Uvula" + "@id": "bts:CarcinomainapolypNOS" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:Carcinomainadenomatouspolyp" }, { - "@id": "bts:Vallecula" + "@id": "bts:Carcinomainpleomorphicadenoma" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:CarcinomainsituinapolypNOS" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:Carcinomainsituinadenomatouspolyp" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:CarcinomainsituNOS" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:CarcinomaanaplasticNOS" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:Carcinomadiffusetype" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:Carcinomaintestinaltype" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:CarcinomametastaticNOS" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:Clitoris" + "@id": "bts:CarcinosarcomaNOS" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:CarcinomaundifferentiatedNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:CementomaNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Site of Resection or Biopsy", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TissueorOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "TissueorOrganofOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Centralneuroblastoma" + }, { - "@id": "bts:AbdomenNOS" + "@id": "bts:Centralneurocytoma" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:Cerebellarliponeurocytoma" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:CerebellarsarcomaNOS" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:CervicalintraepithelialneoplasiagradeIII" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:Cervicalintraepithelialneoplasialowgrade" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:ChondromaNOS" }, { - "@id": "bts:Analcanal" + "@id": "bts:Chondrosarcomagrade2/3" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:ChronicgranulocyticleukemiaNOS" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:ChronicleukemiaNOS" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:Chroniclymphaticleukemia" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:Chroniclymphocyticleukemia" }, { - "@id": "bts:AnusNOS" + "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:Chroniclymphoidleukemia" }, { - "@id": "bts:Appendix" + "@id": "bts:Chronicmonocyticleukemia" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:ChronicmyelocyticleukemiaNOS" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:ChronicmyeloidleukemiaNOS" }, { - "@id": "bts:Bladderneck" + "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" }, { - "@id": "bts:BladderNOS" + "@id": "bts:ChronicmyelomonocyticleukemiaNOS" }, { - "@id": "bts:Blood" + "@id": "bts:ChronicmyelomonocyticleukemiaType1" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:ChronicmyeloproliferativediseaseNOS" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:Chronicmyeloproliferativedisorder" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:Chronicneutrophilicleukemia" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" }, { - "@id": "bts:BoneNOS" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" }, { - "@id": "bts:Brainstem" + "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" }, { - "@id": "bts:BrainNOS" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" }, { - "@id": "bts:BreastNOS" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" }, { - "@id": "bts:Broadligament" + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" }, { - "@id": "bts:Carotidbody" + "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" }, { - "@id": "bts:Caudaequina" + "@id": "bts:Combinedsmallcellcarcinoma" }, { - "@id": "bts:Cecum" + "@id": "bts:Combinedsmallcell-adenocarcinoma" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:Combinedsmallcell-largecarcinoma" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" }, { - "@id": "bts:Cerebrum" + "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:Dermalnevus" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:DermatofibromaNOS" }, { - "@id": "bts:Choroid" + "@id": "bts:DiffuseastrocytomaIDH-mutant" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:DiffuseastrocytomaIDH-wildtype" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:Diffuseastrocytomalowgrade" }, { - "@id": "bts:ColonNOS" + "@id": "bts:DiffuselargeB-celllymphomaNOS" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:Diffusemelanocytosis" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:DuctadenocarcinomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:DuctadenomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:Ductcarcinomadesmoplastictype" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:DuctcarcinomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:Ductcellcarcinoma" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:DuctalcarcinomainsituNOS" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:DuctalcarcinomaNOS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:Dysplasticnevus" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:EndometrialsarcomaNOS" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:EndometrioidadenocarcinomaNOS" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:EndometrioidadenofibromaNOS" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:EndometrioidadenomaNOS" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:EndometrioidcarcinomaNOS" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:Eosinophiladenocarcinoma" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:Eosinophiladenoma" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:Eosinophilcarcinoma" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:Eosinophilicgranuloma" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Eosinophilicleukemia" }, { - "@id": "bts:Duodenum" + "@id": "bts:EpendymomaNOS" }, { - "@id": "bts:Endocervix" + "@id": "bts:EpidermoidcarcinomainsituNOS" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:EpidermoidcarcinomaNOS" }, { - "@id": "bts:Endometrium" + "@id": "bts:Epithelialtumorbenign" }, { - "@id": "bts:Epididymis" + "@id": "bts:Epithelialtumormalignant" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" }, { - "@id": "bts:Ethmoidsinus" + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" }, { - "@id": "bts:Exocervix" + "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" }, { - "@id": "bts:Externalear" + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:Ewingsarcoma" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:GangliogliomaNOS" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:Familialadenomatouspolyposis" }, { - "@id": "bts:EyeNOS" + "@id": "bts:Gastrincelltumor" }, { - "@id": "bts:Eyelid" + "@id": "bts:Gastrincelltumormalignant" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:Gastrinomamalignant" }, { - "@id": "bts:FemalegenitaltractNOS" + "@id": "bts:GastrinomaNOS" }, { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:Gastrointestinalstromaltumormalignant" }, { - "@id": "bts:Frontallobe" + "@id": "bts:Glioblastoma" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:Gliomamalignant" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:GliomaNOS" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:Haemangioblastoma" }, { - "@id": "bts:Gallbladder" + "@id": "bts:Haemangiosarcoma" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:Hepatocarcinoma" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:Hepatocellularadenoma" }, { - "@id": "bts:Glanspenis" + "@id": "bts:HepatocellularcarcinomaNOS" }, { - "@id": "bts:Glottis" + "@id": "bts:Hepatocholangiocarcinoma" }, { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:Hepatoidadenocarcinoma" }, { - "@id": "bts:GumNOS" + "@id": "bts:Hepatoidcarcinoma" }, { - "@id": "bts:Hardpalate" + "@id": "bts:HodgkindiseaseNOS" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:Hodgkingranuloma" }, { - "@id": "bts:HeadfaceorneckNOS" + "@id": "bts:HodgkinlymphomamixedcellularityNOS" }, { - "@id": "bts:Heart" + "@id": "bts:HodgkinlymphomanodularsclerosisNOS" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:HodgkinlymphomaNOS" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:HodgkinparagranulomaNOS" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:Hodgkinsarcoma" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:InfiltratingbasalcellcarcinomaNOS" }, { - "@id": "bts:Ileum" + "@id": "bts:InfiltratingductcarcinomaNOS" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:Infiltratingductandcolloidcarcinoma" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:Infiltratingductandcribriformcarcinoma" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:Inflammatoryadenocarcinoma" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:Inflammatorycarcinoma" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:Interstitialcelltumorbenign" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:Interstitialcelltumormalignant" }, { - "@id": "bts:Isthmusuteri" + "@id": "bts:InterstitialcelltumorNOS" }, { - "@id": "bts:Jejunum" + "@id": "bts:Intracysticpapilloma" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:Intradermalnevus" }, { - "@id": "bts:Labiummajus" + "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" }, { - "@id": "bts:Labiumminus" + "@id": "bts:Intraductalandlobularcarcinoma" }, { - "@id": "bts:Lacrimalgland" + "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" }, { - "@id": "bts:Laryngealcartilage" + "@id": "bts:Intraductalcarcinomaclinging" }, { - "@id": "bts:LarynxNOS" + "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:IntraductalcarcinomaNOS" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:Intraductalcarcinomasolidtype" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:Intraductalmicropapillarycarcinoma" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:Intraductalpapillarycarcinoma" }, { - "@id": "bts:LipNOS" + "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" }, { - "@id": "bts:Liver" + "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" }, { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + "@id": "bts:Intraductaltubulopapillaryneoplasm" }, { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + "@id": "bts:IntraepidermalcarcinomaNOS" }, { - "@id": "bts:Lowergum" + "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" }, { - "@id": "bts:LowerlimbNOS" + "@id": "bts:IntravascularB-celllymphoma" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:Juvenilemyelomonocyticleukemia" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:Kaposisarcoma" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:LargecellcarcinomaNOS" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:Liposarcomadifferentiated" }, { - "@id": "bts:LungNOS" + "@id": "bts:LiposarcomaNOS" }, { - "@id": "bts:LymphnodeNOS" + "@id": "bts:Liposarcomawelldifferentiated" }, { - "@id": "bts:Lymphnodesofaxillaorarm" + "@id": "bts:Livercelladenoma" }, { - "@id": "bts:Lymphnodesofheadfaceandneck" + "@id": "bts:Livercellcarcinoma" }, { - "@id": "bts:Lymphnodesofinguinalregionorleg" + "@id": "bts:Lobularadenocarcinoma" }, { - "@id": "bts:Lymphnodesofmultipleregions" + "@id": "bts:Lobularandductalcarcinoma" }, { - "@id": "bts:Mainbronchus" + "@id": "bts:LobularcarcinomainsituNOS" }, { - "@id": "bts:MajorsalivaryglandNOS" + "@id": "bts:Lobularcarcinomanoninfiltrating" }, { - "@id": "bts:MalegenitalorgansNOS" + "@id": "bts:LobularcarcinomaNOS" }, { - "@id": "bts:Mandible" + "@id": "bts:LymphaticleukemicNOS" }, { - "@id": "bts:Maxillarysinus" + "@id": "bts:LymphoblasticleukemiaNOS" }, { - "@id": "bts:Meckeldiverticulum" + "@id": "bts:Lymphoblastoma" }, { - "@id": "bts:MediastinumNOS" + "@id": "bts:LymphocyticleukemiaNOS" }, { - "@id": "bts:Medullaofadrenalgland" + "@id": "bts:LymphomaNOS" }, { - "@id": "bts:MeningesNOS" + "@id": "bts:Malignancy" }, { - "@id": "bts:Middleear" + "@id": "bts:MalignantlymphomadiffuseNOS" }, { - "@id": "bts:Middlelobelung" + "@id": "bts:MalignantlymphomaHodgkin" }, { - "@id": "bts:Middlethirdofesophagus" + "@id": "bts:MalignantlymphomaimmunoblasticNOS" }, { - "@id": "bts:MouthNOS" + "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" }, { - "@id": "bts:MucosaoflipNOS" + "@id": "bts:MalignantlymphomalargeB-cellNOS" }, { - "@id": "bts:Mucosaoflowerlip" + "@id": "bts:MalignantlymphomalargecellNOS" }, { - "@id": "bts:Mucosaofupperlip" + "@id": "bts:MalignantlymphomalymphoblasticNOS" }, { - "@id": "bts:Myometrium" + "@id": "bts:MalignantlymphomalymphocyticdiffuseNOS" }, { - "@id": "bts:Nasalcavity" + "@id": "bts:MalignantlymphomalymphocyticnodularNOS" }, { - "@id": "bts:NasopharynxNOS" + "@id": "bts:MalignantlymphomalymphocyticNOS" }, { - "@id": "bts:NervoussystemNOS" + "@id": "bts:Malignantlymphomamixedcelltypediffuse" }, { - "@id": "bts:Nipple" + "@id": "bts:Malignantlymphomamixedcelltypefollicular" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:Malignantlymphomamixedcelltypenodular" }, { - "@id": "bts:Olfactorynerve" + "@id": "bts:MalignantlymphomanodularNOS" }, { - "@id": "bts:Opticnerve" + "@id": "bts:Malignantlymphomanon-HodgkinNOS" }, { - "@id": "bts:OrbitNOS" + "@id": "bts:MalignantlymphomaNOS" }, { - "@id": "bts:OropharynxNOS" + "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" }, { - "@id": "bts:Otherill-definedsites" + "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" }, { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + "@id": "bts:Malignantmelanomaingiantpigmentednevus" }, { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" }, { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:Malignantmelanomainjunctionalnevus" }, { - "@id": "bts:Ovary" + "@id": "bts:Malignantmelanomainprecancerousmelanosis" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:MalignantmelanomaNOS" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:Malignantmelanomaregressing" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:Mammarycarcinomainsitu" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id": "bts:Medullaryadenocarcinoma" }, { - "@id": "bts:Overlappinglesionofbrain" + "@id": "bts:MedullarycarcinomaNOS" }, { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + "@id": "bts:Medullaryosteosarcoma" }, { - "@id": "bts:Overlappinglesionofbreast" + "@id": "bts:MedulloblastomaNOS" }, { - "@id": "bts:Overlappinglesionofcervixuteri" + "@id": "bts:Melanoameloblastoma" }, { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:Melanocyticnevus" }, { - 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If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoFollowUp", - "rdfs:subClassOf": [ + "@id": "bts:Tubularadenocarcinoma" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Follow Up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:GeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "GeneSymbol", - "rdfs:subClassOf": [ + "@id": "bts:TubularadenomaNOS" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gene Symbol", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MolecularAnalysisMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularAnalysisMethod", - "rdfs:subClassOf": [ + "@id": "bts:Tubularandroblastomawithlipidstorage" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:TubularandroblastomaNOS" + }, { - "@id": "bts:ComparativeGenomicHybridization" + "@id": "bts:Tubularcarcinoid" }, { - "@id": "bts:CytogeneticsNOS" + "@id": "bts:Tubularcarcinoma" }, { - "@id": "bts:FISH" + "@id": "bts:Tubulo-papillaryadenoma" }, { - "@id": "bts:FlowCytometry" + "@id": "bts:Tubulocysticrenalcellcarcinoma" }, { - "@id": "bts:IHC" + "@id": "bts:Tubulolobularcarcinoma" }, { - "@id": "bts:ISH" + "@id": "bts:Tubulopapillaryadenocarcinoma" }, { - "@id": "bts:Karyotype" + "@id": "bts:TubulovillousadenomaNOS" }, { - "@id": "bts:Microarray" + "@id": "bts:Tumorcellsbenign" }, { - "@id": "bts:MicrosatelliteAnalysis" + "@id": "bts:Tumorcellsmalignant" }, { - "@id": "bts:NuclearStaining" + "@id": "bts:TumorcellsNOS" }, { - "@id": "bts:Other" + "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" }, { - "@id": "bts:RNASequencing" + "@id": "bts:Tumorembolus" }, { - "@id": "bts:RT-PCR" + "@id": "bts:Tumorbenign" }, { - "@id": "bts:SequencingNOS" + "@id": "bts:TumormalignantNOS" }, { - "@id": "bts:SouthernBlotting" + "@id": "bts:Tumormetastatic" }, { - "@id": "bts:TargetedSequencing" + "@id": "bts:TumorNOS" }, { - "@id": "bts:WGS" + "@id": "bts:Tumorsecondary" }, { - "@id": "bts:WXS" + "@id": "bts:Tumorletbenign" }, { - "@id": "bts:Unknown" + "@id": "bts:Typicalcarcinoid" }, { - "@id": "bts:NotReported" + "@id": "bts:Unclassifiedtumorbenign" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Molecular Analysis Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TestResult", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestResult", - "rdfs:subClassOf": [ + "@id": "bts:Unclassifiedtumorborderlinemalignancy" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Unclassifiedtumormalignant" + }, { - "@id": "bts:AbnormalNOS" + "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" }, { - "@id": "bts:CopyNumberReported" + "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" }, { - "@id": "bts:Equivocal" + "@id": "bts:Undifferentiatedepithelioidsarcoma" }, { - "@id": "bts:High" + "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" }, { - "@id": "bts:Intermediate" + "@id": "bts:Undifferentiatedleukaemia" }, { - "@id": "bts:LossofExpression" + "@id": "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id": "bts:Low" + "@id": "bts:Undifferentiatedroundcellsarcoma" }, { - "@id": "bts:Negative" + "@id": "bts:Undifferentiatedsarcoma" }, { - "@id": "bts:Normal" + "@id": "bts:Undifferentiatedspindlecellsarcoma" }, { - "@id": "bts:Overexpressed" + "@id": "bts:Undifferentiateduterinesarcoma" }, { - "@id": "bts:Positive" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Primary Diagnosis", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProgressionorRecurrence", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", + "rdfs:label": "ProgressionorRecurrence", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-ProgressionorRecurrence" }, { - "@id": "bts:TestValueReported" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Test Result", + "sms:displayName": "Progression or Recurrence", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TreatmentType", + "@id": "bts:SiteofResectionorBiopsy", "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of treatment administered.", - "rdfs:label": "TreatmentType", + "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "SiteofResectionorBiopsy", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -10848,1383 +11512,1017 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AblationCryo" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:AblationEthanolInjection" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:AblationMicrowave" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:AblationNOS" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:AblationRadiofrequency" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:AblationRadiosurgical" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:AncillaryTreatment" + "@id": "bts:Analcanal" }, { - "@id": "bts:AntiseizureTreatment" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:BisphosphonateTherapy" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:BlindedStudyTreatmentunknown" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:BrachytherapyHighDose" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:BrachytherapyLowDose" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:BrachytherapyNOS" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Chemoembolization" + "@id": "bts:AnusNOS" }, { - "@id": "bts:Chemoprotectant" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:Chemotherapy" + "@id": "bts:Appendix" }, { - "@id": "bts:ConcurrentChemoradiation" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:Cryoablation" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Embolization" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:EthanolInjectionAblation" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:ExternalBeamRadiation" + "@id": "bts:Bladderneck" }, { - "@id": "bts:HormoneTherapy" + "@id": "bts:BladderNOS" }, { - "@id": "bts:I-131RadiationTherapy" + "@id": "bts:Blood" }, { - "@id": "bts:InternalRadiation" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:Immunotherapy(IncludingVaccines)" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:IsolatedLimbPerfusion(ILP)" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:OrganTransplantation" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Other" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:PharmaceuticalTherapyNOS" + "@id": "bts:BoneNOS" }, { - "@id": "bts:Pleurodesis" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:Radiation2DConventional" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:Radiation3DConformal" + "@id": "bts:Brainstem" }, { - "@id": "bts:RadiationCombination" + "@id": "bts:BrainNOS" }, { - "@id": "bts:RadiationCyberknife" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:RadiationExternalBeam" + "@id": "bts:BreastNOS" }, { - "@id": "bts:RadiationImplants" + "@id": "bts:Broadligament" }, { - "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:RadiationInternal" + "@id": "bts:Carotidbody" }, { - "@id": "bts:RadiationProtonBeam" + "@id": "bts:Caudaequina" }, { - "@id": "bts:RadiationRadioisotope" + "@id": "bts:Cecum" }, { - "@id": "bts:RadiationStereotactic/GammaKnife/SRS" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:RadiationSystemic" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:RadiationTherapyNOS" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:RadioactiveIodineTherapy" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Radioembolization" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:RadiosensitizingAgent" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:StemCellTreatment" + "@id": "bts:Choroid" }, { - "@id": "bts:StemCellTransplantationAutologous" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:StemCellTransplantationDoubleAutologous" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:StemCellTransplantationAllogeneic" + "@id": "bts:ColonNOS" }, { - "@id": "bts:StemCellTransplantationNon-Myeloablative" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:StemCellTransplantationSyngenic" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:StemCellTransplantationHaploidentical" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:StemCellTransplantationNOS" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:StereotacticRadiosurgery" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:SteroidTherapy" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:Surgery" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:TargetedMolecularTherapy" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] - }, - { - "@id": "bts:TumorLargestDimensionDiameter", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", - "rdfs:label": "TumorLargestDimensionDiameter", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Largest Dimension Diameter", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "LungCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lung Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:LungCancerDetectionMethodType" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:LungCancerParticipantProcedureHistory" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:LungAdjacentHistologyType" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:LungTumorLocationAnatomicSite" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:LungTumorLobeBronchialLocation" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:CurrentLungCancerSymptoms" + "@id": "bts:Duodenum" }, { - "@id": "bts:LungTopography" + "@id": "bts:Endocervix" }, { - "@id": "bts:LungCancerHarboringGenomicAberrations" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", - "rdfs:label": "LungCancerDetectionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LowDoseComputedTomography(LDCT)" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:ChestX-ray" + "@id": "bts:Endometrium" }, { - "@id": "bts:ChestCT" + "@id": "bts:Epididymis" }, { - "@id": "bts:Unknown" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Lung Cancer Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerParticipantProcedureHistory", - "@type": "rdfs:Class", - "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", - "rdfs:label": "LungCancerParticipantProcedureHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LobectomyBilateral" + "@id": "bts:Exocervix" }, { - "@id": "bts:LobectomyLeft" + "@id": "bts:Externalear" }, { - "@id": "bts:LobectomyRight" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:LungWedgeResectionBilateral" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:LungWedgeResectionLeft" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:LungWedgeResectionMultiple" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:LungWedgeResectionRight" + "@id": "bts:EyeNOS" }, { - "@id": "bts:PneumonectomyLeft" + "@id": "bts:Eyelid" }, { - 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"schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Lungadenocarcinoma" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:Adenosquamouscarcinoma" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" + "@id": "bts:Glanspenis" }, { - "@id": "bts:Lungadenocarcinomainsitu" + "@id": "bts:Glottis" }, { - "@id": "bts:Largecelllungcarcinoma" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:Largecellneuroendocrinecarcinoma" + "@id": "bts:GumNOS" }, { - "@id": "bts:Lunglymphoepithelioma-likecarcinoma" + "@id": "bts:Hardpalate" }, { - "@id": "bts:Bronchioalveolarcarcinoma" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:ThoracicNUTcarcinoma" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:Sarcomatoidcarcinoma" + "@id": "bts:Heart" }, { - "@id": "bts:Smallcelllungcarcinoma" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:Squamouscelllungcarcinoma" + "@id": "bts:Hepaticflexureofcolon" }, { - 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"@id": "bts:EML4-ALKtranslocation-variant5" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:V600EBRAFmutation" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:V600DBRAFmutation" + "@id": "bts:Roundligament" }, { - "@id": "bts:V600KBRAFmutation" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:V600RBRAFmutation" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:K601EBRAFmutation" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:D963spliceMETmutation" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:D1010NMETmutation" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:D1010spliceMETmutation" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:Intron13mutation" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:Intron14mutation" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:Exon14mutation" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:Exon14deletion" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:Other" + "@id": "bts:SkinNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ColorectalCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Spinalcord" }, { - "@id": "bts:ColorectalCancerDetectionMethodType" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:Spleen" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:StomachNOS" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:Subglottis" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" + "@id": "bts:Supraglottis" }, { - "@id": "bts:MLH1PromoterMethylationStatus" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:Temporallobe" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:TestisNOS" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:ColorectalPolypShape" + "@id": "bts:Thymus" }, { - "@id": "bts:SizeofPolypRemoved" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:ColorectalPolypCount" + "@id": "bts:TongueNOS" }, { - "@id": "bts:ColorectalPolypType" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:ColorectalPolypAdenomaType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", - "rdfs:label": "ColorectalCancerDetectionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Fecaloccultbloodtest" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:Sigmoidoscopy" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:Colonoscopy" + "@id": "bts:Trachea" }, { - "@id": "bts:Virtualcolonoscopy" + "@id": "bts:Transversecolon" }, { - "@id": "bts:DNAstooltest" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:Other" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:Unknown" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Colorectal Cancer Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofPriorColonPolyps", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "HistoryofPriorColonPolyps", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:Uppergum" }, { - "@id": "bts:No" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "History of Prior Colon Polyps", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyColonCancerHistoryIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", - "rdfs:label": "FamilyColonCancerHistoryIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:UpperrespiratorytractNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:Upperthirdofesophagus" }, { - "@id": "bts:No" + "@id": "bts:Upper-innerquadrantofbreast" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Colon Cancer History Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:Urachus" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ureter" + }, { - "@id": "bts:Yes" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:No" + "@id": "bts:Urethra" }, { - "@id": "bts:NotApplicable" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", - "rdfs:subClassOf": [ + "@id": "bts:Uterineadnexa" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:UterusNOS" + }, { - "@id": "bts:Beforeage50" + "@id": "bts:Uvula" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Vallecula" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Endometrial Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", - "rdfs:subClassOf": [ + "@id": "bts:VentralsurfaceoftongueNOS" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:VentricleNOS" + }, { - "@id": "bts:Beforeage50" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:Unknown" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Ovarian Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", - "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", - "rdfs:subClassOf": [ + "@id": "bts:Waldeyerring" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BiliarytractNOS" + }, { - "@id": "bts:Yes-Crohn'sdisease" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:Yes-Ulcerativecolitis" + "@id": "bts:Clitoris" }, { - "@id": "bts:No" + "@id": "bts:Overlappinglesionofbiliarytract" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", - "sms:required": "sms:false", + "sms:displayName": "Site of Resection or Biopsy", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PatientColonoscopyPerformedIndicator", + "@id": "bts:TissueorOrganofOrigin", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", - "rdfs:label": "PatientColonoscopyPerformedIndicator", + "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "TissueorOrganofOrigin", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -12232,1749 +12530,1017 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:No" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:NotApplicable" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Patient Colonoscopy Performed Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerTumorBorderConfiguration", - "@type": "rdfs:Class", - "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", - "rdfs:label": "ColorectalCancerTumorBorderConfiguration", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Acousticnerve" + }, { - "@id": "bts:Indeterminate" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:Infiltrating" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Other" + "@id": "bts:Analcanal" }, { - "@id": "bts:Pushing" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Cancer Tumor Border Configuration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MLH1PromoterMethylationStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", - "rdfs:label": "MLH1PromoterMethylationStatus", - "rdfs:subClassOf": [ + "@id": "bts:Anteriorfloorofmouth" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Anteriormediastinum" + }, { - "@id": "bts:Absent" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:NotAssessed" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Present" - } - ], - "sms:displayName": "MLH1 Promoter Methylation Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerKRASIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", - "rdfs:label": "ColorectalCancerKRASIndicator", - "rdfs:subClassOf": [ + "@id": "bts:AnusNOS" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Aorticbodyandotherparaganglia" + }, { - "@id": "bts:Yes" + "@id": "bts:Appendix" }, { - "@id": "bts:No" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:Unknown" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Cancer KRAS Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColonPolypOccurenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "ColonPolypOccurenceIndicator", - "rdfs:subClassOf": [ + "@id": "bts:Axillarytailofbreast" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BaseoftongueNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:Bladderneck" }, { - "@id": "bts:No" + "@id": "bts:BladderNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Blood" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colon Polyp Occurence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyHistoryColorectalPolyp", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyHistoryColorectalPolyp", - "rdfs:subClassOf": [ + "@id": "bts:Bodyofpancreas" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Bodyofpenis" + }, { - "@id": "bts:Yes" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:No" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Unknown" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Family History Colorectal Polyp", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypNewIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", - "rdfs:label": "ColorectalPolypNewIndicator", - "rdfs:subClassOf": [ + "@id": "bts:BoneNOS" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Bonesofskullandfaceandassociatedjoints" + }, { - "@id": "bts:Yes" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:No" + "@id": "bts:Brainstem" }, { - "@id": "bts:Unknown" + "@id": "bts:BrainNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp New Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypShape", - "@type": "rdfs:Class", - "rdfs:comment": "Shape of polyp identified in the participant", - "rdfs:label": "ColorectalPolypShape", - "rdfs:subClassOf": [ + "@id": "bts:Branchialcleft" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BreastNOS" + }, { - "@id": "bts:Pedunculated" + "@id": "bts:Broadligament" }, { - "@id": "bts:Sessile" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:Flat" + "@id": "bts:Carotidbody" }, { - "@id": "bts:Notstated" + "@id": "bts:Caudaequina" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Shape", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeofPolypRemoved", - "@type": "rdfs:Class", - "rdfs:comment": "Size of the polyp removed in cm", - "rdfs:label": "SizeofPolypRemoved", - "rdfs:subClassOf": [ + "@id": "bts:Cecum" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size of Polyp Removed", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypCount", - "@type": "rdfs:Class", - "rdfs:comment": "The total number of polyps detected", - "rdfs:label": "ColorectalPolypCount", - "rdfs:subClassOf": [ + "@id": "bts:Centralportionofbreast" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Polyp Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of polyp found in the participant", - "rdfs:label": "ColorectalPolypType", - "rdfs:subClassOf": [ + "@id": "bts:CerebellumNOS" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Cerebralmeninges" + }, { - "@id": "bts:Adenoma" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Hyperplastic" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:Mixed" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:Papillomatous" + "@id": "bts:Choroid" }, { - "@id": "bts:Normal" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:Cancer" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:Other" + "@id": "bts:ColonNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Colorectal Polyp Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypAdenomaType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of adenoma associated with the polyp", - "rdfs:label": "ColorectalPolypAdenomaType", - "rdfs:subClassOf": [ + "@id": "bts:Commissureoflip" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Conjunctiva" + }, { - "@id": "bts:Tubular" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Villous" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:Tubulovillous" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:Sessileserrated" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:Traditionalserrated" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:Serratednotspecified" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Notstated" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Adenoma Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "BreastCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:CorneaNOS" + }, { - "@id": "bts:Component" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:BreastCarcinomaDetectionMethodType" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:BreastCarcinomaHistologyCategory" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + "@id": "bts:Duodenum" }, { - 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"rdfs:label": "GliomaSpecificMetastasisSites", - "rdfs:subClassOf": [ + "@id": "bts:Uvula" + }, { - "@id": "bts:NeuroblastomaandGliomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:VaginaNOS" + }, { - "@id": "bts:CSF" + "@id": "bts:Vallecula" }, { - "@id": "bts:Spine" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:Brain" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:Other" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:Leptomeningeal" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Glioma Specific Metastasis Sites", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GliomaSpecificRadiationField", - "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the CNS where radiation was administered in a partcipant with glioma", - "rdfs:label": "GliomaSpecificRadiationField", - "rdfs:subClassOf": [ + "@id": "bts:Waldeyerring" + }, { - "@id": "bts:NeuroblastomaandGliomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BiliarytractNOS" + }, { - "@id": "bts:Craniospinal" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:Focal-tumorbed" + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Glioma Specific Radiation Field", - "sms:required": "sms:false", + "sms:displayName": "Tissue or Organ of Origin", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:NCIAtlasCancerSite", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a supra tentorial ependymoma", - "rdfs:label": "SupraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", + "rdfs:label": "NCIAtlasCancerSite", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -13982,217 +13548,209 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ST-EPN-RELA" + "@id": "bts:Bladder" }, { - "@id": "bts:ST-EPN-YAP1" + "@id": "bts:BrainAndOtherNervousSystem" }, { - "@id": "bts:Unknown" + "@id": "bts:FemaleBreast" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Supra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a infra tentorial ependymoma", - "rdfs:label": "InfraTentorialEpendymomaMolecularSubgroup", - "rdfs:subClassOf": [ + "@id": "bts:InsituFemaleBreast" + }, { - "@id": "bts:NeuroblastomaandGliomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CervixUteri" + }, { - "@id": "bts:PF-EPN-A" + "@id": "bts:LessThanAge" }, { - "@id": "bts:PF-EPN-B" + "@id": "bts:MalignantChildhoodNeoplasm" }, { - "@id": "bts:Myxopapillaryependymoma" + "@id": "bts:ColonAndRectum" }, { - "@id": "bts:Unknown" + "@id": "bts:Esophagus" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Infra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Neuroblastoma MYCN amplification or over-expression status", - "rdfs:label": "NeuroblastomaMYCNGeneAmplificationStatus", - "rdfs:subClassOf": [ + "@id": "bts:KidneyAndRenalPelvis" + }, { - "@id": "bts:NeuroblastomaandGliomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Leukemia" + }, { - "@id": "bts:Amplified" + "@id": "bts:LiverAndBileDuct" }, { - "@id": "bts:Notamplified" + "@id": "bts:LungAndBronchus" }, { - "@id": "bts:Notdone" + "@id": "bts:CutaneousMelanoma" }, { - "@id": "bts:Unknown" + "@id": "bts:Non-Hodgkin'sLymphoma" + }, + { + "@id": "bts:OralCavityAndPharynx" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Pancreas" + }, + { + "@id": "bts:ProstateGland" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:ThyroidGland" + }, + { + "@id": "bts:Uterus" } ], - "sms:displayName": "Neuroblastoma MYCN Gene Amplification Status", + "sms:displayName": "NCI Atlas Cancer Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3", + "@id": "bts:TumorGrade", "@type": "rdfs:Class", - "rdfs:comment": "Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3", - "rdfs:label": "AcuteLymphoblasticLeukemiaTier3", + "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", + "rdfs:label": "TumorGrade", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:G1" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:G2" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:G3" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:G4" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:GX" }, { - "@id": "bts:SpecimenBlastCountPercentageValue" + "@id": "bts:GB" }, { - "@id": "bts:NCIALLRiskGroup" + "@id": "bts:HighGrade" }, { - "@id": "bts:MRDALLDiagnosticSensitivity" + "@id": "bts:IntermediateGrade" }, { - "@id": "bts:CNSLeukemiaStatus" + "@id": "bts:LowGrade" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Tumor Grade", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpecimenBlastCountPercentageValue", + "@id": "bts:PackYearsSmoked", "@type": "rdfs:Class", - "rdfs:comment": "The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis", - "rdfs:label": "SpecimenBlastCountPercentageValue", + "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", + "rdfs:label": "PackYearsSmoked", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Specimen Blast Count Percentage Value", - "sms:required": "sms:false", + "sms:displayName": "Pack Years Smoked", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NCIALLRiskGroup", + "@id": "bts:YearsSmoked", "@type": "rdfs:Class", - "rdfs:comment": "The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.", - "rdfs:label": "NCIALLRiskGroup", + "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", + "rdfs:label": "YearsSmoked", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NCIHighRisk" - }, - { - "@id": "bts:NCIStandardRisk" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "NCI ALL Risk Group", - "sms:required": "sms:false", + "sms:displayName": "Years Smoked", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MRDALLDiagnosticSensitivity", + "@id": "bts:DaystoFollowUp", "@type": "rdfs:Class", - "rdfs:comment": "The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.", - "rdfs:label": "MRDALLDiagnosticSensitivity", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoFollowUp", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Optimal" - }, - { - "@id": "bts:Suboptimal" - }, - { - "@id": "bts:Indeterminate" - }, + "sms:displayName": "Days to Follow Up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:GeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "GeneSymbol", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:MolecularTest" } ], - "sms:displayName": "MRD ALL Diagnostic Sensitivity", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gene Symbol", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CNSLeukemiaStatus", + "@id": "bts:MolecularAnalysisMethod", "@type": "rdfs:Class", - "rdfs:comment": "The status of central nervous system leukemia at the time of diagnosis.", - "rdfs:label": "CNSLeukemiaStatus", + "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularAnalysisMethod", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -14200,94 +13758,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CNS1" + "@id": "bts:ComparativeGenomicHybridization" }, { - "@id": "bts:CNS2" + "@id": "bts:CytogeneticsNOS" }, { - "@id": "bts:CNS3" + "@id": "bts:FISH" }, { - "@id": "bts:CNS2a" + "@id": "bts:FlowCytometry" }, { - "@id": "bts:CNS2b" + "@id": "bts:IHC" }, { - "@id": "bts:CNS2c" + "@id": "bts:ISH" }, { - "@id": "bts:CNS3a" + "@id": "bts:Karyotype" }, { - "@id": "bts:CNS3b" + "@id": "bts:Microarray" }, { - "@id": "bts:CNS3c" + "@id": "bts:MicrosatelliteAnalysis" }, { - "@id": "bts:Notevaluated" + "@id": "bts:NuclearStaining" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "CNS Leukemia Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Ovarian cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "OvarianCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:Other" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ovarian Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:RNASequencing" + }, { - "@id": "bts:Component" + "@id": "bts:RT-PCR" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:SequencingNOS" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:SouthernBlotting" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:TargetedSequencing" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:WGS" }, { - "@id": "bts:OvarianCancerHistologicSubtype" + "@id": "bts:WXS" }, { - "@id": "bts:OvarianCancerSurgicalOutcome" + "@id": "bts:Unknown" }, { - "@id": "bts:OvarianCancerPlatinumStatus" + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Molecular Analysis Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OvarianCancerHistologicSubtype", + "@id": "bts:TestResult", "@type": "rdfs:Class", - "rdfs:comment": "Text term to describe the histological subtype of ovarian cancer in the participant", - "rdfs:label": "OvarianCancerHistologicSubtype", + "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestResult", "rdfs:subClassOf": [ { - "@id": "bts:OvarianCancerTier3" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -14295,88 +13840,63 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:High-gradeserous" - }, - { - "@id": "bts:Low-gradeserous" + "@id": "bts:AbnormalNOS" }, { - "@id": "bts:High-gradeendometrioid" + "@id": "bts:CopyNumberReported" }, { - "@id": "bts:Low-gradeendometrioid" + "@id": "bts:Equivocal" }, { - "@id": "bts:Clearcell" + "@id": "bts:High" }, { - "@id": "bts:Mucinous" + "@id": "bts:Intermediate" }, { - "@id": "bts:Sex-cordstromal" + "@id": "bts:LossofExpression" }, { - "@id": "bts:Germcell" + "@id": "bts:Low" }, { - "@id": "bts:Other" + "@id": "bts:Negative" }, { - "@id": "bts:Unknown" + "@id": "bts:Normal" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Ovarian Cancer Histologic Subtype", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OvarianCancerSurgicalOutcome", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of surgical treatment administered.", - "rdfs:label": "OvarianCancerSurgicalOutcome", - "rdfs:subClassOf": [ - { - "@id": "bts:OvarianCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:R0resection" + "@id": "bts:Overexpressed" }, { - "@id": "bts:Optimalcytoreduction" + "@id": "bts:Positive" }, { - "@id": "bts:Sub-optimalcytoreduction" + "@id": "bts:TestValueReported" }, { - "@id": "bts:Other" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Ovarian Cancer Surgical Outcome", - "sms:required": "sms:false", + "sms:displayName": "Test Result", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OvarianCancerPlatinumStatus", + "@id": "bts:TreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", - "rdfs:label": "OvarianCancerPlatinumStatus", + "rdfs:comment": "Text term that describes the kind of treatment administered.", + "rdfs:label": "TreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:OvarianCancerTier3" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -14384,253 +13904,178 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Platinum-refractory" - }, - { - "@id": "bts:Platinum-sensitive" - }, - { - "@id": "bts:Platinum-resistant" - }, - { - "@id": "bts:Datanotavailable" + "@id": "bts:AblationCryo" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ovarian Cancer Platinum Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ProstateCancerTier3", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Prostate Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:AblationEthanolInjection" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:AblationMicrowave" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:AblationNOS" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:AblationRadiofrequency" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:AblationRadiosurgical" }, { - "@id": "bts:LocationExtentExtraprostaticExtension" + "@id": "bts:AncillaryTreatment" }, { - "@id": "bts:LocationNaturePositiveMargins" + "@id": "bts:AntiseizureTreatment" }, { - "@id": "bts:SeminalVesicleInvasion" + "@id": "bts:BisphosphonateTherapy" }, { - "@id": "bts:ProstateCarcinomaHistologicType" + "@id": "bts:BlindedStudyTreatmentunknown" }, { - "@id": "bts:ProstateCancerLocalExtent" + "@id": "bts:BrachytherapyHighDose" }, { - "@id": "bts:AdditonalFindingsUninvolvedProstate" + "@id": "bts:BrachytherapyLowDose" }, { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:LocationExtentExtraprostaticExtension", - "@type": "rdfs:Class", - "rdfs:comment": "Location and extent of extraprostatic extension", - "rdfs:label": "LocationExtentExtraprostaticExtension", - "rdfs:subClassOf": [ - { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LeftAnterior" + "@id": "bts:BrachytherapyNOS" }, { - "@id": "bts:LeftLateral" + "@id": "bts:Chemoembolization" }, { - "@id": "bts:LeftPosterolateral" + "@id": "bts:Chemoprotectant" }, { - "@id": "bts:LeftPosterior" + "@id": "bts:Chemotherapy" }, { - "@id": "bts:LeftApex" + "@id": "bts:ConcurrentChemoradiation" }, { - "@id": "bts:LeftMid" + "@id": "bts:Cryoablation" }, { - "@id": "bts:LeftBase" + "@id": "bts:Embolization" }, { - "@id": "bts:LeftFocal" + "@id": "bts:EthanolInjectionAblation" }, { - "@id": "bts:LeftNon-focal(established)" + "@id": "bts:ExternalBeamRadiation" }, { - "@id": "bts:RightAnterior" + "@id": "bts:HormoneTherapy" }, { - "@id": "bts:RightLateral" + "@id": "bts:I-131RadiationTherapy" }, { - "@id": "bts:RightPosterolateral" + "@id": "bts:InternalRadiation" }, { - "@id": "bts:RightPosterior" + "@id": "bts:Immunotherapy(IncludingVaccines)" }, { - "@id": "bts:RightApex" + "@id": "bts:IsolatedLimbPerfusion(ILP)" }, { - "@id": "bts:RightMid" + "@id": "bts:OrganTransplantation" }, { - "@id": "bts:RightBase" + "@id": "bts:Other" }, { - "@id": "bts:RightFocal" + "@id": "bts:PharmaceuticalTherapyNOS" }, { - "@id": "bts:RightNon-focal(established)" + "@id": "bts:Pleurodesis" }, { - "@id": "bts:Unknown" + "@id": "bts:Radiation2DConventional" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Location Extent Extraprostatic Extension", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LocationNaturePositiveMargins", - "@type": "rdfs:Class", - "rdfs:comment": "Location and nature of positive margins", - "rdfs:label": "LocationNaturePositiveMargins", - "rdfs:subClassOf": [ - { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LeftAnterior" + "@id": "bts:Radiation3DConformal" }, { - "@id": "bts:LeftLateral" + "@id": "bts:RadiationCombination" }, { - "@id": "bts:LeftPosterolateral" + "@id": "bts:RadiationCyberknife" }, { - "@id": "bts:LeftPosterior" + "@id": "bts:RadiationExternalBeam" }, { - "@id": "bts:LeftApex" + "@id": "bts:RadiationImplants" }, { - "@id": "bts:LeftMid" + "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" }, { - "@id": "bts:LeftBase" + "@id": "bts:RadiationInternal" }, { - "@id": "bts:LeftFocal" + "@id": "bts:RadiationProtonBeam" }, { - "@id": "bts:LeftExtensive" + "@id": "bts:RadiationRadioisotope" }, { - "@id": "bts:LeftPositiveinanareaofextraprostaticextension(EPE)" + "@id": "bts:RadiationStereotactic/GammaKnife/SRS" }, { - "@id": "bts:LeftPositiveinanareaofintraprostaticincision(II)" + "@id": "bts:RadiationSystemic" }, { - "@id": "bts:LeftPositivewhereitisdifficulttodistinguishEPEvsII" + "@id": "bts:RadiationTherapyNOS" }, { - "@id": "bts:RightAnterior" + "@id": "bts:RadioactiveIodineTherapy" }, { - "@id": "bts:RightLateral" + "@id": "bts:Radioembolization" }, { - "@id": "bts:RightPosterolateral" + "@id": "bts:RadiosensitizingAgent" }, { - "@id": "bts:RightPosterior" + "@id": "bts:StemCellTreatment" }, { - "@id": "bts:RightApex" + "@id": "bts:StemCellTransplantationAutologous" }, { - "@id": "bts:RightMid" + "@id": "bts:StemCellTransplantationDoubleAutologous" }, { - "@id": "bts:RightBase" + "@id": "bts:StemCellTransplantationAllogeneic" }, { - "@id": "bts:RightFocal" + "@id": "bts:StemCellTransplantationNon-Myeloablative" }, { - "@id": "bts:RightExtensive" + "@id": "bts:StemCellTransplantationSyngenic" }, { - "@id": "bts:RightPositiveinanareaofextraprostaticextension(EPE)" + "@id": "bts:StemCellTransplantationHaploidentical" }, { - "@id": "bts:RightPositiveinanareaofintraprostaticincision(II)" + "@id": "bts:StemCellTransplantationNOS" }, { - "@id": "bts:RightPositivewhereitisdifficulttodistinguishEPEvsII" + "@id": "bts:StereotacticRadiosurgery" }, { - "@id": "bts:Bladderneck(blockPUM)" + "@id": "bts:SteroidTherapy" }, { - "@id": "bts:Vasdeferens" + "@id": "bts:Surgery" }, { - "@id": "bts:Apicalmargin(blockDUM)" + "@id": "bts:TargetedMolecularTherapy" }, { "@id": "bts:Unknown" @@ -14639,104 +14084,95 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Location Nature Positive Margins", + "sms:displayName": "Treatment Type", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:SeminalVesicleInvasion", + "@id": "bts:TumorLargestDimensionDiameter", "@type": "rdfs:Class", - "rdfs:comment": "An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.", - "rdfs:label": "SeminalVesicleInvasion", + "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", + "rdfs:label": "TumorLargestDimensionDiameter", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:None" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Right" - }, - { - "@id": "bts:Bothsides" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Seminal Vesicle Invasion", + "sms:displayName": "Tumor Largest Dimension Diameter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProstateCarcinomaHistologicType", + "@id": "bts:LungCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "The diagnostic subclassification of an invasive prostate carcinoma.", - "rdfs:label": "ProstateCarcinomaHistologicType", + "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "LungCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Lung Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Prostaticadenocarcinoma(conventionalNOS)" + "@id": "bts:Component" }, { - "@id": "bts:Prostaticductadenocarcinoma" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Acinarprostatemucinous(colloid)adenocarcinoma" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Acinarprostateadenocarcinoma-signet-ringvariant" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Prostaticadenosquamouscarcinoma" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Acinarprostatemucinousadenocarcinoma" + "@id": "bts:LungCancerDetectionMethodType" }, { - "@id": "bts:Prostaticsmallcellcarcinoma" + "@id": "bts:LungCancerParticipantProcedureHistory" }, { - "@id": "bts:Acinarprostateadenocarcinoma-sarcomatoidvariant" + "@id": "bts:LungAdjacentHistologyType" }, { - "@id": "bts:UndifferentiatedcarcinomaNOS" + "@id": "bts:LungTumorLocationAnatomicSite" }, { - "@id": "bts:Other" + "@id": "bts:LungTumorLobeBronchialLocation" + }, + { + "@id": "bts:CurrentLungCancerSymptoms" + }, + { + "@id": "bts:LungTopography" + }, + { + "@id": "bts:LungCancerHarboringGenomicAberrations" } ], - "sms:displayName": "Prostate Carcinoma Histologic Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProstateCancerLocalExtent", + "@id": "bts:LungCancerDetectionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "The response used to categorize the local extent of disease for prostate cancer.", - "rdfs:label": "ProstateCancerLocalExtent", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", + "rdfs:label": "LungCancerDetectionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14744,30 +14180,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:OrganConfined" + "@id": "bts:LowDoseComputedTomography(LDCT)" }, { - "@id": "bts:Extraprostaticextension" + "@id": "bts:ChestX-ray" + }, + { + "@id": "bts:ChestCT" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Prostate Cancer Local Extent", + "sms:displayName": "Lung Cancer Detection Method Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdditonalFindingsUninvolvedProstate", + "@id": "bts:LungCancerParticipantProcedureHistory", "@type": "rdfs:Class", - "rdfs:comment": "Additional findings, uninvolved prostate", - "rdfs:label": "AdditonalFindingsUninvolvedProstate", + "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", + "rdfs:label": "LungCancerParticipantProcedureHistory", "rdfs:subClassOf": [ { - "@id": "bts:ProstateCancerTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14775,148 +14217,113 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:High-gradeprostaticintraepithelialneoplasia(PIN)" + "@id": "bts:LobectomyBilateral" }, { - "@id": "bts:Inflammation" + "@id": "bts:LobectomyLeft" }, { - "@id": "bts:Benignprostatichyperplasia(BPH)" + "@id": "bts:LobectomyRight" }, { - "@id": "bts:ProstaticIntraductaladenocarcinoma" + "@id": "bts:LungWedgeResectionBilateral" }, { - "@id": "bts:Other" + "@id": "bts:LungWedgeResectionLeft" }, { - "@id": "bts:Unknown" + "@id": "bts:LungWedgeResectionMultiple" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Additonal Findings Uninvolved Prostate", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes various morphological and cytological subtypes in protate tumors.", - "rdfs:label": "ProstateCancerCytologicMorphologicSubtypes", - "rdfs:subClassOf": [ + "@id": "bts:LungWedgeResectionRight" + }, { - "@id": "bts:ProstateCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PneumonectomyLeft" + }, { - "@id": "bts:Prostaticbasalcellhyperplasia" + "@id": "bts:PneumonectomyRight" }, { - "@id": "bts:Prostaticclearcellcribiformhyperplasia" + "@id": "bts:Endobronchialbiopsy" }, { - "@id": "bts:Prostaticatypicaladenomatoushyperplasia(adenosisorAAH)" + "@id": "bts:Mediastinoscopy" }, { - "@id": "bts:Lowgradeprostaticintraepithelialneoplasia(PIN)/(PINI)" + "@id": "bts:VATSSclerosis" }, { - "@id": "bts:Highgradeprostaticintraepithelialneoplasia(HGPIN)/(PINII&PINIII)" + "@id": "bts:Brainresection" }, { - "@id": "bts:Other" + "@id": "bts:Segmentectomy" }, { "@id": "bts:Unknown" }, + { + "@id": "bts:Other" + }, { "@id": "bts:NotReported" } ], - "sms:displayName": "Prostate Cancer Cytologic Morphologic Subtypes", + "sms:displayName": "Lung Cancer Participant Procedure History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SarcomaTier3", + "@id": "bts:LungAdjacentHistologyType", "@type": "rdfs:Class", - "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", - "rdfs:label": "SarcomaTier3", + "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", + "rdfs:label": "LungAdjacentHistologyType", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sarcoma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Lungadenocarcinoma" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Adenosquamouscarcinoma" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Lungadenocarcinomainsitu" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Largecelllungcarcinoma" }, { - "@id": "bts:SarcomaSubtype" + "@id": "bts:Largecellneuroendocrinecarcinoma" }, { - "@id": "bts:SarcomaDiagnosisClassificationCategory" + "@id": "bts:Lunglymphoepithelioma-likecarcinoma" }, { - "@id": "bts:SarcomaTumorExtensionType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SarcomaSubtype", - "@type": "rdfs:Class", - "rdfs:comment": "The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.", - "rdfs:label": "SarcomaSubtype", - "rdfs:subClassOf": [ - { - "@id": "bts:SarcomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" + "@id": "bts:Bronchioalveolarcarcinoma" }, { - "@id": "bts:Leiomyosarcoma(uterineorextra-uterine)" + "@id": "bts:ThoracicNUTcarcinoma" }, { - "@id": "bts:OtherSynovialSarcomaOrMalignantPeripheralNerveSheathTumorSarcoma" + "@id": "bts:Sarcomatoidcarcinoma" }, { - "@id": "bts:GastrointestinalStromalTumor" + "@id": "bts:Smallcelllungcarcinoma" }, { - "@id": "bts:Liposarcoma" + "@id": "bts:Squamouscelllungcarcinoma" }, { - "@id": "bts:Undifferentiatedpleomorphicsarcomaormalignantfibroushistiosarcoma" + "@id": "bts:Lungsquamouscellcarcinomainsitu" }, { "@id": "bts:Other" @@ -14928,18 +14335,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sarcoma Subtype", + "sms:displayName": "Lung Adjacent Histology Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SarcomaDiagnosisClassificationCategory", + "@id": "bts:LungTumorLocationAnatomicSite", "@type": "rdfs:Class", - "rdfs:comment": "High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.", - "rdfs:label": "SarcomaDiagnosisClassificationCategory", + "rdfs:comment": "Anatomic location of the tumor inside the lung", + "rdfs:label": "LungTumorLocationAnatomicSite", "rdfs:subClassOf": [ { - "@id": "bts:SarcomaTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14947,13 +14354,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BoneSarcoma" + "@id": "bts:Maincarina" }, { - "@id": "bts:MusculoskeletalSarcoma" + "@id": "bts:Left" }, { - "@id": "bts:SoftTissueSarcoma" + "@id": "bts:Right" }, { "@id": "bts:Unknown" @@ -14962,18 +14369,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sarcoma Diagnosis Classification Category", + "sms:displayName": "Lung Tumor Location Anatomic Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SarcomaTumorExtensionType", + "@id": "bts:LungTumorLobeBronchialLocation", "@type": "rdfs:Class", - "rdfs:comment": "The field to indicate the organs and structures to which the tumor has become adherent or has invaded.", - "rdfs:label": "SarcomaTumorExtensionType", + "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", + "rdfs:label": "LungTumorLobeBronchialLocation", "rdfs:subClassOf": [ { - "@id": "bts:SarcomaTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -14981,22 +14388,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Extraosseous" - }, - { - "@id": "bts:Intracranial" + "@id": "bts:Upperlobe" }, { - "@id": "bts:Lymphnodes" + "@id": "bts:Middlelobe" }, { - "@id": "bts:Parameningeal" + "@id": "bts:Lowerlobe" }, { - "@id": "bts:Thoraciccavity" + "@id": "bts:Stump" }, { - "@id": "bts:Other" + "@id": "bts:Bronchus" }, { "@id": "bts:Unknown" @@ -15005,133 +14409,110 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Sarcoma Tumor Extension Type", + "sms:displayName": "Lung Tumor Lobe Bronchial Location", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PancreaticCancerTier3", + "@id": "bts:CurrentLungCancerSymptoms", "@type": "rdfs:Class", - "rdfs:comment": "Pancreatic cancer specific attributes in Clinical Tier Data 3", - "rdfs:label": "PancreaticCancerTier3", + "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", + "rdfs:label": "CurrentLungCancerSymptoms", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pancreatic Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Asbestosis" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Productivecough" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Non-productivecough" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Wheezing" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Rhonci" }, { - "@id": "bts:PancreasPrecancerHistopathologicGrade" + "@id": "bts:Crackles" }, { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" + "@id": "bts:Hemoptysis" }, { - "@id": "bts:PancreaticDuctFinalPathologyType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PancreasPrecancerHistopathologicGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.", - "rdfs:label": "PancreasPrecancerHistopathologicGrade", - "rdfs:subClassOf": [ + "@id": "bts:Dyspnea" + }, { - "@id": "bts:PancreaticCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Unexplainedweightloss" + }, { - "@id": "bts:IPMN-Adenoma" + "@id": "bts:Unexplainedlossofenergy/fatigue" }, { - "@id": "bts:IPMN-Borderline" + "@id": "bts:Chestpainordiscomfort" }, { - "@id": "bts:IPMN-Carcinomainsitu" + "@id": "bts:Dysphagia" }, { - "@id": "bts:IPMN-Invasivecarcinoma" + "@id": "bts:Pneumonia" }, { - "@id": "bts:PanIN1" + "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" }, { - "@id": "bts:PanIN1A" + "@id": "bts:Airentrydecreased/fair/poor/diminished" }, { - "@id": "bts:PanIN1B" + "@id": "bts:Fair/pooraeration" }, { - "@id": "bts:PanIN2" + "@id": "bts:Shallowinspiration" }, { - "@id": "bts:PanIN3" + "@id": "bts:Breathsoundscoarse/diminished" }, { - "@id": "bts:Unknown" + "@id": "bts:Dullnesstopercussion" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreas Precancer Histopathologic Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype", - "@type": "rdfs:Class", - "rdfs:comment": "The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen", - "rdfs:label": "PancreaticIPMNPathologyEpithelialSubtype", - "rdfs:subClassOf": [ + "@id": "bts:Abnormalbreathsounds" + }, { - "@id": "bts:PancreaticCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Clearlungstoauscultationorpercussion" + }, { - "@id": "bts:GastricFoveolar" + "@id": "bts:Unlabored/normalbreathing" }, { - "@id": "bts:Intestinal" + "@id": "bts:Coldsymptoms/flu/sinus/nasalcongestion" }, { - "@id": "bts:IntraductalTubopapillary" + "@id": "bts:Sinuspain/infection" }, { - "@id": "bts:Pancreatobiliary" + "@id": "bts:Fingerclubbing" }, { - "@id": "bts:Oncocytic" + "@id": "bts:Noevidenceoflungcancerrecurrence" + }, + { + "@id": "bts:PatientisNED" + }, + { + "@id": "bts:Oxygensupplemental-portableO2atnightorcontinuous" + }, + { + "@id": "bts:Prolongedexpiration-long/forcedexpiratoryphase" }, { "@id": "bts:Other" @@ -15143,18 +14524,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", + "sms:displayName": "Current Lung Cancer Symptoms", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PancreaticDuctFinalPathologyType", + "@id": "bts:LungTopography", "@type": "rdfs:Class", - "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", - "rdfs:label": "PancreaticDuctFinalPathologyType", + "rdfs:comment": "Lung PCA specific topography (not covered in previous tiers)", + "rdfs:label": "LungTopography", "rdfs:subClassOf": [ { - "@id": "bts:PancreaticCancerTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -15162,214 +14543,279 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Side-Branch" + "@id": "bts:MC-Carinabetweenrightandleftlungs(maincarina)" }, { - "@id": "bts:MainDuct" + "@id": "bts:TR-Trachea(airwaywallbetweentracheo-esophagealbifurcationandmaincarina)" }, { - "@id": "bts:Mixed" + "@id": "bts:CarinaNOS(Carinanototherwisespecified)" }, { - "@id": "bts:NotSpecified" + "@id": "bts:LUDB-Carinabetweenthelingulaandupperdivisionleftupperlobe" }, { - "@id": "bts:None" + "@id": "bts:CarinabetweenLUDBorificeandlingulaorifice" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreatic Duct Final Pathology Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", - "rdfs:label": "MelanomaTier3", - "rdfs:subClassOf": [ + "@id": "bts:LUDB-orificeairwaywallbetweenLUDBandLB3(LB1+2carinae)" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Melanoma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:LingulaorificeairwaywallbetweenLUDBandLB4/5carinae" + }, { - "@id": "bts:Component" + "@id": "bts:RMB-Rightmainstembronchus(airwaywallbetweenMC&RULcarina)" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:LMB-Leftmainstembronchus(airwaywallbetweenMC&LULcarina)" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:RLNOS(Rightlungnototherwisespecified)" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:RB1/2-Carinabetweenapicalandposteriorsegmentsrightupperlobe(CarinabetweenRB1orificeandRB2orifice)" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:RB6A/B-CarinabetweenapicalandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" + "@id": "bts:RB6A/C-CarinabetweenapicalandmedialsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:CutaneousMelanomaTumorRegressionRange" + "@id": "bts:RB6B/C-CarinabetweenmedialandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:MelanomaSpecimenClarkLevelValue" + "@id": "bts:RB7A/B-CarinabetweenmedialandlateralsubsegmentsmedialbasalsegmentRLL" }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins" + "@id": "bts:RB8/9-CarinabetweenanteriorandlateralsegmentsRLL(CarinabetweenRB8orificeandRB9orifice)" }, { - "@id": "bts:MelanomaLesionSize" + "@id": "bts:RB8A/B-CarinabetweenmedialandlateralsubsegmentsanteriorsegmentRLL" }, { - "@id": "bts:HistoryofAtypicalNevi" + "@id": "bts:RB9/10-CarinabetweenlateralandposteriorsegmentsRLL" }, { - "@id": "bts:FitzpatrickSkinTone" + "@id": "bts:RB9A/B-CarinabetweenmedialandlateralsubsegmentslateralsegmentRLL" }, { - "@id": "bts:HistoryofChronicUVExposure" + "@id": "bts:RB10A/B-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:HistoryofBlisteringSunburn" + "@id": "bts:RB10A/C-CarinabetweenmedialandapicalsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:HistoryofTanningBedUse" + "@id": "bts:RB1A/B-CarinabetweenmedialandlateralsubsegmentsapicalsegmentRUL" }, { - "@id": "bts:ImmediateFamilyHistoryMelanoma" + "@id": "bts:RB10B/C-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:MelanomaBiopsyResectionSites" + "@id": "bts:RB6-CarinaofsuperiorsegmentRLL(CarinabetweenRB6orificeandlowerportionofRLLorifice)" }, { - "@id": "bts:CutaneousMelanomaUlceration" + "@id": "bts:RB6orificeAirwaywallbetweenRB6andRB6A/B/Ccarinae" }, { - "@id": "bts:CutaneousMelanomaAdditionalFindings" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes", - "@type": "rdfs:Class", - "rdfs:comment": "Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaTumorInfiltratingLymphocytes", - "rdfs:subClassOf": [ + "@id": "bts:BronchusIntermediusBronchus(airwaywall)betweenrightupperandrightmiddlelobes" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RB1/3-CarinabetweenapicalandanteriorsegmentsRUL(CarinabetweenRB1orificeandRB3orifice)" + }, { - "@id": "bts:Absent" + "@id": "bts:RB2/3-CarinabetweenanteriorandposteriorsegmentsRUL(CarinabetweenRB2orificeandRB3orifice)" }, { - "@id": "bts:Brisk" + "@id": "bts:RB2A/B-Carinabetweenthemedialandlateralsubsegmentsoftheposteriorsegment(RUL)" }, { - "@id": "bts:Nonbrisk" + "@id": "bts:RB3A/B-CarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentRUL" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaTumorRegressionRange", - "@type": "rdfs:Class", - "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", - "rdfs:label": "CutaneousMelanomaTumorRegressionRange", - "rdfs:subClassOf": [ + "@id": "bts:RB4/5-Carinabetweenthelateralandmedialsegmentsrightmiddlelobe(CarinabetweenRB4orificeandRB5orifice)" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RB4A/B-Carinabetweenthemedialandlateralsubsegmentsofthelateralsegmentoftherightmiddlelobe" + }, { - "@id": "bts:Absent" + "@id": "bts:RB5A/B-Carinabetweenthemedialandlateralsubsegmentsofthemedialsegmentoftherightmiddlelobe" }, { - "@id": "bts:Presentinvolving75%ormore" + "@id": "bts:RULCarinaebetweenRULorificeandbronchusintermedius" }, { - "@id": "bts:Presentinvolvinglessthan75%" + "@id": "bts:RULorificeAirwaywallbetweenRULandRB1/RB2/RB3" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaSpecimenClarkLevelValue", - "@type": "rdfs:Class", - "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", - "rdfs:label": "MelanomaSpecimenClarkLevelValue", - "rdfs:subClassOf": [ + "@id": "bts:RB1orificeApicalsegment-rightupperlobe(airwaywallbetweenRB1andRB1A/Bcarinae)" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RB2orificePosteriorsegment-rightupperlobe(airwaywallbetweenRB2andRB2A/Bcarinae)" + }, { - "@id": "bts:I" + "@id": "bts:RB3orificeAnteriorsegment-rightupperlobe(airwaywallbetweenRB3andRB3A/Bcarinae)" }, { - "@id": "bts:II" + "@id": "bts:RML-CarinabetweenRMLorificeandRLLorifice" }, { - "@id": "bts:III" + "@id": "bts:RMLorificeAirwaywallbetweenRMLandRB4/5" }, { - "@id": "bts:IV" + "@id": "bts:RB4orificeLateralsegmentrightmiddlelobe(airwaywallbetweenRB4andRB4A/Bcarinae)" }, { - "@id": "bts:V" + "@id": "bts:RB5orificeMedialsegmentrightmiddlelobe(airwaywallbetweenRB5andRB5A/Bcarinae)" }, { - "@id": "bts:NoSourceDocumentation" + "@id": "bts:RLLorificeAirwaywallbetweenRMLandRB6-10carinae" + }, + { + "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" + }, + { + "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" + }, + { + "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" + }, + { + "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" + }, + { + "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" + }, + { + "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" + }, + { + "@id": "bts:LLNOS(Leftlungnototherwisespecified)" + }, + { + "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" + }, + { + "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" + }, + { + "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" + }, + { + "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" + }, + { + "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" + }, + { + "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" + }, + { + "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" + }, + { + "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" + }, + { + "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" + }, + { + "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" + }, + { + "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" + }, + { + "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" + }, + { + "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + }, + { + "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" + }, + { + "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + }, + { + "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" + }, + { + "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" + }, + { + "@id": "bts:LB6orificeAirwaywallbetweenLB6andLB6A/Bcarinae" + }, + { + "@id": "bts:LB1A/CCarinabetweentheapicalandlateralsubsegmentsoftheapicalsegmentleftupperlobe" + }, + { + "@id": "bts:LB1B/CCarinabetweenthemedialandlateralsubsegmentsoftheapicalsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LB2A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LB2A/CCarinabetweentheapicalandmedialsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LB2B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentleftupperlobe" + }, + { + "@id": "bts:LB1+2/3Carinabetweentheapico-posteriorandanteriorsegmentsoftheleftupperlobe(CarinabetweenLB1+2orificeandLB3orifice)" + }, + { + "@id": "bts:LB3A/BCarinabetweentheapicalandlateralsubsegmentsoftheanteriorsegmentoftheleftupperlobe" + }, + { + "@id": "bts:LULCarinabetweentheLULorificeandLLLorifice(airways)" + }, + { + "@id": "bts:LULorificeAirwaywallbetweenLULandLUDB" + }, + { + "@id": "bts:LB3orificeAnteriorsegmentleftupperlobe(airwaywallbetweenLB3andLB3A/Bcarinae)" + }, + { + "@id": "bts:LB4orificeSuperiorsegmentlingula(airwaywallbetweenLB4andLB4A/Bcarinae)" + }, + { + "@id": "bts:LB5orificeInferiorsegmentlingula(airwaywallbetweenLB5andLB5A/Bcarinae)" + }, + { + "@id": "bts:LLLorificeAirwaywallbetweenLULcarinaandLB6-10carinae" + }, + { + "@id": "bts:LB9orificeLateralsegmentleftlowerlobe(airwaywallbetweenLB9andLB9A/Bcarinae)" + }, + { + "@id": "bts:LB8orificeAnteriorsegmentleftlowerlobe(airwaywallbetweenLB8andLB8A/Bcarinae)" + }, + { + "@id": "bts:LB10orificePosteriorsegmentleftlowerlobe(airwaywallbetweenLB10andLB10A/Bcarinae)" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Melanoma Specimen Clark Level Value", + "sms:displayName": "Lung Topography", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins", + "@id": "bts:LungCancerHarboringGenomicAberrations", "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate presence of tumor at resection margins", - "rdfs:label": "CutaneousMelanomaSurgicalMargins", + "rdfs:comment": "Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)", + "rdfs:label": "LungCancerHarboringGenomicAberrations", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -15377,10 +14823,121 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Positive" + "@id": "bts:G12AKRASmutation" }, { - "@id": "bts:Negative" + "@id": "bts:G12CKRASmutation" + }, + { + "@id": "bts:G12DKRASmutation" + }, + { + "@id": "bts:G12RKRASmutation" + }, + { + "@id": "bts:G12SKRASmutation" + }, + { + "@id": "bts:G12VKRASmutation" + }, + { + "@id": "bts:G13DKRASmutation" + }, + { + "@id": "bts:G13RKRASmutation" + }, + { + "@id": "bts:G13CKRASmutation" + }, + { + "@id": "bts:G13AKRASmutation" + }, + { + "@id": "bts:G13VKRASmutation" + }, + { + "@id": "bts:Q61LKRASmutation" + }, + { + "@id": "bts:Q61HKRASmutation" + }, + { + "@id": "bts:A146TKRASmutation" + }, + { + "@id": "bts:G719XEGFRmutation" + }, + { + "@id": "bts:T790MEGFRmutation" + }, + { + "@id": "bts:C797SEGFRmutation" + }, + { + "@id": "bts:L858REGFRmutation" + }, + { + "@id": "bts:L861QEGFRmutation" + }, + { + "@id": "bts:Exon19deletion" + }, + { + "@id": "bts:Exon20insertion" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant1" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant2" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant3" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant4" + }, + { + "@id": "bts:EML4-ALKtranslocation-variant5" + }, + { + "@id": "bts:V600EBRAFmutation" + }, + { + "@id": "bts:V600DBRAFmutation" + }, + { + "@id": "bts:V600KBRAFmutation" + }, + { + "@id": "bts:V600RBRAFmutation" + }, + { + "@id": "bts:K601EBRAFmutation" + }, + { + "@id": "bts:D963spliceMETmutation" + }, + { + "@id": "bts:D1010NMETmutation" + }, + { + "@id": "bts:D1010spliceMETmutation" + }, + { + "@id": "bts:Intron13mutation" + }, + { + "@id": "bts:Intron14mutation" + }, + { + "@id": "bts:Exon14mutation" + }, + { + "@id": "bts:Exon14deletion" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -15389,69 +14946,109 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Cutaneous Melanoma Surgical Margins", + "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MelanomaLesionSize", + "@id": "bts:ColorectalCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", - "rdfs:label": "MelanomaLesionSize", + "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ColorectalCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Melanoma Lesion Size", + "sms:displayName": "Colorectal Cancer Tier 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofAtypicalNevi", - "@type": "rdfs:Class", - "rdfs:comment": "Patient has a history of atypical nevi", - "rdfs:label": "HistoryofAtypicalNevi", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:Yes(morethan50)" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Yes(lessthan50)" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:No" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Unknown" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:NotReported" + "@id": "bts:ColorectalCancerDetectionMethodType" + }, + { + "@id": "bts:HistoryofPriorColonPolyps" + }, + { + "@id": "bts:FamilyColonCancerHistoryIndicator" + }, + { + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + }, + { + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + }, + { + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + }, + { + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + }, + { + "@id": "bts:PatientColonoscopyPerformedIndicator" + }, + { + "@id": "bts:ColorectalCancerTumorBorderConfiguration" + }, + { + "@id": "bts:MLH1PromoterMethylationStatus" + }, + { + "@id": "bts:ColorectalCancerKRASIndicator" + }, + { + "@id": "bts:ColonPolypOccurenceIndicator" + }, + { + "@id": "bts:FamilyHistoryColorectalPolyp" + }, + { + "@id": "bts:ColorectalPolypNewIndicator" + }, + { + "@id": "bts:ColorectalPolypShape" + }, + { + "@id": "bts:SizeofPolypRemoved" + }, + { + "@id": "bts:ColorectalPolypCount" + }, + { + "@id": "bts:ColorectalPolypType" + }, + { + "@id": "bts:ColorectalPolypAdenomaType" } ], - "sms:displayName": "History of Atypical Nevi", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FitzpatrickSkinTone", + "@id": "bts:ColorectalCancerDetectionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "The Fitzpatrick classification of skin phototype", - "rdfs:label": "FitzpatrickSkinTone", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", + "rdfs:label": "ColorectalCancerDetectionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15459,42 +15056,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:I" + "@id": "bts:Fecaloccultbloodtest" }, { - "@id": "bts:II" + "@id": "bts:Sigmoidoscopy" }, { - "@id": "bts:III" + "@id": "bts:Colonoscopy" }, { - "@id": "bts:IV" + "@id": "bts:Virtualcolonoscopy" }, { - "@id": "bts:V" + "@id": "bts:DNAstooltest" }, { - "@id": "bts:VI" + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Fitzpatrick Skin Tone", + "sms:displayName": "Colorectal Cancer Detection Method Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofChronicUVExposure", + "@id": "bts:HistoryofPriorColonPolyps", "@type": "rdfs:Class", - "rdfs:comment": "History of chronic UV exposure", - "rdfs:label": "HistoryofChronicUVExposure", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "HistoryofPriorColonPolyps", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15502,33 +15099,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Outdooroccupational" - }, - { - "@id": "bts:Outdoorrecreational" + "@id": "bts:Yes" }, { - "@id": "bts:Therapeutic" + "@id": "bts:No" }, { - "@id": "bts:None" + "@id": "bts:NotApplicable" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "History of Chronic UV Exposure", + "sms:displayName": "History of Prior Colon Polyps", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofBlisteringSunburn", + "@id": "bts:FamilyColonCancerHistoryIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Patient has history of blistering sunburn", - "rdfs:label": "HistoryofBlisteringSunburn", + "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", + "rdfs:label": "FamilyColonCancerHistoryIndicator", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15542,24 +15136,24 @@ "@id": "bts:No" }, { - "@id": "bts:Unknown" + "@id": "bts:NotApplicable" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "History of Blistering Sunburn", + "sms:displayName": "Family Colon Cancer History Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofTanningBedUse", + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "History of tanning bed use of the patient", - "rdfs:label": "HistoryofTanningBedUse", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15567,36 +15161,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Never" - }, - { - "@id": "bts:Lessthan10times" - }, - { - "@id": "bts:10-50times" + "@id": "bts:Yes" }, { - "@id": "bts:50-100times" + "@id": "bts:No" }, { - "@id": "bts:Morethan100times" + "@id": "bts:NotApplicable" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "History of Tanning Bed Use", + "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryMelanoma", + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryMelanoma", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15611,20 +15199,23 @@ }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Immediate Family History Melanoma", + "sms:displayName": "Immediate Family History Endometrial Cancer", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MelanomaBiopsyResectionSites", + "@id": "bts:ImmediateFamilyHistoryOvarianCancer", "@type": "rdfs:Class", - "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", - "rdfs:label": "MelanomaBiopsyResectionSites", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15632,84 +15223,129 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Skinofscalp" - }, - { - "@id": "bts:Skinofeyelid" + "@id": "bts:Beforeage50" }, { - "@id": "bts:Skinofnose" + "@id": "bts:Notbeforeage50" }, { - "@id": "bts:Skinoflip" + "@id": "bts:Unknown" }, { - "@id": "bts:Skinofear" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Immediate Family History Ovarian Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", + "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofneck" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofotherpartsofface" + "@id": "bts:Yes-Crohn'sdisease" }, { - "@id": "bts:Skinofchest" + "@id": "bts:Yes-Ulcerativecolitis" }, { - "@id": "bts:Skinofback" + "@id": "bts:No" }, { - "@id": "bts:Skinofabdomen" + "@id": "bts:Unknown" }, { - "@id": "bts:Skinoftrunk-other" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PatientColonoscopyPerformedIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", + "rdfs:label": "PatientColonoscopyPerformedIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofbreast" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:Yes" }, { - "@id": "bts:Skinofpalm" + "@id": "bts:No" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Skinofsole" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Patient Colonoscopy Performed Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalCancerTumorBorderConfiguration", + "@type": "rdfs:Class", + "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", + "rdfs:label": "ColorectalCancerTumorBorderConfiguration", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofpenis" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinofscrotum" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Skinofvulva" + "@id": "bts:Infiltrating" }, { - "@id": "bts:Skinother" + "@id": "bts:Other" }, { - "@id": "bts:SkinNOS" + "@id": "bts:Pushing" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Melanoma Biopsy Resection Sites", + "sms:displayName": "Colorectal Cancer Tumor Border Configuration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaUlceration", + "@id": "bts:MLH1PromoterMethylationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaUlceration", + "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", + "rdfs:label": "MLH1PromoterMethylationStatus", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15720,27 +15356,27 @@ "@id": "bts:Absent" }, { - "@id": "bts:Present" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Unknown" + "@id": "bts:NotAssessed" }, { - "@id": "bts:NotReported" + "@id": "bts:Present" } ], - "sms:displayName": "Cutaneous Melanoma Ulceration", + "sms:displayName": "MLH1 Promoter Methylation Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaAdditionalFindings", + "@id": "bts:ColorectalCancerKRASIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaAdditionalFindings", + "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", + "rdfs:label": "ColorectalCancerKRASIndicator", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15748,28 +15384,41 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ActinicKeratosis" - }, - { - "@id": "bts:NevusRemnant" + "@id": "bts:Yes" }, { - "@id": "bts:SolarElastosis" + "@id": "bts:No" }, { - "@id": "bts:FibrosingRegression" + "@id": "bts:Unknown" }, { - "@id": "bts:NestingMelanoma" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Cancer KRAS Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColonPolypOccurenceIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "ColonPolypOccurenceIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:PagetoidSpread" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:VascularProliferation" + "@id": "bts:Yes" }, { - "@id": "bts:Other" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -15778,37 +15427,49 @@ "@id": "bts:NotApplicable" } ], - "sms:displayName": "Cutaneous Melanoma Additional Findings", + "sms:displayName": "Colon Polyp Occurence Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoBirth", + "@id": "bts:FamilyHistoryColorectalPolyp", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoBirth", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyHistoryColorectalPolyp", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Birth", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Family History Colorectal Polyp", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:CountryofResidence", + "@id": "bts:ColorectalPolypNewIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Country of Residence at enrollment", - "rdfs:label": "CountryofResidence", + "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", + "rdfs:label": "ColorectalPolypNewIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -15816,773 +15477,982 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Afghanistan" + "@id": "bts:Yes" }, { - "@id": "bts:Albania" + "@id": "bts:No" }, { - "@id": "bts:Algeria" + "@id": "bts:Unknown" }, { - "@id": "bts:Andorra" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp New Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypShape", + "@type": "rdfs:Class", + "rdfs:comment": "Shape of polyp identified in the participant", + "rdfs:label": "ColorectalPolypShape", + "rdfs:subClassOf": [ { - "@id": "bts:Angola" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Anguilla" + "@id": "bts:Pedunculated" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:Sessile" }, { - "@id": "bts:Argentina" + "@id": "bts:Flat" }, { - "@id": "bts:Armenia" + "@id": "bts:Notstated" }, { - "@id": "bts:Aruba" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp Shape", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SizeofPolypRemoved", + "@type": "rdfs:Class", + "rdfs:comment": "Size of the polyp removed in cm", + "rdfs:label": "SizeofPolypRemoved", + "rdfs:subClassOf": [ { - "@id": "bts:Australia" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Size of Polyp Removed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypCount", + "@type": "rdfs:Class", + "rdfs:comment": "The total number of polyps detected", + "rdfs:label": "ColorectalPolypCount", + "rdfs:subClassOf": [ { - "@id": "bts:Austria" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Colorectal Polyp Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypType", + "@type": "rdfs:Class", + "rdfs:comment": "Type of polyp found in the participant", + "rdfs:label": "ColorectalPolypType", + "rdfs:subClassOf": [ { - "@id": "bts:Azerbaijan" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Bahamas" + "@id": "bts:Adenoma" }, { - "@id": "bts:Bahrain" + "@id": "bts:Hyperplastic" }, { - "@id": "bts:Bangladesh" + "@id": "bts:Mixed" }, { - "@id": "bts:Barbados" + "@id": "bts:Papillomatous" }, { - "@id": "bts:Belarus" + "@id": "bts:Normal" }, { - "@id": "bts:Belgium" + "@id": "bts:Cancer" }, { - "@id": "bts:Belize" + "@id": "bts:Other" }, { - "@id": "bts:Benin" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Colorectal Polyp Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ColorectalPolypAdenomaType", + "@type": "rdfs:Class", + "rdfs:comment": "Type of adenoma associated with the polyp", + "rdfs:label": "ColorectalPolypAdenomaType", + "rdfs:subClassOf": [ { - "@id": "bts:Bermuda" - }, + "@id": "bts:ColorectalCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Bhutan" + "@id": "bts:Tubular" }, { - "@id": "bts:Bolivia" + "@id": "bts:Villous" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:Tubulovillous" }, { - "@id": "bts:Botswana" + "@id": "bts:Sessileserrated" }, { - "@id": "bts:Brazil" + "@id": "bts:Traditionalserrated" }, { - "@id": "bts:Brunei" + "@id": "bts:Serratednotspecified" }, { - "@id": "bts:Bulgaria" + "@id": "bts:Notstated" }, { - "@id": "bts:BurkinaFaso" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp Adenoma Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "BreastCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:Burundi" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Cambodia" + "@id": "bts:Component" }, { - "@id": "bts:Cameroon" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Canada" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:CapeVerde" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:BreastCarcinomaDetectionMethodType" }, { - "@id": "bts:Chad" + "@id": "bts:BreastCarcinomaHistologyCategory" }, { - "@id": "bts:Chile" + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" }, { - "@id": "bts:China" + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" }, { - "@id": "bts:Colombia" + "@id": "bts:BreastBiopsyProcedureFindingType" }, { - "@id": "bts:Comoros" + "@id": "bts:BreastQuadrantSite" }, { - "@id": "bts:Congo" + "@id": "bts:BreastCancerAssessmentTests" }, { - "@id": "bts:CookIslands" + "@id": "bts:BreastCancerGenomicTestPerformed" }, { - "@id": "bts:CostaRica" + "@id": "bts:MammaprintRiskGroup" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:OncotypeRiskGroup" }, { - "@id": "bts:Croatia" + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" }, { - "@id": "bts:Cuba" + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" }, { - "@id": "bts:Curacao" + "@id": "bts:BreastCancerAllredEstrogenReceptorScore" }, { - "@id": "bts:Cyprus" + "@id": "bts:PriorInvasiveBreastDisease" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:BreastCarcinomaERStatusPercentageValue" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:BreastCarcinomaPRStatusPercentageValue" }, { - "@id": "bts:Denmark" + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" }, { - "@id": "bts:Djibouti" + "@id": "bts:BreastCarcinomaCentromere17CopyNumber" }, { - "@id": "bts:Dominica" + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" }, { - "@id": "bts:DominicanRepublic" + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" }, { - "@id": "bts:Ecuador" + "@id": "bts:BreastCarcinomaSurgicalProcedureName" }, { - "@id": "bts:Egypt" + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" }, { - "@id": "bts:ElSalvador" + "@id": "bts:BreastCarcinomaHER2Status" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:Eritrea" + "@id": "bts:BreastCarcinomaERStainingIntensity" }, { - "@id": "bts:Estonia" + "@id": "bts:BreastCarcinomaPRStainingIntensity" }, { - "@id": "bts:Eswatini" + "@id": "bts:OncotypeScore" }, { - "@id": "bts:Ethiopia" + "@id": "bts:BreastImagingPerformedType" }, { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" }, { - "@id": "bts:FederatedStatesofMicronesia" - }, + "@id": "bts:BIRADSMammographyBreastDensityCategory" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaDetectionMethodType", + "@type": "rdfs:Class", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", + "rdfs:label": "BreastCarcinomaDetectionMethodType", + "rdfs:subClassOf": [ { - "@id": "bts:Fiji" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Finland" + "@id": "bts:ClinicalExam" }, { - "@id": "bts:France" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:FrenchGuiana" + "@id": "bts:NippleDischarge" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:Other" }, { - "@id": "bts:Gabon" + "@id": "bts:ScreeningMammography" }, { - "@id": "bts:Gambia" + "@id": "bts:ScreeningMRI" }, { - "@id": "bts:Georgia" + "@id": "bts:Selfexam" }, { - "@id": "bts:Germany" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Detection Method Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHistologyCategory", + "@type": "rdfs:Class", + "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", + "rdfs:label": "BreastCarcinomaHistologyCategory", + "rdfs:subClassOf": [ { - "@id": "bts:Ghana" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Gibraltar" + "@id": "bts:Infiltratingductalcarcinoma" }, { - "@id": "bts:Greece" + "@id": "bts:Infiltratinglobularcarcinoma" }, { - "@id": "bts:Greenland" + "@id": "bts:InvasivemammarycarcinomaNOS" }, { - "@id": "bts:Grenada" + "@id": "bts:Invasivemixedductalandlobularcarcinoma" }, { - "@id": "bts:Guadeloupe" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Carcinoma Histology Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", + "@type": "rdfs:Class", + "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", + "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", + "rdfs:subClassOf": [ { - "@id": "bts:Guam" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Guatemala" + "@id": "bts:Alveolartype" }, { - "@id": "bts:Guernsey" + "@id": "bts:Classicaltype" }, { - "@id": "bts:Guinea" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Guinea-Bissau" - }, - { - "@id": "bts:Guyana" - }, - { - "@id": "bts:Haiti" - }, - { - "@id": "bts:HolySee" - }, - { - "@id": "bts:Honduras" - }, - { - "@id": "bts:HongKong" - }, - { - "@id": "bts:Hungary" - }, - { - "@id": "bts:Iceland" - }, - { - "@id": "bts:India" - }, - { - "@id": "bts:Indonesia" - }, - { - "@id": "bts:Iran" - }, - { - "@id": "bts:Iraq" - }, - { - "@id": "bts:Ireland" - }, - { - "@id": "bts:IsleofMan" - }, - { - "@id": "bts:Israel" - }, - { - "@id": "bts:Italy" - }, - { - "@id": "bts:Jamaica" - }, - { - "@id": "bts:Japan" - }, - { - "@id": "bts:Jersey" - }, - { - "@id": "bts:Jordan" - }, - { - "@id": "bts:Kazakhstan" - }, - { - "@id": "bts:Kenya" - }, - { - "@id": "bts:Kiribati" - }, - { - "@id": "bts:Kosovo" - }, - { - "@id": "bts:Kuwait" - }, - { - "@id": "bts:Kyrgyzstan" - }, - { - "@id": "bts:Laos" - }, - { - "@id": "bts:Latvia" - }, - { - "@id": "bts:Lebanon" - }, - { - "@id": "bts:Lesotho" - }, - { - "@id": "bts:Liberia" - }, - { - "@id": "bts:Libya" - }, - { - "@id": "bts:Liechtenstein" - }, - { - "@id": "bts:Lithuania" - }, - { - "@id": "bts:Luxembourg" - }, - { - "@id": "bts:Macau" - }, - { - "@id": "bts:Madagascar" - }, - { - "@id": "bts:Malawi" - }, - { - "@id": "bts:Malaysia" - }, - { - "@id": "bts:Maldives" - }, - { - "@id": "bts:Mali" - }, - { - "@id": "bts:Malta" - }, - { - "@id": "bts:MarshallIslands" - }, - { - "@id": "bts:Martinique" - }, - { - "@id": "bts:Mauritania" - }, - { - "@id": "bts:Mauritius" - }, - { - "@id": "bts:Mayotte" - }, - { - "@id": "bts:Mexico" - }, - { - "@id": "bts:Moldova" - }, - { - "@id": "bts:Monaco" + "@id": "bts:Pleomorphictype" }, { - "@id": "bts:Mongolia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", + "@type": "rdfs:Class", + "rdfs:comment": "The histologic subtype for the most common type of invasive breast carcinoma.", + "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", + "rdfs:subClassOf": [ { - "@id": "bts:Montenegro" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Montserrat" + "@id": "bts:Classicaltype" }, { - "@id": "bts:Morocco" + "@id": "bts:Invasivecarcinoma-typecannotbedetermined" }, { - "@id": "bts:Mozambique" + "@id": "bts:Invasivecribriformcarcinoma" }, { - "@id": "bts:Myanmar" + "@id": "bts:Invasivemicropapillarycarcinoma" }, { - "@id": "bts:Namibia" + "@id": "bts:Invasivepapillarycarcinoma" }, { - "@id": "bts:Nauru" + "@id": "bts:Invasivetubularcarcinoma" }, { - "@id": "bts:Nepal" + "@id": "bts:Medullarycarcinoma" }, { - "@id": "bts:Netherlands" + "@id": "bts:Mucinouscarcinoma" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:Tubulolobularcarcinoma" }, { - "@id": "bts:NewZealand" + "@id": "bts:Other" }, { - "@id": "bts:Nicaragua" + "@id": "bts:Unknown" }, { - "@id": "bts:Niger" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Invasive Ductal Breast Carcinoma Histologic Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastBiopsyProcedureFindingType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.", + "rdfs:label": "BreastBiopsyProcedureFindingType", + "rdfs:subClassOf": [ { - "@id": "bts:Nigeria" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Niue" + "@id": "bts:Atypicalhyperplasia" }, { - "@id": "bts:NorthKorea" + "@id": "bts:DCIS" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:LCIS" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:Cancer" }, { - "@id": "bts:Norway" + "@id": "bts:Nocancer" }, { - "@id": "bts:Oman" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Biopsy Procedure Finding Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastQuadrantSite", + "@type": "rdfs:Class", + "rdfs:comment": "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", + "rdfs:label": "BreastQuadrantSite", + "rdfs:subClassOf": [ { - "@id": "bts:Pakistan" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Palau" + "@id": "bts:Upperouterquadrant" }, { - "@id": "bts:Panama" + "@id": "bts:Lowerouterquadrant" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:Upperinnerquadrant" }, { - "@id": "bts:Paraguay" + "@id": "bts:Lowerinnerquadrant" }, { - "@id": "bts:Peru" + "@id": "bts:Central" }, { - "@id": "bts:Philippines" + "@id": "bts:Nipple" }, { - "@id": "bts:Poland" + "@id": "bts:Unknown" }, { - "@id": "bts:Portugal" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Quadrant Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAssessmentTests", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", + "rdfs:label": "BreastCancerAssessmentTests", + "rdfs:subClassOf": [ { - "@id": "bts:PuertoRico" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Qatar" + "@id": "bts:EstrogenreceptorIHC" }, { - "@id": "bts:Reunion" + "@id": "bts:ProgesteronereceptorIHC" }, { - "@id": "bts:Romania" + "@id": "bts:HER2IHC" }, { - "@id": "bts:Russia" + "@id": "bts:HER2FISH-CISH" }, { - "@id": "bts:Rwanda" + "@id": "bts:HER2FISH" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Other" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:Unknown" }, { - "@id": "bts:SaintLucia" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Cancer Assessment Tests", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerGenomicTestPerformed", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", + "rdfs:label": "BreastCancerGenomicTestPerformed", + "rdfs:subClassOf": [ { - "@id": "bts:SaintPierreandMiquelon" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:Oncotype" }, { - "@id": "bts:Samoa" + "@id": "bts:MammaPrint" }, { - "@id": "bts:SanMarino" + "@id": "bts:Other" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:Unknown" }, { - "@id": "bts:Senegal" - }, + "@id": "bts:Notperformed" + } + ], + "sms:displayName": "Breast Cancer Genomic Test Performed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MammaprintRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "rdfs:label": "MammaprintRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:Serbia" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Seychelles" + "@id": "bts:Highrisk" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:Singapore" + "@id": "bts:Lowrisk" }, { - "@id": "bts:Slovakia" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Slovenia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Mammaprint Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OncotypeRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "rdfs:label": "OncotypeRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:SolomonIslands" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Somalia" + "@id": "bts:Highrisk" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:SouthKorea" + "@id": "bts:Lowrisk" }, { - "@id": "bts:SouthSudan" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Spain" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Oncotype Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaEstrogenReceptorStatus", + "rdfs:subClassOf": [ { - "@id": "bts:SriLanka" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StateofPalestine" + "@id": "bts:Borderline" }, { - "@id": "bts:Sudan" + "@id": "bts:Equivocal" }, { - "@id": "bts:Suriname" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:Negative" }, { - "@id": "bts:Sweden" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Switzerland" + "@id": "bts:PerformedbutNotAvailable" }, { - "@id": "bts:Syria" + "@id": "bts:Positive" }, { - "@id": "bts:Taiwan" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Estrogen Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Tajikistan" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Tanzania" + "@id": "bts:Borderline" }, { - "@id": "bts:Thailand" + "@id": "bts:Equivocal" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Togo" + "@id": "bts:Negative" }, { - "@id": "bts:Tokelau" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Tonga" + "@id": "bts:PerformedbutNotAvailable" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:Positive" }, { - "@id": "bts:Tunisia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAllredEstrogenReceptorScore", + "@type": "rdfs:Class", + "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "rdfs:label": "BreastCancerAllredEstrogenReceptorScore", + "rdfs:subClassOf": [ { - "@id": "bts:Turkey" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Turkmenistan" + "@id": "bts:0" }, { - "@id": "bts:Tuvalu" + "@id": "bts:1" }, { - "@id": "bts:Uganda" + "@id": "bts:2" }, { - "@id": "bts:Ukraine" + "@id": "bts:3" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:4" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:5" }, { - "@id": "bts:UnitedStates" + "@id": "bts:6" }, { - "@id": "bts:Uruguay" + "@id": "bts:7" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:8" }, { - "@id": "bts:Vanuatu" + "@id": "bts:10" }, { - "@id": "bts:Venezuela" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Cancer Allred Estrogen Receptor Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorInvasiveBreastDisease", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate prior invasive breast condition in the participant", + "rdfs:label": "PriorInvasiveBreastDisease", + "rdfs:subClassOf": [ { - "@id": "bts:Vietnam" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:DCIS" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:LCIS" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Other" }, { - "@id": "bts:Yemen" + "@id": "bts:Unknown" }, { - "@id": "bts:Zambia" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Prior Invasive Breast Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaERStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStatusPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:Zimbabwe" + "@id": "bts:BreastCancerTier3" } ], - "sms:displayName": "Country of Residence", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma ER Status Percentage Value", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AgeIsObfuscated", + "@id": "bts:BreastCarcinomaPRStatusPercentageValue", "@type": "rdfs:Class", - "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "rdfs:label": "AgeIsObfuscated", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStatusPercentageValue", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label": "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:subClassOf": [ { - "@id": "bts:True" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaCentromere17CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", + "rdfs:label": "BreastCarcinomaCentromere17CopyNumber", + "rdfs:subClassOf": [ { - "@id": "bts:False" + "@id": "bts:BreastCancerTier3" } ], - "sms:displayName": "Age Is Obfuscated", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearOfBirth", + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label": "YearOfBirth", + "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year Of Birth", + "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OccupationDurationYears", + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", + "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Occupation Duration Years", + "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrematureAtBirth", + "@id": "bts:BreastCarcinomaSurgicalProcedureName", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", + "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "rdfs:label": "BreastCarcinomaSurgicalProcedureName", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16590,47 +16460,62 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Lumpectomy" }, { - "@id": "bts:No" + "@id": "bts:Radicalmastectomy" }, { - "@id": "bts:Unknown" + "@id": "bts:Modifiedradicalmastectomy" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" + }, + { + "@id": "bts:Partialmastectomy" + }, + { + "@id": "bts:Re-excision" + }, + { + "@id": "bts:Simplemastectomy" + }, + { + "@id": "bts:Surgerynotperformed" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Premature At Birth", + "sms:displayName": "Breast Carcinoma Surgical Procedure Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WeeksGestationatBirth", + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", + "rdfs:comment": "HER2 ratio of the participant at diagnosis", + "rdfs:label": "BreastCarcinomaHER2RatioDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Weeks Gestation at Birth", + "sms:displayName": "Breast Carcinoma HER2 Ratio Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelativewithCancerHistory", + "@id": "bts:BreastCarcinomaHER2Status", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", + "rdfs:comment": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Status", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16638,30 +16523,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-CancerHistoryRelative" + "@id": "bts:Positive" }, { - "@id": "bts:None" + "@id": "bts:Negative" }, { - "@id": "bts:Unknown" + "@id": "bts:Amplified" }, { - "@id": "bts:NotReported" + "@id": "bts:Non-amplified" + }, + { + "@id": "bts:Equivocal" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Relative with Cancer History", + "sms:displayName": "Breast Carcinoma HER2 Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SmokingExposure", + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", + "rdfs:comment": "Did the patient receive hormonal therapy for prevention of breast cancer?", + "rdfs:label": "HormoneTherapyBreastCancerPreventionIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16669,27 +16566,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-SmokingExposure" + "@id": "bts:Yes" }, { - "@id": "bts:No-SmokingExposure" + "@id": "bts:No" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", + "sms:displayName": "Hormone Therapy Breast Cancer Prevention Indicator", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholExposure", + "@id": "bts:BreastCarcinomaERStainingIntensity", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", + "rdfs:comment": "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStainingIntensity", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16697,27 +16597,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AlcoholExposure" + "@id": "bts:Strong" }, { - "@id": "bts:No-AlcoholExposure" + "@id": "bts:Moderate" }, { - "@id": "bts:NotReported" + "@id": "bts:Weak" + }, + { + "@id": "bts:Weak-Moderate" + }, + { + "@id": "bts:Moderate-Strong" + }, + { + "@id": "bts:Weak-Strong" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", + "sms:displayName": "Breast Carcinoma ER Staining Intensity", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AsbestosExposure", + "@id": "bts:BreastCarcinomaPRStainingIntensity", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", + "rdfs:comment": "Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStainingIntensity", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16725,30 +16640,59 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Strong" }, { - "@id": "bts:No" + "@id": "bts:Moderate" }, { - "@id": "bts:Unknown" + "@id": "bts:Weak" }, { - "@id": "bts:NotReported" + "@id": "bts:Weak-Moderate" + }, + { + "@id": "bts:Moderate-Strong" + }, + { + "@id": "bts:Weak-Strong" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Asbestos Exposure", + "sms:displayName": "Breast Carcinoma PR Staining Intensity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CoalDustExposure", + "@id": "bts:OncotypeScore", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", + "rdfs:comment": "OncotypeDX recurrence score", + "rdfs:label": "OncotypeScore", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Oncotype Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastImagingPerformedType", + "@type": "rdfs:Class", + "rdfs:comment": "The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).", + "rdfs:label": "BreastImagingPerformedType", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16756,27 +16700,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Mammogram" }, { - "@id": "bts:No" + "@id": "bts:Ultrasound" + }, + { + "@id": "bts:MRI" + }, + { + "@id": "bts:PET/CT" + }, + { + "@id": "bts:CT" + }, + { + "@id": "bts:Multipleimagingmodalities" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Coal Dust Exposure", + "sms:displayName": "Breast Imaging Performed Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.", + "rdfs:label": "MultifocalBreastCarcinomaPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16791,20 +16750,23 @@ }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", + "sms:displayName": "Multifocal Breast Carcinoma Present Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RadonExposure", + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", + "rdfs:comment": "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.", + "rdfs:label": "MulticentricBreastCarcinomaPresentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16821,21 +16783,21 @@ "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Radon Exposure", + "sms:displayName": "Multicentric Breast Carcinoma Present Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RespirableCrystallineSilicaExposure", + "@id": "bts:BIRADSMammographyBreastDensityCategory", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:comment": "The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.", + "rdfs:label": "BIRADSMammographyBreastDensityCategory", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -16843,5783 +16805,6015 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Predominantlyfatty" }, { - "@id": "bts:No" + "@id": "bts:Scatteredfibroglandulardensities" + }, + { + "@id": "bts:Heterogeneouslydense" + }, + { + "@id": "bts:Extremelydense" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:displayName": "BIRADS Mammography Breast Density Category", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdverseEvent", + "@id": "bts:NeuroblastomaandGliomaTier3", "@type": "rdfs:Class", - "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", - "rdfs:label": "AdverseEvent", + "rdfs:comment": "Brain cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "NeuroblastomaandGliomaTier3", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdominalDistension" - }, - { - "@id": "bts:AbdominalInfection" - }, + "sms:displayName": "Neuroblastoma and Glioma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:AbdominalPain" + "@id": "bts:Component" }, { - "@id": "bts:AbdominalSoftTissueNecrosis" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:AbducensNerveDisorder" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:AccessoryNerveDisorder" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Acidosis" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:AcousticNerveDisorderNOS" + "@id": "bts:CNSTumorPrimaryAnatomicSite" }, { - "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:AcuteCoronarySyndrome" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:AcuteKidneyInjury" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:AdrenalInsufficiency" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:AdultRespiratoryDistressSyndrome" - }, + "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CNSTumorPrimaryAnatomicSite", + "@type": "rdfs:Class", + "rdfs:comment": "Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2", + "rdfs:label": "CNSTumorPrimaryAnatomicSite", + "rdfs:subClassOf": [ { - "@id": "bts:Agitation" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Akathisia" + "@id": "bts:Thalamus" }, { - "@id": "bts:AlanineAminotransferaseIncreased" + "@id": "bts:Ventricles" }, { - "@id": "bts:AlcoholIntolerance" + "@id": "bts:Intracranial/Leptomeningeal" }, { - "@id": "bts:AlkalinePhosphataseIncreased" + "@id": "bts:Suprasellar/Hypothalamic/Pituitary" }, { - "@id": "bts:Alkalosis" + "@id": "bts:Cerebellar/Posteriorfossa" }, { - "@id": "bts:AllergicReaction" + "@id": "bts:Brainstem-Medulla" }, { - "@id": "bts:AllergicRhinitis" + "@id": "bts:Brainstem-Midbrain/Tectum" }, { - "@id": "bts:Alopecia" + "@id": "bts:Brainstem-Pons" }, { - "@id": "bts:Amnesia" + "@id": "bts:Spinalcord-Cervical" }, { - "@id": "bts:AnalFistula" + "@id": "bts:Spinalcord-Thoracic" }, { - "@id": "bts:AnalHemorrhage" + "@id": "bts:Spinalcord-Lumbar" }, { - "@id": "bts:AnalMucositis" + "@id": "bts:Opticpathway" }, { - "@id": "bts:AnalNecrosis" + "@id": "bts:OtherlocationsNOS" }, { - "@id": "bts:AnalPain" + "@id": "bts:Paraspinalganglion" }, { - "@id": "bts:AnalStenosis" + "@id": "bts:Basalganglia" }, { - "@id": "bts:AnalUlcer" + "@id": "bts:Hippocampus" }, { - "@id": "bts:Anaphylaxis" + "@id": "bts:Meninges/Dura" }, { - "@id": "bts:Anemia" - }, + "@id": "bts:Otherlymphnodes" + } + ], + "sms:displayName": "CNS Tumor Primary Anatomic Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GliomaSpecificMetastasisSites", + "@type": "rdfs:Class", + "rdfs:comment": "Evidence of active brain metastasis including leptomeningeal involvement", + "rdfs:label": "GliomaSpecificMetastasisSites", + "rdfs:subClassOf": [ { - "@id": "bts:AnkleFracture" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:AnorectalInfection" + "@id": "bts:CSF" }, { - "@id": "bts:Anorexia" + "@id": "bts:Spine" }, { - "@id": "bts:Anorgasmia" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Anxiety" + "@id": "bts:Brain" }, { - "@id": "bts:AorticInjury" + "@id": "bts:Other" }, { - "@id": "bts:AorticValveDisease" + "@id": "bts:Leptomeningeal" }, { - "@id": "bts:Aphonia" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Glioma Specific Metastasis Sites", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GliomaSpecificRadiationField", + "@type": "rdfs:Class", + "rdfs:comment": "A description of the location on or within the CNS where radiation was administered in a partcipant with glioma", + "rdfs:label": "GliomaSpecificRadiationField", + "rdfs:subClassOf": [ { - "@id": "bts:Apnea" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Appendicitis" + "@id": "bts:Craniospinal" }, { - "@id": "bts:AppendicitisPerforated" + "@id": "bts:Focal-tumorbed" }, { - "@id": "bts:Arachnoiditis" + "@id": "bts:Unknown" }, { - "@id": "bts:ArterialInjury" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Glioma Specific Radiation Field", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the molecular subgroup in a supra tentorial ependymoma", + "rdfs:label": "SupraTentorialEpendymomaMolecularSubgroup", + "rdfs:subClassOf": [ { - "@id": "bts:ArteritisInfective" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Arthralgia" + "@id": "bts:ST-EPN-RELA" }, { - "@id": "bts:Arthritis" + "@id": "bts:ST-EPN-YAP1" }, { - "@id": "bts:Ascites" + "@id": "bts:Unknown" }, { - "@id": "bts:AspartateAminotransferaseIncreased" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Supra Tentorial Ependymoma Molecular Subgroup", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the molecular subgroup in a infra tentorial ependymoma", + "rdfs:label": "InfraTentorialEpendymomaMolecularSubgroup", + "rdfs:subClassOf": [ { - "@id": "bts:Aspiration" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Asystole" + "@id": "bts:PF-EPN-A" }, { - "@id": "bts:Ataxia" + "@id": "bts:PF-EPN-B" }, { - "@id": "bts:Atelectasis" + "@id": "bts:Myxopapillaryependymoma" }, { - "@id": "bts:AtrialFibrillation" + "@id": "bts:Unknown" }, { - "@id": "bts:AtrialFlutter" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Infra Tentorial Ependymoma Molecular Subgroup", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Neuroblastoma MYCN amplification or over-expression status", + "rdfs:label": "NeuroblastomaMYCNGeneAmplificationStatus", + "rdfs:subClassOf": [ { - "@id": "bts:AtrioventricularBlockComplete" - }, + "@id": "bts:NeuroblastomaandGliomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:AtrioventricularBlockFirstDegree" + "@id": "bts:Amplified" }, { - "@id": "bts:AutoimmuneDisorder" + "@id": "bts:Notamplified" }, { - "@id": "bts:AvascularNecrosis" + "@id": "bts:Notdone" }, { - "@id": "bts:Azoospermia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Neuroblastoma MYCN Gene Amplification Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AcuteLymphoblasticLeukemiaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3", + "rdfs:label": "AcuteLymphoblasticLeukemiaTier3", + "rdfs:subClassOf": [ { - "@id": "bts:BackPain" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:BileDuctStenosis" + "@id": "bts:Component" }, { - "@id": "bts:BiliaryAnastomoticLeak" + "@id": "bts:HTANParticipantID" }, { - 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoBirth", + "rdfs:subClassOf": [ { - "@id": "bts:Leukoencephalopathy" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Birth", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:CountryofResidence", + "@type": "rdfs:Class", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", + "rdfs:subClassOf": [ { - "@id": "bts:LibidoDecreased" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LibidoIncreased" + "@id": "bts:Afghanistan" }, { - "@id": "bts:LipInfection" + "@id": "bts:Albania" }, { - "@id": "bts:LipPain" + "@id": "bts:Algeria" }, { - "@id": "bts:LipaseIncreased" + "@id": "bts:Andorra" }, { - "@id": "bts:Lipohypertrophy" + "@id": "bts:Angola" }, { - 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"@id": "bts:PelvicSoftTissueNecrosis" + "@id": "bts:Jordan" }, { - "@id": "bts:PenileInfection" + "@id": "bts:Kazakhstan" }, { - "@id": "bts:PenilePain" + "@id": "bts:Kenya" }, { - "@id": "bts:PerforationBileDuct" + "@id": "bts:Kiribati" }, { - "@id": "bts:PericardialEffusion" + "@id": "bts:Kosovo" }, { - "@id": "bts:PericardialTamponade" + "@id": "bts:Kuwait" }, { - "@id": "bts:Pericarditis" + "@id": "bts:Kyrgyzstan" }, { - "@id": "bts:PerinealPain" + "@id": "bts:Laos" }, { - "@id": "bts:PeriodontalDisease" + "@id": "bts:Latvia" }, { - "@id": "bts:PeriorbitalEdema" + "@id": "bts:Lebanon" }, { - "@id": "bts:PeriorbitalInfection" + "@id": "bts:Lesotho" }, { - "@id": "bts:PeripheralIschemia" + "@id": "bts:Liberia" }, { - "@id": "bts:PeripheralMotorNeuropathy" + "@id": "bts:Libya" }, { - "@id": "bts:PeripheralNerveInfection" + "@id": "bts:Liechtenstein" }, { - "@id": "bts:PeripheralSensoryNeuropathy" + "@id": "bts:Lithuania" }, { - "@id": "bts:PeritonealInfection" + "@id": "bts:Luxembourg" }, { - 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"@id": "bts:PleuralHemorrhage" + "@id": "bts:Montserrat" }, { - "@id": "bts:PleuralInfection" + "@id": "bts:Morocco" }, { - "@id": "bts:PleuriticPain" + "@id": "bts:Mozambique" }, { - "@id": "bts:Pneumonitis" + "@id": "bts:Myanmar" }, { - "@id": "bts:Pneumothorax" + "@id": "bts:Namibia" }, { - "@id": "bts:PortalHypertension" + "@id": "bts:Nauru" }, { - "@id": "bts:PortalVeinThrombosis" + "@id": "bts:Nepal" }, { - "@id": "bts:PostnasalDrip" + "@id": "bts:Netherlands" }, { - "@id": "bts:PostoperativeHemorrhage" + "@id": "bts:NewCaledonia" }, { - "@id": "bts:PostoperativeThoracicProcedureComplication" + "@id": "bts:NewZealand" }, { - "@id": "bts:PrecociousPuberty" + "@id": "bts:Nicaragua" }, { - "@id": "bts:Pregnancy" + "@id": "bts:Niger" }, { - "@id": "bts:PuerperiumandPerinatalConditionsOther" + "@id": "bts:Nigeria" }, { - "@id": "bts:PrematureDelivery" + "@id": "bts:Niue" }, { - "@id": "bts:PrematureMenopause" + "@id": "bts:NorthKorea" }, { - "@id": "bts:Presyncope" + "@id": "bts:NorthMacedonia" }, { - "@id": "bts:Proctitis" + "@id": "bts:NorthernMarianaIslands" }, { - "@id": "bts:ProductiveCough" + "@id": "bts:Norway" }, { - "@id": "bts:ProlapseofIntestinalStoma" + "@id": "bts:Oman" }, { - "@id": "bts:ProlapseofUrostomy" + "@id": "bts:Pakistan" }, { - "@id": "bts:ProstateInfection" + "@id": "bts:Palau" }, { - "@id": "bts:ProstaticHemorrhage" + "@id": "bts:Panama" }, { - "@id": "bts:ProstaticObstruction" + "@id": "bts:PapuaNewGuinea" }, { - "@id": "bts:ProstaticPain" + "@id": "bts:Paraguay" }, { - "@id": "bts:Proteinuria" + "@id": "bts:Peru" }, { - "@id": "bts:Pruritus" + "@id": "bts:Philippines" }, { - "@id": "bts:PsychiatricDisordersOther" + "@id": "bts:Poland" }, { - "@id": "bts:Psychosis" + "@id": "bts:Portugal" }, { - "@id": "bts:PulmonaryEdema" + "@id": "bts:PuertoRico" }, { - "@id": "bts:PulmonaryFibrosis" + "@id": "bts:Qatar" }, { - "@id": "bts:PulmonaryFistula" + "@id": "bts:Reunion" }, { - "@id": "bts:PulmonaryHypertension" + "@id": "bts:Romania" }, { - "@id": "bts:PulmonaryValveDisease" + "@id": "bts:Russia" }, { - "@id": "bts:Purpura" + "@id": "bts:Rwanda" }, { - "@id": "bts:PyramidalTractSyndrome" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:RadiationRecallReaction(Dermatologic)" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:Radiculitis" + "@id": "bts:SaintLucia" }, { - "@id": "bts:RashAcneiform" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:RashMaculo-Papular" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:RashPustular" + "@id": "bts:Samoa" }, { - "@id": "bts:RectalAnastomoticLeak" + "@id": "bts:SanMarino" }, { - "@id": "bts:RectalFistula" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:RectalHemorrhage" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:RectalMucositis" + "@id": "bts:Senegal" }, { - "@id": "bts:RectalNecrosis" + "@id": "bts:Serbia" }, { - "@id": "bts:RectalObstruction" + "@id": "bts:Seychelles" }, { - "@id": "bts:RectalPain" + "@id": "bts:SierraLeone" }, { - "@id": "bts:RectalPerforation" + "@id": "bts:Singapore" }, { - "@id": "bts:RectalStenosis" + "@id": "bts:Slovakia" }, { - "@id": "bts:RectalUlcer" + "@id": "bts:Slovenia" }, { - "@id": "bts:RecurrentLaryngealNervePalsy" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:RenalandUrinaryDisordersOther" + "@id": "bts:Somalia" }, { - "@id": "bts:RenalCalculi" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:RenalColic" + "@id": "bts:SouthKorea" }, { - "@id": "bts:RenalHemorrhage" + "@id": "bts:SouthSudan" }, { - "@id": "bts:ReproductiveSystemandBreastDisordersOther" + "@id": "bts:Spain" }, { - "@id": "bts:RespiratoryFailure" + "@id": "bts:SriLanka" }, { - "@id": "bts:Respiratory" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:ThoracicandMediastinalDisordersOther" + "@id": "bts:Sudan" }, { - "@id": "bts:Restlessness" + "@id": "bts:Suriname" }, { - "@id": "bts:RestrictiveCardiomyopathy" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:RetinalDetachment" + "@id": "bts:Sweden" }, { - "@id": "bts:RetinalTear" + "@id": "bts:Switzerland" }, { - "@id": "bts:RetinalVascularDisorder" + "@id": "bts:Syria" }, { - "@id": "bts:RetinoicAcidSyndrome" + "@id": "bts:Taiwan" }, { - "@id": "bts:Retinopathy" + "@id": "bts:Tajikistan" }, { - "@id": "bts:RetroperitonealHemorrhage" + "@id": "bts:Tanzania" }, { - "@id": "bts:ReversiblePosteriorLeukoencephalopathySyndrome" + "@id": "bts:Thailand" }, { - "@id": "bts:RhinitisInfective" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:RightVentricularDysfunction" + "@id": "bts:Togo" }, { - "@id": "bts:SalivaryDuctInflammation" + "@id": "bts:Tokelau" }, { - "@id": "bts:SalivaryGlandFistula" + "@id": "bts:Tonga" }, { - "@id": "bts:SalivaryGlandInfection" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:ScalpPain" + "@id": "bts:Tunisia" }, { - "@id": "bts:ScleralDisorder" + "@id": "bts:Turkey" }, { - "@id": "bts:Scoliosis" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:ScrotalInfection" + "@id": "bts:Tuvalu" }, { - "@id": "bts:ScrotalPain" + "@id": "bts:Uganda" }, { - "@id": "bts:Seizure" + "@id": "bts:Ukraine" }, { - "@id": "bts:Sepsis" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:Seroma" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:SerumAmylaseIncreased" + "@id": "bts:UnitedStates" }, { - "@id": "bts:SerumSickness" + "@id": "bts:Uruguay" }, { - "@id": "bts:SickSinusSyndrome" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:SinusBradycardia" + "@id": "bts:Vanuatu" }, { - "@id": "bts:SinusDisorder" + "@id": "bts:Venezuela" }, { - "@id": "bts:SinusPain" + "@id": "bts:Vietnam" }, { - "@id": "bts:SinusTachycardia" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:Sinusitis" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:SkinandSubcutaneousTissueDisordersOther" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:SkinAtrophy" + "@id": "bts:WesternSahara" }, { - "@id": "bts:SkinHyperpigmentation" + "@id": "bts:Yemen" }, { - "@id": "bts:SkinHypopigmentation" + "@id": "bts:Zambia" }, { - "@id": "bts:SkinInduration" - }, + "@id": "bts:Zimbabwe" + } + ], + "sms:displayName": "Country of Residence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeIsObfuscated", + "@type": "rdfs:Class", + "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "rdfs:label": "AgeIsObfuscated", + "rdfs:subClassOf": [ { - "@id": "bts:SkinInfection" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SkinUlceration" + "@id": "bts:True" }, { - "@id": "bts:SleepApnea" - }, + "@id": "bts:False" + } + ], + "sms:displayName": "Age Is Obfuscated", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:YearOfBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label": "YearOfBirth", + "rdfs:subClassOf": [ { - "@id": "bts:SmallIntestinalAnastomoticLeak" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Year Of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OccupationDurationYears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of years a patient worked in a specific occupation.", + "rdfs:label": "OccupationDurationYears", + "rdfs:subClassOf": [ { - "@id": "bts:SmallIntestinalMucositis" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Occupation Duration Years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrematureAtBirth", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", + "rdfs:label": "PrematureAtBirth", + "rdfs:subClassOf": [ { - "@id": "bts:SmallIntestinalObstruction" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SmallIntestinalPerforation" + "@id": "bts:Yes" }, { - "@id": "bts:SmallIntestinalStenosis" + "@id": "bts:No" }, { - "@id": "bts:SmallIntestineInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:SmallIntestineUlcer" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Premature At Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WeeksGestationatBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", + "rdfs:label": "WeeksGestationatBirth", + "rdfs:subClassOf": [ { - "@id": "bts:Sneezing" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Weeks Gestation at Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RelativewithCancerHistory", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "rdfs:label": "RelativewithCancerHistory", + "rdfs:subClassOf": [ { - "@id": "bts:SocialCircumstancesOther" - }, + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SoftTissueInfection" + "@id": "bts:Yes-CancerHistoryRelative" }, { - "@id": "bts:SoftTissueNecrosisLowerLimb" + "@id": "bts:None" }, { - "@id": "bts:SoftTissueNecrosisUpperLimb" + "@id": "bts:Unknown" }, { - "@id": "bts:Somnolence" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Relative with Cancer History", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SmokingExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if individual has smoking exposure", + "rdfs:label": "SmokingExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-SmokingExposure" }, { - "@id": "bts:SoreThroat" + "@id": "bts:No-SmokingExposure" }, { - "@id": "bts:Spasticity" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Smoking Exposure", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AlcoholExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if individual has alcohol exposure", + "rdfs:label": "AlcoholExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AlcoholExposure" }, { - "@id": "bts:SpermaticCordAnastomoticLeak" + "@id": "bts:No-AlcoholExposure" }, { - "@id": "bts:SpermaticCordHemorrhage" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Alcohol Exposure", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AsbestosExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", + "rdfs:label": "AsbestosExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SpermaticCordObstruction" + "@id": "bts:No" }, { - "@id": "bts:SpinalFracture" + "@id": "bts:Unknown" }, { - "@id": "bts:SpleenDisorder" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Asbestos Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CoalDustExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", + "rdfs:label": "CoalDustExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SplenicInfection" + "@id": "bts:No" }, { - "@id": "bts:StenosisofGastrointestinalStoma" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Coal Dust Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", + "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Stevens-JohnsonSyndrome" + "@id": "bts:No" }, { - "@id": "bts:StomaSiteInfection" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Environmental Tobacco Smoke Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RadonExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", + "rdfs:label": "RadonExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:StomachPain" + "@id": "bts:No" }, { - "@id": "bts:StomalUlcer" + "@id": "bts:Unknown" }, { - "@id": "bts:Stridor" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Radon Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RespirableCrystallineSilicaExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", + "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Stroke" + "@id": "bts:No" }, { - "@id": "bts:SuddenDeathNOS" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdverseEvent", + "@type": "rdfs:Class", + "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", + "rdfs:label": "AdverseEvent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdominalDistension" }, { - "@id": "bts:SuicidalIdeation" + "@id": "bts:AbdominalInfection" }, { - "@id": "bts:SuicideAttempt" + "@id": "bts:AbdominalPain" }, { - "@id": "bts:SuperficialSoftTissueFibrosis" + "@id": "bts:AbdominalSoftTissueNecrosis" }, { - "@id": "bts:SuperficialThrombophlebitis" + "@id": "bts:AbducensNerveDisorder" }, { - "@id": "bts:SuperiorVenaCavaSyndrome" + "@id": "bts:AccessoryNerveDisorder" }, { - "@id": "bts:SupraventricularTachycardia" + "@id": "bts:Acidosis" }, { - "@id": "bts:SurgicalandMedicalProceduresOther" + "@id": "bts:AcousticNerveDisorderNOS" }, { - "@id": "bts:Syncope" + "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" }, { - "@id": "bts:Telangiectasia" + "@id": "bts:AcuteCoronarySyndrome" }, { - "@id": "bts:TesticularDisorder" + "@id": "bts:AcuteKidneyInjury" }, { - "@id": "bts:TesticularHemorrhage" + "@id": "bts:AdrenalInsufficiency" }, { - "@id": "bts:TesticularPain" + "@id": "bts:AdultRespiratoryDistressSyndrome" }, { - "@id": "bts:ThromboembolicEvent" + "@id": "bts:Agitation" }, { - "@id": "bts:ThromboticThrombocytopenicPurpura" + "@id": "bts:Akathisia" }, { - "@id": "bts:Tinnitus" + "@id": "bts:AlanineAminotransferaseIncreased" }, { - "@id": "bts:ToothDevelopmentDisorder" + "@id": "bts:AlcoholIntolerance" }, { - "@id": "bts:ToothDiscoloration" + "@id": "bts:AlkalinePhosphataseIncreased" }, { - "@id": "bts:ToothInfection" + "@id": "bts:Alkalosis" }, { - "@id": "bts:Toothache" + "@id": "bts:AllergicReaction" }, { - "@id": "bts:ToxicEpidermalNecrolysis" + "@id": "bts:AllergicRhinitis" }, { - "@id": "bts:TrachealFistula" + "@id": "bts:Alopecia" }, { - "@id": "bts:TrachealHemorrhage" + "@id": "bts:Amnesia" }, { - "@id": "bts:TrachealMucositis" + "@id": "bts:AnalFistula" }, { - "@id": "bts:TrachealObstruction" + "@id": "bts:AnalHemorrhage" }, { - "@id": "bts:TrachealStenosis" + "@id": "bts:AnalMucositis" }, { - "@id": "bts:Tracheitis" + "@id": "bts:AnalNecrosis" }, { - "@id": "bts:TracheostomySiteBleeding" + "@id": "bts:AnalPain" }, { - "@id": "bts:TransientIschemicAttacks" + "@id": "bts:AnalStenosis" }, { - "@id": "bts:TreatmentRelatedSecondaryMalignancy" + "@id": "bts:AnalUlcer" }, { - "@id": "bts:Tremor" + "@id": "bts:Anaphylaxis" }, { - "@id": "bts:TricuspidValveDisease" + "@id": "bts:Anemia" }, { - "@id": "bts:TrigeminalNerveDisorder" + "@id": "bts:AnkleFracture" }, { - "@id": "bts:Trismus" + "@id": "bts:AnorectalInfection" }, { - "@id": "bts:TumorLysisSyndrome" + "@id": "bts:Anorexia" }, { - "@id": "bts:TumorPain" + "@id": "bts:Anorgasmia" }, { - "@id": "bts:Typhlitis" + "@id": "bts:Anxiety" }, { - "@id": "bts:UnequalLimbLength" + "@id": "bts:AorticInjury" }, { - "@id": "bts:UnintendedPregnancy" + "@id": "bts:AorticValveDisease" }, { - "@id": "bts:UpperGastrointestinalHemorrhage" + "@id": "bts:Aphonia" }, { - "@id": "bts:UpperRespiratoryInfection" + "@id": "bts:Apnea" }, { - "@id": "bts:UretericAnastomoticLeak" + "@id": "bts:Appendicitis" }, { - "@id": "bts:UrethralAnastomoticLeak" + "@id": "bts:AppendicitisPerforated" }, { - "@id": "bts:UrethralInfection" + "@id": "bts:Arachnoiditis" }, { - "@id": "bts:UrinaryFistula" + "@id": "bts:ArterialInjury" }, { - "@id": "bts:UrinaryFrequency" + "@id": "bts:ArteritisInfective" }, { - "@id": "bts:UrinaryIncontinence" + "@id": "bts:Arthralgia" }, { - "@id": "bts:UrinaryRetention" + "@id": "bts:Arthritis" }, { - "@id": "bts:UrinaryTractInfection" + "@id": "bts:Ascites" }, { - "@id": "bts:UrinaryTractObstruction" + "@id": "bts:AspartateAminotransferaseIncreased" }, { - "@id": "bts:UrinaryTractPain" + "@id": "bts:Aspiration" }, { - "@id": "bts:UrinaryUrgency" + "@id": "bts:Asystole" }, { - "@id": "bts:UrineDiscoloration" + "@id": "bts:Ataxia" }, { - "@id": "bts:UrineOutputDecreased" + "@id": "bts:Atelectasis" }, { - "@id": "bts:UrostomyLeak" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:UrostomyObstruction" + "@id": "bts:AtrialFlutter" }, { - "@id": "bts:UrostomySiteBleeding" + "@id": "bts:AtrioventricularBlockComplete" }, { - "@id": "bts:UrostomyStenosis" + "@id": "bts:AtrioventricularBlockFirstDegree" }, { - "@id": "bts:Urticaria" + "@id": "bts:AutoimmuneDisorder" }, { - "@id": "bts:UterineAnastomoticLeak" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:UterineFistula" + "@id": "bts:Azoospermia" }, { - "@id": "bts:UterineHemorrhage" + "@id": "bts:BackPain" }, { - "@id": "bts:UterineInfection" + "@id": "bts:BileDuctStenosis" }, { - "@id": "bts:UterineObstruction" + "@id": "bts:BiliaryAnastomoticLeak" }, { - "@id": "bts:UterinePain" + "@id": "bts:BiliaryFistula" }, { - "@id": "bts:UterinePerforation" + "@id": "bts:BiliaryTractInfection" }, { - "@id": "bts:Uveitis" + "@id": "bts:BladderAnastomoticLeak" }, { - "@id": "bts:VaginalAnastomoticLeak" + "@id": "bts:BladderInfection" }, { - "@id": "bts:VaginalDischarge" + "@id": "bts:BladderPerforation" }, { - "@id": "bts:VaginalDryness" + "@id": "bts:BladderSpasm" }, { - "@id": "bts:VaginalFistula" + "@id": "bts:Bloating" }, { - "@id": "bts:VaginalHemorrhage" + "@id": "bts:BloodandLymphaticSystemDisordersOther" }, { - "@id": "bts:VaginalInfection" + "@id": "bts:BloodAntidiureticHormoneAbnormal" }, { - "@id": "bts:VaginalInflammation" + "@id": "bts:BloodBilirubinIncreased" }, { - "@id": "bts:VaginalObstruction" + "@id": "bts:BloodCorticotrophinDecreased" }, { - "@id": "bts:VaginalPain" + "@id": "bts:BloodGonadotrophinAbnormal" }, { - "@id": "bts:VaginalPerforation" + "@id": "bts:BloodProlactinAbnormal" }, { - "@id": "bts:VaginalStricture" + "@id": "bts:BlurredVision" }, { - "@id": "bts:Vaginismus" + "@id": "bts:BodyOdor" }, { - "@id": "bts:VagusNerveDisorder" + "@id": "bts:BoneInfection" }, { - "@id": "bts:VasDeferensAnastomoticLeak" + "@id": "bts:BoneMarrowHypocellular" }, { - "@id": "bts:VascularAccessComplication" + "@id": "bts:BonePain" }, { - "@id": "bts:VascularDisordersOther" + "@id": "bts:BrachialPlexopathy" }, { - "@id": "bts:Vasculitis" + "@id": "bts:BreastAtrophy" }, { - "@id": "bts:VasovagalReaction" + "@id": "bts:BreastInfection" }, { - "@id": "bts:VenousInjury" + "@id": "bts:BreastPain" }, { - "@id": "bts:VentricularArrhythmia" + "@id": "bts:BronchialFistula" }, { - "@id": "bts:VentricularFibrillation" + "@id": "bts:BronchialInfection" }, { - "@id": "bts:VentricularTachycardia" + "@id": "bts:BronchialObstruction" }, { - "@id": "bts:Vertigo" + "@id": "bts:BronchialStricture" }, { - "@id": "bts:VestibularDisorder" + "@id": "bts:BronchopleuralFistula" }, { - "@id": "bts:Virilization" + "@id": "bts:BronchopulmonaryHemorrhage" }, { - "@id": "bts:VisceralArterialIschemia" + "@id": "bts:Bronchospasm" }, { - "@id": "bts:VitalCapacityAbnormal" + "@id": "bts:Bruising" }, { - "@id": "bts:VitreousHemorrhage" + "@id": "bts:BullousDermatitis" }, { - "@id": "bts:VoiceAlteration" + "@id": "bts:Burn" }, { - "@id": "bts:Vomiting" + "@id": "bts:ButtockPain" }, { - "@id": "bts:VulvalInfection" + "@id": "bts:CapillaryLeakSyndrome" }, { - "@id": "bts:WateringEyes" + "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" }, { - "@id": "bts:WeightGain" + "@id": "bts:CardiacArrest" }, { - "@id": "bts:WeightLoss" + "@id": "bts:CardiacDisordersOther" }, { - "@id": "bts:Wheezing" + "@id": "bts:CardiacTroponinIIncreased" }, { - "@id": "bts:WhiteBloodCellDecreased" + "@id": "bts:CardiacTroponinTIncreased" }, { - "@id": "bts:Wolff-Parkinson-WhiteSyndrome" + "@id": "bts:Cataract" }, { - "@id": "bts:WoundComplication" + "@id": "bts:CatheterRelatedInfection" }, { - "@id": "bts:WoundDehiscence" + "@id": "bts:CD4LymphocytesDecreased" }, { - "@id": "bts:WoundInfection" + "@id": "bts:CecalHemorrhage" }, { - "@id": "bts:WristFracture" - } - ], - "sms:displayName": "Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BarrettsEsophagusGobletCellsPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", - "rdfs:label": "BarrettsEsophagusGobletCellsPresent", - "rdfs:subClassOf": [ + "@id": "bts:CecalInfection" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CentralNervousSystemNecrosis" + }, { - "@id": "bts:Yes" + "@id": "bts:CerebrospinalFluidLeakage" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Barretts Esophagus Goblet Cells Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BMI", - "@type": "rdfs:Class", - "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", - "rdfs:label": "BMI", - "rdfs:subClassOf": [ + "@id": "bts:CervicitisInfection" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "BMI", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CauseofResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", - "rdfs:label": "CauseofResponse", - "rdfs:subClassOf": [ + "@id": "bts:Cheilitis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cause of Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Comorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", - "rdfs:label": "Comorbidity", - "rdfs:subClassOf": [ + "@id": "bts:ChestPainCardiac" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ChestWallPain" + }, { - "@id": "bts:AcuteRenalFailure" + "@id": "bts:Chills" }, { - "@id": "bts:Adenocarcinoma" + "@id": "bts:Cholecystitis" }, { - "@id": "bts:AdrenocorticalInsufficiency" + "@id": "bts:CholesterolHigh" }, { - "@id": "bts:AdenomatousPolyposisColi" + "@id": "bts:ChronicKidneyDisease" }, { - "@id": "bts:Allergies" + "@id": "bts:Chylothorax" }, { - "@id": "bts:Alpha-1Antitrypsin" + "@id": "bts:CognitiveDisturbance" }, { - "@id": "bts:Anemia" + "@id": "bts:Colitis" }, { - "@id": "bts:Anxiety" + "@id": "bts:ColonicFistula" }, { - "@id": "bts:Arrhythmia" + "@id": "bts:ColonicHemorrhage" }, { - "@id": "bts:Arthritis" + "@id": "bts:ColonicObstruction" }, { - "@id": "bts:Asthma" + "@id": "bts:ColonicPerforation" }, { - "@id": "bts:AtrialFibrillation" + "@id": "bts:ColonicStenosis" }, { - "@id": "bts:AvascularNecrosis" + "@id": "bts:ColonicUlcer" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:ConcentrationImpairment" }, { - "@id": "bts:BasalCellCarcinoma" + "@id": "bts:ConductionDisorder" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:Confusion" }, { - "@id": "bts:Behcet'sDisease" + "@id": "bts:Congenital" }, { - "@id": "bts:BiliaryDisorder" + "@id": "bts:FamilialandGeneticDisordersOther" }, { - "@id": "bts:BloodClots" + "@id": "bts:Conjunctivitis" }, { - "@id": "bts:BoneFracture(s)" + "@id": "bts:ConjunctivitisInfective" }, { - "@id": "bts:Bronchitis" + "@id": "bts:Constipation" }, { - "@id": "bts:CalciumChannelBlockers" + "@id": "bts:ConstrictivePericarditis" }, { - "@id": "bts:Cancer" + "@id": "bts:CornealInfection" }, { - "@id": "bts:Cataracts" + "@id": "bts:CornealUlcer" }, { - "@id": "bts:CeliacDisease" + "@id": "bts:Cough" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:CPKIncreased" }, { - "@id": "bts:UnknownEtiology" + "@id": "bts:CranialNerveInfection" }, { - "@id": "bts:CerebrovascularDisease" + "@id": "bts:CreatinineIncreased" }, { - "@id": "bts:Cholelithiasis" + "@id": "bts:Cushingoid" }, { - "@id": "bts:ChronicRenalFailure" + "@id": "bts:CystitisNoninfective" }, { - "@id": "bts:ColonPolyps" + "@id": "bts:CytokineReleaseSyndrome" }, { - "@id": "bts:CommonVariableImmunodeficiency" + "@id": "bts:DeathNeonatal" }, { - "@id": "bts:CongestiveHeartFailure(CHF)" + "@id": "bts:DeathNOS" }, { - "@id": "bts:ConnectiveTissueDisorder" + "@id": "bts:Dehydration" }, { - "@id": "bts:COPD" + "@id": "bts:DelayedOrgasm" }, { - "@id": "bts:CoronaryArteryDisease" + "@id": "bts:DelayedPuberty" }, { - "@id": "bts:Crohn'sDisease" + "@id": "bts:Delirium" }, { - "@id": "bts:CryptogenicOrganizingPneumonia" + "@id": "bts:Delusions" }, { - "@id": "bts:DeepVeinThrombosis/Thromboembolism" + "@id": "bts:DentalCaries" }, { - "@id": "bts:Denys-DrashSyndrome" + "@id": "bts:DepressedLevelofConsciousness" }, { "@id": "bts:Depression" }, { - "@id": "bts:Diabetes" + "@id": "bts:DermatitisRadiation" }, { - "@id": "bts:TypeII" + "@id": "bts:DeviceRelatedInfection" }, { - "@id": "bts:DiabeticNeuropathy" + "@id": "bts:Diarrhea" }, { - "@id": "bts:DietControlledDiabetes" + "@id": "bts:DisseminatedIntravascularCoagulation" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:Dizziness" }, { - "@id": "bts:DVT/PE" + "@id": "bts:DryEye" }, { - "@id": "bts:Dyslipidemia" + "@id": "bts:DryMouth" }, { - "@id": "bts:Epilepsy" + "@id": "bts:DrySkin" }, { - "@id": "bts:Eczema" + "@id": "bts:DuodenalFistula" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:DuodenalHemorrhage" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:DuodenalInfection" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:DuodenalObstruction" }, { - "@id": "bts:Fibrosis" + "@id": "bts:DuodenalPerforation" }, { - "@id": "bts:GastroesophagealRefluxDisease" + "@id": "bts:DuodenalStenosis" }, { - "@id": "bts:GERD" + "@id": "bts:DuodenalUlcer" }, { - "@id": "bts:Glaucoma" + "@id": "bts:Dysarthria" }, { - "@id": "bts:GlycogenStorageDisease" + "@id": "bts:Dysesthesia" }, { - "@id": "bts:Gout" + "@id": "bts:Dysgeusia" }, { - "@id": "bts:GonadalDysfunction" + "@id": "bts:Dysmenorrhea" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:Dyspareunia" }, { - "@id": "bts:H.pyloriInfection" + "@id": "bts:Dyspepsia" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:Dysphagia" }, { - "@id": "bts:Headache" + "@id": "bts:Dysphasia" }, { - "@id": "bts:HeartDisease" + "@id": "bts:Dyspnea" }, { - "@id": "bts:Hemihypertrophy" + "@id": "bts:EarandLabyrinthDisordersOther" }, { - "@id": "bts:HemorrhagicCystitis" + "@id": "bts:EarPain" }, { - "@id": "bts:Hepatitis" + "@id": "bts:EdemaCerebral" }, { - "@id": "bts:HepatitisAInfection" + "@id": "bts:EdemaFace" }, { - "@id": "bts:HepatitisBInfection" + "@id": "bts:EdemaLimbs" }, { - "@id": "bts:HepatitisCInfection" + "@id": "bts:EdemaTrunk" }, { - "@id": "bts:ChronicHepatitis" + "@id": "bts:EjaculationDisorder" }, { - "@id": "bts:HereditaryNon-polyposisColonCancer" + "@id": "bts:EjectionFractionDecreased" }, { - "@id": "bts:Herpes" + "@id": "bts:ElectrocardiogramQTCorrectedIntervalProlonged" }, { - "@id": "bts:HighGradeLiverDysplasticNodule" + "@id": "bts:EncephalitisInfection" }, { - "@id": "bts:HIV/AIDS" + "@id": "bts:EncephalomyelitisInfection" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:Encephalopathy" }, { - "@id": "bts:HUS/TTP" + "@id": "bts:EndocarditisInfective" }, { - "@id": "bts:Hypercholesterolemia" + "@id": "bts:EndocrineDisordersOther" }, { - "@id": "bts:Hypercalcemia" + "@id": "bts:Endophthalmitis" }, { - "@id": "bts:Hyperglycemia" + "@id": "bts:Enterocolitis" }, { - "@id": "bts:Hyperlipidemia" + "@id": "bts:EnterocolitisInfectious" }, { - "@id": "bts:Hypertension" + "@id": "bts:EnterovesicalFistula" }, { - "@id": "bts:Hypospadias" + "@id": "bts:Epistaxis" }, { - "@id": "bts:Hypothyroidism" + "@id": "bts:ErectileDysfunction" }, { - "@id": "bts:InflammatoryBowelDisease" + "@id": "bts:ErythemaMultiforme" }, { - "@id": "bts:InsulinControlledDiabetes" + "@id": "bts:Erythroderma" }, { - "@id": "bts:InterstitialPneumontisorARDS" + "@id": "bts:EsophagealAnastomoticLeak" }, { - "@id": "bts:IntraductalPapillaryMucinousNeoplasm" + "@id": "bts:EsophagealFistula" }, { - "@id": "bts:IronOverload" + "@id": "bts:EsophagealHemorrhage" }, { - "@id": "bts:IschemicHeartDisease" + "@id": "bts:EsophagealInfection" }, { - "@id": "bts:ITP" + "@id": "bts:EsophagealNecrosis" }, { - "@id": "bts:JointReplacement" + "@id": "bts:EsophagealObstruction" }, { - "@id": "bts:KidneyDisease" + "@id": "bts:EsophagealPain" }, { - "@id": "bts:LiverCirrhosis(LiverDisease)" + "@id": "bts:EsophagealPerforation" }, { - "@id": "bts:LiverToxicity(Non-Infectious)" + "@id": "bts:EsophagealStenosis" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:EsophagealUlcer" }, { - "@id": "bts:LowGradeLiverDysplasticNodule" + "@id": "bts:EsophagealVaricesHemorrhage" }, { - "@id": "bts:Lupus" + "@id": "bts:Esophagitis" }, { - "@id": "bts:LynchSyndrome" + "@id": "bts:Euphoria" }, { - "@id": "bts:MAI" + "@id": "bts:Exostosis" }, { - "@id": "bts:MyastheniaGravis" + "@id": "bts:ExternalEarInflammation" }, { - "@id": "bts:MyocardialInfarction" + "@id": "bts:ExternalEarPain" }, { - "@id": "bts:NeuroendocrineTumor" + "@id": "bts:ExtraocularMuscleParesis" }, { - "@id": "bts:NonalcoholicSteatohepatitis" + "@id": "bts:ExtrapyramidalDisorder" }, { - "@id": "bts:Obesity" + "@id": "bts:EyeDisordersOther" }, { - "@id": "bts:Organtransplant(site)" + "@id": "bts:EyeInfection" }, { - "@id": "bts:Osteoarthritis" + "@id": "bts:EyePain" }, { - "@id": "bts:OsteoporosisorOsteopenia" + "@id": "bts:EyelidFunctionDisorder" }, { - "@id": "bts:Other" + "@id": "bts:FacialMuscleWeakness" }, { - "@id": "bts:OtherCancerWithin5Years" + "@id": "bts:FacialNerveDisorder" }, { - "@id": "bts:OtherNonmalignantSystemicDisease" + "@id": "bts:FacialPain" }, { - "@id": "bts:OtherPulmonaryComplications" + "@id": "bts:Fall" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:FallopianTubeAnastomoticLeak" }, { - "@id": "bts:Pain(Various)" + "@id": "bts:FallopianTubeObstruction" }, { - "@id": "bts:PepticUlcer(Ulcer)" + "@id": "bts:FallopianTubePerforation" }, { - "@id": "bts:PeripheralNeuropathy" + "@id": "bts:FallopianTubeStenosis" }, { - "@id": "bts:PeripheralVascularDisease" + "@id": "bts:FatAtrophy" }, { - "@id": "bts:Peutz-JeghersDisease" + "@id": "bts:Fatigue" }, { - "@id": "bts:PregnancyinPatientorPartner" + "@id": "bts:FebrileNeutropenia" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:FecalIncontinence" }, { - "@id": "bts:Psoriasis" + "@id": "bts:FemaleGenitalTractFistula" }, { - "@id": "bts:PulmonaryFibrosis" + "@id": "bts:FeminizationAcquired" }, { - "@id": "bts:PulmonaryHemorrhage" + "@id": "bts:FetalDeath" }, { - "@id": "bts:RenalFailure(RequiringDialysis)" + "@id": "bts:FetalGrowthRetardation" }, { - "@id": "bts:RenalDialysis" + "@id": "bts:Fever" }, { - "@id": "bts:RenalInsufficiency" + "@id": "bts:FibrinogenDecreased" }, { - "@id": "bts:RheumatologicDisease" + "@id": "bts:FibrosisDeepConnectiveTissue" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:FlankPain" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:FlashingLights" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:Flatulence" }, { - "@id": "bts:Seizure" + "@id": "bts:Floaters" }, { - "@id": "bts:Sleepapnea" + "@id": "bts:FluLikeSymptoms" }, { - "@id": "bts:Smoking" + "@id": "bts:Flushing" }, { - "@id": "bts:Steatosis" + "@id": "bts:ForcedExpiratoryVolumeDecreased" }, { - "@id": "bts:Stroke" + "@id": "bts:Fracture" }, { - "@id": "bts:TransientIschemicAttack" + "@id": "bts:GaitDisturbance" }, { - "@id": "bts:Tuberculosis" + "@id": "bts:GallbladderFistula" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:GallbladderInfection" }, { - "@id": "bts:Tyrosinemia" + "@id": "bts:GallbladderNecrosis" }, { - "@id": "bts:UlcerativeColitis" + "@id": "bts:GallbladderObstruction" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:GallbladderPain" }, { - "@id": "bts:Unknown" + "@id": "bts:GallbladderPerforation" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ComorbidityMethodofDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", - "rdfs:label": "ComorbidityMethodofDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:GastricAnastomoticLeak" + }, { - "@id": "bts:Histology" + "@id": "bts:GastricFistula" }, { - "@id": "bts:Pathology" + "@id": "bts:GastricHemorrhage" }, { - "@id": "bts:Radiology" + "@id": "bts:GastricNecrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:GastricPerforation" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity Method of Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoAdverseEvent", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoAdverseEvent", - "rdfs:subClassOf": [ + "@id": "bts:GastricStenosis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoComorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoComorbidity", - "rdfs:subClassOf": [ + "@id": "bts:GastricUlcer" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DiabetesTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", - "rdfs:label": "DiabetesTreatmentType", - "rdfs:subClassOf": [ + "@id": "bts:Gastritis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:GastroesophagealRefluxDisease" + }, { - "@id": "bts:Alpha-GlucosidaseInhibitor" + "@id": "bts:GastrointestinalAnastomoticLeak" }, { - "@id": "bts:Biguanide" + "@id": "bts:GastrointestinalDisordersOther" }, { - "@id": "bts:Diet" + "@id": "bts:GastrointestinalFistula" }, { - "@id": "bts:InjectedInsulin" + "@id": "bts:GastrointestinalPain" }, { - "@id": "bts:Insulin" + "@id": "bts:GastrointestinalStomaNecrosis" }, { - "@id": "bts:OralHypoglycemic" + "@id": "bts:Gastroparesis" }, { - "@id": "bts:Sulfonylurea" + "@id": "bts:GeneralDisordersandAdministrationSiteConditionsOther" }, { - "@id": "bts:Thiazolidinedione" + "@id": "bts:GeneralizedMuscleWeakness" }, { - "@id": "bts:Other" + "@id": "bts:GenitalEdema" }, { - "@id": "bts:Unknown" + "@id": "bts:GGTIncreased" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Diabetes Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DiseaseResponse", - "@type": "rdfs:Class", - "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", - "rdfs:label": "DiseaseResponse", - "rdfs:subClassOf": [ + "@id": "bts:GingivalPain" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Glaucoma" + }, { - "@id": "bts:AJ-AdjuvantTherapy" + "@id": "bts:GlossopharyngealNerveDisorder" }, { - "@id": "bts:BED-BiochemicalEvidenceofDisease" + "@id": "bts:GlucoseIntolerance" }, { - "@id": "bts:CPD-ClinicalProgression" + "@id": "bts:GrowthAccelerated" }, { - "@id": "bts:CR-CompleteResponse" + "@id": "bts:GrowthHormoneAbnormal" }, { - "@id": "bts:CRU-CompleteResponseUnconfirmed" + "@id": "bts:GrowthSuppression" }, { - "@id": "bts:DU-DiseaseUnchanged" + "@id": "bts:GumInfection" }, { - "@id": "bts:IMR-Immunoresponse" + "@id": "bts:Gynecomastia" }, { - "@id": "bts:IPD-Immunoprogression" + "@id": "bts:Hallucinations" }, { - "@id": "bts:MR-Minimal/Marginalresponse" + "@id": "bts:HaptoglobinDecreased" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:HeadSoftTissueNecrosis" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:Headache" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:HearingImpaired" }, { - "@id": "bts:NR-NoResponse" + "@id": "bts:HeartFailure" }, { - "@id": "bts:PA-PalliativeTherapy" + "@id": "bts:Hematoma" }, { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:Hematosalpinx" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:Hematuria" }, { - "@id": "bts:PDM-PersistentDistantMetastasis" + "@id": "bts:HemoglobinIncreased" }, { - "@id": "bts:PLD-PersistentLocoregionalDisease" + "@id": "bts:Hemoglobinuria" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:Hemolysis" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:HemolyticUremicSyndrome" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:HemorrhoidalHemorrhage" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:Hemorrhoids" }, { - "@id": "bts:RP-Response" + "@id": "bts:HepaticFailure" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:HepaticHemorrhage" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:HepaticInfection" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:HepaticNecrosis" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:HepaticPain" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:HepatitisViral" }, { - "@id": "bts:TF-TumorFree" + "@id": "bts:HepatobiliaryDisordersOther" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:Hiccups" }, { - "@id": "bts:WT-WithTumor" + "@id": "bts:HipFracture" }, { - "@id": "bts:Unknown" + "@id": "bts:Hirsutism" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Disease Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DLCORefPredictivePercent", - "@type": "rdfs:Class", - "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", - "rdfs:label": "DLCORefPredictivePercent", - "rdfs:subClassOf": [ + "@id": "bts:Hoarseness" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DLCO Ref Predictive Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ECOGPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The ECOG functional performance status of the patient/participant.", - "rdfs:label": "ECOGPerformanceStatus", - "rdfs:subClassOf": [ + "@id": "bts:HotFlashes" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hydrocephalus" + }, { - "@id": "bts:\"0\"" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:\"1\"" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:\"2\"" + "@id": "bts:Hyperhidrosis" }, { - "@id": "bts:\"3\"" + "@id": "bts:Hyperkalemia" }, { - "@id": "bts:\"4\"" + "@id": "bts:Hypermagnesemia" }, { - "@id": "bts:\"5\"" + "@id": "bts:Hypernatremia" }, { - "@id": "bts:\"0.0\"" + "@id": "bts:Hyperparathyroidism" }, { - "@id": "bts:\"1.0\"" + "@id": "bts:Hypersomnia" }, { - "@id": "bts:\"2.0\"" + "@id": "bts:Hypertension" }, { - "@id": "bts:\"3.0\"" + "@id": "bts:Hyperthyroidism" }, { - "@id": "bts:\"4.0\"" + "@id": "bts:Hypertrichosis" }, { - "@id": "bts:\"5.0\"" + "@id": "bts:Hypertriglyceridemia" }, { - "@id": "bts:Unknown" + "@id": "bts:Hyperuricemia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "ECOG Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", - "rdfs:label": "FEV1FVCPostBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hypoalbuminemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 FVC Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", - "rdfs:label": "FEV1FVCPreBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hypocalcemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV 1 FVC Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", - "rdfs:label": "FEV1RefPostBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:HypoglossalNerveDisorder" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", - "rdfs:label": "FEV1RefPreBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:Hypoglycemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Height", - "@type": "rdfs:Class", - "rdfs:comment": "The height of the patient in centimeters.", - "rdfs:label": "Height", - "rdfs:subClassOf": [ + "@id": "bts:Hypohidrosis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Height", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "HepatitisSustainedVirologicalResponse", - "rdfs:subClassOf": [ + "@id": "bts:Hypokalemia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hypomagnesemia" + }, { - "@id": "bts:Yes" + "@id": "bts:Hyponatremia" }, { - "@id": "bts:No" + "@id": "bts:Hypoparathyroidism" }, { - "@id": "bts:Unknown" + "@id": "bts:Hypophosphatemia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hepatitis Sustained Virological Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HPVPositiveType", - "@type": "rdfs:Class", - "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", - "rdfs:label": "HPVPositiveType", - "rdfs:subClassOf": [ + "@id": "bts:Hypotension" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hypothermia" + }, { - "@id": "bts:\"16\"" + "@id": "bts:Hypothyroidism" }, { - "@id": "bts:\"18\"" + "@id": "bts:Hypoxia" }, { - "@id": "bts:\"26\"" + "@id": "bts:IlealFistula" }, { - "@id": "bts:\"31\"" + "@id": "bts:IlealHemorrhage" }, { - "@id": "bts:\"33\"" + "@id": "bts:IlealObstruction" }, { - "@id": "bts:\"35\"" + "@id": "bts:IlealPerforation" }, { - "@id": "bts:\"39\"" + "@id": "bts:IlealStenosis" }, { - "@id": "bts:\"45\"" + "@id": "bts:IlealUlcer" }, { - "@id": "bts:\"51\"" + "@id": "bts:Ileus" }, { - "@id": "bts:\"52\"" + "@id": "bts:ImmuneSystemDisordersOther" }, { - "@id": "bts:\"53\"" + "@id": "bts:InfectionsandInfestationsOther" }, { - "@id": "bts:\"56\"" + "@id": "bts:InfectiveMyositis" }, { - "@id": "bts:\"58\"" + "@id": "bts:InfusionRelatedReaction" }, { - "@id": "bts:\"59\"" + "@id": "bts:InfusionSiteExtravasation" }, { - "@id": "bts:\"63\"" + "@id": "bts:InjectionSiteReaction" }, { - "@id": "bts:\"66\"" + "@id": "bts:InjurytoCarotidArtery" }, { - "@id": "bts:\"68\"" + "@id": "bts:InjurytoInferiorVenaCava" }, { - "@id": "bts:\"70\"" + "@id": "bts:InjurytoJugularVein" }, { - "@id": "bts:\"73\"" + "@id": "bts:InjurytoSuperiorVenaCava" }, { - "@id": "bts:\"82\"" + "@id": "bts:Injury" }, { - "@id": "bts:Other" + "@id": "bts:PoisoningandProceduralComplicationsOther" }, { - "@id": "bts:Unknown" + "@id": "bts:INRIncreased" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "HPV Positive Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KarnofskyPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", - "rdfs:label": "KarnofskyPerformanceStatus", - "rdfs:subClassOf": [ + "@id": "bts:Insomnia" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IntestinalStomaLeak" + }, { - "@id": "bts:\"0\"" + "@id": "bts:IntestinalStomaObstruction" }, { - "@id": "bts:\"10\"" + "@id": "bts:IntestinalStomaSiteBleeding" }, { - "@id": "bts:\"20\"" + "@id": "bts:Intra-AbdominalHemorrhage" }, { - "@id": "bts:\"30\"" + "@id": "bts:IntracranialHemorrhage" }, { - "@id": "bts:\"40\"" + "@id": "bts:IntraoperativeArterialInjury" }, { - "@id": "bts:\"50\"" + "@id": "bts:IntraoperativeBreastInjury" }, { - "@id": "bts:\"60\"" + "@id": "bts:IntraoperativeCardiacInjury" }, { - "@id": "bts:\"70\"" + "@id": "bts:IntraoperativeEarInjury" }, { - "@id": "bts:\"80\"" + "@id": "bts:IntraoperativeEndocrineInjury" }, { - "@id": "bts:\"90\"" + "@id": "bts:IntraoperativeGastrointestinalInjury" }, { - "@id": "bts:\"100\"" + "@id": "bts:IntraoperativeHeadandNeckInjury" }, { - "@id": "bts:Unknown" + "@id": "bts:IntraoperativeHemorrhage" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Karnofsky Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MenopauseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's menopause status.", - "rdfs:label": "MenopauseStatus", - "rdfs:subClassOf": [ + "@id": "bts:IntraoperativeHepatobiliaryInjury" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IntraoperativeMusculoskeletalInjury" + }, { - "@id": "bts:Premenopausal" + "@id": "bts:IntraoperativeNeurologicalInjury" }, { - "@id": "bts:Perimenopausal" + "@id": "bts:IntraoperativeOcularInjury" }, { - "@id": "bts:Postmenopausal" + "@id": "bts:IntraoperativeRenalInjury" }, { - "@id": "bts:Unknown" + "@id": "bts:IntraoperativeReproductiveTractInjury" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Menopause Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreatitisOnsetYear", - "@type": "rdfs:Class", - "rdfs:comment": "Date of onset of pancreatitis.", - "rdfs:label": "PancreatitisOnsetYear", - "rdfs:subClassOf": [ + "@id": "bts:IntraoperativeRespiratoryInjury" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pancreatitis Onset Year", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:RefluxTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", - "rdfs:label": "RefluxTreatmentType", - "rdfs:subClassOf": [ + "@id": "bts:IntraoperativeSkinInjury" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IntraoperativeSplenicInjury" + }, { - "@id": "bts:Antacids" + "@id": "bts:IntraoperativeUrinaryInjury" }, { - "@id": "bts:H2Blockers" + "@id": "bts:IntraoperativeVenousInjury" }, { - "@id": "bts:MedicallyTreated" + "@id": "bts:InvestigationsOther" }, { - "@id": "bts:NoTreatment" + "@id": "bts:IronOverload" }, { - "@id": "bts:NotApplicable" + "@id": "bts:IrregularMenstruation" }, { - "@id": "bts:NotReported" + "@id": "bts:Irritability" }, { - "@id": "bts:ProtonPumpInhibitors" + "@id": "bts:IschemiaCerebrovascular" }, { - "@id": "bts:SurgicallyTreated" + "@id": "bts:IVthNerveDisorder" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Reflux Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RiskFactor", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactor", - "rdfs:subClassOf": [ + "@id": "bts:JejunalFistula" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:JejunalHemorrhage" + }, { - "@id": "bts:AlcoholConsumption" + "@id": "bts:JejunalObstruction" }, { - "@id": "bts:AlcoholicLiverDisease" + "@id": "bts:JejunalPerforation" }, { - "@id": "bts:AllergyAnimalNOS" + "@id": "bts:JejunalStenosis" }, { - "@id": "bts:AllergyAnt" + "@id": "bts:JejunalUlcer" }, { - "@id": "bts:AllergyBee" + "@id": "bts:JointEffusion" }, { - "@id": "bts:AllergyCat" + "@id": "bts:JointInfection" }, { - "@id": "bts:AllergyDairyorLactose" + "@id": "bts:JointRangeofMotionDecreased" }, { - "@id": "bts:AllergyDog" + "@id": "bts:JointRangeofMotionDecreasedCervicalSpine" }, { - "@id": "bts:AllergyEggs" + "@id": "bts:JointRangeofMotionDecreasedLumbarSpine" }, { - "@id": "bts:AllergyFoodNOS" + "@id": "bts:Keratitis" }, { - "@id": "bts:AllergyFruit" + "@id": "bts:KidneyAnastomoticLeak" }, { - "@id": "bts:AllergyMeat" + "@id": "bts:KidneyInfection" }, { - "@id": "bts:AllergyMoldorDust" + "@id": "bts:Kyphosis" }, { - "@id": "bts:AllergyNuts" + "@id": "bts:LactationDisorder" }, { - "@id": "bts:AllergyProcessedFoods" + "@id": "bts:LargeIntestinalAnastomoticLeak" }, { - "@id": "bts:AllergySeafood" + "@id": "bts:LaryngealEdema" }, { - "@id": "bts:AllergyWasp" + "@id": "bts:LaryngealFistula" }, { - "@id": "bts:Alpha-1AntitrypsinDeficiency" + "@id": "bts:LaryngealHemorrhage" }, { - "@id": "bts:AutoimmuneAtrophicChronicGastritis" + "@id": "bts:LaryngealInflammation" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:LaryngealMucositis" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:LaryngealObstruction" }, { - "@id": "bts:Behcet'sDisease" + "@id": "bts:LaryngealStenosis" }, { - "@id": "bts:Cancer" + "@id": "bts:Laryngitis" }, { - "@id": "bts:Cholelithiasis" + "@id": "bts:LaryngopharyngealDysesthesia" }, { - "@id": "bts:ChronicHepatitis" + "@id": "bts:Laryngospasm" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:LeftVentricularSystolicDysfunction" }, { - "@id": "bts:ColonPolyps" + "@id": "bts:Lethargy" }, { - "@id": "bts:Commonvariableimmunedeficiency(CVID)" + "@id": "bts:LeukemiaSecondarytoOncologyChemotherapy" }, { - "@id": "bts:Denys-DrashSyndrome" + "@id": "bts:Leukocytosis" }, { - "@id": "bts:DiabetesNOS" + "@id": "bts:Leukoencephalopathy" }, { - "@id": "bts:DiabetesTypeI" + "@id": "bts:LibidoDecreased" }, { - "@id": "bts:DiabetesTypeII" + "@id": "bts:LibidoIncreased" }, { - "@id": "bts:Diet" + "@id": "bts:LipInfection" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:LipPain" }, { - "@id": "bts:Endometriosis" + "@id": "bts:LipaseIncreased" }, { - "@id": "bts:Endosalpingiosis" + "@id": "bts:Lipohypertrophy" }, { - "@id": "bts:Eczema" + "@id": "bts:LocalizedEdema" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:Lordosis" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:LowerGastrointestinalHemorrhage" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:LungInfection" }, { - "@id": "bts:Fibrosis" + "@id": "bts:LymphGlandInfection" }, { - "@id": "bts:GastricPolyp(s)" + "@id": "bts:LymphLeakage" }, { - "@id": "bts:Gilbert'sSyndrome" + "@id": "bts:LymphNodePain" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:Lymphedema" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:Lymphocele" }, { - "@id": "bts:HayFever" + "@id": "bts:LymphocyteCountDecreased" }, { - "@id": "bts:Headache" + "@id": "bts:LymphocyteCountIncreased" }, { - "@id": "bts:HelicobacterPylori-AssociatedGastritis" + "@id": "bts:Malabsorption" }, { - "@id": "bts:HematologicDisorderNOS" + "@id": "bts:Malaise" }, { - "@id": "bts:Hemihypertrophy" + "@id": "bts:Mania" }, { - "@id": "bts:Hemochromatosis" + "@id": "bts:MediastinalHemorrhage" }, { - "@id": "bts:HepaticEncephalopathy" + "@id": "bts:MediastinalInfection" }, { - "@id": "bts:HepatitisBInfection" + "@id": "bts:MemoryImpairment" }, { - "@id": "bts:HepatitisCInfection" + "@id": "bts:Meningismus" }, { - "@id": "bts:HepatitisNOS" + "@id": "bts:Meningitis" }, { - "@id": "bts:HighGradeDysplasia" + "@id": "bts:Menopause" }, { - "@id": "bts:HIV" + "@id": "bts:Menorrhagia" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:MetabolismandNutritionDisordersOther" }, { - "@id": "bts:Hypospadias" + "@id": "bts:MiddleEarInflammation" }, { - "@id": "bts:IntestinalMetaplasia" + "@id": "bts:MitralValveDisease" }, { - "@id": "bts:IronOverload" + "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:MobitzTypeI" }, { - "@id": "bts:LowGradeDysplasia" + "@id": "bts:MovementsInvoluntary" }, { - "@id": "bts:LymphocyticThyroiditis" + "@id": "bts:MucosalInfection" }, { - "@id": "bts:LynchSyndrome" + "@id": "bts:MucositisOral" }, { - "@id": "bts:MyastheniaGravis" + "@id": "bts:Multi-OrganFailure" }, { - "@id": "bts:NonalcoholicFattyLiverDisease" + "@id": "bts:MuscleWeaknessLeft-Sided" }, { - "@id": "bts:NonalcoholicSteatohepatitis" + "@id": "bts:MuscleWeaknessLowerLimb" }, { - "@id": "bts:Obesity" + "@id": "bts:MuscleWeaknessRight-Sided" }, { - "@id": "bts:OralContraceptives" + "@id": "bts:MuscleWeaknessTrunk" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:MuscleWeaknessUpperLimb" }, { - "@id": "bts:ParasiticDiseaseofBiliaryTract" + "@id": "bts:MusculoskeletalandConnectiveTissueDisordersOther" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:MusculoskeletalDeformity" }, { - "@id": "bts:RecurrentPyogenicCholangitis" + "@id": "bts:Myalgia" }, { - "@id": "bts:RefluxDisease" + "@id": "bts:Myelitis" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:MyelodysplasticSyndrome" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:Myocarditis" }, { - "@id": "bts:Seizure" + "@id": "bts:Myositis" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:NailDiscoloration" }, { - "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + "@id": "bts:NailInfection" }, { - "@id": "bts:Steatosis" + "@id": "bts:NailLoss" }, { - "@id": "bts:Tattoo" + "@id": "bts:NailRidging" }, { - "@id": "bts:ThyroidNodularHyperplasia" + "@id": "bts:NasalCongestion" }, { - "@id": "bts:TobaccoNOS" + "@id": "bts:Nausea" }, { - "@id": "bts:TobaccoSmokeless" + "@id": "bts:NeckEdema" }, { - "@id": "bts:TobaccoSmoking" + "@id": "bts:NeckPain" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:NeckSoftTissueNecrosis" }, { - "@id": "bts:UndescendedTestis" + "@id": "bts:NeoplasmsBenign" }, { - "@id": "bts:VisionChanges" + "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:NervousSystemDisordersOther" }, { - "@id": "bts:Unknown" + "@id": "bts:Neuralgia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Risk Factor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RiskFactorTreatment", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactorTreatment", - "rdfs:subClassOf": [ + "@id": "bts:NeutrophilCountDecreased" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:NightBlindness" + }, { - "@id": "bts:Yes" + "@id": "bts:NippleDeformity" }, { - "@id": "bts:No" + "@id": "bts:Non-CardiacChestPain" }, { - "@id": "bts:Unknown" + "@id": "bts:Nystagmus" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Risk Factor Treatment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ViralHepatitisSerologies", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", - "rdfs:label": "ViralHepatitisSerologies", - "rdfs:subClassOf": [ + "@id": "bts:Obesity" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ObstructionGastric" + }, { - "@id": "bts:HBVCoreAntibody" + "@id": "bts:OculomotorNerveDisorder" }, { - "@id": "bts:HBVDNA" + "@id": "bts:OlfactoryNerveDisorder" }, { - "@id": "bts:HBVGenotype" + "@id": "bts:Oligospermia" }, { - "@id": "bts:HBVSurfaceAntibody" + "@id": "bts:OpticNerveDisorder" }, { - "@id": "bts:HCVGenotype" + "@id": "bts:OralCavityFistula" }, { - "@id": "bts:HepatitisBSurfaceAntigen" + "@id": "bts:OralDysesthesia" }, { - "@id": "bts:HepatitisCAntibody" + "@id": "bts:OralHemorrhage" }, { - "@id": "bts:HepatitisCVirusRNA" + "@id": "bts:OralPain" }, { - "@id": "bts:Unknown" + "@id": "bts:OsteonecrosisofJaw" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Viral Hepatitis Serologies", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Weight", - "@type": "rdfs:Class", - "rdfs:comment": "The weight of the patient measured in kilograms.", - "rdfs:label": "Weight", - "rdfs:subClassOf": [ + "@id": "bts:Osteoporosis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdverseEventGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "AdverseEventGrade", - "rdfs:subClassOf": [ + "@id": "bts:OtitisExterna" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:OtitisMedia" + }, { - "@id": "bts:Grade1" + "@id": "bts:OvarianHemorrhage" }, { - "@id": "bts:Grade2" + "@id": "bts:OvarianInfection" }, { - "@id": "bts:Grade3" + "@id": "bts:OvarianRupture" }, { - "@id": "bts:Grade4" + "@id": "bts:OvulationPain" }, { - "@id": "bts:Grade5" - } - ], - "sms:displayName": "Adverse Event Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AIDSRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", - "rdfs:label": "AIDSRiskFactors", - "rdfs:subClassOf": [ + "@id": "bts:Pain" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PaininExtremity" + }, { - "@id": "bts:Candidiasis" + "@id": "bts:PainofSkin" }, { - "@id": "bts:Coccidioidomycosis" + "@id": "bts:Palmar-PlantarErythrodysesthesiaSyndrome" }, { - "@id": "bts:Cryptococcosis" + "@id": "bts:Palpitations" }, { - "@id": "bts:Cytomegalovirus" + "@id": "bts:PancreasInfection" }, { - "@id": "bts:Encephalopathy" + "@id": "bts:PancreaticAnastomoticLeak" }, { - "@id": "bts:HerpesSimplexVirus" + "@id": "bts:PancreaticDuctStenosis" }, { - "@id": "bts:Histoplasmosis" + "@id": "bts:PancreaticEnzymesDecreased" }, { - "@id": "bts:Isosporiasis" + "@id": "bts:PancreaticFistula" }, { - "@id": "bts:MycobacteriumaviumComplex" + "@id": "bts:PancreaticHemorrhage" }, { - "@id": "bts:Mycobacteriumtuberculosis" + "@id": "bts:PancreaticNecrosis" }, { - "@id": "bts:Mycobacterium" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:NOS" + "@id": "bts:Papilledema" }, { - "@id": "bts:Nocardiosis" + "@id": "bts:PapulopustularRash" }, { - "@id": "bts:PneumocystisPneumonia" + "@id": "bts:Paresthesia" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Paronychia" }, { - "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" + "@id": "bts:ParoxysmalAtrialTachycardia" }, { - "@id": "bts:SalmonellaSepticemia" + "@id": "bts:PelvicFloorMuscleWeakness" }, { - "@id": "bts:Toxoplasmosis" + "@id": "bts:PelvicInfection" }, { - "@id": "bts:WastingSyndrome" - } - ], - "sms:displayName": "AIDS Risk Factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BodySurfaceArea", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", - "rdfs:label": "BodySurfaceArea", - "rdfs:subClassOf": [ + "@id": "bts:PelvicPain" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Body Surface Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CD4Count", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", - "rdfs:label": "CD4Count", - "rdfs:subClassOf": [ + "@id": "bts:PelvicSoftTissueNecrosis" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "CD4 Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CDCHIVRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", - "rdfs:label": "CDCHIVRiskFactors", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Hemophiliac" - }, - { - "@id": "bts:HeterosexualContact" - }, - { - "@id": "bts:HomosexualContact" - }, - { - "@id": "bts:IntravenousDrugUser" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:TransfusionRecipient" + "@id": "bts:PenileInfection" }, { - "@id": "bts:Unknown" + "@id": "bts:PenilePain" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "CDC HIV Risk Factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoImaging", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoImaging", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Imaging", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:EvidenceofRecurrenceType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", - "rdfs:label": "EvidenceofRecurrenceType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BiopsywithHistologicConfirmation" + "@id": "bts:PerforationBileDuct" }, { - "@id": "bts:ConvincingImageSource" + "@id": "bts:PericardialEffusion" }, { - "@id": "bts:PositiveBiomarkers" - } - ], - "sms:displayName": "Evidence of Recurrence Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HAARTTreatmentIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", - "rdfs:label": "HAARTTreatmentIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:PericardialTamponade" }, { - "@id": "bts:No" + "@id": "bts:Pericarditis" }, { - "@id": "bts:Unknown" + "@id": "bts:PerinealPain" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "HAART Treatment Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HIVViralLoad", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", - "rdfs:label": "HIVViralLoad", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HIV Viral Load", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HormonalContraceptiveUse", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", - "rdfs:label": "HormonalContraceptiveUse", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CurrentUser" + "@id": "bts:PeriodontalDisease" }, { - "@id": "bts:FormerUser" + "@id": "bts:PeriorbitalEdema" }, { - "@id": "bts:NeverUsed" + "@id": "bts:PeriorbitalInfection" }, { - "@id": "bts:Unknown" + "@id": "bts:PeripheralIschemia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hormonal Contraceptive Use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HysterectomyMarginsInvolved", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", - "rdfs:label": "HysterectomyMarginsInvolved", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bladder" + "@id": "bts:PeripheralMotorNeuropathy" }, { - "@id": "bts:MacroscopicParametrium" + "@id": "bts:PeripheralNerveInfection" }, { - "@id": "bts:MicroscopicParametrium" + "@id": "bts:PeripheralSensoryNeuropathy" }, { - "@id": "bts:None" + "@id": "bts:PeritonealInfection" }, { - "@id": "bts:Vagina" + "@id": "bts:PeritonealNecrosis" }, { - "@id": "bts:Unknown" + "@id": "bts:PersonalityChange" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hysterectomy Margins Involved", - "sms:required": "sms:false", - 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"@id": "bts:LowerlimbNOS" + "@id": "bts:UretericAnastomoticLeak" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:UrethralAnastomoticLeak" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:UrethralInfection" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:UrinaryFistula" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:UrinaryFrequency" }, { - "@id": "bts:LungNOS" + "@id": "bts:UrinaryIncontinence" }, { - "@id": "bts:LymphnodeNOS" + "@id": "bts:UrinaryRetention" }, { - "@id": "bts:Lymphnodesofaxillaorarm" + "@id": "bts:UrinaryTractInfection" }, { - "@id": "bts:Lymphnodesofheadfaceandneck" + "@id": "bts:UrinaryTractObstruction" }, { - "@id": "bts:Lymphnodesofinguinalregionorleg" + "@id": "bts:UrinaryTractPain" }, { - "@id": "bts:Lymphnodesofmultipleregions" + "@id": "bts:UrinaryUrgency" }, { - "@id": "bts:Mainbronchus" + "@id": "bts:UrineDiscoloration" }, { - "@id": "bts:MajorsalivaryglandNOS" + "@id": "bts:UrineOutputDecreased" }, { - "@id": "bts:MalegenitalorgansNOS" + "@id": "bts:UrostomyLeak" }, { - "@id": "bts:Mandible" + "@id": "bts:UrostomyObstruction" }, { - "@id": "bts:Maxillarysinus" + "@id": "bts:UrostomySiteBleeding" }, { - "@id": "bts:Meckeldiverticulum" + "@id": "bts:UrostomyStenosis" }, { - "@id": "bts:MediastinumNOS" + "@id": "bts:Urticaria" }, { - "@id": "bts:Medullaofadrenalgland" + "@id": "bts:UterineAnastomoticLeak" }, { - "@id": "bts:MeningesNOS" + "@id": "bts:UterineFistula" }, { - "@id": "bts:Middleear" + "@id": "bts:UterineHemorrhage" }, { - "@id": "bts:Middlelobelung" + "@id": "bts:UterineInfection" }, { - "@id": "bts:Middlethirdofesophagus" + "@id": "bts:UterineObstruction" }, { - "@id": "bts:MouthNOS" + "@id": "bts:UterinePain" }, { - "@id": "bts:MucosaoflipNOS" + "@id": "bts:UterinePerforation" }, { - "@id": "bts:Mucosaoflowerlip" + "@id": "bts:Uveitis" }, { - "@id": "bts:Mucosaofupperlip" + "@id": "bts:VaginalAnastomoticLeak" }, { - "@id": "bts:Myometrium" + "@id": "bts:VaginalDischarge" }, { - "@id": "bts:Nasalcavity" + "@id": "bts:VaginalDryness" }, { - "@id": "bts:NasopharynxNOS" + "@id": "bts:VaginalFistula" }, { - "@id": "bts:NervoussystemNOS" + "@id": "bts:VaginalHemorrhage" }, { - "@id": "bts:Nipple" + "@id": "bts:VaginalInfection" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:VaginalInflammation" }, { - "@id": "bts:Olfactorynerve" + "@id": "bts:VaginalObstruction" }, { - "@id": "bts:Opticnerve" + "@id": "bts:VaginalPain" }, { - "@id": "bts:OrbitNOS" + "@id": "bts:VaginalPerforation" }, { - "@id": "bts:OropharynxNOS" + "@id": "bts:VaginalStricture" }, { - "@id": "bts:Otherill-definedsites" + "@id": "bts:Vaginismus" }, { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + "@id": "bts:VagusNerveDisorder" }, { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + "@id": "bts:VasDeferensAnastomoticLeak" }, { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:VascularAccessComplication" }, { - "@id": "bts:Ovary" + "@id": "bts:VascularDisordersOther" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:Vasculitis" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:VasovagalReaction" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:VenousInjury" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id": "bts:VentricularArrhythmia" }, { - "@id": "bts:Overlappinglesionofbrain" + "@id": "bts:VentricularFibrillation" }, { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + "@id": "bts:VentricularTachycardia" }, { - "@id": "bts:Overlappinglesionofbreast" + "@id": "bts:Vertigo" }, { - "@id": "bts:Overlappinglesionofcervixuteri" + "@id": "bts:VestibularDisorder" }, { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:Virilization" }, { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + "@id": "bts:VisceralArterialIschemia" }, { - "@id": "bts:Overlappinglesionofcorpusuteri" + "@id": "bts:VitalCapacityAbnormal" }, { - "@id": "bts:Overlappinglesionofdigestivesystem" + "@id": "bts:VitreousHemorrhage" }, { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + "@id": "bts:VoiceAlteration" }, { - "@id": "bts:Overlappinglesionofesophagus" + "@id": "bts:Vomiting" }, { - "@id": "bts:Overlappinglesionofeyeandadnexa" + "@id": "bts:VulvalInfection" }, { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" + "@id": "bts:WateringEyes" }, { - "@id": "bts:Overlappinglesionoffloorofmouth" + "@id": "bts:WeightGain" }, { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + "@id": "bts:WeightLoss" }, { - "@id": "bts:Overlappinglesionofhypopharynx" + "@id": "bts:Wheezing" }, { - "@id": "bts:Overlappinglesionofill-definedsites" + "@id": "bts:WhiteBloodCellDecreased" }, { - "@id": "bts:Overlappinglesionoflarynx" + "@id": "bts:Wolff-Parkinson-WhiteSyndrome" }, { - "@id": "bts:Overlappinglesionoflip" + "@id": "bts:WoundComplication" }, { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + "@id": "bts:WoundDehiscence" }, { - "@id": "bts:Overlappinglesionoflung" + "@id": "bts:WoundInfection" }, { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" - }, + "@id": "bts:WristFracture" + } + ], + "sms:displayName": "Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", + "rdfs:label": "BarrettsEsophagusGobletCellsPresent", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofmalegenitalorgans" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionofnasopharynx" + "@id": "bts:Yes" }, { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" - }, + "@id": "bts:No" + } + ], + "sms:displayName": "Barretts Esophagus Goblet Cells Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BMI", + "@type": "rdfs:Class", + "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", + "rdfs:label": "BMI", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofpalate" + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "BMI", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CauseofResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", + "rdfs:label": "CauseofResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cause of Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Comorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", + "rdfs:label": "Comorbidity", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AcuteRenalFailure" }, { - "@id": "bts:Overlappinglesionofpancreas" + "@id": "bts:Adenocarcinoma" }, { - "@id": "bts:Overlappinglesionofpenis" + "@id": "bts:AdrenocorticalInsufficiency" }, { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + "@id": "bts:AdenomatousPolyposisColi" }, { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + "@id": "bts:Allergies" }, { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + "@id": "bts:Alpha-1Antitrypsin" }, { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + "@id": "bts:Anemia" }, { - "@id": "bts:Overlappinglesionofskin" + "@id": "bts:Anxiety" }, { - "@id": "bts:Overlappinglesionofsmallintestine" + "@id": "bts:Arrhythmia" }, { - "@id": "bts:Overlappinglesionofstomach" + "@id": "bts:Arthritis" }, { - "@id": "bts:Overlappinglesionoftongue" + "@id": "bts:Asthma" }, { - "@id": "bts:Overlappinglesionoftonsil" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:Overlappinglesionofurinaryorgans" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:Overlappinglesionofvulva" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:Overlappinglesionsoforopharynx" + "@id": "bts:BasalCellCarcinoma" }, { - "@id": "bts:PalateNOS" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:PancreasNOS" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:Pancreaticduct" + "@id": "bts:BiliaryDisorder" }, { - "@id": "bts:Parametrium" + "@id": "bts:BloodClots" }, { - "@id": "bts:Parathyroidgland" + "@id": "bts:BoneFracture(s)" }, { - "@id": "bts:Paraurethralgland" + "@id": "bts:Bronchitis" }, { - "@id": "bts:Parietallobe" + "@id": "bts:CalciumChannelBlockers" }, { - "@id": "bts:Parotidgland" + "@id": "bts:Cancer" }, { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + "@id": "bts:Cataracts" }, { - "@id": "bts:Pelviclymphnodes" + "@id": "bts:CeliacDisease" }, { - "@id": "bts:PelvisNOS" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:PenisNOS" + "@id": "bts:UnknownEtiology" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + "@id": "bts:CerebrovascularDisease" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + "@id": "bts:ChronicRenalFailure" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + "@id": "bts:CommonVariableImmunodeficiency" }, { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + "@id": "bts:CongestiveHeartFailure(CHF)" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + "@id": "bts:ConnectiveTissueDisorder" }, { - "@id": "bts:PeritoneumNOS" + "@id": "bts:COPD" }, { - "@id": "bts:PharynxNOS" + "@id": "bts:CoronaryArteryDisease" }, { - "@id": "bts:Pinealgland" + "@id": "bts:Crohn'sDisease" }, { - "@id": "bts:Pituitarygland" + "@id": "bts:CryptogenicOrganizingPneumonia" }, { - "@id": "bts:Placenta" + "@id": "bts:DeepVeinThrombosis/Thromboembolism" }, { - "@id": "bts:PleuraNOS" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:Postcricoidregion" + "@id": "bts:Depression" }, { - "@id": "bts:Posteriormediastinum" + "@id": "bts:Diabetes" }, { - "@id": "bts:Posteriorwallofbladder" + "@id": "bts:TypeII" }, { - "@id": "bts:Posteriorwallofhypopharynx" + "@id": "bts:DiabeticNeuropathy" }, { - "@id": "bts:Posteriorwallofnasopharynx" + "@id": "bts:DietControlledDiabetes" }, { - "@id": "bts:Posteriorwalloforopharynx" + "@id": "bts:Diverticulitis" }, { - "@id": "bts:Prepuce" + "@id": "bts:DVT/PE" }, { - "@id": "bts:Prostategland" + "@id": "bts:Dyslipidemia" }, { - "@id": "bts:Pylorus" + "@id": "bts:Epilepsy" }, { - "@id": "bts:Pyriformsinus" + "@id": "bts:Eczema" }, { - "@id": "bts:Rectosigmoidjunction" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:RectumNOS" + "@id": "bts:FamilialAdenomatousPolyposis" }, { - "@id": "bts:Renalpelvis" + "@id": "bts:FanconiAnemia" }, { - "@id": "bts:ReticuloendothelialsystemNOS" + "@id": "bts:Fibrosis" }, { - "@id": "bts:Retina" + "@id": "bts:GastroesophagealRefluxDisease" }, { - "@id": "bts:Retromolararea" + "@id": "bts:GERD" }, { - "@id": "bts:Retroperitoneum" + "@id": "bts:Glaucoma" }, { - "@id": "bts:Ribsternumclavicleandassociatedjoints" + "@id": "bts:GlycogenStorageDisease" }, { - "@id": "bts:Roundligament" + "@id": "bts:Gout" }, { - "@id": "bts:ScrotumNOS" + "@id": "bts:GonadalDysfunction" }, { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + "@id": "bts:GorlinSyndrome" }, { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:H.pyloriInfection" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:Hashimoto'sThyroiditis" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:Headache" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:HeartDisease" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:Hemihypertrophy" }, { - "@id": "bts:Skinofscalpandneck" + "@id": "bts:HemorrhagicCystitis" }, { - "@id": "bts:Skinoftrunk" + "@id": "bts:Hepatitis" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:HepatitisAInfection" }, { - "@id": "bts:SkinNOS" + "@id": "bts:HepatitisBInfection" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:HepatitisCInfection" }, { - "@id": "bts:SoftpalateNOS" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:Specifiedpartsofperitoneum" + "@id": "bts:HereditaryNon-polyposisColonCancer" }, { - "@id": "bts:Spermaticcord" + "@id": "bts:Herpes" }, { - "@id": "bts:Sphenoidsinus" + "@id": "bts:HighGradeLiverDysplasticNodule" }, { - "@id": "bts:Spinalcord" + "@id": "bts:HIV/AIDS" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:HumanPapillomavirusInfection" }, { - "@id": "bts:Spleen" + "@id": "bts:HUS/TTP" }, { - "@id": "bts:Splenicflexureofcolon" + "@id": "bts:Hypercholesterolemia" }, { - "@id": "bts:StomachNOS" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:Subglottis" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:Hyperlipidemia" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:Hypertension" }, { - "@id": "bts:Superiorwallofnasopharynx" + "@id": "bts:Hypospadias" }, { - "@id": "bts:Supraglottis" + "@id": "bts:Hypothyroidism" }, { - "@id": "bts:Tailofpancreas" + "@id": "bts:InflammatoryBowelDisease" }, { - "@id": "bts:Temporallobe" + "@id": "bts:InsulinControlledDiabetes" }, { - "@id": "bts:TestisNOS" + "@id": "bts:InterstitialPneumontisorARDS" }, { - "@id": "bts:Thoracicesophagus" + "@id": "bts:IntraductalPapillaryMucinousNeoplasm" }, { - "@id": "bts:ThoraxNOS" + "@id": "bts:IronOverload" }, { - "@id": "bts:Thymus" + "@id": "bts:IschemicHeartDisease" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:ITP" }, { - "@id": "bts:TongueNOS" + "@id": "bts:JointReplacement" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:KidneyDisease" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:LiverCirrhosis(LiverDisease)" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:LiverToxicity(Non-Infectious)" }, { - "@id": "bts:Trachea" + "@id": "bts:Li-FraumeniSyndrome" }, { - "@id": "bts:Transversecolon" + "@id": "bts:LowGradeLiverDysplasticNodule" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:Lupus" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:LynchSyndrome" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:MAI" }, { - "@id": "bts:Uppergum" + "@id": "bts:MyastheniaGravis" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:NeuroendocrineTumor" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:NonalcoholicSteatohepatitis" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:Obesity" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:Organtransplant(site)" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:Osteoarthritis" }, { - "@id": "bts:Urachus" + "@id": "bts:OsteoporosisorOsteopenia" }, { - "@id": "bts:Ureter" + "@id": "bts:Other" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:OtherCancerWithin5Years" }, { - "@id": "bts:Urethra" + "@id": "bts:OtherNonmalignantSystemicDisease" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:OtherPulmonaryComplications" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:UterusNOS" + "@id": "bts:Pain(Various)" }, { - "@id": "bts:Uvula" + "@id": "bts:PepticUlcer(Ulcer)" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:PeripheralNeuropathy" }, { - "@id": "bts:Vallecula" + "@id": "bts:PeripheralVascularDisease" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:Peutz-JeghersDisease" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:PregnancyinPatientorPartner" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:PrimarySclerosingCholangitis" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:Psoriasis" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:PulmonaryFibrosis" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:PulmonaryHemorrhage" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:RenalFailure(RequiringDialysis)" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:RenalDialysis" }, { - "@id": "bts:Clitoris" + "@id": "bts:RenalInsufficiency" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:RheumatologicDisease" + }, + { + "@id": "bts:RheumatoidArthritis" + }, + { + "@id": "bts:Rubinstein-TaybiSyndrome" + }, + { + "@id": "bts:Sarcoidosis" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:Sleepapnea" + }, + { + "@id": "bts:Smoking" + }, + { + "@id": "bts:Steatosis" + }, + { + "@id": "bts:Stroke" + }, + { + "@id": "bts:TransientIschemicAttack" + }, + { + "@id": "bts:Tuberculosis" + }, + { + "@id": "bts:TurcotSyndrome" + }, + { + "@id": "bts:Tyrosinemia" + }, + { + "@id": "bts:UlcerativeColitis" + }, + { + "@id": "bts:WagrSyndrome" }, { "@id": "bts:Unknown" @@ -22628,37 +22822,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Anatomic Site", + "sms:displayName": "Comorbidity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoTreatmentStart", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoTreatmentStart", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Treatment Start", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:InitialDiseaseStatus", + "@id": "bts:ComorbidityMethodofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", - "rdfs:label": "InitialDiseaseStatus", + "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", + "rdfs:label": "ComorbidityMethodofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22666,16 +22841,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:InitialDiagnosis" - }, - { - "@id": "bts:ProgressiveDisease" + "@id": "bts:Histology" }, { - "@id": "bts:RecurrentDisease" + "@id": "bts:Pathology" }, { - "@id": "bts:ResidualDisease" + "@id": "bts:Radiology" }, { "@id": "bts:Unknown" @@ -22684,52 +22856,56 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Initial Disease Status", + "sms:displayName": "Comorbidity Method of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RegimenorLineofTherapy", + "@id": "bts:DaystoAdverseEvent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the regimen or line of therapy.", - "rdfs:label": "RegimenorLineofTherapy", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoAdverseEvent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Regimen or Line of Therapy", + "sms:displayName": "Days to Adverse Event", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:TherapeuticAgents", + "@id": "bts:DaystoComorbidity", "@type": "rdfs:Class", - "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", - "rdfs:label": "TherapeuticAgents", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoComorbidity", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Therapeutic Agents", + "sms:displayName": "Days to Comorbidity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:TreatmentIntentType", + "@id": "bts:DiabetesTreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", - "rdfs:label": "TreatmentIntentType", + "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", + "rdfs:label": "DiabetesTreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22737,22 +22913,31 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Adjuvant" + "@id": "bts:Alpha-GlucosidaseInhibitor" }, { - "@id": "bts:CancerControl" + "@id": "bts:Biguanide" }, { - "@id": "bts:Cure" + "@id": "bts:Diet" }, { - "@id": "bts:Neoadjuvant" + "@id": "bts:InjectedInsulin" }, { - "@id": "bts:Palliative" + "@id": "bts:Insulin" }, { - "@id": "bts:Prevention" + "@id": "bts:OralHypoglycemic" + }, + { + "@id": "bts:Sulfonylurea" + }, + { + "@id": "bts:Thiazolidinedione" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -22761,18 +22946,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Intent Type", + "sms:displayName": "Diabetes Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChemoConcurrenttoRadiation", + "@id": "bts:DiseaseResponse", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", - "rdfs:label": "ChemoConcurrenttoRadiation", + "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", + "rdfs:label": "DiseaseResponse", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22780,10 +22965,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:No" + "@id": "bts:BED-BiochemicalEvidenceofDisease" + }, + { + "@id": "bts:CPD-ClinicalProgression" + }, + { + "@id": "bts:CR-CompleteResponse" + }, + { + "@id": "bts:CRU-CompleteResponseUnconfirmed" + }, + { + "@id": "bts:DU-DiseaseUnchanged" + }, + { + "@id": "bts:IMR-Immunoresponse" + }, + { + "@id": "bts:IPD-Immunoprogression" + }, + { + "@id": "bts:MR-Minimal/Marginalresponse" + }, + { + "@id": "bts:MX-MixedResponse" + }, + { + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + }, + { + "@id": "bts:NPB-NoPalliativeBenefit" + }, + { + "@id": "bts:NR-NoResponse" + }, + { + "@id": "bts:PA-PalliativeTherapy" + }, + { + "@id": "bts:PB-PalliativeBenefit" + }, + { + "@id": "bts:PD-ProgressiveDisease" + }, + { + "@id": "bts:PDM-PersistentDistantMetastasis" + }, + { + "@id": "bts:PLD-PersistentLocoregionalDisease" + }, + { + "@id": "bts:PPD-Pseudoprogression" + }, + { + "@id": "bts:PR-PartialResponse" + }, + { + "@id": "bts:PSR-Pseudoresponse" + }, + { + "@id": "bts:RD-ResponsiveDisease" + }, + { + "@id": "bts:RP-Response" + }, + { + "@id": "bts:RPD-RadiographicProgressiveDisease" + }, + { + "@id": "bts:SCR-StringentCompleteResponse" + }, + { + "@id": "bts:SD-StableDisease" + }, + { + "@id": "bts:SPD-SurgicalProgression" + }, + { + "@id": "bts:TE-TooEarly" + }, + { + "@id": "bts:TF-TumorFree" + }, + { + "@id": "bts:VGPR-VeryGoodPartialResponse" + }, + { + "@id": "bts:WT-WithTumor" }, { "@id": "bts:Unknown" @@ -22792,35 +23064,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Chemo Concurrent to Radiation", + "sms:displayName": "Disease Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NumberofCycles", + "@id": "bts:DLCORefPredictivePercent", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", - "rdfs:label": "NumberofCycles", + "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", + "rdfs:label": "DLCORefPredictivePercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Cycles", + "sms:displayName": "DLCO Ref Predictive Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReasonTreatmentEnded", + "@id": "bts:ECOGPerformanceStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", - "rdfs:label": "ReasonTreatmentEnded", + "rdfs:comment": "The ECOG functional performance status of the patient/participant.", + "rdfs:label": "ECOGPerformanceStatus", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22828,137 +23100,145 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AdverseTherapyEvent" + "@id": "bts:\"0\"" }, { - "@id": "bts:CourseofTherapyCompleted" + "@id": "bts:\"1\"" }, { - "@id": "bts:Death" + "@id": "bts:\"2\"" }, { - "@id": "bts:DiseaseProgression" + "@id": "bts:\"3\"" }, { - "@id": "bts:Other" + "@id": "bts:\"4\"" }, { - "@id": "bts:WithdrawalbySubject" + "@id": "bts:\"5\"" + }, + { + "@id": "bts:\"0.0\"" + }, + { + "@id": "bts:\"1.0\"" + }, + { + "@id": "bts:\"2.0\"" + }, + { + "@id": "bts:\"3.0\"" + }, + { + "@id": "bts:\"4.0\"" + }, + { + "@id": "bts:\"5.0\"" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Reason Treatment Ended", + "sms:displayName": "ECOG Performance Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentArm", + "@id": "bts:FEV1FVCPostBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", - "rdfs:label": "TreatmentArm", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", + "rdfs:label": "FEV1FVCPostBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:A081105" - }, - { - "@id": "bts:E4512" - }, - { - "@id": "bts:EA5142" - } - ], - "sms:displayName": "Treatment Arm", + "sms:displayName": "FEV1 FVC Post Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDose", + "@id": "bts:FEV1FVCPreBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", - "rdfs:label": "TreatmentDose", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", + "rdfs:label": "FEV1FVCPreBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Treatment Dose", + "sms:displayName": "FEV 1 FVC Pre Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDoseUnits", + "@id": "bts:FEV1RefPostBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", - "rdfs:label": "TreatmentDoseUnits", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", + "rdfs:label": "FEV1RefPostBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CGy" - }, - { - "@id": "bts:Gy" - } - ], - "sms:displayName": "Treatment Dose Units", + "sms:displayName": "FEV1 Ref Post Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentEffectIndicator", + "@id": "bts:FEV1RefPreBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", - "rdfs:label": "TreatmentEffectIndicator", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", + "rdfs:label": "FEV1RefPreBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:NotReported" - }, + "sms:displayName": "FEV1 Ref Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Height", + "@type": "rdfs:Class", + "rdfs:comment": "The height of the patient in centimeters.", + "rdfs:label": "Height", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:FollowUp" } ], - "sms:displayName": "Treatment Effect Indicator", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Height", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentFrequency", + "@id": "bts:HepatitisSustainedVirologicalResponse", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", - "rdfs:label": "TreatmentFrequency", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "HepatitisSustainedVirologicalResponse", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -22966,31 +23246,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EveryHour" - }, - { - "@id": "bts:FiveTimesDaily" - }, - { - "@id": "bts:FourTimesDaily" - }, - { - "@id": "bts:ThreeTimesDaily" - }, - { - "@id": "bts:TwiceDaily" - }, - { - "@id": "bts:Every24Hours" - }, - { - "@id": "bts:EveryOtherDay" - }, - { - "@id": "bts:TwiceWeekly" + "@id": "bts:Yes" }, { - "@id": "bts:OnceWeekly" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -22999,35 +23258,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Frequency", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:YearofDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", - "rdfs:label": "YearofDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Year of Diagnosis", + "sms:displayName": "Hepatitis Sustained Virological Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrecancerousConditionType", + "@id": "bts:HPVPositiveType", "@type": "rdfs:Class", - "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", - "rdfs:label": "PrecancerousConditionType", + "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", + "rdfs:label": "HPVPositiveType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23035,132 +23277,87 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DuctalCarcinomaInSitu" - }, - { - "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" - }, - { - "@id": "bts:AtypicalAdenomatousLungHyperplasia" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:PancreaticIntraepithelialNeoplasia" - }, - { - "@id": "bts:ProstaticIntraepithelialNeoplasia" - }, - { - "@id": "bts:Melanocytichyperplasia" - }, - { - "@id": "bts:Atypicalmelanocyticproliferation" - }, - { - "@id": "bts:Melanomainsitu" - }, - { - "@id": "bts:Superficialspreading" - }, - { - "@id": "bts:Lentigomalignatype" - }, - { - "@id": "bts:Acral-lentiginous" - }, - { - "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" - }, - { - "@id": "bts:Persistentmelanomainsitu" - }, - { - "@id": "bts:Melanomainsitunototherwiseclassified" - }, - { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:\"16\"" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:\"18\"" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:\"26\"" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:\"31\"" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:\"33\"" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:\"35\"" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:\"39\"" }, { - "@id": "bts:Invasivemelanoma" + "@id": "bts:\"45\"" }, { - "@id": "bts:NormalWDA" + "@id": "bts:\"51\"" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:\"52\"" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:\"53\"" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:\"56\"" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:\"58\"" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:\"59\"" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:\"63\"" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:\"66\"" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:\"68\"" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:\"70\"" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:\"73\"" }, { - "@id": "bts:Hamartoma" + "@id": "bts:\"82\"" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Other" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Precancerous Condition Type", + "sms:displayName": "HPV Positive Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofDiagnosis", + "@id": "bts:KarnofskyPerformanceStatus", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", - "rdfs:label": "MethodofDiagnosis", + "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", + "rdfs:label": "KarnofskyPerformanceStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23168,73 +23365,37 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" - }, - { - "@id": "bts:BloodDraw" - }, - { - "@id": "bts:BoneMarrowAspirate" - }, - { - "@id": "bts:CoreBiopsy" - }, - { - "@id": "bts:Cytology" - }, - { - "@id": "bts:Cystoscopy" - }, - { - "@id": "bts:Debulking" - }, - { - "@id": "bts:DiagnosticImaging" - }, - { - "@id": "bts:DilationandCurettageProcedure" - }, - { - "@id": "bts:Enucleation" - }, - { - "@id": "bts:ExcisionalBiopsy" - }, - { - "@id": "bts:FineNeedleAspiration" + "@id": "bts:\"0\"" }, { - "@id": "bts:IncisionalBiopsy" + "@id": "bts:\"10\"" }, { - "@id": "bts:Laparoscopy" + "@id": "bts:\"20\"" }, { - "@id": "bts:Laparotomy" + "@id": "bts:\"30\"" }, { - "@id": "bts:Other" + "@id": "bts:\"40\"" }, { - "@id": "bts:PapSmear" + "@id": "bts:\"50\"" }, { - "@id": "bts:PhysicalExam" + "@id": "bts:\"60\"" }, { - "@id": "bts:PathologicReview" + "@id": "bts:\"70\"" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:\"80\"" }, { - "@id": "bts:Thoracentesis" + "@id": "bts:\"90\"" }, { - "@id": "bts:UltrasoundGuidedBiopsy" + "@id": "bts:\"100\"" }, { "@id": "bts:Unknown" @@ -23243,18 +23404,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Method of Diagnosis", + "sms:displayName": "Karnofsky Performance Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorMalignancy", + "@id": "bts:MenopauseStatus", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", - "rdfs:label": "PriorMalignancy", + "rdfs:comment": "Text term used to describe the patient's menopause status.", + "rdfs:label": "MenopauseStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23262,67 +23423,52 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Premenopausal" }, { - "@id": "bts:No" + "@id": "bts:Perimenopausal" }, { - "@id": "bts:Unknown" + "@id": "bts:Postmenopausal" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:NotReported" } ], - "sms:displayName": "Prior Malignancy", + "sms:displayName": "Menopause Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorTreatment", + "@id": "bts:PancreatitisOnsetYear", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", - "rdfs:label": "PriorTreatment", + "rdfs:comment": "Date of onset of pancreatitis.", + "rdfs:label": "PancreatitisOnsetYear", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Treatment", + "sms:displayName": "Pancreatitis Onset Year", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:MetastasisatDiagnosis", + "@id": "bts:RefluxTreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", - "rdfs:label": "MetastasisatDiagnosis", + "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", + "rdfs:label": "RefluxTreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23330,36 +23476,45 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DistantMetastasis" + "@id": "bts:Antacids" }, { - "@id": "bts:MetastasisNOS" + "@id": "bts:H2Blockers" }, { - "@id": "bts:NoMetastasis" + "@id": "bts:MedicallyTreated" }, { - "@id": "bts:RegionalMetastasis" + "@id": "bts:NoTreatment" }, { - "@id": "bts:Unknown" + "@id": "bts:NotApplicable" }, { "@id": "bts:NotReported" + }, + { + "@id": "bts:ProtonPumpInhibitors" + }, + { + "@id": "bts:SurgicallyTreated" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Metastasis at Diagnosis", + "sms:displayName": "Reflux Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MetastasisatDiagnosisSite", + "@id": "bts:RiskFactor", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", - "rdfs:label": "MetastasisatDiagnosisSite", + "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactor", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23367,97 +23522,277 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Abdomen" + "@id": "bts:AlcoholConsumption" }, { - "@id": "bts:AdrenalGland" + "@id": "bts:AlcoholicLiverDisease" }, { - "@id": "bts:Ascites" + "@id": "bts:AllergyAnimalNOS" }, { - "@id": "bts:Bone" + "@id": "bts:AllergyAnt" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:AllergyBee" }, { - "@id": "bts:Brain" + "@id": "bts:AllergyCat" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:AllergyDairyorLactose" }, { - "@id": "bts:CentralNervousSystem" + "@id": "bts:AllergyDog" }, { - "@id": "bts:Colon" + "@id": "bts:AllergyEggs" }, { - "@id": "bts:DistantNodes" + "@id": "bts:AllergyFoodNOS" }, { - "@id": "bts:DistantOrgan" + "@id": "bts:AllergyFruit" }, { - "@id": "bts:Groin" + "@id": "bts:AllergyMeat" }, { - "@id": "bts:Kidney" + "@id": "bts:AllergyMoldorDust" }, { - "@id": "bts:Liver" + "@id": "bts:AllergyNuts" }, { - "@id": "bts:Lung" + "@id": "bts:AllergyProcessedFoods" }, { - "@id": "bts:LymphNode" + "@id": "bts:AllergySeafood" }, { - "@id": "bts:Axillary" + "@id": "bts:AllergyWasp" }, { - "@id": "bts:Inguinal" + "@id": "bts:Alpha-1AntitrypsinDeficiency" }, { - "@id": "bts:LymphNodeNOS" + "@id": "bts:AutoimmuneAtrophicChronicGastritis" }, { - "@id": "bts:Mediastinum" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:Omentum" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:Ovary" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:Pelvis" + "@id": "bts:Cancer" }, { - "@id": "bts:PeritonealCavity" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:Peritoneum" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:Pleura" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:Scalp" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:Skin" + "@id": "bts:Commonvariableimmunedeficiency(CVID)" }, { - "@id": "bts:SmallIntestine" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:SoftTissue" + "@id": "bts:DiabetesNOS" }, { - "@id": "bts:SpinalCord" + "@id": "bts:DiabetesTypeI" + }, + { + "@id": "bts:DiabetesTypeII" + }, + { + "@id": "bts:Diet" + }, + { + "@id": "bts:Diverticulitis" + }, + { + "@id": "bts:Endometriosis" + }, + { + "@id": "bts:Endosalpingiosis" + }, + { + "@id": "bts:Eczema" + }, + { + "@id": "bts:Epstein-BarrVirus" + }, + { + "@id": "bts:FamilialAdenomatousPolyposis" + }, + { + "@id": "bts:FanconiAnemia" + }, + { + "@id": "bts:Fibrosis" + }, + { + "@id": "bts:GastricPolyp(s)" + }, + { + "@id": "bts:Gilbert'sSyndrome" + }, + { + "@id": "bts:GorlinSyndrome" + }, + { + "@id": "bts:Hashimoto'sThyroiditis" + }, + { + "@id": "bts:HayFever" + }, + { + "@id": "bts:Headache" + }, + { + "@id": "bts:HelicobacterPylori-AssociatedGastritis" + }, + { + "@id": "bts:HematologicDisorderNOS" + }, + { + "@id": "bts:Hemihypertrophy" + }, + { + "@id": "bts:Hemochromatosis" + }, + { + "@id": "bts:HepaticEncephalopathy" + }, + { + "@id": "bts:HepatitisBInfection" + }, + { + "@id": "bts:HepatitisCInfection" + }, + { + "@id": "bts:HepatitisNOS" + }, + { + "@id": "bts:HighGradeDysplasia" + }, + { + "@id": "bts:HIV" + }, + { + "@id": "bts:HumanPapillomavirusInfection" + }, + { + "@id": "bts:Hypospadias" + }, + { + "@id": "bts:IntestinalMetaplasia" + }, + { + "@id": "bts:IronOverload" + }, + { + "@id": "bts:Li-FraumeniSyndrome" + }, + { + "@id": "bts:LowGradeDysplasia" + }, + { + "@id": "bts:LymphocyticThyroiditis" + }, + { + "@id": "bts:LynchSyndrome" + }, + { + "@id": "bts:MyastheniaGravis" + }, + { + "@id": "bts:NonalcoholicFattyLiverDisease" + }, + { + "@id": "bts:NonalcoholicSteatohepatitis" + }, + { + "@id": "bts:Obesity" + }, + { + "@id": "bts:OralContraceptives" + }, + { + "@id": "bts:Pancreatitis" + }, + { + "@id": "bts:ParasiticDiseaseofBiliaryTract" + }, + { + "@id": "bts:PrimarySclerosingCholangitis" + }, + { + "@id": "bts:RecurrentPyogenicCholangitis" + }, + { + "@id": "bts:RefluxDisease" + }, + { + "@id": "bts:RheumatoidArthritis" + }, + { + "@id": "bts:Rubinstein-TaybiSyndrome" + }, + { + "@id": "bts:Sarcoidosis" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + }, + { + "@id": "bts:Steatosis" + }, + { + "@id": "bts:Tattoo" + }, + { + "@id": "bts:ThyroidNodularHyperplasia" + }, + { + "@id": "bts:TobaccoNOS" + }, + { + "@id": "bts:TobaccoSmokeless" + }, + { + "@id": "bts:TobaccoSmoking" + }, + { + "@id": "bts:TurcotSyndrome" + }, + { + "@id": "bts:UndescendedTestis" + }, + { + "@id": "bts:VisionChanges" + }, + { + "@id": "bts:WagrSyndrome" }, { "@id": "bts:Unknown" @@ -23466,18 +23801,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Metastasis at Diagnosis Site", + "sms:displayName": "Risk Factor", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FirstSymptomPriortoDiagnosis", + "@id": "bts:RiskFactorTreatment", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", - "rdfs:label": "FirstSymptomPriortoDiagnosis", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactorTreatment", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23485,22 +23820,59 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AlteredMentalStatus" + "@id": "bts:Yes" }, { - "@id": "bts:Headaches" + "@id": "bts:No" }, { - "@id": "bts:MotororMovementChanges" + "@id": "bts:Unknown" }, { - "@id": "bts:Seizures" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Risk Factor Treatment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ViralHepatitisSerologies", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", + "rdfs:label": "ViralHepatitisSerologies", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:HBVCoreAntibody" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:HBVDNA" }, { - "@id": "bts:VisualChanges" + "@id": "bts:HBVGenotype" + }, + { + "@id": "bts:HBVSurfaceAntibody" + }, + { + "@id": "bts:HCVGenotype" + }, + { + "@id": "bts:HepatitisBSurfaceAntigen" + }, + { + "@id": "bts:HepatitisCAntibody" + }, + { + "@id": "bts:HepatitisCVirusRNA" }, { "@id": "bts:Unknown" @@ -23509,57 +23881,69 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "First Symptom Prior to Diagnosis", + "sms:displayName": "Viral Hepatitis Serologies", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoDiagnosis", + "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDiagnosis", + "rdfs:comment": "The weight of the patient measured in kilograms.", + "rdfs:label": "Weight", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Diagnosis", + "sms:displayName": "Weight", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:PercentTumorInvasion", + "@id": "bts:AdverseEventGrade", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "AdverseEventGrade", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Invasion", + "schema:rangeIncludes": [ + { + "@id": "bts:Grade1" + }, + { + "@id": "bts:Grade2" + }, + { + "@id": "bts:Grade3" + }, + { + "@id": "bts:Grade4" + }, + { + "@id": "bts:Grade5" + } + ], + "sms:displayName": "Adverse Event Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ResidualDisease", + "@id": "bts:AIDSRiskFactors", "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", + "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", + "rdfs:label": "AIDSRiskFactors", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" - }, - { - "@id": "bts:InitialDiseaseStatus" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23567,67 +23951,109 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:R0" + "@id": "bts:Candidiasis" }, { - "@id": "bts:R1" + "@id": "bts:Coccidioidomycosis" }, { - "@id": "bts:R2" + "@id": "bts:Cryptococcosis" }, { - "@id": "bts:RX" + "@id": "bts:Cytomegalovirus" }, { - "@id": "bts:Unknown" + "@id": "bts:Encephalopathy" }, { - "@id": "bts:NotReported" + "@id": "bts:HerpesSimplexVirus" + }, + { + "@id": "bts:Histoplasmosis" + }, + { + "@id": "bts:Isosporiasis" + }, + { + "@id": "bts:MycobacteriumaviumComplex" + }, + { + "@id": "bts:Mycobacteriumtuberculosis" + }, + { + "@id": "bts:Mycobacterium" + }, + { + "@id": "bts:NOS" + }, + { + "@id": "bts:Nocardiosis" + }, + { + "@id": "bts:PneumocystisPneumonia" + }, + { + "@id": "bts:Pneumonia" + }, + { + "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" + }, + { + "@id": "bts:SalmonellaSepticemia" + }, + { + "@id": "bts:Toxoplasmosis" + }, + { + "@id": "bts:WastingSyndrome" } ], - "sms:displayName": "Residual Disease", + "sms:displayName": "AIDS Risk Factors", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SynchronousMalignancy", + "@id": "bts:BodySurfaceArea", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", + "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", + "rdfs:label": "BodySurfaceArea", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Body Surface Area", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CD4Count", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", + "rdfs:label": "CD4Count", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:FollowUp" } ], - "sms:displayName": "Synchronous Malignancy", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CD4 Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorConfinedtoOrganofOrigin", + "@id": "bts:CDCHIVRiskFactors", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", + "rdfs:label": "CDCHIVRiskFactors", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23635,10 +24061,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Hemophiliac" }, { - "@id": "bts:No" + "@id": "bts:HeterosexualContact" + }, + { + "@id": "bts:HomosexualContact" + }, + { + "@id": "bts:IntravenousDrugUser" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:TransfusionRecipient" }, { "@id": "bts:Unknown" @@ -23647,83 +24085,113 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Tumor Confined to Organ of Origin", + "sms:displayName": "CDC HIV Risk Factors", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorFocality", + "@id": "bts:DaystoImaging", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", - "rdfs:label": "TumorFocality", + "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoImaging", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Days to Imaging", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:EvidenceofRecurrenceType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", + "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:subClassOf": [ { - "@id": "bts:Multifocal" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Unifocal" + "@id": "bts:BiopsywithHistologicConfirmation" }, { - "@id": "bts:Unknown" + "@id": "bts:ConvincingImageSource" }, { - "@id": "bts:NotReported" + "@id": "bts:PositiveBiomarkers" } ], - "sms:displayName": "Tumor Focality", + "sms:displayName": "Evidence of Recurrence Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GrossTumorWeight", + "@id": "bts:HAARTTreatmentIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", - "rdfs:label": "GrossTumorWeight", + "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", + "rdfs:label": "HAARTTreatmentIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gross Tumor Weight", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HAART Treatment Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreslowThickness", + "@id": "bts:HIVViralLoad", "@type": "rdfs:Class", - "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", - "rdfs:label": "BreslowThickness", + "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", + "rdfs:label": "HIVViralLoad", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breslow Thickness", + "sms:displayName": "HIV Viral Load", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionPresent", + "@id": "bts:HormonalContraceptiveUse", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", - "rdfs:label": "VascularInvasionPresent", + "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", + "rdfs:label": "HormonalContraceptiveUse", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23731,33 +24199,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-VascularInvasionPresent" + "@id": "bts:CurrentUser" }, { - "@id": "bts:No" + "@id": "bts:FormerUser" }, { - "@id": "bts:Unknown" + "@id": "bts:NeverUsed" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:NotReported" } ], - "sms:displayName": "Vascular Invasion Present", + "sms:displayName": "Hormonal Contraceptive Use", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionType", + "@id": "bts:HysterectomyMarginsInvolved", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", + "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", + "rdfs:label": "HysterectomyMarginsInvolved", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23765,19 +24233,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Extramural" + "@id": "bts:Bladder" }, { - "@id": "bts:Intramural" + "@id": "bts:MacroscopicParametrium" }, { - "@id": "bts:Macro" + "@id": "bts:MicroscopicParametrium" }, { - "@id": "bts:Micro" + "@id": "bts:None" }, { - "@id": "bts:NoVascularInvasion" + "@id": "bts:Vagina" }, { "@id": "bts:Unknown" @@ -23786,18 +24254,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Vascular Invasion Type", + "sms:displayName": "Hysterectomy Margins Involved", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AnaplasiaPresent", + "@id": "bts:HysterectomyType", "@type": "rdfs:Class", - "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", - "rdfs:label": "AnaplasiaPresent", + "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", + "rdfs:label": "HysterectomyType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23805,10 +24273,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AnaplasiaPresent" + "@id": "bts:HysterectomyNOS" }, { - "@id": "bts:No" + "@id": "bts:Notperformed" + }, + { + "@id": "bts:RadicalHysterectomy" + }, + { + "@id": "bts:SimpleHysterectomy" }, { "@id": "bts:Unknown" @@ -23817,18 +24291,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Anaplasia Present", + "sms:displayName": "Hysterectomy Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AnaplasiaPresentType", + "@id": "bts:ImagingResult", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", - "rdfs:label": "AnaplasiaPresentType", + "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", + "rdfs:label": "ImagingResult", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23836,22 +24310,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" - }, - { - "@id": "bts:Diffuse" - }, - { - "@id": "bts:Equivocal" + "@id": "bts:Positive" }, { - "@id": "bts:Focal" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Present" + "@id": "bts:Negative" }, { - "@id": "bts:Sclerosis" + "@id": "bts:NotPerformed" }, { "@id": "bts:Unknown" @@ -23860,18 +24328,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Anaplasia Present Type", + "sms:displayName": "Imaging Result", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Laterality", + "@id": "bts:ImagingType", "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", - "rdfs:label": "Laterality", + "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", + "rdfs:label": "ImagingType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23879,39 +24347,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Bilateral" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Midline" - }, - { - "@id": "bts:Right" + "@id": "bts:99mTcBoneScintigraphy" }, { - "@id": "bts:Unilateral" + "@id": "bts:CTScan" }, { - "@id": "bts:Unknown" + "@id": "bts:MRI" }, { - "@id": "bts:NotReported" + "@id": "bts:PET" } ], - "sms:displayName": "Laterality", + "sms:displayName": "Imaging Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PerineuralInvasionPresent", + "@id": "bts:ImmunosuppressiveTreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", + "rdfs:comment": "The text term used to describe the type of immunosuppresive treatment the patient received.", + "rdfs:label": "ImmunosuppressiveTreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23919,10 +24378,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Anti-TNFTherapy" }, { - "@id": "bts:No" + "@id": "bts:Azathioprine" + }, + { + "@id": "bts:Cyclophosphamide" + }, + { + "@id": "bts:Methotrexate" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -23931,18 +24402,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Perineural Invasion Present", + "sms:displayName": "Immunosuppressive Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphaticInvasionPresent", + "@id": "bts:NadirCD4Count", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", - "rdfs:label": "LymphaticInvasionPresent", + "rdfs:comment": "Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).", + "rdfs:label": "NadirCD4Count", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nadir CD4 Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnancyOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of pregnancy the patient had", + "rdfs:label": "PregnancyOutcome", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -23950,10 +24438,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:EctopicPregnancy" }, { - "@id": "bts:No" + "@id": "bts:InducedAbortion" + }, + { + "@id": "bts:LiveBirth" + }, + { + "@id": "bts:Miscarriage" + }, + { + "@id": "bts:Stillbirth" }, { "@id": "bts:Unknown" @@ -23962,52 +24459,52 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lymphatic Invasion Present", + "sms:displayName": "Pregnancy Outcome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesPositive", + "@id": "bts:RecistTargetedRegionsNumber", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", - "rdfs:label": "LymphNodesPositive", + "rdfs:comment": "Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria", + "rdfs:label": "RecistTargetedRegionsNumber", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Positive", + "sms:displayName": "Recist Targeted Regions Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesTested", + "@id": "bts:RecistTargetedRegionsSum", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", - "rdfs:label": "LymphNodesTested", + "rdfs:comment": "Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.", + "rdfs:label": "RecistTargetedRegionsSum", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Tested", + "sms:displayName": "Recist Targeted Regions Sum", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeritonealFluidCytologicalStatus", + "@id": "bts:ScanTracerUsed", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", + "rdfs:comment": "The text term used to describe the type of tracer used during the imaging or scan of the patient.", + "rdfs:label": "ScanTracerUsed", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -24015,36 +24512,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Atypical" - }, - { - "@id": "bts:Malignant" + "@id": "bts:Acetate" }, { - "@id": "bts:Non-Malignant" + "@id": "bts:Axumin" }, { - "@id": "bts:Unsatisfactory" + "@id": "bts:Choline" }, { - "@id": "bts:Unknown" + "@id": "bts:PSMA" }, { - "@id": "bts:NotReported" + "@id": "bts:SodiumFluoride" } ], - "sms:displayName": "Peritoneal Fluid Cytological Status", + "sms:displayName": "Scan Tracer Used", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClassificationofTumor", + "@id": "bts:TreatmentorTherapy", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", - "rdfs:label": "ClassificationofTumor", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.", + "rdfs:label": "TreatmentorTherapy", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -24052,39 +24546,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Primary" - }, - { - "@id": "bts:Metastasis" - }, - { - "@id": "bts:Recurrence" + "@id": "bts:Yes" }, { - "@id": "bts:Other" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" } ], - "sms:displayName": "Classification of Tumor", + "sms:displayName": "Treatment or Therapy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BestOverallResponse", + "@id": "bts:TreatmentEffect", "@type": "rdfs:Class", - "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", - "rdfs:label": "BestOverallResponse", + "rdfs:comment": "The text term used to describe the pathologic effect a treatment(s) had on the tumor.", + "rdfs:label": "TreatmentEffect", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -24092,113 +24577,110 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AJ-AdjuvantTherapy" - }, - { - "@id": "bts:CPD-ClinicalProgression" - }, - { - "@id": "bts:CR-CompleteResponse" - }, - { - "@id": "bts:CRU-CompleteResponseUnconfirmed" - }, - { - "@id": "bts:DU-DiseaseUnchanged" - }, - { - "@id": "bts:IMR-Immunoresponse" - }, - { - "@id": "bts:IPD-Immunoprogression" - }, - { - "@id": "bts:MR-Minimal/MarginalResponse" + "@id": "bts:CompleteNecrosis(NoViableTumor)" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:IncompleteNecrosis(ViableTumorPresent)" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:NoNecrosis" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:Unknown" }, { - "@id": "bts:NR-NoResponse" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Effect", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the patient's final outcome after the treatment was administered.", + "rdfs:label": "TreatmentOutcome", + "rdfs:subClassOf": [ { - "@id": "bts:PA-PalliativeTherapy" - }, + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:CompleteResponse" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:MixedResponse" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:NoMeasurableDisease" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:NoResponse" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:PartialResponse" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:PersistentDisease" }, { - "@id": "bts:RP-Response" + "@id": "bts:ProgressiveDisease" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:StableDisease" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:TreatmentOngoing" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:TreatmentStoppedDuetoToxicity" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:VeryGoodPartialResponse" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:Unknown" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:NotReported" } ], - "sms:displayName": "Best Overall Response", + "sms:displayName": "Treatment Outcome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitoticCount", + "@id": "bts:DaystoTreatmentEnd", "@type": "rdfs:Class", - "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", + "rdfs:comment": "Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentEnd", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mitotic Count", + "sms:displayName": "Days to Treatment End", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:AJCCClinicalM", + "@id": "bts:TreatmentAnatomicSite", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalM", + "rdfs:comment": "The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment", + "rdfs:label": "TreatmentAnatomicSite", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -24206,1389 +24688,994 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:M0" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:M1" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:M1a" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:M1b" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:M1c" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:MX" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:Analcanal" }, { - "@id": "bts:Unknown" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical M", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalN", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalN", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:N0" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:N0(i+)" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:N0(i-)" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:N0(mol+)" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:N1" + "@id": "bts:AnusNOS" }, { - "@id": "bts:N1a" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:N1b" + "@id": "bts:Appendix" }, { - "@id": "bts:N1bI" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:N1bII" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:N1bIII" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:N1bIV" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:N1c" + "@id": "bts:Bladderneck" }, { - "@id": "bts:N1mi" + "@id": "bts:BladderNOS" }, { - "@id": "bts:N2" + "@id": "bts:Blood" }, { - "@id": "bts:N2a" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:N2b" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:N2c" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:N3" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:N3a" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:N3b" + "@id": "bts:BoneNOS" }, { - "@id": "bts:N3c" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:N4" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:NX" + "@id": "bts:Brainstem" }, { - "@id": "bts:Unknown" + "@id": "bts:BrainNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical N", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalStage", - "@type": "rdfs:Class", - "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", - "rdfs:label": "AJCCClinicalStage", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Branchialcleft" + }, { - "@id": "bts:Stage0" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Stage0a" + "@id": "bts:Broadligament" }, { - "@id": "bts:Stage0is" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:StageI" + "@id": "bts:Carotidbody" }, { - "@id": "bts:StageIA" + "@id": "bts:Caudaequina" }, { - "@id": "bts:StageIA1" + "@id": "bts:Cecum" }, { - "@id": "bts:StageIA2" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:StageIB" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:StageIB1" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:StageIB2" + "@id": "bts:Cerebrum" }, { - "@id": "bts:StageIC" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:StageII" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:StageIIA" + "@id": "bts:Choroid" }, { - "@id": "bts:StageIIA1" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:StageIIA2" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:StageIIB" + "@id": "bts:ColonNOS" }, { - "@id": "bts:StageIIC" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:StageIIC1" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:StageIII" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:StageIIIA" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:StageIIIB" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:StageIIIC" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:StageIS" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:StageIV" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:StageIVA" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:StageIVB" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:StageIVC" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:StageTis" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:StageX" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Unknown" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalT", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalT", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:T0" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:T1" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:T1a" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:T1a1" + "@id": "bts:Duodenum" }, { - "@id": "bts:T1a2" + "@id": "bts:Endocervix" }, { - "@id": "bts:T1b" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:T1b1" + "@id": "bts:Endometrium" }, { - "@id": "bts:T1b2" + "@id": "bts:Epididymis" }, { - "@id": "bts:T1c" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:T1mi" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:T2" + "@id": "bts:Exocervix" }, { - "@id": "bts:T2a" + "@id": "bts:Externalear" }, { - "@id": "bts:T2a1" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:T2a2" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:T2b" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:T2c" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:T2d" + "@id": "bts:EyeNOS" }, { - "@id": "bts:T3" + "@id": "bts:Eyelid" }, { - "@id": "bts:T3a" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:T3b" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:T3c" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:T3d" + "@id": "bts:Frontallobe" }, { - "@id": "bts:T4" + "@id": "bts:Frontalsinus" }, { - "@id": "bts:T4a" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:T4b" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:T4c" + "@id": "bts:Gallbladder" }, { - "@id": "bts:T4d" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:T4e" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:TX" + "@id": "bts:Glanspenis" }, { - "@id": "bts:Ta" + "@id": "bts:Glottis" }, { - "@id": "bts:Tis" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:GumNOS" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:Hardpalate" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:Unknown" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical T", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicM", - "@type": "rdfs:Class", - "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicM", - "rdfs:subClassOf": [ + "@id": "bts:Heart" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HematopoieticsystemNOS" + }, { - "@id": "bts:M0" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:M1" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:M1a" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:M1b" + "@id": "bts:Ileum" }, { - "@id": "bts:M1c" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:MX" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:Unknown" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Pathologic M", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicN", - "@type": "rdfs:Class", - "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", - "rdfs:label": "AJCCPathologicN", - "rdfs:subClassOf": [ + "@id": "bts:Intrathoraciclymphnodes" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IsletsofLangerhans" + }, { - "@id": "bts:N0" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:N0(i+)" + "@id": "bts:Jejunum" }, { - "@id": "bts:N0(i-)" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:N0(mol+)" + "@id": "bts:Labiummajus" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:Labiumminus" }, { - "@id": "bts:N1" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:N1a" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:N1b" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:N1bI" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:N1bII" + "@id": "bts:Lateralwallofbladder" }, { - "@id": "bts:N1bIII" + "@id": "bts:Lateralwallofnasopharynx" }, { - "@id": "bts:N1bIV" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:N1c" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:N1mi" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:N2" + "@id": "bts:LipNOS" }, { - "@id": "bts:N2a" + "@id": "bts:Liver" }, { - "@id": "bts:N2b" + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:N2c" + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" }, { - "@id": "bts:N3" + "@id": "bts:Lowergum" }, { - "@id": "bts:N3a" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:N3b" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:N3c" + "@id": "bts:Lowerthirdofesophagus" }, { - "@id": "bts:N4" + "@id": "bts:Lower-innerquadrantofbreast" }, { - "@id": "bts:NX" + "@id": "bts:Lower-outerquadrantofbreast" }, { - "@id": "bts:Unknown" + "@id": "bts:LungNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Pathologic N", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicStage", - "@type": "rdfs:Class", - "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", - "rdfs:label": "AJCCPathologicStage", - "rdfs:subClassOf": [ + "@id": "bts:LymphnodeNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lymphnodesofaxillaorarm" + }, { - "@id": "bts:Stage0" + "@id": "bts:Lymphnodesofheadfaceandneck" }, { - "@id": "bts:Stage0a" + "@id": "bts:Lymphnodesofinguinalregionorleg" }, { - "@id": "bts:Stage0is" + "@id": "bts:Lymphnodesofmultipleregions" }, { - "@id": "bts:StageI" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:StageIA" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:StageIA1" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:StageIA2" + "@id": "bts:Mandible" }, { - "@id": "bts:StageIB" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:StageIB1" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:StageIB2" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:StageIC" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:StageII" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:StageIIA" + "@id": "bts:Middleear" }, { - "@id": "bts:StageIIA1" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:StageIIA2" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:StageIIB" + "@id": "bts:MouthNOS" }, { - "@id": "bts:StageIIC" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:StageIIC1" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:StageIII" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:StageIIIA" + "@id": "bts:Myometrium" }, { - "@id": "bts:StageIIIB" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:StageIIIC" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:Nipple" }, { - "@id": "bts:StageIS" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:StageIV" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:StageIVA" + "@id": "bts:Opticnerve" }, { - "@id": "bts:StageIVB" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:StageIVC" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:StageTis" + "@id": "bts:Otherill-definedsites" }, { - "@id": "bts:StageX" + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id": "bts:Unknown" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Pathologic Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicT", - "@type": "rdfs:Class", - "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicT", - "rdfs:subClassOf": [ + "@id": "bts:Otherspecifiedpartsofpancreas" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ovary" + }, { - "@id": "bts:T0" + "@id": "bts:Overlappinglesionofaccessorysinuses" }, { - "@id": "bts:T1" + "@id": "bts:Overlappinglesionofbladder" }, { - "@id": "bts:T1a" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" }, { - "@id": "bts:T1a1" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id": "bts:T1a2" + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:T1b" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:T1b1" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:T1b2" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:T1c" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:T1mi" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:T2" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:T2a" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:T2a1" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:T2a2" + "@id": "bts:Overlappinglesionofesophagus" }, { - "@id": "bts:T2b" + "@id": "bts:Overlappinglesionofeyeandadnexa" }, { - "@id": "bts:T2c" + "@id": "bts:Overlappinglesionoffemalegenitalorgans" }, { - "@id": "bts:T2d" + "@id": "bts:Overlappinglesionoffloorofmouth" }, { - "@id": "bts:T3" + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" }, { - "@id": "bts:T3a" + "@id": "bts:Overlappinglesionofhypopharynx" }, { - "@id": "bts:T3b" + "@id": "bts:Overlappinglesionofill-definedsites" }, { - "@id": "bts:T3c" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:T3d" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:T4" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:T4a" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:T4b" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:T4c" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:T4d" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:T4e" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:TX" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:Ta" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:Tis" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:Unknown" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Pathologic T", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCStagingSystemEdition", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", - 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Risk level is used to assign treatment intensity.", - "rdfs:label": "CogNeuroblastomaRiskGroup", - "rdfs:subClassOf": [ + "@id": "bts:Parametrium" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Parathyroidgland" + }, { - "@id": "bts:HighRisk" + "@id": "bts:Paraurethralgland" }, { - "@id": "bts:IntermediateRisk" + "@id": "bts:Parietallobe" }, { - "@id": "bts:LowRisk" + "@id": "bts:Parotidgland" }, { - "@id": "bts:Unknown" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Cog Neuroblastoma Risk Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CogRhabdomyosarcomaRiskGroup", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).", - "rdfs:label": "CogRhabdomyosarcomaRiskGroup", - "rdfs:subClassOf": [ + "@id": "bts:Pelviclymphnodes" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PelvisNOS" + }, { - "@id": "bts:HighRisk" + "@id": "bts:PenisNOS" }, { - "@id": "bts:IntermediateRisk" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" }, { - "@id": "bts:LowRisk" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" }, { - "@id": "bts:Unknown" + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Cog Rhabdomyosarcoma Risk Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GleasonGradeGroup", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. 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"rdfs:subClassOf": [ + "@id": "bts:TongueNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:TonsilNOS" + }, { - "@id": "bts:1" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:2" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:3" + "@id": "bts:Trachea" }, { - "@id": "bts:4" + "@id": "bts:Transversecolon" }, { - "@id": "bts:Unknown" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "IRS Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ISSStage", - "@type": "rdfs:Class", - "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", - "rdfs:label": "ISSStage", - "rdfs:subClassOf": [ + "@id": "bts:Undescendedtestis" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Unknownprimarysite" + }, { - "@id": "bts:I" + "@id": "bts:Uppergum" }, { - "@id": "bts:II" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:III" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:NotReported" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "ISS Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphNodeInvolvedSite", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", - "rdfs:label": "LymphNodeInvolvedSite", - "rdfs:subClassOf": [ + "@id": "bts:Upperthirdofesophagus" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Upper-innerquadrantofbreast" + }, { - "@id": "bts:Axillary" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:Cervical" + "@id": "bts:Urachus" }, { - "@id": "bts:Epitrochlear" + "@id": "bts:Ureter" }, { - "@id": "bts:Femoral" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:Hilar" + "@id": "bts:Urethra" }, { - "@id": "bts:Iliac-common" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:Iliac-external" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:Iliac" + "@id": "bts:UterusNOS" }, { - "@id": "bts:NOS" + "@id": "bts:Uvula" }, { - "@id": "bts:Inguinal" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:Mediastinal" + "@id": "bts:Vallecula" }, { - "@id": "bts:Mesenteric" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:None" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:Occipital" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:Paraaortic" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:Parotid" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:Popliteal" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:Retroperitoneal" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:Splenic" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:Submandibular" + "@id": "bts:Clitoris" }, { - "@id": "bts:Supraclavicular" + "@id": "bts:Overlappinglesionofbiliarytract" }, { "@id": "bts:Unknown" @@ -25597,35 +25684,37 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lymph Node Involved Site", + "sms:displayName": "Treatment Anatomic Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MarginDistance", + "@id": "bts:DaystoTreatmentStart", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", - "rdfs:label": "MarginDistance", + "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentStart", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Margin Distance", + "sms:displayName": "Days to Treatment Start", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:MarginsInvolvedSite", + "@id": "bts:InitialDiseaseStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", - "rdfs:label": "MarginsInvolvedSite", + "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", + "rdfs:label": "InitialDiseaseStatus", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25633,110 +25722,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GerotaFascia" - }, - { - "@id": "bts:Parenchyma" - }, - { - "@id": "bts:PerinephricFat" + "@id": "bts:InitialDiagnosis" }, { - "@id": "bts:Renal" + "@id": "bts:ProgressiveDisease" }, { - "@id": "bts:RenalCapsule" + "@id": "bts:RecurrentDisease" }, { - "@id": "bts:RenalSinus" + "@id": "bts:ResidualDisease" }, { - "@id": "bts:RenalVein" + "@id": "bts:Unknown" }, { - "@id": "bts:Ureter" + "@id": "bts:NotReported" } ], - "sms:displayName": "Margins Involved Site", + "sms:displayName": "Initial Disease Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedulloblastomaMolecularClassification", + "@id": "bts:RegimenorLineofTherapy", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", - "rdfs:label": "MedulloblastomaMolecularClassification", + "rdfs:comment": "The text term used to describe the regimen or line of therapy.", + "rdfs:label": "RegimenorLineofTherapy", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NotDetermined" - }, - { - "@id": "bts:Non-WNT/non-SHHActivated" - }, - { - "@id": "bts:SHH-Activated" - }, - { - "@id": "bts:WNT-Activated" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Medulloblastoma Molecular Classification", + "sms:displayName": "Regimen or Line of Therapy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicropapillaryFeatures", + "@id": "bts:TherapeuticAgents", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", - "rdfs:label": "MicropapillaryFeatures", + "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", + "rdfs:label": "TherapeuticAgents", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Micropapillary Features", + "sms:displayName": "Therapeutic Agents", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitosisKaryorrhexisIndex", + "@id": "bts:TreatmentIntentType", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", - "rdfs:label": "MitosisKaryorrhexisIndex", + "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", + "rdfs:label": "TreatmentIntentType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25744,47 +25793,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:High" - }, - { - "@id": "bts:Intermediate" + "@id": "bts:Adjuvant" }, { - "@id": "bts:Low" + "@id": "bts:CancerControl" }, { - "@id": "bts:Unknown" + "@id": "bts:Cure" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mitosis Karyorrhexis Index", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NonNodalRegionalDisease", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", - "rdfs:label": "NonNodalRegionalDisease", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" + "@id": "bts:Neoadjuvant" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Palliative" }, { - "@id": "bts:Present" + "@id": "bts:Prevention" }, { "@id": "bts:Unknown" @@ -25793,18 +25817,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Non Nodal Regional Disease", + "sms:displayName": "Treatment Intent Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NonNodalTumorDeposits", + "@id": "bts:ChemoConcurrenttoRadiation", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", - "rdfs:label": "NonNodalTumorDeposits", + "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", + "rdfs:label": "ChemoConcurrenttoRadiation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25824,52 +25848,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Non Nodal Tumor Deposits", + "sms:displayName": "Chemo Concurrent to Radiation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OvarianSpecimenStatus", + "@id": "bts:NumberofCycles", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", - "rdfs:label": "OvarianSpecimenStatus", + "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", + "rdfs:label": "NumberofCycles", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:OvarianCapsuleIntact" - }, - { - "@id": "bts:OvarianCapsuleRuptured" - }, - { - "@id": "bts:OvarianCapsuleFragmented" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Ovarian Specimen Status", + "sms:displayName": "Number of Cycles", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OvarianSurfaceInvolvement", + "@id": "bts:ReasonTreatmentEnded", "@type": "rdfs:Class", - "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", - "rdfs:label": "OvarianSurfaceInvolvement", + "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", + "rdfs:label": "ReasonTreatmentEnded", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25877,33 +25884,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:AdverseTherapyEvent" }, { - "@id": "bts:Present" + "@id": "bts:CourseofTherapyCompleted" }, { - "@id": "bts:Indeterminate" + "@id": "bts:Death" }, { - "@id": "bts:Unknown" + "@id": "bts:DiseaseProgression" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" + }, + { + "@id": "bts:WithdrawalbySubject" } ], - "sms:displayName": "Ovarian Surface Involvement", + "sms:displayName": "Reason Treatment Ended", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PregnantatDiagnosis", + "@id": "bts:TreatmentArm", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", - "rdfs:label": "PregnantatDiagnosis", + "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", + "rdfs:label": "TreatmentArm", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25911,64 +25921,44 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" + "@id": "bts:A081105" }, { - "@id": "bts:Unknown" + "@id": "bts:E4512" }, { - "@id": "bts:NotReported" + "@id": "bts:EA5142" } ], - "sms:displayName": "Pregnant at Diagnosis", + "sms:displayName": "Treatment Arm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrimaryGleasonGrade", + "@id": "bts:TreatmentDose", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "PrimaryGleasonGrade", + "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", + "rdfs:label": "TreatmentDose", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pattern1" - }, - { - "@id": "bts:Pattern2" - }, - { - "@id": "bts:Pattern3" - }, - { - "@id": "bts:Pattern4" - }, - { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Primary Gleason Grade", + "sms:displayName": "Treatment Dose", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SecondaryGleasonGrade", + "@id": "bts:TreatmentDoseUnits", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "SecondaryGleasonGrade", + "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", + "rdfs:label": "TreatmentDoseUnits", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -25976,33 +25966,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pattern1" - }, - { - "@id": "bts:Pattern2" - }, - { - "@id": "bts:Pattern3" - }, - { - "@id": "bts:Pattern4" + "@id": "bts:CGy" }, { - "@id": "bts:Pattern5" + "@id": "bts:Gy" } ], - "sms:displayName": "Secondary Gleason Grade", + "sms:displayName": "Treatment Dose Units", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SupratentorialLocalization", + "@id": "bts:TreatmentEffectIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", - "rdfs:label": "SupratentorialLocalization", + "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", + "rdfs:label": "TreatmentEffectIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -26010,53 +25991,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CerebralCortex" - }, - { - "@id": "bts:DeepGray" + "@id": "bts:Yes" }, { - "@id": "bts:SpinalCord" + "@id": "bts:No" }, { - "@id": "bts:WhiteMatter" + "@id": "bts:NotReported" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Supratentorial Localization", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorDepth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", - "rdfs:label": "TumorDepth", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Depth", + "sms:displayName": "Treatment Effect Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WHOCNSGrade", + "@id": "bts:TreatmentFrequency", "@type": "rdfs:Class", - "rdfs:comment": "WHO CNS Grade", - "rdfs:label": "WHOCNSGrade", + "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", + "rdfs:label": "TreatmentFrequency", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Therapy" } ], "schema:isPartOf": { @@ -26064,56 +26022,31 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GradeI" - }, - { - "@id": "bts:GradeII" + "@id": "bts:EveryHour" }, { - "@id": "bts:GradeIII" + "@id": "bts:FiveTimesDaily" }, { - "@id": "bts:GradeIV" + "@id": "bts:FourTimesDaily" }, { - "@id": "bts:GradeNotAssigned" + "@id": "bts:ThreeTimesDaily" }, { - "@id": "bts:Unknown" + "@id": "bts:TwiceDaily" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "WHO CNS Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WHONTEGrade", - "@type": "rdfs:Class", - "rdfs:comment": "WHO NTE Grade", - "rdfs:label": "WHONTEGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:G1" + "@id": "bts:Every24Hours" }, { - "@id": "bts:G2" + "@id": "bts:EveryOtherDay" }, { - "@id": "bts:G3" + "@id": "bts:TwiceWeekly" }, { - "@id": "bts:GX" + "@id": "bts:OnceWeekly" }, { "@id": "bts:Unknown" @@ -26122,35 +26055,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "WHO NTE Grade", + "sms:displayName": "Treatment Frequency", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AAChange", + "@id": "bts:YearofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "AAChange", + "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", + "rdfs:label": "YearofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "AA Change", + "sms:displayName": "Year of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Antigen", + "@id": "bts:PrecancerousConditionType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Antigen", + "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", + "rdfs:label": "PrecancerousConditionType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26158,108 +26091,132 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BCL6" + "@id": "bts:DuctalCarcinomaInSitu" }, { - "@id": "bts:CA-125" + "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" }, { - "@id": "bts:CA19-9" + "@id": "bts:AtypicalAdenomatousLungHyperplasia" }, { - "@id": "bts:CCND1" + "@id": "bts:Other" }, { - "@id": "bts:CD10" + "@id": "bts:PancreaticIntraepithelialNeoplasia" }, { - "@id": "bts:CD117" + "@id": "bts:ProstaticIntraepithelialNeoplasia" }, { - "@id": "bts:CD138" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:CD14" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:CD15" + "@id": "bts:Melanomainsitu" }, { - "@id": "bts:CD19" + "@id": "bts:Superficialspreading" }, { - "@id": "bts:CD20" + "@id": "bts:Lentigomalignatype" }, { - "@id": "bts:CD22" + "@id": "bts:Acral-lentiginous" }, { - "@id": "bts:CD23" + "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" }, { - "@id": "bts:CD25" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:CD3" + "@id": "bts:Melanomainsitunototherwiseclassified" }, { - "@id": "bts:CD30" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:CD33" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:CD34" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:CD45" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:CD5" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:CD56" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:CD7" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:CD79A" + "@id": "bts:Invasivemelanoma" }, { - "@id": "bts:CEA" + "@id": "bts:NormalWDA" }, { - "@id": "bts:HLA-DR" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:Mesothelin" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:NSE" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:SquamousCellCarcinomaAntigen" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:Unknown" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:NotReported" + "@id": "bts:Severedysplasia" + }, + { + "@id": "bts:Atypicaladenomatoushyperplasia" + }, + { + "@id": "bts:Adenocarcinomainsitu-nonmucinous" + }, + { + "@id": "bts:Adenocarcinomainsitu-mucinous" + }, + { + "@id": "bts:BenigntumorNOS" + }, + { + "@id": "bts:Hamartoma" + }, + { + "@id": "bts:CarcinomaNOS" + }, + { + "@id": "bts:Nodiagnosispossible" + }, + { + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Antigen", + "sms:displayName": "Precancerous Condition Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClinicalBiospecimenType", + "@id": "bts:MethodofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "ClinicalBiospecimenType", + "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", + "rdfs:label": "MethodofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26267,70 +26224,73 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Blood" + "@id": "bts:Autopsy" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:Biopsy" }, { - "@id": "bts:BuccalMucosa" + "@id": "bts:BloodDraw" }, { - "@id": "bts:BuffyCoat" + "@id": "bts:BoneMarrowAspirate" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:CoreBiopsy" }, { - "@id": "bts:ConnectiveTissue" + "@id": "bts:Cytology" }, { - "@id": "bts:EmbryonicFluid" + "@id": "bts:Cystoscopy" }, { - "@id": "bts:EmbryonicTissue" + "@id": "bts:Debulking" }, { - "@id": "bts:Feces" + "@id": "bts:DiagnosticImaging" }, { - "@id": "bts:Granulocyte" + "@id": "bts:DilationandCurettageProcedure" }, { - "@id": "bts:MuscleTissue" + "@id": "bts:Enucleation" }, { - "@id": "bts:NerveTissue" + "@id": "bts:ExcisionalBiopsy" }, { - "@id": "bts:PeritonealFluid" + "@id": "bts:FineNeedleAspiration" }, { - "@id": "bts:Plasma" + "@id": "bts:IncisionalBiopsy" }, { - "@id": "bts:PleuralFluid" + "@id": "bts:Laparoscopy" }, { - "@id": "bts:Saliva" + "@id": "bts:Laparotomy" }, { - "@id": "bts:Serum" + "@id": "bts:Other" }, { - "@id": "bts:Skin" + "@id": "bts:PapSmear" }, { - "@id": "bts:SoftTissue" + "@id": "bts:PhysicalExam" }, { - "@id": "bts:TissueNOS" + "@id": "bts:PathologicReview" }, { - "@id": "bts:UninvolvedTissueNOS" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:Urine" + "@id": "bts:Thoracentesis" + }, + { + "@id": "bts:UltrasoundGuidedBiopsy" }, { "@id": "bts:Unknown" @@ -26339,69 +26299,123 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Clinical Biospecimen Type", + "sms:displayName": "Method of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BloodTestNormalRangeUpper", + "@id": "bts:PriorMalignancy", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeUpper", + "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", + "rdfs:label": "PriorMalignancy", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Test Normal Range Upper", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Malignancy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BloodTestNormalRangeLower", + "@id": "bts:PriorTreatment", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", + "rdfs:label": "PriorTreatment", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Test Normal Range Lower", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Treatment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellCount", + "@id": "bts:MetastasisatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CellCount", + "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", + "rdfs:label": "MetastasisatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Count", + "schema:rangeIncludes": [ + { + "@id": "bts:DistantMetastasis" + }, + { + "@id": "bts:MetastasisNOS" + }, + { + "@id": "bts:NoMetastasis" + }, + { + "@id": "bts:RegionalMetastasis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Metastasis at Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Chromosome", + "@id": "bts:MetastasisatDiagnosisSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Chromosome", + "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", + "rdfs:label": "MetastasisatDiagnosisSite", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26409,82 +26423,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Chr1" + "@id": "bts:Abdomen" }, { - "@id": "bts:Chr2" + "@id": "bts:AdrenalGland" }, { - "@id": "bts:Chr3" + "@id": "bts:Ascites" }, { - "@id": "bts:Chr4" + "@id": "bts:Bone" }, { - "@id": "bts:Chr5" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:Chr6" + "@id": "bts:Brain" }, { - "@id": "bts:Chr7" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:Chr8" + "@id": "bts:CentralNervousSystem" }, { - "@id": "bts:Chr9" + "@id": "bts:Colon" }, { - "@id": "bts:Chr10" + "@id": "bts:DistantNodes" }, { - "@id": "bts:Chr11" + "@id": "bts:DistantOrgan" }, { - "@id": "bts:Chr12" + "@id": "bts:Groin" }, { - "@id": "bts:Chr13" + "@id": "bts:Kidney" }, { - "@id": "bts:Chr14" + "@id": "bts:Liver" }, { - "@id": "bts:Chr15" + "@id": "bts:Lung" }, { - "@id": "bts:Chr16" + "@id": "bts:LymphNode" }, { - "@id": "bts:Chr17" + "@id": "bts:Axillary" }, { - "@id": "bts:Chr18" + "@id": "bts:Inguinal" }, { - "@id": "bts:Chr19" + "@id": "bts:LymphNodeNOS" }, { - "@id": "bts:Chr20" + "@id": "bts:Mediastinum" }, { - "@id": "bts:Chr21" + "@id": "bts:Omentum" }, { - "@id": "bts:Chr22" + "@id": "bts:Ovary" }, { - "@id": "bts:Chr23" + "@id": "bts:Pelvis" }, { - "@id": "bts:ChrM" + "@id": "bts:PeritonealCavity" }, { - "@id": "bts:ChrX" + "@id": "bts:Peritoneum" }, { - "@id": "bts:ChrY" + "@id": "bts:Pleura" + }, + { + "@id": "bts:Scalp" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:SmallIntestine" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:SpinalCord" }, { "@id": "bts:Unknown" @@ -26493,18 +26522,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Chromosome", + "sms:displayName": "Metastasis at Diagnosis Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clonality", + "@id": "bts:FirstSymptomPriortoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Clonality", + "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", + "rdfs:label": "FirstSymptomPriortoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26512,75 +26541,118 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Clonal" + "@id": "bts:AlteredMentalStatus" }, { - "@id": "bts:Non-clonal" + "@id": "bts:Headaches" + }, + { + "@id": "bts:MotororMovementChanges" + }, + { + "@id": "bts:Seizures" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:VisualChanges" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Clonality", + "sms:displayName": "First Symptom Prior to Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CopyNumber", + "@id": "bts:DaystoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CopyNumber", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Copy Number", + "sms:displayName": "Days to Diagnosis", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:Cytoband", + "@id": "bts:PercentTumorInvasion", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Cytoband", + "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", + "rdfs:label": "PercentTumorInvasion", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cytoband", + "sms:displayName": "Percent Tumor Invasion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Exon", + "@id": "bts:ResidualDisease", "@type": "rdfs:Class", - "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Exon", + "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", + "rdfs:label": "ResidualDisease", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:InitialDiseaseStatus" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Exon", + "schema:rangeIncludes": [ + { + "@id": "bts:R0" + }, + { + "@id": "bts:R1" + }, + { + "@id": "bts:R2" + }, + { + "@id": "bts:RX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Residual Disease", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoneFamily", + "@id": "bts:SynchronousMalignancy", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", - "rdfs:label": "HistoneFamily", + "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", + "rdfs:label": "SynchronousMalignancy", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26588,19 +26660,41 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:H1" + "@id": "bts:Yes" }, { - "@id": "bts:H2A" + "@id": "bts:No" }, { - "@id": "bts:H2B" + "@id": "bts:Unknown" }, { - "@id": "bts:H3" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Synchronous Malignancy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorConfinedtoOrganofOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", + "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:H4" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -26609,18 +26703,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Histone Family", + "sms:displayName": "Tumor Confined to Organ of Origin", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoneVariant", + "@id": "bts:TumorFocality", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "HistoneVariant", + "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", + "rdfs:label": "TumorFocality", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26628,55 +26722,118 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CENP-A" + "@id": "bts:Multifocal" }, { - "@id": "bts:H2A-Bbd" + "@id": "bts:Unifocal" }, { - "@id": "bts:H2A.X" + "@id": "bts:Unknown" }, { - "@id": "bts:H2A.Z" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Focality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GrossTumorWeight", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", + "rdfs:label": "GrossTumorWeight", + "rdfs:subClassOf": [ { - "@id": "bts:H2A.Z.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gross Tumor Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreslowThickness", + "@type": "rdfs:Class", + "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", + "rdfs:label": "BreslowThickness", + "rdfs:subClassOf": [ { - "@id": "bts:H2A.Z.2" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breslow Thickness", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", + "rdfs:label": "VascularInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:H2A.Z.2.2" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:H3.1" + "@id": "bts:Yes-VascularInvasionPresent" }, { - "@id": "bts:H3.2" + "@id": "bts:No" }, { - "@id": "bts:H3.3" + "@id": "bts:Unknown" }, { - "@id": "bts:H3.5" + "@id": "bts:NotReported" }, { - "@id": "bts:H3.X" - }, + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Vascular Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", + "rdfs:label": "VascularInvasionType", + "rdfs:subClassOf": [ { - "@id": "bts:H3.Y" + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Extramural" }, { - "@id": "bts:H3t(H3.4)" + "@id": "bts:Intramural" }, { - "@id": "bts:MH2A" + "@id": "bts:Macro" }, { - "@id": "bts:MH2A.1" + "@id": "bts:Micro" }, { - "@id": "bts:MH2A.2" + "@id": "bts:NoVascularInvasion" }, { "@id": "bts:Unknown" @@ -26685,35 +26842,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Histone Variant", + "sms:displayName": "Vascular Invasion Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Intron", + "@id": "bts:AnaplasiaPresent", "@type": "rdfs:Class", - "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", - "rdfs:label": "Intron", + "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", + "rdfs:label": "AnaplasiaPresent", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Intron", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AnaplasiaPresent" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LaboratoryTest", + "@id": "bts:AnaplasiaPresentType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", - "rdfs:label": "LaboratoryTest", + "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", + "rdfs:label": "AnaplasiaPresentType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26721,139 +26892,124 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbsoluteNeutrophil" + "@id": "bts:Absent" }, { - "@id": "bts:Albumin" + "@id": "bts:Diffuse" }, { - "@id": "bts:AlphaFetoprotein" + "@id": "bts:Equivocal" }, { - "@id": "bts:B-cellgenotyping" + "@id": "bts:Focal" }, { - "@id": "bts:Basophil" + "@id": "bts:Present" }, { - "@id": "bts:Beta2Microglobulin" + "@id": "bts:Sclerosis" }, { - "@id": "bts:BloodUreaNitrogen" + "@id": "bts:Unknown" }, { - "@id": "bts:C-ReactiveProtein" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Laterality", + "@type": "rdfs:Class", + "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", + "rdfs:label": "Laterality", + "rdfs:subClassOf": [ { - "@id": "bts:Calcium" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Cellularity" + "@id": "bts:Bilateral" }, { - "@id": "bts:CirculatingTumorCells" + "@id": "bts:Left" }, { - "@id": "bts:Creatinine" + "@id": "bts:Midline" }, { - "@id": "bts:Eosinophil" + "@id": "bts:Right" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:Unilateral" }, { - "@id": "bts:Glucose" + "@id": "bts:Unknown" }, { - "@id": "bts:Hematocrit" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laterality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerineuralInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", + "rdfs:label": "PerineuralInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:Hemoglobin" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HPV-E6/E7" + "@id": "bts:Yes" }, { - "@id": "bts:HumanChorionicGonadotropin" + "@id": "bts:No" }, { - "@id": "bts:HumanPapillomavirus" + "@id": "bts:Unknown" }, { - "@id": "bts:ImmunoglobulinA" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Perineural Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LymphaticInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", + "rdfs:label": "LymphaticInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:ImmunoglobulinG" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ImmunoglobulinM" + "@id": "bts:Yes" }, { - "@id": "bts:LactateDehydrogenase" - }, - { - "@id": "bts:Leukocytes" - }, - { - "@id": "bts:LuteinizingHormone" - }, - { - "@id": "bts:Lymphoblasts" - }, - { - "@id": "bts:Lymphocytes" - }, - { - "@id": "bts:MProtein" - }, - { - "@id": "bts:Metamyelocytes" - }, - { - "@id": "bts:Myeloblasts" - }, - { - "@id": "bts:Myelocytes" - }, - { - "@id": "bts:NeutrophilBands" - }, - { - "@id": "bts:Platelets" - }, - { - "@id": "bts:Prolymphocytes" - }, - { - "@id": "bts:Promonocytes" - }, - { - "@id": "bts:Promyelocytes" - }, - { - "@id": "bts:SegmentedNeutrophil" - }, - { - "@id": "bts:SerumFreeImmunoglobulinLightChain" - }, - { - "@id": "bts:Kappa" - }, - { - "@id": "bts:Lambda" - }, - { - "@id": "bts:NOS" - }, - { - "@id": "bts:Testosterone" - }, - { - "@id": "bts:TotalBilirubin" - }, - { - "@id": "bts:TotalProtein" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -26862,69 +27018,52 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Laboratory Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LociAbnormalCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", - "rdfs:label": "LociAbnormalCount", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loci Abnormal Count", + "sms:displayName": "Lymphatic Invasion Present", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LociCount", + "@id": "bts:LymphNodesPositive", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci tested.", - "rdfs:label": "LociCount", + "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", + "rdfs:label": "LymphNodesPositive", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loci Count", + "sms:displayName": "Lymph Nodes Positive", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Locus", + "@id": "bts:LymphNodesTested", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", - "rdfs:label": "Locus", + "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", + "rdfs:label": "LymphNodesTested", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Locus", + "sms:displayName": "Lymph Nodes Tested", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MismatchRepairMutation", + "@id": "bts:PeritonealFluidCytologicalStatus", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MismatchRepairMutation", + "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", + "rdfs:label": "PeritonealFluidCytologicalStatus", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26932,10 +27071,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Atypical" }, { - "@id": "bts:No" + "@id": "bts:Malignant" + }, + { + "@id": "bts:Non-Malignant" + }, + { + "@id": "bts:Unsatisfactory" }, { "@id": "bts:Unknown" @@ -26944,18 +27089,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Mismatch Repair Mutation", + "sms:displayName": "Peritoneal Fluid Cytological Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MolecularConsequence", + "@id": "bts:ClassificationofTumor", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularConsequence", + "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", + "rdfs:label": "ClassificationofTumor", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -26963,157 +27108,153 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:3PrimeUTRVariant" - }, - { - "@id": "bts:5PrimeUTRVariant" + "@id": "bts:Primary" }, { - "@id": "bts:CodingSequenceVariant" + "@id": "bts:Metastasis" }, { - "@id": "bts:DownstreamGeneVariant" + "@id": "bts:Recurrence" }, { - "@id": "bts:FeatureElongation" + "@id": "bts:Other" }, { - "@id": "bts:FeatureTruncation" + "@id": "bts:Unknown" }, { - "@id": "bts:FrameshiftVariant" + "@id": "bts:NotReported" }, { - "@id": "bts:IncompleteTerminalCodonVariant" - }, + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Classification of Tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BestOverallResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", + "rdfs:label": "BestOverallResponse", + "rdfs:subClassOf": [ { - "@id": "bts:InframeDeletion" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:InframeInsertion" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:IntergenicVariant" + "@id": "bts:CPD-ClinicalProgression" }, { - "@id": "bts:IntronVariant" + "@id": "bts:CR-CompleteResponse" }, { - "@id": "bts:MaturemiRNAVariant" + "@id": "bts:CRU-CompleteResponseUnconfirmed" }, { - "@id": "bts:MissenseVariant" + "@id": "bts:DU-DiseaseUnchanged" }, { - "@id": "bts:NMDTranscriptVariant" + "@id": "bts:IMR-Immunoresponse" }, { - "@id": "bts:Non-codingTranscriptExonVariant" + "@id": "bts:IPD-Immunoprogression" }, { - "@id": "bts:Non-codingTranscriptVariant" + "@id": "bts:MR-Minimal/MarginalResponse" }, { - "@id": "bts:ProteinAlteringVariant" + "@id": "bts:MX-MixedResponse" }, { - "@id": "bts:RegulatoryRegionAblation" + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" }, { - "@id": "bts:RegulatoryRegionAmplification" + "@id": "bts:NPB-NoPalliativeBenefit" }, { - "@id": "bts:RegulatoryRegionVariant" + "@id": "bts:NR-NoResponse" }, { - "@id": "bts:SpliceAcceptorVariant" + "@id": "bts:PA-PalliativeTherapy" }, { - "@id": "bts:SpliceDonorVariant" + "@id": "bts:PB-PalliativeBenefit" }, { - "@id": "bts:SpliceRegionVariant" + "@id": "bts:PD-ProgressiveDisease" }, { - "@id": "bts:StartLost" + "@id": "bts:PPD-Pseudoprogression" }, { - "@id": "bts:StopGain" + "@id": "bts:PR-PartialResponse" }, { - "@id": "bts:StopLost" + "@id": "bts:PSR-Pseudoresponse" }, { - "@id": "bts:StopRetainedVariant" + "@id": "bts:RD-ResponsiveDisease" }, { - "@id": "bts:SynonymousVariant" + "@id": "bts:RP-Response" }, { - "@id": "bts:TFBindingSiteVariant" + "@id": "bts:RPD-RadiographicProgressiveDisease" }, { - "@id": "bts:TFBSAblation" + "@id": "bts:SCR-StringentCompleteResponse" }, { - "@id": "bts:TFBSAmplification" + "@id": "bts:SD-StableDisease" }, { - "@id": "bts:TranscriptAblation" + "@id": "bts:SPD-SurgicalProgression" }, { - "@id": "bts:TranscriptAmplification" + "@id": "bts:TE-TooEarly" }, { - "@id": "bts:UpstreamGeneVariant" + "@id": "bts:VGPR-VeryGoodPartialResponse" } ], - "sms:displayName": "Molecular Consequence", + "sms:displayName": "Best Overall Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pathogenicity", + "@id": "bts:MitoticCount", "@type": "rdfs:Class", - "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", - "rdfs:label": "Pathogenicity", + "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", + "rdfs:label": "MitoticCount", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Benign" - }, - { - "@id": "bts:LikelyBenign" - }, - { - "@id": "bts:LikelyPathogenic" - }, - { - "@id": "bts:Pathogenic" - }, - { - "@id": "bts:UncertainSignificance" - } - ], - "sms:displayName": "Pathogenicity", + "sms:displayName": "Mitotic Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ploidy", + "@id": "bts:AJCCClinicalM", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", - "rdfs:label": "Ploidy", + "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalM", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27121,22 +27262,25 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aneuploid" + "@id": "bts:M0" }, { - "@id": "bts:Diploid" + "@id": "bts:M1" }, { - "@id": "bts:Hyperdiploid" + "@id": "bts:M1a" }, { - "@id": "bts:Hypodiploid" + "@id": "bts:M1b" }, { - "@id": "bts:NearDiploid" + "@id": "bts:M1c" }, { - "@id": "bts:Tetraploid" + "@id": "bts:MX" + }, + { + "@id": "bts:CM0(i+)" }, { "@id": "bts:Unknown" @@ -27145,188 +27289,115 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Ploidy", + "sms:displayName": "AJCC Clinical M", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SecondExon", + "@id": "bts:AJCCClinicalN", "@type": "rdfs:Class", - "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", - "rdfs:label": "SecondExon", + "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalN", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Second Exon", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondGeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SecondGeneSymbol", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second Gene Symbol", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SpecializedMolecularTest", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SpecializedMolecularTest", - "rdfs:subClassOf": [ + "@id": "bts:N0" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Specialized Molecular Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestAnalyteType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestAnalyteType", - "rdfs:subClassOf": [ + "@id": "bts:N0(i+)" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:N0(i-)" + }, { - "@id": "bts:DNA" + "@id": "bts:N0(mol+)" }, { - "@id": "bts:MRNA" + "@id": "bts:N0(mol-)" }, { - "@id": "bts:MiRNA" + "@id": "bts:N1" }, { - "@id": "bts:ProteinAnalyte" + "@id": "bts:N1a" }, { - "@id": "bts:TotalRNA" + "@id": "bts:N1b" }, { - "@id": "bts:Unknown" + "@id": "bts:N1bI" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Test Analyte Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestUnits", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestUnits", - "rdfs:subClassOf": [ + "@id": "bts:N1bII" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Test Units", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestValue", - "@type": "rdfs:Class", - "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", - "rdfs:label": "TestValue", - "rdfs:subClassOf": [ + "@id": "bts:N1bIII" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Test Value", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Transcript", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Transcript", - "rdfs:subClassOf": [ + "@id": "bts:N1bIV" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VariantOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "VariantOrigin", - "rdfs:subClassOf": [ + "@id": "bts:N1c" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:N1mi" + }, { - "@id": "bts:Germline" + "@id": "bts:N2" }, { - "@id": "bts:Somatic" + "@id": "bts:N2a" + }, + { + "@id": "bts:N2b" + }, + { + "@id": "bts:N2c" + }, + { + "@id": "bts:N3" + }, + { + "@id": "bts:N3a" + }, + { + "@id": "bts:N3b" + }, + { + "@id": "bts:N3c" + }, + { + "@id": "bts:N4" + }, + { + "@id": "bts:NX" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Variant Origin", + "sms:displayName": "AJCC Clinical N", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VariantType", + "@id": "bts:AJCCClinicalStage", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of genetic variation.", - "rdfs:label": "VariantType", + "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", + "rdfs:label": "AJCCClinicalStage", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27334,70 +27405,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Alleles" + "@id": "bts:Stage0" }, { - "@id": "bts:Amplification" + "@id": "bts:Stage0a" }, { - "@id": "bts:Chrimerism" + "@id": "bts:Stage0is" }, { - "@id": "bts:Conversion" + "@id": "bts:StageI" }, { - "@id": "bts:Deletion" + "@id": "bts:StageIA" }, { - "@id": "bts:Deletion-Insertion" + "@id": "bts:StageIA1" }, { - "@id": "bts:Duplication" + "@id": "bts:StageIA2" }, { - "@id": "bts:Extension" + "@id": "bts:StageIB" }, { - "@id": "bts:Gain" + "@id": "bts:StageIB1" }, { - "@id": "bts:Hypermethylation" + "@id": "bts:StageIB2" }, { - "@id": "bts:Insertion" + "@id": "bts:StageIC" }, { - "@id": "bts:Inversion" + "@id": "bts:StageII" }, { - "@id": "bts:Loss" + "@id": "bts:StageIIA" }, { - "@id": "bts:Methylation" + "@id": "bts:StageIIA1" }, { - "@id": "bts:Mosaicism" + "@id": "bts:StageIIA2" }, { - "@id": "bts:Other" + "@id": "bts:StageIIB" }, { - "@id": "bts:PartialMethylation" + "@id": "bts:StageIIC" }, { - "@id": "bts:Rearrangement" + "@id": "bts:StageIIC1" }, { - "@id": "bts:RepeatedSequences" + "@id": "bts:StageIII" }, { - "@id": "bts:Splice" + "@id": "bts:StageIIIA" }, { - "@id": "bts:Substitution" + "@id": "bts:StageIIIB" }, { - "@id": "bts:Translocation" + "@id": "bts:StageIIIC" + }, + { + "@id": "bts:StageIIIC1" + }, + { + "@id": "bts:StageIIIC2" + }, + { + "@id": "bts:StageIS" + }, + { + "@id": "bts:StageIV" + }, + { + "@id": "bts:StageIVA" + }, + { + "@id": "bts:StageIVB" + }, + { + "@id": "bts:StageIVC" + }, + { + "@id": "bts:StageTis" + }, + { + "@id": "bts:StageX" }, { "@id": "bts:Unknown" @@ -27406,18 +27504,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Variant Type", + "sms:displayName": "AJCC Clinical Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zygosity", + "@id": "bts:AJCCClinicalT", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", - "rdfs:label": "Zygosity", + "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalT", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27425,223 +27523,172 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Heterozygous" + "@id": "bts:T0" }, { - "@id": "bts:Hemizygous" + "@id": "bts:T1" }, { - "@id": "bts:Homozygous" + "@id": "bts:T1a" }, { - "@id": "bts:Nullizygous" + "@id": "bts:T1a1" }, { - "@id": "bts:Unknown" + "@id": "bts:T1a2" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Zygosity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SourceHTANBiospecimenID", - "@type": "rdfs:Class", - "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", - "rdfs:label": "SourceHTANBiospecimenID", - "rdfs:subClassOf": [ + "@id": "bts:T1b" + }, { - "@id": "bts:Biosample" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Source HTAN Biospecimen ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", - "rdfs:label": "CollectionDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:T1b1" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:AdjacentBiospecimenIDs", - "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenIDs", - "rdfs:subClassOf": [ + "@id": "bts:T1b2" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adjacent Biospecimen IDs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Biospecimen Type", - "rdfs:label": "BiospecimenType", - "rdfs:subClassOf": [ + "@id": "bts:T1c" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:T1mi" + }, { - "@id": "bts:TissueBiospecimenType" + "@id": "bts:T2" }, { - "@id": "bts:BloodBiospecimenType" + "@id": "bts:T2a" }, { - "@id": "bts:AnalyteBiospecimenType" + "@id": "bts:T2a1" }, { - "@id": "bts:MouthRinseBiospecimenType" + "@id": "bts:T2a2" }, { - "@id": "bts:StoolBiospecimenType" + "@id": "bts:T2b" }, { - "@id": "bts:UrineBiospecimenType" + "@id": "bts:T2c" }, { - "@id": "bts:AscitesBiospecimenType" + "@id": "bts:T2d" }, { - "@id": "bts:SputumBiospecimenType" + "@id": "bts:T3" }, { - "@id": "bts:FluidsBiospecimenType" + "@id": "bts:T3a" }, { - "@id": "bts:BoneMarrowBiospecimenType" + "@id": "bts:T3b" }, { - "@id": "bts:CellsBiospecimenType" - } - ], - "sms:displayName": "Biospecimen Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", - "rdfs:subClassOf": [ + "@id": "bts:T3c" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:T3d" + }, { - "@id": "bts:Autopsy" + "@id": "bts:T4" }, { - "@id": "bts:Biopsy" + "@id": "bts:T4a" }, { - "@id": "bts:FineNeedleAspirate" + "@id": "bts:T4b" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:T4c" }, { - "@id": "bts:PunchBiopsy" + "@id": "bts:T4d" }, { - "@id": "bts:ShaveBiopsy" + "@id": "bts:T4e" }, { - "@id": "bts:Excision" + "@id": "bts:TX" }, { - "@id": "bts:Re-excision" + "@id": "bts:Ta" }, { - "@id": "bts:SentinelNodeBiopsy" + "@id": "bts:Tis" }, { - "@id": "bts:Lymphadenectomy-RegionalNodes" + "@id": "bts:Tis(DCIS)" }, { - "@id": "bts:OtherAcquisitionMethod" + "@id": "bts:Tis(LCIS)" }, { - "@id": "bts:Noninducedsputum" + "@id": "bts:Tis(Paget's)" }, { - "@id": "bts:Inducedsputum" + "@id": "bts:Unknown" }, { - "@id": "bts:BAL(bronchialalveolarlavage)" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Clinical T", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCPathologicM", + "@type": "rdfs:Class", + "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", + "rdfs:label": "AJCCPathologicM", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:M0" }, { - "@id": "bts:Cytobrush" + "@id": "bts:M1" }, { - "@id": "bts:Blooddraw" + "@id": "bts:M1a" }, { - "@id": "bts:Fluidcollection" + "@id": "bts:M1b" }, { - "@id": "bts:Forcepsbiopsy" + "@id": "bts:M1c" }, { - "@id": "bts:Coreneedlebiopsy" + "@id": "bts:MX" }, { - "@id": "bts:Endoscopicbiopsy" + "@id": "bts:CM0(i+)" }, { - "@id": "bts:Notspecified" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Acquisition Method Type", - "sms:required": "sms:true", + "sms:displayName": "AJCC Pathologic M", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FixativeType", + "@id": "bts:AJCCPathologicN", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", + "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", + "rdfs:label": "AJCCPathologicN", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27649,87 +27696,96 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Acetone" + "@id": "bts:N0" }, { - "@id": "bts:Alcohol" + "@id": "bts:N0(i+)" }, { - "@id": "bts:Formalin" + "@id": "bts:N0(i-)" }, { - "@id": "bts:Glutaraldehyde" + "@id": "bts:N0(mol+)" }, { - "@id": "bts:OCTmedia" + "@id": "bts:N0(mol-)" }, { - "@id": "bts:RNAlater" + "@id": "bts:N1" }, { - "@id": "bts:Saline" + "@id": "bts:N1a" }, { - "@id": "bts:95%Ethanol" + "@id": "bts:N1b" }, { - "@id": "bts:Dimidoester" + "@id": "bts:N1bI" }, { - "@id": "bts:Carbodiimide" + "@id": "bts:N1bII" }, { - "@id": "bts:Dimethylacetamide" + "@id": "bts:N1bIII" }, { - "@id": "bts:Para-benzoquinone" + "@id": "bts:N1bIV" }, { - "@id": "bts:PAXgenetissue" + "@id": "bts:N1c" }, { - "@id": "bts:TCLlysisbuffer" + "@id": "bts:N1mi" }, { - "@id": "bts:NP40lysisbuffer" + "@id": "bts:N2" }, { - "@id": "bts:Methacarn" + "@id": "bts:N2a" }, { - "@id": "bts:Cryo-store" + "@id": "bts:N2b" }, { - "@id": "bts:Carnoy'sFixative" + "@id": "bts:N2c" }, { - "@id": "bts:Polaxamer" + "@id": "bts:N3" }, { - "@id": "bts:Other" + "@id": "bts:N3a" }, { - "@id": "bts:None" + "@id": "bts:N3b" + }, + { + "@id": "bts:N3c" + }, + { + "@id": "bts:N4" + }, + { + "@id": "bts:NX" }, { "@id": "bts:Unknown" }, { - "@id": "bts:Unfixed" + "@id": "bts:NotReported" } ], - "sms:displayName": "Fixative Type", - "sms:required": "sms:true", + "sms:displayName": "AJCC Pathologic N", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StorageMethod", + "@id": "bts:AJCCPathologicStage", "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", + "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", + "rdfs:label": "AJCCPathologicStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27737,194 +27793,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Ambienttemperature" + "@id": "bts:Stage0" }, { - "@id": "bts:Cutslide" + "@id": "bts:Stage0a" }, { - "@id": "bts:Fresh" + "@id": "bts:Stage0is" }, { - "@id": "bts:Frozenat-20C" + "@id": "bts:StageI" }, { - "@id": "bts:Frozenat-70C" + "@id": "bts:StageIA" }, { - "@id": "bts:Frozenat-80C" + "@id": "bts:StageIA1" }, { - "@id": "bts:Frozenat-150C" + "@id": "bts:StageIA2" }, { - "@id": "bts:Frozeninliquidnitrogen" + "@id": "bts:StageIB" }, { - "@id": "bts:Frozeninvaporphase" + "@id": "bts:StageIB1" }, { - "@id": "bts:Paraffinblock" + "@id": "bts:StageIB2" }, { - "@id": "bts:RNAlaterat4C" + "@id": "bts:StageIC" }, { - "@id": "bts:RNAlaterat25C" + "@id": "bts:StageII" }, { - "@id": "bts:RNAlaterat-20C" + "@id": "bts:StageIIA" }, { - "@id": "bts:Refrigeratedat4degrees" + "@id": "bts:StageIIA1" }, { - "@id": "bts:Refrigeratedvacuumchamber" + "@id": "bts:StageIIA2" }, { - "@id": "bts:4Cinvacuumchamber" + "@id": "bts:StageIIB" }, { - "@id": "bts:Desiccantat4C" + "@id": "bts:StageIIC" }, { - "@id": "bts:NotApplicable" + "@id": "bts:StageIIC1" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", - "rdfs:label": "ProcessingDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:ProtocolLink", - "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label": "ProtocolLink", - "rdfs:subClassOf": [ - { - "@id": "bts:InformationContentEntity" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Protocol Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteDataSource", - "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Site Data Source", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionMedia", - "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:DMEM" + "@id": "bts:StageIII" }, { - "@id": "bts:DMEM+Serum" + "@id": "bts:StageIIIA" }, { - "@id": "bts:RPMI" + "@id": "bts:StageIIIB" }, { - "@id": "bts:RPMI+Serum" + "@id": "bts:StageIIIC" }, { - "@id": "bts:PBS" + "@id": "bts:StageIIIC1" }, { - "@id": "bts:PBS+Serum" + "@id": "bts:StageIIIC2" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Collection Media", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MountingMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Aqueouswaterbased" + "@id": "bts:StageIS" }, { - "@id": "bts:Non-AqueousSolventbased" + "@id": "bts:StageIV" }, { - "@id": "bts:Xylene" + "@id": "bts:StageIVA" }, { - "@id": "bts:Toluene" + "@id": "bts:StageIVB" }, { - "@id": "bts:AntifadewithDAPI" + "@id": "bts:StageIVC" }, { - "@id": "bts:AntifadewithoutDAPI" + "@id": "bts:StageTis" }, { - "@id": "bts:PBS" + "@id": "bts:StageX" }, { "@id": "bts:Unknown" @@ -27933,35 +27892,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Mounting Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingLocation", - "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Location", + "sms:displayName": "AJCC Pathologic Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentBy", + "@id": "bts:AJCCPathologicT", "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", + "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", + "rdfs:label": "AJCCPathologicT", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -27969,190 +27911,126 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pathologist" + "@id": "bts:T0" }, { - "@id": "bts:ResearchScientist" + "@id": "bts:T1" }, { - "@id": "bts:Other" + "@id": "bts:T1a" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment By", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Digital" - }, - { - "@id": "bts:Microscopy" + "@id": "bts:T1a1" }, { - "@id": "bts:Other" + "@id": "bts:T1a2" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PreinvasiveMorphology", - "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", - "rdfs:label": "PreinvasiveMorphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Melanocytichyperplasia" + "@id": "bts:T1b" }, { - "@id": "bts:Atypicalmelanocyticproliferation" + "@id": "bts:T1b1" }, { - "@id": "bts:Melanomainsitu-superficialspreading" + "@id": "bts:T1b2" }, { - "@id": "bts:Melanomainsitu-lentigomalignatype" + "@id": "bts:T1c" }, { - "@id": "bts:Melanomainsitu-acral-lentiginous" + "@id": "bts:T1mi" }, { - "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" + "@id": "bts:T2" }, { - "@id": "bts:Persistentmelanomainsitu" + "@id": "bts:T2a" }, { - "@id": "bts:Melanomainsitu-nototherwiseclassified" + "@id": "bts:T2a1" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:T2a2" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:T2b" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:T2c" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:T2d" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:T3" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:T3a" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:T3b" }, { - "@id": "bts:Invasivemelanoma-other" + "@id": "bts:T3c" }, { - "@id": "bts:NormalWDA" + "@id": "bts:T3d" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:T4" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:T4a" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:T4b" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:T4c" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:T4d" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:T4e" }, { - "@id": "bts:SquamousCarcinomainsitu" + "@id": "bts:TX" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:Ta" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:Tis" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:Tis(DCIS)" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:Tis(LCIS)" }, { - "@id": "bts:Hamartoma" + "@id": "bts:Tis(Paget's)" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Nodiagnosispossible" - } - ], - "sms:displayName": "Preinvasive Morphology", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorInfiltratingLymphocytes", - "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", + "sms:displayName": "AJCC Pathologic T", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DegreeofDysplasia", + "@id": "bts:AJCCStagingSystemEdition", "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", + "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", + "rdfs:label": "AJCCStagingSystemEdition", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28160,257 +28038,419 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" + "@id": "bts:1st" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:2nd" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:3rd" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:4th" }, { - "@id": "bts:CarcinomainSitu" + "@id": "bts:5th" + }, + { + "@id": "bts:6th" + }, + { + "@id": "bts:7th" + }, + { + "@id": "bts:8th" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Degree of Dysplasia", + "sms:displayName": "AJCC Staging System Edition", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DysplasiaFraction", + "@id": "bts:CogNeuroblastomaRiskGroup", "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", + "rdfs:comment": "Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.", + "rdfs:label": "CogNeuroblastomaRiskGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dysplasia Fraction", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NumberProliferatingCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:HighRisk" + }, + { + "@id": "bts:IntermediateRisk" + }, + { + "@id": "bts:LowRisk" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number Proliferating Cells", + "sms:displayName": "Cog Neuroblastoma Risk Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentEosinophilInfiltration", + "@id": "bts:CogRhabdomyosarcomaRiskGroup", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).", + "rdfs:label": "CogRhabdomyosarcomaRiskGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Eosinophil Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:HighRisk" + }, + { + "@id": "bts:IntermediateRisk" + }, + { + "@id": "bts:LowRisk" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cog Rhabdomyosarcoma Risk Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentGranulocyteInfiltration", + "@id": "bts:GleasonGradeGroup", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", + "rdfs:comment": "The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "GleasonGradeGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Granulocyte Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Group1" + }, + { + "@id": "bts:Group2" + }, + { + "@id": "bts:Group3" + }, + { + "@id": "bts:Group4" + }, + { + "@id": "bts:Group5" + } + ], + "sms:displayName": "Gleason Grade Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentInflamInfiltration", + "@id": "bts:GleasonGradeTertiary", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", + "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", + "rdfs:label": "GleasonGradeTertiary", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Inflam Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Gleason Grade Tertiary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentLymphocyteInfiltration", + "@id": "bts:GleasonPatternsPercent", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", + "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", + "rdfs:label": "GleasonPatternsPercent", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Lymphocyte Infiltration", + "sms:displayName": "Gleason Patterns Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentMonocyteInfiltration", + "@id": "bts:GreatestTumorDimension", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", + "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", + "rdfs:label": "GreatestTumorDimension", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Monocyte Infiltration", + "sms:displayName": "Greatest Tumor Dimension", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNecrosis", + "@id": "bts:IGCCCGStage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", + "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", + "rdfs:label": "IGCCCGStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Necrosis", + "schema:rangeIncludes": [ + { + "@id": "bts:GoodPrognosis" + }, + { + "@id": "bts:IntermediatePrognosis" + }, + { + "@id": "bts:PoorPrognosis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "IGCCCG Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNeutrophilInfiltration", + "@id": "bts:INPCGrade", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", + "rdfs:label": "INPCGrade", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Neutrophil Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Differentiating" + }, + { + "@id": "bts:PoorlyDifferentiated" + }, + { + "@id": "bts:Undifferentiated" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNormalCells", + "@id": "bts:INPCHistologicGroup", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", + "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", + "rdfs:label": "INPCHistologicGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Normal Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:Favorable" + }, + { + "@id": "bts:Unfavorable" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Histologic Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentStromalCells", + "@id": "bts:INRGStage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", + "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", + "rdfs:label": "INRGStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Stromal Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:L1" + }, + { + "@id": "bts:L2" + }, + { + "@id": "bts:M" + }, + { + "@id": "bts:Ms" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INRG Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorCells", + "@id": "bts:INSSStage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", + "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", + "rdfs:label": "INSSStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:Stage1" + }, + { + "@id": "bts:Stage2A" + }, + { + "@id": "bts:Stage2B" + }, + { + "@id": "bts:Stage3" + }, + { + "@id": "bts:Stage4" + }, + { + "@id": "bts:Stage4S" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INSS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorNuclei", + "@id": "bts:InternationalPrognosticIndex", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", + "rdfs:comment": "The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.", + "rdfs:label": "InternationalPrognosticIndex", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Nuclei", + "schema:rangeIncludes": [ + { + "@id": "bts:LowRisk" + }, + { + "@id": "bts:Low-IntermediateRisk" + }, + { + "@id": "bts:High-IntermediateRisk" + }, + { + "@id": "bts:HighRisk" + } + ], + "sms:displayName": "International Prognostic Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FiducialMarker", + "@id": "bts:IRSGroup", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", + "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSGroup", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28418,19 +28458,34 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NuclearStain-DAPI" + "@id": "bts:GroupI" }, { - "@id": "bts:FluorescentBeads" + "@id": "bts:GroupIa" }, { - "@id": "bts:GridSlides-Hemocytometer" + "@id": "bts:GroupIb" }, { - "@id": "bts:AdhesiveMarkers" + "@id": "bts:GroupII" }, { - "@id": "bts:Other" + "@id": "bts:GroupIIa" + }, + { + "@id": "bts:GroupIIc" + }, + { + "@id": "bts:GroupIII" + }, + { + "@id": "bts:GroupIIIa" + }, + { + "@id": "bts:GroupIIIb" + }, + { + "@id": "bts:GroupIV" }, { "@id": "bts:Unknown" @@ -28439,18 +28494,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Fiducial Marker", + "sms:displayName": "IRS Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlicingMethod", + "@id": "bts:IRSStage", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", + "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28458,22 +28513,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Vibratome" - }, - { - "@id": "bts:Cryosectioning" - }, - { - "@id": "bts:Tissuemolds" + "@id": "bts:1" }, { - "@id": "bts:Slidingmicrotome" + "@id": "bts:2" }, { - "@id": "bts:Sectioning" + "@id": "bts:3" }, { - "@id": "bts:Other" + "@id": "bts:4" }, { "@id": "bts:Unknown" @@ -28482,173 +28531,157 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Slicing Method", + "sms:displayName": "IRS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LysisBuffer", + "@id": "bts:ISSStage", "@type": "rdfs:Class", - "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", - "rdfs:label": "LysisBuffer", + "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", + "rdfs:label": "ISSStage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lysis Buffer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MethodofNucleicAcidIsolation", - "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", - "rdfs:label": "MethodofNucleicAcidIsolation", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Method of Nucleic Acid Isolation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Biosample", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Biosample", - "rdfs:subClassOf": [ + "@id": "bts:I" + }, { - "@id": "bts:Thing" + "@id": "bts:II" + }, + { + "@id": "bts:III" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Biosample", + "sms:displayName": "ISS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SRRSBiospecimen", + "@id": "bts:LymphNodeInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", - "rdfs:label": "SRRSBiospecimen", + "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", + "rdfs:label": "LymphNodeInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Biospecimen", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "schema:rangeIncludes": [ { - "@id": "bts:Patient" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Axillary" + }, { - "@id": "bts:Component" + "@id": "bts:Cervical" }, { - "@id": "bts:HTANBiospecimenID" + "@id": "bts:Epitrochlear" }, { - "@id": "bts:SourceHTANBiospecimenID" + "@id": "bts:Femoral" }, { - "@id": "bts:HTANParentID" + "@id": "bts:Hilar" }, { - "@id": "bts:AdjacentBiospecimenIDs" + "@id": "bts:Iliac-common" }, { - "@id": "bts:BiospecimenType" + "@id": "bts:Iliac-external" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Iliac" }, { - "@id": "bts:CollectionDaysfromIndex" + "@id": "bts:NOS" }, { - "@id": "bts:AcquisitionMethodType" + "@id": "bts:Inguinal" }, { - "@id": "bts:IschemicTime" + "@id": "bts:Mediastinal" }, { - "@id": "bts:IschemicTemperature" + "@id": "bts:Mesenteric" }, { - "@id": "bts:CollectionMedia" + "@id": "bts:None" }, { - "@id": "bts:TopographyCode" + "@id": "bts:Occipital" }, { - "@id": "bts:AdditionalTopography" + "@id": "bts:Paraaortic" }, { - "@id": "bts:FixativeType" + "@id": "bts:Parotid" }, { - "@id": "bts:StorageMethod" + "@id": "bts:Popliteal" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:Retroperitoneal" }, { - "@id": "bts:HistologicMorphologyCode" + "@id": "bts:Splenic" }, { - "@id": "bts:PreservationMethod" + "@id": "bts:Submandibular" }, { - "@id": "bts:ProcessingDaysfromIndex" + "@id": "bts:Supraclavicular" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], + "sms:displayName": "Lymph Node Involved Site", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IschemicTime", + "@id": "bts:MarginDistance", "@type": "rdfs:Class", - "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", - "rdfs:label": "IschemicTime", + "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", + "rdfs:label": "MarginDistance", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ischemic Time", + "sms:displayName": "Margin Distance", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IschemicTemperature", + "@id": "bts:MarginsInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", - "rdfs:label": "IschemicTemperature", + "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", + "rdfs:label": "MarginsInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -28656,39 +28689,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:WarmIschemia" + "@id": "bts:GerotaFascia" }, { - "@id": "bts:ColdIschemia" + "@id": "bts:Parenchyma" }, { - "@id": "bts:Ambientair" + "@id": "bts:PerinephricFat" }, { - "@id": "bts:4Cwetice" + "@id": "bts:Renal" }, { - "@id": "bts:Negative-20C" + "@id": "bts:RenalCapsule" }, { - "@id": "bts:DryIce" + "@id": "bts:RenalSinus" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:RenalVein" }, { - "@id": "bts:Unknown" + "@id": "bts:Ureter" } ], - "sms:displayName": "Ischemic Temperature", + "sms:displayName": "Margins Involved Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TopographyCode", + "@id": "bts:MedulloblastomaMolecularClassification", "@type": "rdfs:Class", - "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", - "rdfs:label": "TopographyCode", + "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", + "rdfs:label": "MedulloblastomaMolecularClassification", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -28699,973 +28732,1558 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:C00.0" - }, - { - "@id": "bts:C00.1" + "@id": "bts:NotDetermined" }, { - "@id": "bts:C00.2" + "@id": "bts:Non-WNT/non-SHHActivated" }, { - "@id": "bts:C00.3" + "@id": "bts:SHH-Activated" }, { - "@id": "bts:C00.4" + "@id": "bts:WNT-Activated" }, { - "@id": "bts:C00.5" + "@id": "bts:Unknown" }, { - "@id": "bts:C00.6" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Medulloblastoma Molecular Classification", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MicropapillaryFeatures", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", + "rdfs:label": "MicropapillaryFeatures", + "rdfs:subClassOf": [ { - "@id": "bts:C00.8" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C01.9" + "@id": "bts:Absent" }, { - "@id": "bts:C02.0" + "@id": "bts:Present" }, { - "@id": "bts:C02.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C02.2" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Micropapillary Features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MitosisKaryorrhexisIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", + "rdfs:label": "MitosisKaryorrhexisIndex", + "rdfs:subClassOf": [ { - "@id": "bts:C02.3" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C02.4" + "@id": "bts:High" }, { - "@id": "bts:C02.8" + "@id": "bts:Intermediate" }, { - "@id": "bts:C02.9" + "@id": "bts:Low" }, { - "@id": "bts:C03.0" + "@id": "bts:Unknown" }, { - "@id": "bts:C03.1" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mitosis Karyorrhexis Index", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NonNodalRegionalDisease", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", + "rdfs:label": "NonNodalRegionalDisease", + "rdfs:subClassOf": [ { - "@id": "bts:C03.9" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C04.0" + "@id": "bts:Absent" }, { - "@id": "bts:C04.1" + "@id": "bts:Indeterminate" }, { - "@id": "bts:C04.8" + "@id": "bts:Present" }, { - "@id": "bts:C04.9" + "@id": "bts:Unknown" }, { - "@id": "bts:C05.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Regional Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NonNodalTumorDeposits", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", + "rdfs:label": "NonNodalTumorDeposits", + "rdfs:subClassOf": [ { - "@id": "bts:C05.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C05.2" + "@id": "bts:Yes" }, { - "@id": "bts:C05.8" + "@id": "bts:No" }, { - "@id": "bts:C05.9" + "@id": "bts:Unknown" }, { - "@id": "bts:C06.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Tumor Deposits", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianSpecimenStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", + "rdfs:label": "OvarianSpecimenStatus", + "rdfs:subClassOf": [ { - "@id": "bts:C06.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C06.2" + "@id": "bts:OvarianCapsuleIntact" }, { - "@id": "bts:C06.8" + "@id": "bts:OvarianCapsuleRuptured" }, { - "@id": "bts:C06.9" + "@id": "bts:OvarianCapsuleFragmented" }, { - "@id": "bts:C07.9" + "@id": "bts:Unknown" }, { - "@id": "bts:C08.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ovarian Specimen Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianSurfaceInvolvement", + "@type": "rdfs:Class", + "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", + "rdfs:label": "OvarianSurfaceInvolvement", + "rdfs:subClassOf": [ { - "@id": "bts:C08.1" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C08.8" + "@id": "bts:Absent" }, { - "@id": "bts:C08.9" + "@id": "bts:Present" }, { - "@id": "bts:C09.0" + "@id": "bts:Indeterminate" }, { - "@id": "bts:C09.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C09.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ovarian Surface Involvement", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnantatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", + "rdfs:label": "PregnantatDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:C09.9" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C10.0" + "@id": "bts:Yes" }, { - "@id": "bts:C10.1" + "@id": "bts:No" }, { - "@id": "bts:C10.2" + "@id": "bts:Unknown" }, { - "@id": "bts:C10.3" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pregnant at Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryGleasonGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "PrimaryGleasonGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C10.4" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C10.8" + "@id": "bts:Pattern1" }, { - "@id": "bts:C10.9" + "@id": "bts:Pattern2" }, { - "@id": "bts:C11.0" + "@id": "bts:Pattern3" }, { - "@id": "bts:C11.1" + "@id": "bts:Pattern4" }, { - "@id": "bts:C11.2" - }, + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Primary Gleason Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondaryGleasonGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "SecondaryGleasonGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C11.3" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C11.8" + "@id": "bts:Pattern1" }, { - "@id": "bts:C11.9" + "@id": "bts:Pattern2" }, { - "@id": "bts:C12.9" + "@id": "bts:Pattern3" }, { - "@id": "bts:C13.0" + "@id": "bts:Pattern4" }, { - "@id": "bts:C13.1" - }, + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Secondary Gleason Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SupratentorialLocalization", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", + "rdfs:label": "SupratentorialLocalization", + "rdfs:subClassOf": [ { - "@id": "bts:C13.2" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C13.8" + "@id": "bts:CerebralCortex" }, { - "@id": "bts:C13.9" + "@id": "bts:DeepGray" }, { - "@id": "bts:C14.0" + "@id": "bts:SpinalCord" }, { - "@id": "bts:C14.2" + "@id": "bts:WhiteMatter" }, { - "@id": "bts:C14.8" + "@id": "bts:Unknown" }, { - "@id": "bts:C15.0" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Supratentorial Localization", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorDepth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", + "rdfs:label": "TumorDepth", + "rdfs:subClassOf": [ { - "@id": "bts:C15.1" - }, - { - "@id": "bts:C15.2" - }, - { - "@id": "bts:C15.3" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tumor Depth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHOCNSGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO CNS Grade", + "rdfs:label": "WHOCNSGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C15.4" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C15.5" + "@id": "bts:GradeI" }, { - "@id": "bts:C15.8" + "@id": "bts:GradeII" }, { - "@id": "bts:C15.9" + "@id": "bts:GradeIII" }, { - "@id": "bts:C16.0" + "@id": "bts:GradeIV" }, { - "@id": "bts:C16.1" + "@id": "bts:GradeNotAssigned" }, { - "@id": "bts:C16.2" + "@id": "bts:Unknown" }, { - "@id": "bts:C16.3" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO CNS Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHONTEGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO NTE Grade", + "rdfs:label": "WHONTEGrade", + "rdfs:subClassOf": [ { - "@id": "bts:C16.4" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C16.5" + "@id": "bts:G1" }, { - "@id": "bts:C16.6" + "@id": "bts:G2" }, { - "@id": "bts:C16.8" + "@id": "bts:G3" }, { - "@id": "bts:C16.9" + "@id": "bts:GX" }, { - "@id": "bts:C17.0" + "@id": "bts:Unknown" }, { - "@id": "bts:C17.1" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO NTE Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AAChange", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "AAChange", + "rdfs:subClassOf": [ { - "@id": "bts:C17.2" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "AA Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Antigen", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Antigen", + "rdfs:subClassOf": [ { - "@id": "bts:C17.3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C17.8" + "@id": "bts:BCL6" }, { - "@id": "bts:C17.9" + "@id": "bts:CA-125" }, { - "@id": "bts:C18.0" + "@id": "bts:CA19-9" }, { - "@id": "bts:C18.1" + "@id": "bts:CCND1" }, { - "@id": "bts:C18.2" + "@id": "bts:CD10" }, { - "@id": "bts:C18.3" + "@id": "bts:CD117" }, { - "@id": "bts:C18.4" + "@id": "bts:CD138" }, { - "@id": "bts:C18.5" + "@id": "bts:CD14" }, { - "@id": "bts:C18.6" + "@id": "bts:CD15" }, { - "@id": "bts:C18.7" + "@id": "bts:CD19" }, { - "@id": "bts:C18.8" + "@id": "bts:CD20" }, { - "@id": "bts:C18.9" + "@id": "bts:CD22" }, { - "@id": "bts:C19.9" + "@id": "bts:CD23" }, { - "@id": "bts:C20.9" + "@id": "bts:CD25" }, { - "@id": "bts:C21.0" + "@id": "bts:CD3" }, { - "@id": "bts:C21.1" + "@id": "bts:CD30" }, { - "@id": "bts:C21.2" + "@id": "bts:CD33" }, { - "@id": "bts:C21.8" + "@id": "bts:CD34" }, { - "@id": "bts:C22.0" + "@id": "bts:CD45" }, { - "@id": "bts:C22.1" + "@id": "bts:CD5" }, { - "@id": "bts:C23.9" + "@id": "bts:CD56" }, { - "@id": "bts:C24.0" + "@id": "bts:CD7" }, { - "@id": "bts:C24.1" + "@id": "bts:CD79A" }, { - "@id": "bts:C24.8" + "@id": "bts:CEA" }, { - "@id": "bts:C24.9" + "@id": "bts:HLA-DR" }, { - "@id": "bts:C25.0" + "@id": "bts:Mesothelin" }, { - "@id": "bts:C25.1" + "@id": "bts:NSE" }, { - "@id": "bts:C25.2" + "@id": "bts:SquamousCellCarcinomaAntigen" }, { - "@id": "bts:C25.3" + "@id": "bts:Unknown" }, { - "@id": "bts:C25.4" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Antigen", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalBiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "ClinicalBiospecimenType", + "rdfs:subClassOf": [ { - "@id": "bts:C25.7" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C25.8" + "@id": "bts:Blood" }, { - "@id": "bts:C25.9" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:C26.0" + "@id": "bts:BuccalMucosa" }, { - "@id": "bts:C26.8" + "@id": "bts:BuffyCoat" }, { - "@id": "bts:C26.9" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:C30.0" + "@id": "bts:ConnectiveTissue" }, { - "@id": "bts:C30.1" + "@id": "bts:EmbryonicFluid" }, { - "@id": "bts:C31.0" + "@id": "bts:EmbryonicTissue" }, { - "@id": "bts:C31.1" + "@id": "bts:Feces" }, { - "@id": "bts:C31.2" + "@id": "bts:Granulocyte" }, { - "@id": "bts:C31.3" + "@id": "bts:MuscleTissue" }, { - "@id": "bts:C31.8" + "@id": "bts:NerveTissue" }, { - "@id": "bts:C31.9" + "@id": "bts:PeritonealFluid" }, { - "@id": "bts:C32.0" + "@id": "bts:Plasma" }, { - "@id": "bts:C32.1" + "@id": "bts:PleuralFluid" }, { - "@id": "bts:C32.2" + "@id": "bts:Saliva" }, { - "@id": "bts:C32.3" + "@id": "bts:Serum" }, { - "@id": "bts:C32.8" + "@id": "bts:Skin" }, { - "@id": "bts:C32.9" + "@id": "bts:SoftTissue" }, { - "@id": "bts:C33.9" + "@id": "bts:TissueNOS" }, { - "@id": "bts:C34.0" + "@id": "bts:UninvolvedTissueNOS" }, { - "@id": "bts:C34.1" + "@id": "bts:Urine" }, { - "@id": "bts:C34.2" + "@id": "bts:Unknown" }, { - "@id": "bts:C34.3" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Clinical Biospecimen Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeUpper", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeUpper", + "rdfs:subClassOf": [ { - "@id": "bts:C34.8" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Upper", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeLower", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:subClassOf": [ { - "@id": "bts:C34.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Lower", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CellCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CellCount", + "rdfs:subClassOf": [ { - "@id": "bts:C37.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Chromosome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Chromosome", + "rdfs:subClassOf": [ { - "@id": "bts:C38.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C38.1" + "@id": "bts:Chr1" }, { - "@id": "bts:C38.2" + "@id": "bts:Chr2" }, { - "@id": "bts:C38.3" + "@id": "bts:Chr3" }, { - "@id": "bts:C38.4" + "@id": "bts:Chr4" }, { - "@id": "bts:C38.8" + "@id": "bts:Chr5" }, { - "@id": "bts:C39.0" + "@id": "bts:Chr6" }, { - "@id": "bts:C39.8" + "@id": "bts:Chr7" }, { - "@id": "bts:C39.9" + "@id": "bts:Chr8" }, { - "@id": "bts:C40.0" + "@id": "bts:Chr9" }, { - "@id": "bts:C40.1" + "@id": "bts:Chr10" }, { - "@id": "bts:C40.3" + "@id": "bts:Chr11" }, { - "@id": "bts:C40.8" + "@id": "bts:Chr12" }, { - "@id": "bts:C40.9" + "@id": "bts:Chr13" }, { - "@id": "bts:C41.0" + "@id": "bts:Chr14" }, { - "@id": "bts:C41.1" + "@id": "bts:Chr15" }, { - "@id": "bts:C41.2" + "@id": "bts:Chr16" }, { - "@id": "bts:C41.3" + "@id": "bts:Chr17" }, { - "@id": "bts:C41.4" + "@id": "bts:Chr18" }, { - "@id": "bts:C41.8" + "@id": "bts:Chr19" }, { - "@id": "bts:C41.9" + "@id": "bts:Chr20" }, { - "@id": "bts:C42.0" + "@id": "bts:Chr21" }, { - "@id": "bts:C42.1" + "@id": "bts:Chr22" }, { - "@id": "bts:C42.2" + "@id": "bts:Chr23" }, { - "@id": "bts:C42.3" + "@id": "bts:ChrM" }, { - "@id": "bts:C42.4" + "@id": "bts:ChrX" }, { - "@id": "bts:C44.0" + "@id": "bts:ChrY" }, { - "@id": "bts:C44.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C44.2" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Chromosome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Clonality", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Clonality", + "rdfs:subClassOf": [ { - "@id": "bts:C44.3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C44.4" + "@id": "bts:Clonal" }, { - "@id": "bts:C44.5" - }, + "@id": "bts:Non-clonal" + } + ], + "sms:displayName": "Clonality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CopyNumber", + "rdfs:subClassOf": [ { - "@id": "bts:C44.6" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Copy Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cytoband", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Cytoband", + "rdfs:subClassOf": [ { - "@id": "bts:C44.7" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cytoband", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Exon", + "@type": "rdfs:Class", + "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Exon", + "rdfs:subClassOf": [ { - "@id": "bts:C47.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneFamily", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "rdfs:label": "HistoneFamily", + "rdfs:subClassOf": [ { - "@id": "bts:C47.1" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C47.2" + "@id": "bts:H1" }, { - "@id": "bts:C47.3" + "@id": "bts:H2A" }, { - "@id": "bts:C47.4" + "@id": "bts:H2B" }, { - "@id": "bts:C47.5" + "@id": "bts:H3" }, { - "@id": "bts:C47.6" + "@id": "bts:H4" }, { - "@id": "bts:C47.8" + "@id": "bts:Unknown" }, { - "@id": "bts:C47.9" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Family", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneVariant", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "HistoneVariant", + "rdfs:subClassOf": [ { - "@id": "bts:C48.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C48.1" + "@id": "bts:CENP-A" }, { - "@id": "bts:C48.2" + "@id": "bts:H2A-Bbd" }, { - "@id": "bts:C48.8" + "@id": "bts:H2A.X" }, { - "@id": "bts:C49.0" + "@id": "bts:H2A.Z" }, { - "@id": "bts:C49.1" + "@id": "bts:H2A.Z.1" }, { - "@id": "bts:C49.2" + "@id": "bts:H2A.Z.2" }, { - "@id": "bts:C49.3" + "@id": "bts:H2A.Z.2.2" }, { - "@id": "bts:C49.4" + "@id": "bts:H3.1" }, { - "@id": "bts:C49.5" + "@id": "bts:H3.2" }, { - "@id": "bts:C49.6" + "@id": "bts:H3.3" }, { - "@id": "bts:C49.8" + "@id": "bts:H3.5" }, { - "@id": "bts:C49.9" + "@id": "bts:H3.X" }, { - "@id": "bts:C50.0" + "@id": "bts:H3.Y" }, { - "@id": "bts:C50.1" + "@id": "bts:H3t(H3.4)" }, { - "@id": "bts:C50.2" + "@id": "bts:MH2A" }, { - "@id": "bts:C50.3" + "@id": "bts:MH2A.1" }, { - "@id": "bts:C50.4" + "@id": "bts:MH2A.2" }, { - "@id": "bts:C50.5" + "@id": "bts:Unknown" }, { - "@id": "bts:C50.6" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Variant", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Intron", + "@type": "rdfs:Class", + "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", + "rdfs:label": "Intron", + "rdfs:subClassOf": [ { - "@id": "bts:C50.8" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Intron", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LaboratoryTest", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", + "rdfs:label": "LaboratoryTest", + "rdfs:subClassOf": [ { - "@id": "bts:C50.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C51.0" + "@id": "bts:AbsoluteNeutrophil" }, { - "@id": "bts:C51.1" + "@id": "bts:Albumin" }, { - "@id": "bts:C51.2" + "@id": "bts:AlphaFetoprotein" }, { - "@id": "bts:C51.8" + "@id": "bts:B-cellgenotyping" }, { - "@id": "bts:C51.9" + "@id": "bts:Basophil" }, { - "@id": "bts:C52.9" + "@id": "bts:Beta2Microglobulin" }, { - "@id": "bts:C53.0" + "@id": "bts:BloodUreaNitrogen" }, { - "@id": "bts:C53.1" + "@id": "bts:C-ReactiveProtein" }, { - "@id": "bts:C53.8" + "@id": "bts:Calcium" }, { - "@id": "bts:C53.9" + "@id": "bts:Cellularity" }, { - "@id": "bts:C54.0" + "@id": "bts:CirculatingTumorCells" }, { - "@id": "bts:C54.1" + "@id": "bts:Creatinine" }, { - "@id": "bts:C54.2" + "@id": "bts:Eosinophil" }, { - "@id": "bts:C54.3" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:C54.8" + "@id": "bts:Glucose" }, { - "@id": "bts:C54.9" + "@id": "bts:Hematocrit" }, { - "@id": "bts:C55.9" + "@id": "bts:Hemoglobin" }, { - "@id": "bts:C56.9" + "@id": "bts:HPV-E6/E7" }, { - "@id": "bts:C57.0" + "@id": "bts:HumanChorionicGonadotropin" }, { - "@id": "bts:C57.1" + "@id": "bts:HumanPapillomavirus" }, { - "@id": "bts:C57.2" + "@id": "bts:ImmunoglobulinA" }, { - "@id": "bts:C57.3" + "@id": "bts:ImmunoglobulinG" }, { - "@id": "bts:C57.4" + "@id": "bts:ImmunoglobulinM" }, { - "@id": "bts:C57.7" + "@id": "bts:LactateDehydrogenase" }, { - "@id": "bts:C57.8" + "@id": "bts:Leukocytes" }, { - "@id": "bts:C57.9" + "@id": "bts:LuteinizingHormone" }, { - "@id": "bts:C60.0" + "@id": "bts:Lymphoblasts" }, { - "@id": "bts:C60.1" + "@id": "bts:Lymphocytes" }, { - "@id": "bts:C60.2" + "@id": "bts:MProtein" }, { - "@id": "bts:C60.8" + "@id": "bts:Metamyelocytes" }, { - "@id": "bts:C60.9" + "@id": "bts:Myeloblasts" }, { - "@id": "bts:C61.9" + "@id": "bts:Myelocytes" }, { - "@id": "bts:C62.0" + "@id": "bts:NeutrophilBands" }, { - "@id": "bts:C62.1" + "@id": "bts:Platelets" }, { - "@id": "bts:C62.9" + "@id": "bts:Prolymphocytes" }, { - "@id": "bts:C63.0" + "@id": "bts:Promonocytes" }, { - "@id": "bts:C63.1" + "@id": "bts:Promyelocytes" }, { - "@id": "bts:C63.2" + "@id": "bts:SegmentedNeutrophil" }, { - "@id": "bts:C63.7" + "@id": "bts:SerumFreeImmunoglobulinLightChain" }, { - "@id": "bts:C63.8" + "@id": "bts:Kappa" }, { - "@id": "bts:C63.9" + "@id": "bts:Lambda" }, { - "@id": "bts:C64.9" + "@id": "bts:NOS" }, { - "@id": "bts:C65.9" + "@id": "bts:Testosterone" }, { - "@id": "bts:C66.9" + "@id": "bts:TotalBilirubin" }, { - "@id": "bts:C67.0" + "@id": "bts:TotalProtein" }, { - "@id": "bts:C67.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C67.2" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laboratory Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociAbnormalCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", + "rdfs:label": "LociAbnormalCount", + "rdfs:subClassOf": [ { - "@id": "bts:C67.4" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Abnormal Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci tested.", + "rdfs:label": "LociCount", + "rdfs:subClassOf": [ { - "@id": "bts:C67.6" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Locus", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label": "Locus", + "rdfs:subClassOf": [ { - "@id": "bts:C67.7" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Locus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MismatchRepairMutation", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MismatchRepairMutation", + "rdfs:subClassOf": [ { - "@id": "bts:C67.8" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C67.9" + "@id": "bts:Yes" }, { - "@id": "bts:C68.0" + "@id": "bts:No" }, { - "@id": "bts:C68.1" + "@id": "bts:Unknown" }, { - "@id": "bts:C68.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mismatch Repair Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularConsequence", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularConsequence", + "rdfs:subClassOf": [ { - "@id": "bts:C68.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C69.0" + "@id": "bts:3PrimeUTRVariant" }, { - "@id": "bts:C69.1" + "@id": "bts:5PrimeUTRVariant" }, { - "@id": "bts:C69.2" + "@id": "bts:CodingSequenceVariant" }, { - "@id": "bts:C69.3" + "@id": "bts:DownstreamGeneVariant" }, { - "@id": "bts:C69.4" + "@id": "bts:FeatureElongation" }, { - "@id": "bts:C69.5" + "@id": "bts:FeatureTruncation" }, { - "@id": "bts:C69.6" + "@id": "bts:FrameshiftVariant" }, { - "@id": "bts:C69.8" + "@id": "bts:IncompleteTerminalCodonVariant" }, { - "@id": "bts:C69.9" + "@id": "bts:InframeDeletion" }, { - "@id": "bts:C70.0" + "@id": "bts:InframeInsertion" }, { - "@id": "bts:C70.1" + "@id": "bts:IntergenicVariant" }, { - "@id": "bts:C70.9" + "@id": "bts:IntronVariant" }, { - "@id": "bts:C71.0" + "@id": "bts:MaturemiRNAVariant" }, { - "@id": "bts:C71.1" + "@id": "bts:MissenseVariant" }, { - "@id": "bts:C71.2" + "@id": "bts:NMDTranscriptVariant" }, { - "@id": "bts:C71.3" + "@id": "bts:Non-codingTranscriptExonVariant" }, { - "@id": "bts:C71.4" + "@id": "bts:Non-codingTranscriptVariant" }, { - "@id": "bts:C71.5" + "@id": "bts:ProteinAlteringVariant" }, { - "@id": "bts:C71.6" + "@id": "bts:RegulatoryRegionAblation" }, { - "@id": "bts:C71.7" + "@id": "bts:RegulatoryRegionAmplification" }, { - "@id": "bts:C71.8" + "@id": "bts:RegulatoryRegionVariant" }, { - "@id": "bts:C71.9" + "@id": "bts:SpliceAcceptorVariant" }, { - "@id": "bts:C72.0" + "@id": "bts:SpliceDonorVariant" }, { - "@id": "bts:C72.1" + "@id": "bts:SpliceRegionVariant" }, { - "@id": "bts:C72.2" + "@id": "bts:StartLost" }, { - "@id": "bts:C72.3" + "@id": "bts:StopGain" }, { - "@id": "bts:C72.4" + "@id": "bts:StopLost" }, { - "@id": "bts:C72.5" + "@id": "bts:StopRetainedVariant" }, { - "@id": "bts:C72.8" + "@id": "bts:SynonymousVariant" }, { - "@id": "bts:C72.9" + "@id": "bts:TFBindingSiteVariant" }, { - "@id": "bts:C73.9" + "@id": "bts:TFBSAblation" }, { - "@id": "bts:C74.0" + "@id": "bts:TFBSAmplification" }, { - "@id": "bts:C74.1" + "@id": "bts:TranscriptAblation" }, { - "@id": "bts:C74.9" + "@id": "bts:TranscriptAmplification" }, { - "@id": "bts:C75.0" - }, + "@id": "bts:UpstreamGeneVariant" + } + ], + "sms:displayName": "Molecular Consequence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pathogenicity", + "@type": "rdfs:Class", + "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "rdfs:label": "Pathogenicity", + "rdfs:subClassOf": [ { - "@id": "bts:C75.1" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C75.2" + "@id": "bts:Benign" }, { - "@id": "bts:C75.3" + "@id": "bts:LikelyBenign" }, { - "@id": "bts:C75.4" + "@id": "bts:LikelyPathogenic" }, { - "@id": "bts:C75.5" + "@id": "bts:Pathogenic" }, { - "@id": "bts:C75.8" - }, + "@id": "bts:UncertainSignificance" + } + ], + "sms:displayName": "Pathogenicity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ploidy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", + "rdfs:label": "Ploidy", + "rdfs:subClassOf": [ { - "@id": "bts:C75.9" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C76.0" + "@id": "bts:Aneuploid" }, { - "@id": "bts:C76.1" + "@id": "bts:Diploid" }, { - "@id": "bts:C76.2" + "@id": "bts:Hyperdiploid" }, { - "@id": "bts:C76.3" + "@id": "bts:Hypodiploid" }, { - "@id": "bts:C76.4" + "@id": "bts:NearDiploid" }, { - "@id": "bts:C76.5" + "@id": "bts:Tetraploid" }, { - "@id": "bts:C76.7" + "@id": "bts:Unknown" }, { - "@id": "bts:C76.8" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ploidy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondExon", + "@type": "rdfs:Class", + "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label": "SecondExon", + "rdfs:subClassOf": [ { - "@id": "bts:C77.0" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondGeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SecondGeneSymbol", + "rdfs:subClassOf": [ { - "@id": "bts:C77.1" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Gene Symbol", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpecializedMolecularTest", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SpecializedMolecularTest", + "rdfs:subClassOf": [ { - "@id": "bts:C77.2" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Specialized Molecular Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestAnalyteType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestAnalyteType", + "rdfs:subClassOf": [ { - "@id": "bts:C77.3" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C77.4" + "@id": "bts:DNA" }, { - "@id": "bts:C77.5" + "@id": "bts:MRNA" }, { - "@id": "bts:C77.8" + "@id": "bts:MiRNA" }, { - "@id": "bts:C77.9" + "@id": "bts:ProteinAnalyte" }, { - "@id": "bts:C80.9" + "@id": "bts:TotalRNA" }, { "@id": "bts:Unknown" @@ -29674,123 +30292,97 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Topography Code", + "sms:displayName": "Test Analyte Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdditionalTopography", + "@id": "bts:TestUnits", "@type": "rdfs:Class", - "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", - "rdfs:label": "AdditionalTopography", + "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestUnits", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Skinofscalp" - }, - { - "@id": "bts:Skinofeyelid" - }, - { - "@id": "bts:Skinofnose" - }, - { - "@id": "bts:Skinoflip" - }, - { - "@id": "bts:Skinofear" - }, - { - "@id": "bts:Skinofneck" - }, - { - "@id": "bts:Skinofotherpartsofface" - }, - { - "@id": "bts:Skinofchest" - }, - { - "@id": "bts:Skinofback" - }, - { - "@id": "bts:Skinofabdomen" - }, - { - "@id": "bts:Skinoftrunk" - }, - { - "@id": "bts:Skinofbreast" - }, - { - "@id": "bts:Skinofupperlimbandshoulder" - }, - { - "@id": "bts:Skinofpalm" - }, - { - "@id": "bts:Skinoflowerlimbandhip" - }, - { - "@id": "bts:Skinofsole" - }, - { - "@id": "bts:Skinofpenis" - }, - { - "@id": "bts:Skinofscrotum" - }, - { - "@id": "bts:Skinofvulva" - }, - { - "@id": "bts:SkinNOS" - }, - { - "@id": "bts:HilarAirway" - }, + "sms:displayName": "Test Units", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestValue", + "@type": "rdfs:Class", + "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", + "rdfs:label": "TestValue", + "rdfs:subClassOf": [ { - "@id": "bts:Peri-tumoralAirway" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Transcript", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Transcript", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:MolecularTest" } ], - "sms:displayName": "Additional Topography", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Transcript", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologicMorphologyCode", + "@id": "bts:VariantOrigin", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", - "rdfs:label": "HistologicMorphologyCode", + "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "VariantOrigin", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Histologic Morphology Code", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Germline" + }, + { + "@id": "bts:Somatic" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Variant Origin", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PreservationMethod", + "@id": "bts:VariantType", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the method used to preserve the sample.", - "rdfs:label": "PreservationMethod", + "rdfs:comment": "The text term used to describe the type of genetic variation.", + "rdfs:label": "VariantType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -29798,58 +30390,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Cryopreserved" + "@id": "bts:Alleles" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" + "@id": "bts:Amplification" }, { - "@id": "bts:Cryopreservationindryice-deadtissue" + "@id": "bts:Chrimerism" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-livecells" + "@id": "bts:Conversion" }, { - "@id": "bts:Formalinfixedparaffinembedded-FFPE" + "@id": "bts:Deletion" }, { - "@id": "bts:Formalinfixed-unbuffered" + "@id": "bts:Deletion-Insertion" }, { - "@id": "bts:Formalinfixed-buffered" + "@id": "bts:Duplication" }, { - "@id": "bts:Fresh" + "@id": "bts:Extension" }, { - "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + "@id": "bts:Gain" }, { - "@id": "bts:OCT" + "@id": "bts:Hypermethylation" }, { - "@id": "bts:SnapFrozen" + "@id": "bts:Insertion" }, { - "@id": "bts:Frozen" + "@id": "bts:Inversion" }, { - "@id": "bts:Negative80DegC" + "@id": "bts:Loss" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:Methylation" }, { - "@id": "bts:Freshdissociated" + "@id": "bts:Mosaicism" }, { - "@id": "bts:Freshdissociatedandsinglecellsorted" + "@id": "bts:Other" }, { - "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + "@id": "bts:PartialMethylation" }, { - "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + "@id": "bts:Rearrangement" + }, + { + "@id": "bts:RepeatedSequences" + }, + { + "@id": "bts:Splice" + }, + { + "@id": "bts:Substitution" + }, + { + "@id": "bts:Translocation" }, { "@id": "bts:Unknown" @@ -29858,221 +30462,242 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Preservation Method", - "sms:required": "sms:true", + "sms:displayName": "Variant Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OtherAssay", + "@id": "bts:Zygosity", "@type": "rdfs:Class", - "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", - "rdfs:label": "OtherAssay", + "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", + "rdfs:label": "Zygosity", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - }, - { - "@id": "bts:DataType" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Assay", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Heterozygous" }, { - "@id": "bts:Filename" + "@id": "bts:Hemizygous" }, { - "@id": "bts:FileFormat" + "@id": "bts:Homozygous" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Nullizygous" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Unknown" }, { - "@id": "bts:AssayType" + "@id": "bts:NotReported" } ], + "sms:displayName": "Zygosity", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AssayType", + "@id": "bts:SourceHTANBiospecimenID", "@type": "rdfs:Class", - "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", - "rdfs:label": "AssayType", + "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", + "rdfs:label": "SourceHTANBiospecimenID", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Assay Type", - "sms:required": "sms:true", + "sms:displayName": "Source HTAN Biospecimen ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExSeqMinimal", + "@id": "bts:CollectionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Minimal metadata for the ExSeq assay", - "rdfs:label": "ExSeqMinimal", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", + "rdfs:label": "CollectionDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq Minimal", + "sms:displayName": "Collection Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:AdjacentBiospecimenIDs", + "@type": "rdfs:Class", + "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", + "rdfs:label": "AdjacentBiospecimenIDs", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adjacent Biospecimen IDs", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:BiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "Biospecimen Type", + "rdfs:label": "BiospecimenType", + "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" } ], - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:TissueBiospecimenType" }, { - "@id": "bts:Filename" + "@id": "bts:BloodBiospecimenType" }, { - "@id": "bts:FileFormat" + "@id": "bts:AnalyteBiospecimenType" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:MouthRinseBiospecimenType" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:StoolBiospecimenType" }, { - "@id": "bts:AssayType" + "@id": "bts:UrineBiospecimenType" + }, + { + "@id": "bts:AscitesBiospecimenType" + }, + { + "@id": "bts:SputumBiospecimenType" + }, + { + "@id": "bts:FluidsBiospecimenType" + }, + { + "@id": "bts:BoneMarrowBiospecimenType" + }, + { + "@id": "bts:CellsBiospecimenType" } ], + "sms:displayName": "Biospecimen Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel1", + "@id": "bts:AcquisitionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", - "rdfs:label": "ScRNA-seqLevel1", + "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", + "rdfs:label": "AcquisitionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANDataFileID" + "@id": "bts:Autopsy" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:Biopsy" }, { - "@id": "bts:CryopreservedCellsinSample" + "@id": "bts:FineNeedleAspirate" }, { - "@id": "bts:SingleCellIsolationMethod" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:PunchBiopsy" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:ShaveBiopsy" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:Excision" }, { - "@id": "bts:Read1" + "@id": "bts:Re-excision" }, { - "@id": "bts:Read2" + "@id": "bts:SentinelNodeBiopsy" }, { - "@id": "bts:EndBias" + "@id": "bts:Lymphadenectomy-RegionalNodes" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:OtherAcquisitionMethod" }, { - "@id": "bts:SpikeIn" + "@id": "bts:Noninducedsputum" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:Inducedsputum" }, { - "@id": "bts:TotalNumberofInputCells" + "@id": "bts:BAL(bronchialalveolarlavage)" }, { - "@id": "bts:InputCellsandNuclei" + "@id": "bts:Cytobrush" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:Blooddraw" }, { - "@id": "bts:SingleCellDissociationDaysfromIndex" + "@id": "bts:Fluidcollection" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:Forcepsbiopsy" }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex" + "@id": "bts:Coreneedlebiopsy" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Endoscopicbiopsy" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:Notspecified" } ], + "sms:displayName": "Acquisition Method Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidSource", + "@id": "bts:FixativeType", "@type": "rdfs:Class", - "rdfs:comment": "The source of the input nucleic molecule", - "rdfs:label": "NucleicAcidSource", + "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", + "rdfs:label": "FixativeType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30080,126 +30705,87 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:SingleCell" + "@id": "bts:Acetone" }, { - "@id": "bts:BulkWholeCell" + "@id": "bts:Alcohol" }, { - "@id": "bts:SingleNucleus" + "@id": "bts:Formalin" }, { - "@id": "bts:BulkNuclei" + "@id": "bts:Glutaraldehyde" }, { - "@id": "bts:Micro-region" - } - ], - "sms:displayName": "Nucleic Acid Source", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CryopreservedCellsinSample", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", - "rdfs:label": "CryopreservedCellsinSample", - "rdfs:subClassOf": [ + "@id": "bts:OCTmedia" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RNAlater" + }, { - "@id": "bts:Yes" + "@id": "bts:Saline" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Cryopreserved Cells in Sample", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SingleCellIsolationMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", - "rdfs:label": "SingleCellIsolationMethod", - "rdfs:subClassOf": [ + "@id": "bts:95%Ethanol" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Dimidoester" + }, { - "@id": "bts:MicrofluidicsChip" + "@id": "bts:Carbodiimide" }, { - "@id": "bts:Droplets" + "@id": "bts:Dimethylacetamide" }, { - "@id": "bts:FACS" + "@id": "bts:Para-benzoquinone" }, { - "@id": "bts:Plates" + "@id": "bts:PAXgenetissue" }, { - "@id": "bts:10x" + "@id": "bts:TCLlysisbuffer" }, { - "@id": "bts:NucleiIsolation" - } - ], - "sms:displayName": "Single Cell Isolation Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DissociationMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", - "rdfs:label": "DissociationMethod", - "rdfs:subClassOf": [ + "@id": "bts:NP40lysisbuffer" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Methacarn" + }, { - "@id": "bts:GentleMACS" + "@id": "bts:Cryo-store" }, { - "@id": "bts:Dounce" + "@id": "bts:Carnoy'sFixative" }, { - "@id": "bts:EnzymaticDigestion" + "@id": "bts:Polaxamer" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Other" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unfixed" } ], - "sms:displayName": "Dissociation Method", + "sms:displayName": "Fixative Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryConstructionMethod", + "@id": "bts:StorageMethod", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "LibraryConstructionMethod", + "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", + "rdfs:label": "StorageMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30207,131 +30793,128 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" + "@id": "bts:Ambienttemperature" }, { - "@id": "bts:Smart-SeqV4" + "@id": "bts:Cutslide" }, { - "@id": "bts:10xV1.0" + "@id": "bts:Fresh" }, { - "@id": "bts:10xV1.1" + "@id": "bts:Frozenat-20C" }, { - "@id": "bts:10xV2" + "@id": "bts:Frozenat-70C" }, { - "@id": "bts:10xV3" + "@id": "bts:Frozenat-80C" }, { - "@id": "bts:10xV3.1" + "@id": "bts:Frozenat-150C" }, { - "@id": "bts:CEL-seq2" + "@id": "bts:Frozeninliquidnitrogen" }, { - "@id": "bts:Drop-seq" + "@id": "bts:Frozeninvaporphase" }, { - "@id": "bts:InDropsV2" + "@id": "bts:Paraffinblock" }, { - "@id": "bts:InDropsV3" + "@id": "bts:RNAlaterat4C" }, { - "@id": "bts:TruDrop" + "@id": "bts:RNAlaterat25C" }, { - "@id": "bts:Sci-ATAC-seq" + "@id": "bts:RNAlaterat-20C" }, { - "@id": "bts:NexteraXT" + "@id": "bts:Refrigeratedat4degrees" }, { - "@id": "bts:10xMultiome" + "@id": "bts:Refrigeratedvacuumchamber" }, { - "@id": "bts:10xFLEX" + "@id": "bts:4Cinvacuumchamber" }, { - "@id": "bts:10xGEM3'" + "@id": "bts:Desiccantat4C" }, { - "@id": "bts:10xGEM5'" + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Library Construction Method", + "sms:displayName": "Storage Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ReadIndicator", + "@id": "bts:ProcessingDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", - "rdfs:label": "ReadIndicator", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", + "rdfs:label": "ProcessingDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:R1" - }, - { - "@id": "bts:R2" - }, - { - "@id": "bts:R1&R2" - }, - { - "@id": "bts:I1" - }, + "sms:displayName": "Processing Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:ProtocolLink", + "@type": "rdfs:Class", + "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label": "ProtocolLink", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:InformationContentEntity" } ], - "sms:displayName": "Read Indicator", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Protocol Link", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Read1", + "@id": "bts:SiteDataSource", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "Read1", + "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", + "rdfs:label": "SiteDataSource", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" - }, - { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "Read1", - "sms:required": "sms:true", + "sms:displayName": "Site Data Source", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Read2", + "@id": "bts:CollectionMedia", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "Read2", + "rdfs:comment": "Material Specimen is collected into post procedure", + "rdfs:label": "CollectionMedia", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30339,24 +30922,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:DMEM" }, { - "@id": "bts:CDNA" + "@id": "bts:DMEM+Serum" + }, + { + "@id": "bts:RPMI" + }, + { + "@id": "bts:RPMI+Serum" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:PBS+Serum" + }, + { + "@id": "bts:None" } ], - "sms:displayName": "Read2", - "sms:required": "sms:true", + "sms:displayName": "Collection Media", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EndBias", + "@id": "bts:MountingMedium", "@type": "rdfs:Class", - "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "rdfs:label": "EndBias", + "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", + "rdfs:label": "MountingMedium", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30364,27 +30962,62 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:3Prime" + "@id": "bts:Aqueouswaterbased" }, { - "@id": "bts:5Prime" + "@id": "bts:Non-AqueousSolventbased" }, { - "@id": "bts:FullLengthTranscript" + "@id": "bts:Xylene" + }, + { + "@id": "bts:Toluene" + }, + { + "@id": "bts:AntifadewithDAPI" + }, + { + "@id": "bts:AntifadewithoutDAPI" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "End Bias", - "sms:required": "sms:true", + "sms:displayName": "Mounting Medium", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReverseTranscriptionPrimer", + "@id": "bts:ProcessingLocation", "@type": "rdfs:Class", - "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", - "rdfs:label": "ReverseTranscriptionPrimer", + "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", + "rdfs:label": "ProcessingLocation", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistologyAssessmentBy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", + "rdfs:label": "HistologyAssessmentBy", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30392,30 +31025,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Oligo-dT" + "@id": "bts:Pathologist" }, { - "@id": "bts:Poly-dT" + "@id": "bts:ResearchScientist" }, { - "@id": "bts:Featurebarcoding" + "@id": "bts:Other" }, { - "@id": "bts:Random" + "@id": "bts:Unknown" } ], - "sms:displayName": "Reverse Transcription Primer", - "sms:required": "sms:true", + "sms:displayName": "Histology Assessment By", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpikeIn", + "@id": "bts:HistologyAssessmentMedium", "@type": "rdfs:Class", - "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", - "rdfs:label": "SpikeIn", + "rdfs:comment": "The method of assessment used to characterize histology", + "rdfs:label": "HistologyAssessmentMedium", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30423,30 +31056,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ERCC" + "@id": "bts:Digital" }, { - "@id": "bts:OtherSpikeIn" + "@id": "bts:Microscopy" }, { - "@id": "bts:NoSpikeIn" + "@id": "bts:Other" }, { - "@id": "bts:PhiX" + "@id": "bts:Unknown" } ], - "sms:displayName": "Spike In", - "sms:required": "sms:true", + "sms:displayName": "Histology Assessment Medium", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SequencingPlatform", + "@id": "bts:PreinvasiveMorphology", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "SequencingPlatform", + "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", + "rdfs:label": "PreinvasiveMorphology", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -30454,565 +31087,530 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:IlluminaNextSeq500" - }, - { - "@id": "bts:IlluminaNextSeq550" - }, - { - "@id": "bts:IlluminaNextSeq2500" - }, - { - "@id": "bts:IlluminaNovaSeq6000" - }, - { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:Melanomainsitu-superficialspreading" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:Melanomainsitu-lentigomalignatype" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:Melanomainsitu-acral-lentiginous" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:Melanomainsitu-nototherwiseclassified" }, { - "@id": "bts:IlluminaGenomeAnalyzerII" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:IlluminaGenomeAnalyzerIIx" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:IlluminaHiSeq2000" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:IlluminaHiSeq2500" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:IlluminaHiSeq4000" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:IonTorrentPGM" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:IonTorrentProton" + "@id": "bts:Invasivemelanoma-other" }, { - "@id": "bts:IonTorrentS5" + "@id": "bts:NormalWDA" }, { - "@id": "bts:PacBioRS" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:GridION" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:PromethION" + "@id": "bts:SquamousCarcinomainsitu" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:Atypicaladenomatoushyperplasia" }, { - "@id": "bts:Revio" + "@id": "bts:Adenocarcinomainsitu-nonmucinous" }, { - "@id": "bts:IlluminaNextSeq1000" + "@id": "bts:Adenocarcinomainsitu-mucinous" }, { - "@id": "bts:IlluminaNextSeq2000" + "@id": "bts:BenigntumorNOS" }, { - "@id": "bts:Other" + "@id": "bts:Hamartoma" }, { - "@id": "bts:Unknown" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:Nodiagnosispossible" } ], - "sms:displayName": "Sequencing Platform", - "sms:required": "sms:true", + "sms:displayName": "Preinvasive Morphology", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofInputCells", + "@id": "bts:TumorInfiltratingLymphocytes", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells loaded/placed on plates", - "rdfs:label": "TotalNumberofInputCells", + "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", + "rdfs:label": "TumorInfiltratingLymphocytes", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Input Cells", - "sms:required": "sms:true", + "sms:displayName": "Tumor Infiltrating Lymphocytes", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InputCellsandNuclei", + "@id": "bts:DegreeofDysplasia", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", - "rdfs:label": "InputCellsandNuclei", + "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", + "rdfs:label": "DegreeofDysplasia", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Input Cells and Nuclei", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" + }, + { + "@id": "bts:Milddysplasia" + }, + { + "@id": "bts:Moderatedysplasia" + }, + { + "@id": "bts:Severedysplasia" + }, + { + "@id": "bts:CarcinomainSitu" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Degree of Dysplasia", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationDaysfromIndex", + "@id": "bts:DysplasiaFraction", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "LibraryPreparationDaysfromIndex", + "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", + "rdfs:label": "DysplasiaFraction", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Days from Index", + "sms:displayName": "Dysplasia Fraction", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:SingleCellDissociationDaysfromIndex", + "@id": "bts:NumberProliferatingCells", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SingleCellDissociationDaysfromIndex", + "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", + "rdfs:label": "NumberProliferatingCells", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell Dissociation Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Number Proliferating Cells", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex", + "@id": "bts:PercentEosinophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", + "rdfs:label": "PercentEosinophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Library Construction Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Percent Eosinophil Infiltration", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex", + "@id": "bts:PercentGranulocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "NucleicAcidCaptureDaysfromIndex", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", + "rdfs:label": "PercentGranulocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleic Acid Capture Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Percent Granulocyte Infiltration", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:TechnicalReplicateGroup", + "@id": "bts:PercentInflamInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", - "rdfs:label": "TechnicalReplicateGroup", + "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", + "rdfs:label": "PercentInflamInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Technical Replicate Group", + "sms:displayName": "Percent Inflam Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel2", + "@id": "bts:PercentLymphocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", - "rdfs:label": "ScRNA-seqLevel2", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", + "rdfs:label": "PercentLymphocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 2", + "sms:displayName": "Percent Lymphocyte Infiltration", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:GenomeAnnotationURL" - }, - { - "@id": "bts:Checksum" - }, - { - "@id": "bts:WhitelistCellBarcodeFileLink" - }, - { - "@id": "bts:CellBarcodeTag" - }, - { - "@id": "bts:UMITag" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:PercentMonocyteInfiltration", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", + "rdfs:label": "PercentMonocyteInfiltration", + "rdfs:subClassOf": [ { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:Biospecimen" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Percent Monocyte Infiltration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowType", + "@id": "bts:PercentNecrosis", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScRNAseqWorkflowType", + "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNecrosis", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellRanger" - }, - { - "@id": "bts:STARsolo" - }, - { - "@id": "bts:HCAOptimus" - }, - { - "@id": "bts:DropEST" - }, - { - "@id": "bts:SEQC" - }, - { - "@id": "bts:Cufflinks" - }, - { - "@id": "bts:DEXSeq" - }, - { - "@id": "bts:HTSeq-FPKM" - }, - { - "@id": "bts:Cellannotation" - }, - { - "@id": "bts:Differentiationtrajectoryanalysis" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "scRNAseq Workflow Type", - "sms:required": "sms:true", + "sms:displayName": "Percent Necrosis", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowVersion", + "@id": "bts:PercentNeutrophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", - "rdfs:label": "WorkflowVersion", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", + "rdfs:label": "PercentNeutrophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Version", - "sms:required": "sms:true", + "sms:displayName": "Percent Neutrophil Infiltration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription", + "@id": "bts:PercentNormalCells", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", - "rdfs:label": "ScRNAseqWorkflowParametersDescription", + "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNormalCells", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNAseq Workflow Parameters Description", - "sms:required": "sms:true", + "sms:displayName": "Percent Normal Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowLink", + "@id": "bts:PercentStromalCells", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "WorkflowLink", + "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", + "rdfs:label": "PercentStromalCells", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Link", - "sms:required": "sms:true", + "sms:displayName": "Percent Stromal Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReference", + "@id": "bts:PercentTumorCells", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", - "rdfs:label": "GenomicReference", + "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", + "rdfs:label": "PercentTumorCells", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference", - "sms:required": "sms:true", + "sms:displayName": "Percent Tumor Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:PercentTumorNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", + "rdfs:label": "PercentTumorNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", - "sms:required": "sms:true", + "sms:displayName": "Percent Tumor Nuclei", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomeAnnotationURL", + "@id": "bts:FiducialMarker", "@type": "rdfs:Class", - "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", - "rdfs:label": "GenomeAnnotationURL", + "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", + "rdfs:label": "FiducialMarker", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genome Annotation URL", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:NuclearStain-DAPI" + }, + { + "@id": "bts:FluorescentBeads" + }, + { + "@id": "bts:GridSlides-Hemocytometer" + }, + { + "@id": "bts:AdhesiveMarkers" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Fiducial Marker", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WhitelistCellBarcodeFileLink", + "@id": "bts:SlicingMethod", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible cell barcodes. URL", - "rdfs:label": "WhitelistCellBarcodeFileLink", + "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", + "rdfs:label": "SlicingMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whitelist Cell Barcode File Link", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Vibratome" + }, + { + "@id": "bts:Cryosectioning" + }, + { + "@id": "bts:Tissuemolds" + }, + { + "@id": "bts:Slidingmicrotome" + }, + { + "@id": "bts:Sectioning" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Slicing Method", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeTag", + "@id": "bts:LysisBuffer", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", - "rdfs:label": "CellBarcodeTag", + "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", + "rdfs:label": "LysisBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Tag", - "sms:required": "sms:true", + "sms:displayName": "Lysis Buffer", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UMITag", + "@id": "bts:MethodofNucleicAcidIsolation", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", - "rdfs:label": "UMITag", + "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. 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Comma-delimited list of filenames", - "rdfs:label": "LinkedMatrices", + "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", + "rdfs:label": "IschemicTime", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Linked Matrices", + "sms:displayName": "Ischemic Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberReads", + "@id": "bts:IschemicTemperature", "@type": "rdfs:Class", - "rdfs:comment": "Median number of reads per cell. Number", - "rdfs:label": "CellMedianNumberReads", + "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", + "rdfs:label": "IschemicTemperature", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Reads", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CellMedianNumberGenes", - "@type": "rdfs:Class", - "rdfs:comment": "Median number of genes detected per cell. Number", - "rdfs:label": "CellMedianNumberGenes", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScRNA-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Median Number Genes", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CellTotal", - "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", - "rdfs:label": "CellTotal", - "rdfs:subClassOf": [ + "@id": "bts:WarmIschemia" + }, { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ColdIschemia" + }, + { + "@id": "bts:Ambientair" + }, + { + "@id": "bts:4Cwetice" + }, + { + "@id": "bts:Negative-20C" + }, + { + "@id": "bts:DryIce" + }, + { + "@id": "bts:LiquidNitrogen" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Total", - "sms:required": "sms:true", + "sms:displayName": "Ischemic Temperature", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel4", + "@id": "bts:TopographyCode", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScRNA-seqLevel4", + "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", + "rdfs:label": "TopographyCode", "rdfs:subClassOf": [ { - 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"rdfs:label": "Slide-seqLevel1", - "rdfs:subClassOf": [ + "@id": "bts:C02.0" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:C02.1" + }, { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:C02.2" + }, { - "@id": "bts:Component" + "@id": "bts:C02.3" }, { - "@id": "bts:Filename" + "@id": "bts:C02.4" }, { - "@id": "bts:FileFormat" + "@id": "bts:C02.8" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:C02.9" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:C03.0" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:C03.1" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:C03.9" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:C04.0" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:C04.1" }, { - "@id": "bts:EndBias" + "@id": "bts:C04.8" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:C04.9" }, { - 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} - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C57.3" + }, { - "@id": "bts:PairedEnd" + "@id": "bts:C57.4" }, { - "@id": "bts:SingleRead" + "@id": "bts:C57.7" }, { - "@id": "bts:Mid-length" + "@id": "bts:C57.8" }, { - "@id": "bts:LongRead" + "@id": "bts:C57.9" + }, + { + "@id": "bts:C60.0" + }, + { + "@id": "bts:C60.1" + }, + { + "@id": "bts:C60.2" + }, + { + "@id": "bts:C60.8" + }, + { + "@id": "bts:C60.9" + }, + { + "@id": "bts:C61.9" + }, + { + "@id": "bts:C62.0" + }, + { + "@id": "bts:C62.1" + }, + { + "@id": "bts:C62.9" + }, + { + "@id": "bts:C63.0" + }, + { + "@id": "bts:C63.1" + }, + { + "@id": "bts:C63.2" + }, + { + "@id": "bts:C63.7" + }, + { + "@id": "bts:C63.8" + }, + { + "@id": "bts:C63.9" + }, + { + "@id": "bts:C64.9" + }, + { + "@id": "bts:C65.9" + }, + { + "@id": "bts:C66.9" + }, + { + "@id": "bts:C67.0" + }, + { + "@id": "bts:C67.1" + }, + { + "@id": "bts:C67.2" + }, + { + "@id": "bts:C67.4" + }, + { + "@id": "bts:C67.6" + }, + { + "@id": "bts:C67.7" + }, + { + "@id": "bts:C67.8" + }, + { + "@id": "bts:C67.9" + }, + { + "@id": "bts:C68.0" + }, + { + "@id": "bts:C68.1" + }, + { + "@id": "bts:C68.8" + }, + { + "@id": "bts:C68.9" + }, + { + "@id": "bts:C69.0" + }, + { + "@id": "bts:C69.1" + }, + { + "@id": "bts:C69.2" + }, + { + "@id": "bts:C69.3" + }, + { + "@id": "bts:C69.4" + }, + { + "@id": "bts:C69.5" + }, + { + "@id": "bts:C69.6" + }, + { + "@id": "bts:C69.8" + }, + { + "@id": "bts:C69.9" + }, + { + "@id": "bts:C70.0" + }, + { + "@id": "bts:C70.1" + }, + { + "@id": "bts:C70.9" + }, + { + "@id": "bts:C71.0" + }, + { + "@id": "bts:C71.1" + }, + { + "@id": "bts:C71.2" + }, + { + "@id": "bts:C71.3" + }, + { + "@id": "bts:C71.4" + }, + { + "@id": "bts:C71.5" + }, + { + "@id": "bts:C71.6" + }, + { + "@id": "bts:C71.7" + }, + { + "@id": "bts:C71.8" + }, + { + "@id": "bts:C71.9" + }, + { + "@id": "bts:C72.0" + }, + { + "@id": "bts:C72.1" + }, + { + "@id": "bts:C72.2" + }, + { + "@id": "bts:C72.3" + }, + { + "@id": "bts:C72.4" + }, + { + "@id": "bts:C72.5" + }, + { + "@id": "bts:C72.8" + }, + { + "@id": "bts:C72.9" + }, + { + "@id": "bts:C73.9" + }, + { + "@id": "bts:C74.0" + }, + { + "@id": "bts:C74.1" + }, + { + "@id": "bts:C74.9" + }, + { + "@id": "bts:C75.0" + }, + { + "@id": "bts:C75.1" + }, + { + "@id": "bts:C75.2" + }, + { + "@id": "bts:C75.3" + }, + { + "@id": "bts:C75.4" + }, + { + "@id": "bts:C75.5" + }, + { + "@id": "bts:C75.8" + }, + { + "@id": "bts:C75.9" + }, + { + "@id": "bts:C76.0" + }, + { + "@id": "bts:C76.1" + }, + { + "@id": "bts:C76.2" + }, + { + "@id": "bts:C76.3" + }, + { + "@id": "bts:C76.4" + }, + { + "@id": "bts:C76.5" + }, + { + "@id": "bts:C76.7" + }, + { + "@id": "bts:C76.8" + }, + { + "@id": "bts:C77.0" + }, + { + "@id": "bts:C77.1" + }, + { + "@id": "bts:C77.2" + }, + { + "@id": "bts:C77.3" + }, + { + "@id": "bts:C77.4" + }, + { + "@id": "bts:C77.5" + }, + { + "@id": "bts:C77.8" + }, + { + "@id": "bts:C77.9" + }, + { + "@id": "bts:C80.9" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Topography Code", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Micro-regionSeqPlatform", + "@id": "bts:AdditionalTopography", "@type": "rdfs:Class", - "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", - "rdfs:label": "Micro-regionSeqPlatform", + "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", + "rdfs:label": "AdditionalTopography", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -32381,58 +32749,104 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RarecytePick-Seq" + "@id": "bts:Skinofscalp" }, { - "@id": "bts:LaserCaptureMicrodissection" - } - ], - "sms:displayName": "Micro-region Seq Platform", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ROITag", - "@type": "rdfs:Class", - "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", - "rdfs:label": "ROITag", - "rdfs:subClassOf": [ + "@id": "bts:Skinofeyelid" + }, { - "@id": "bts:Sequencing" + "@id": "bts:Skinofnose" + }, + { + "@id": "bts:Skinoflip" + }, + { + "@id": "bts:Skinofear" + }, + { + "@id": "bts:Skinofneck" + }, + { + "@id": "bts:Skinofotherpartsofface" + }, + { + "@id": "bts:Skinofchest" + }, + { + "@id": "bts:Skinofback" + }, + { + "@id": "bts:Skinofabdomen" + }, + { + "@id": "bts:Skinoftrunk" + }, + { + "@id": "bts:Skinofbreast" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:Skinofpalm" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:HilarAirway" + }, + { + "@id": "bts:Peri-tumoralAirway" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI Tag", + "sms:displayName": "Additional Topography", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReadLength", + "@id": "bts:HistologicMorphologyCode", "@type": "rdfs:Class", - "rdfs:comment": "The length of the sequencing reads. Can be integer, null", - "rdfs:label": "ReadLength", + "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:label": "HistologicMorphologyCode", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Read Length", + "sms:displayName": "Histologic Morphology Code", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibrarySelectionMethod", + "@id": "bts:PreservationMethod", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "LibrarySelectionMethod", + "rdfs:comment": "Text term that represents the method used to preserve the sample.", + "rdfs:label": "PreservationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -32440,90 +32854,134 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HybridSelection" + "@id": "bts:Cryopreserved" }, { - "@id": "bts:PCR" + "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" }, { - "@id": "bts:AffinityEnrichment" + "@id": "bts:Cryopreservationindryice-deadtissue" }, { - "@id": "bts:Poly-TEnrichment" + "@id": "bts:Cryopreservationinliquidnitrogen-livecells" }, { - "@id": "bts:Random" + "@id": "bts:Formalinfixedparaffinembedded-FFPE" }, { - "@id": "bts:RRNADepletion" + "@id": "bts:Formalinfixed-unbuffered" }, { - "@id": "bts:MiRNASizeFractionation" + "@id": "bts:Formalinfixed-buffered" }, { - "@id": "bts:Other" + "@id": "bts:Fresh" + }, + { + "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + }, + { + "@id": "bts:OCT" + }, + { + "@id": "bts:SnapFrozen" + }, + { + "@id": "bts:Frozen" + }, + { + "@id": "bts:Negative80DegC" + }, + { + "@id": "bts:LiquidNitrogen" + }, + { + "@id": "bts:Freshdissociated" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsorted" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + }, + { + "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Library Selection Method", + "sms:displayName": "Preservation Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitName", + "@id": "bts:AssayType", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitName", + "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", + "rdfs:label": "AssayType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Name", + "sms:displayName": "Assay Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitVendor", + "@id": "bts:ExSeqMinimal", "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVendor", + "rdfs:comment": "Minimal metadata for the ExSeq assay", + "rdfs:label": "ExSeqMinimal", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Vendor", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVersion", - "rdfs:subClassOf": [ + "sms:displayName": "ExSeq Minimal", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Version", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterName", + "@id": "bts:ScRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Name of the sequencing adapter. String", - "rdfs:label": "AdapterName", + "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", + "rdfs:label": "ScRNA-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32532,15 +32990,97 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Name", + "sms:displayName": "scRNA-seq Level 1", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:NucleicAcidSource" + }, + { + "@id": "bts:CryopreservedCellsinSample" + }, + { + "@id": "bts:SingleCellIsolationMethod" + }, + { + "@id": "bts:DissociationMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" + }, + { + "@id": "bts:ReadIndicator" + }, + { + "@id": "bts:Read1" + }, + { + "@id": "bts:Read2" + }, + { + "@id": "bts:EndBias" + }, + { + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:SpikeIn" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:TotalNumberofInputCells" + }, + { + "@id": "bts:InputCellsandNuclei" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SingleCellDissociationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:TechnicalReplicateGroup" + } + ], "sms:validationRules": [] }, { - "@id": "bts:AdapterSequence", + "@id": "bts:NucleicAcidSource", "@type": "rdfs:Class", - "rdfs:comment": "Base sequence of the sequencing adapter. String", - "rdfs:label": "AdapterSequence", + "rdfs:comment": "The source of the input nucleic molecule", + "rdfs:label": "NucleicAcidSource", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32549,154 +33089,97 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Sequence", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:SingleCell" + }, + { + "@id": "bts:BulkWholeCell" + }, + { + "@id": "bts:SingleNucleus" + }, + { + "@id": "bts:BulkNuclei" + }, + { + "@id": "bts:Micro-region" + } + ], + "sms:displayName": "Nucleic Acid Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerName", + "@id": "bts:CryopreservedCellsinSample", "@type": "rdfs:Class", - "rdfs:comment": "Name of the base caller. String", - "rdfs:label": "BaseCallerName", + "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", + "rdfs:label": "CryopreservedCellsinSample", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Name", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Cryopreserved Cells in Sample", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerVersion", + "@id": "bts:SingleCellIsolationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Version of the base caller. String", - "rdfs:label": "BaseCallerVersion", + "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", + "rdfs:label": "SingleCellIsolationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Version", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FlowCellBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", - "rdfs:label": "FlowCellBarcode", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Flow Cell Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMaximumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMaximumLength", - "rdfs:subClassOf": [ + "@id": "bts:MicrofluidicsChip" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Maximum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMeanLength", - "@type": "rdfs:Class", - "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentMeanLength", - "rdfs:subClassOf": [ + "@id": "bts:Droplets" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Mean Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMinimumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMinimumLength", - "rdfs:subClassOf": [ + "@id": "bts:FACS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Minimum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentStandardDeviationLength", - "@type": "rdfs:Class", - "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentStandardDeviationLength", - "rdfs:subClassOf": [ + "@id": "bts:Plates" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Standard Deviation Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LaneNumber", - "@type": "rdfs:Class", - "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", - "rdfs:label": "LaneNumber", - "rdfs:subClassOf": [ + "@id": "bts:10x" + }, { - "@id": "bts:Sequencing" + "@id": "bts:NucleiIsolation" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lane Number", - "sms:required": "sms:false", + "sms:displayName": "Single Cell Isolation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryStrand", + "@id": "bts:DissociationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Library stranded-ness.", - "rdfs:label": "LibraryStrand", + "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", + "rdfs:label": "DissociationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32704,27 +33187,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Unstranded" + "@id": "bts:GentleMACS" }, { - "@id": "bts:FirstStranded" + "@id": "bts:Dounce" }, { - "@id": "bts:SecondStranded" + "@id": "bts:EnzymaticDigestion" }, { "@id": "bts:NotApplicable" } ], - "sms:displayName": "Library Strand", - "sms:required": "sms:false", + "sms:displayName": "Dissociation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MultiplexBarcode", + "@id": "bts:LibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", - "rdfs:label": "MultiplexBarcode", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "LibraryConstructionMethod", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32733,49 +33216,71 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Multiplex Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeSelectionRange", - "@type": "rdfs:Class", - "rdfs:comment": "Range of size selection. String", - "rdfs:label": "SizeSelectionRange", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size Selection Range", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TargetDepth", - "@type": "rdfs:Class", - "rdfs:comment": "The targeted read depth prior to sequencing. Integer", - "rdfs:label": "TargetDepth", - "rdfs:subClassOf": [ + "@id": "bts:Smart-seq2" + }, { - "@id": "bts:Sequencing" + "@id": "bts:Smart-SeqV4" + }, + { + "@id": "bts:10xV1.0" + }, + { + "@id": "bts:10xV1.1" + }, + { + "@id": "bts:10xV2" + }, + { + "@id": "bts:10xV3" + }, + { + "@id": "bts:10xV3.1" + }, + { + "@id": "bts:CEL-seq2" + }, + { + "@id": "bts:Drop-seq" + }, + { + "@id": "bts:InDropsV2" + }, + { + "@id": "bts:InDropsV3" + }, + { + "@id": "bts:TruDrop" + }, + { + "@id": "bts:Sci-ATAC-seq" + }, + { + "@id": "bts:NexteraXT" + }, + { + "@id": "bts:10xMultiome" + }, + { + "@id": "bts:10xFLEX" + }, + { + "@id": "bts:10xGEM3'" + }, + { + "@id": "bts:10xGEM5'" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Target Depth", - "sms:required": "sms:false", + "sms:displayName": "Library Construction Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ToTrimAdapterSequence", + "@id": "bts:ReadIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Does the user suggest adapter trimming?", - "rdfs:label": "ToTrimAdapterSequence", + "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", + "rdfs:label": "ReadIndicator", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -32786,75 +33291,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-TrimAdapterSequence" + "@id": "bts:R1" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "To Trim Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TranscriptIntegrityNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", - "rdfs:label": "TranscriptIntegrityNumber", - "rdfs:subClassOf": [ + "@id": "bts:R2" + }, { - "@id": "bts:Sequencing" + "@id": "bts:R1&R2" + }, + { + "@id": "bts:I1" + }, + { + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript Integrity Number", - "sms:required": "sms:false", + "sms:displayName": "Read Indicator", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RIN", + "@id": "bts:Read1", "@type": "rdfs:Class", - "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", - "rdfs:label": "RIN", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "Read1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RIN", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DV200", - "@type": "rdfs:Class", - "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", - "rdfs:label": "DV200", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DV200", - "sms:required": "sms:false", + "sms:displayName": "Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterContent", + "@id": "bts:Read2", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "AdapterContent", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "Read2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32862,33 +33350,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:NotReported" + "@id": "bts:CDNA" } ], - "sms:displayName": "Adapter Content", - "sms:required": "sms:false", + "sms:displayName": "Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BasicStatistics", + "@id": "bts:EndBias", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "BasicStatistics", + "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", + "rdfs:label": "EndBias", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32896,50 +33375,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" + "@id": "bts:3Prime" }, { - "@id": "bts:Unknown" + "@id": "bts:5Prime" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Basic Statistics", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Encoding", - "@type": "rdfs:Class", - "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", - "rdfs:label": "Encoding", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:FullLengthTranscript" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Encoding", - "sms:required": "sms:false", + "sms:displayName": "End Bias", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:KmerContent", + "@id": "bts:ReverseTranscriptionPrimer", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "KmerContent", + "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", + "rdfs:label": "ReverseTranscriptionPrimer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32947,33 +33403,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:Oligo-dT" }, { - "@id": "bts:WARN" + "@id": "bts:Poly-dT" }, { - "@id": "bts:Unknown" + "@id": "bts:Featurebarcoding" }, { - "@id": "bts:NotReported" + "@id": "bts:Random" } ], - "sms:displayName": "Kmer Content", - "sms:required": "sms:false", + "sms:displayName": "Reverse Transcription Primer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OverrepresentedSequences", + "@id": "bts:SpikeIn", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "OverrepresentedSequences", + "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", + "rdfs:label": "SpikeIn", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -32981,33 +33434,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:ERCC" }, { - "@id": "bts:WARN" + "@id": "bts:OtherSpikeIn" }, { - "@id": "bts:Unknown" + "@id": "bts:NoSpikeIn" }, { - "@id": "bts:NotReported" + "@id": "bts:PhiX" } ], - "sms:displayName": "Overrepresented Sequences", - "sms:required": "sms:false", + "sms:displayName": "Spike In", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseNContent", + "@id": "bts:SequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseNContent", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "SequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Device" } ], "schema:isPartOf": { @@ -33015,183 +33465,103 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:IlluminaNextSeq500" }, { - "@id": "bts:PASS" + "@id": "bts:IlluminaNextSeq550" }, { - "@id": "bts:WARN" + "@id": "bts:IlluminaNextSeq2500" }, { - "@id": "bts:Unknown" + "@id": "bts:IlluminaNovaSeq6000" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base N Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseSequenceContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceContent", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaMiSeq" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:454GSFLXTitanium" + }, { - "@id": "bts:FAIL" + "@id": "bts:ABSOLiD4" }, { - "@id": "bts:PASS" + "@id": "bts:ABSOLiD2" }, { - "@id": "bts:WARN" + "@id": "bts:ABSOLiD3" }, { - "@id": "bts:Unknown" + "@id": "bts:CompleteGenomics" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseSequenceQuality", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceQuality", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaHiSeqXTen" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IlluminaHiSeqXFive" + }, { - "@id": "bts:FAIL" + "@id": "bts:IlluminaGenomeAnalyzerII" }, { - "@id": "bts:PASS" + "@id": "bts:IlluminaGenomeAnalyzerIIx" }, { - "@id": "bts:WARN" + "@id": "bts:IlluminaHiSeq2000" }, { - "@id": "bts:Unknown" + "@id": "bts:IlluminaHiSeq2500" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Quality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceGCContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceGCContent", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaHiSeq4000" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IlluminaNextSeq" + }, { - "@id": "bts:FAIL" + "@id": "bts:IonTorrentPGM" }, { - "@id": "bts:PASS" + "@id": "bts:IonTorrentProton" }, { - "@id": "bts:WARN" + "@id": "bts:IonTorrentS5" }, { - "@id": "bts:Unknown" + "@id": "bts:PacBioRS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence GC Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceQualityScore", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceQualityScore", - "rdfs:subClassOf": [ + "@id": "bts:NovaSeq6000" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:NovaSeqS4" + }, { - "@id": "bts:FAIL" + "@id": "bts:UltimaGenomicsUG100" }, { - "@id": "bts:PASS" + "@id": "bts:OxfordNanoporeminION" }, { - "@id": "bts:WARN" + "@id": "bts:GridION" }, { - "@id": "bts:Unknown" + "@id": "bts:PromethION" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence Quality Score", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerTileSequenceQuality", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerTileSequenceQuality", - "rdfs:subClassOf": [ + "@id": "bts:PacBioSequel2" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Revio" + }, { - "@id": "bts:FAIL" + "@id": "bts:IlluminaNextSeq1000" }, { - "@id": "bts:PASS" + "@id": "bts:IlluminaNextSeq2000" }, { - "@id": "bts:WARN" + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -33200,15 +33570,15 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Per Tile Sequence Quality", - "sms:required": "sms:false", + "sms:displayName": "Sequencing Platform", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentGCContent", + "@id": "bts:TotalNumberofInputCells", "@type": "rdfs:Class", - "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", - "rdfs:label": "PercentGCContent", + "rdfs:comment": "Number of cells loaded/placed on plates", + "rdfs:label": "TotalNumberofInputCells", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33217,49 +33587,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent GC Content", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Input Cells", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceDuplicationLevels", + "@id": "bts:InputCellsandNuclei", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceDuplicationLevels", + "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label": "InputCellsandNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Duplication Levels", - "sms:required": "sms:false", + "sms:displayName": "Input Cells and Nuclei", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceLengthDistribution", + "@id": "bts:LibraryPreparationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceLengthDistribution", + "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "LibraryPreparationDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33268,49 +33621,36 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Length Distribution", + "sms:displayName": "Library Preparation Days from Index", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:TotalReads", + "@id": "bts:SingleCellDissociationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Total number of reads per sample. Integer", - "rdfs:label": "TotalReads", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SingleCellDissociationDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Reads", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Single Cell Dissociation Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:QCWorkflowType", + "@id": "bts:SequencingLibraryConstructionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", - "rdfs:label": "QCWorkflowType", + "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33319,15 +33659,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Sequencing Library Construction Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:QCWorkflowVersion", + "@id": "bts:NucleicAcidCaptureDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Major version for a workflow. String", - "rdfs:label": "QCWorkflowVersion", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "NucleicAcidCaptureDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33336,15 +33678,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Version", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Nucleic Acid Capture Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:QCWorkflowLink", + "@id": "bts:TechnicalReplicateGroup", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used. String", - "rdfs:label": "QCWorkflowLink", + "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", + "rdfs:label": "TechnicalReplicateGroup", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33353,15 +33697,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Link", + "sms:displayName": "Technical Replicate Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel2", + "@id": "bts:ScRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq alignment protocol description", - "rdfs:label": "BulkRNA-seqLevel2", + "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", + "rdfs:label": "ScRNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33370,11 +33714,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 2", + "sms:displayName": "scRNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel1" + "@id": "bts:ScRNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -33394,102 +33738,49 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:MSIWorkflowLink" - }, - { - "@id": "bts:MSIScore" + "@id": "bts:ScRNAseqWorkflowType" }, { - "@id": "bts:MSIStatus" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ScRNAseqWorkflowParametersDescription" }, { - "@id": "bts:TotalReads" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:GenomicReference" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Checksum" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:WhitelistCellBarcodeFileLink" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:CellBarcodeTag" }, { - "@id": "bts:ShortReads" + "@id": "bts:UMITag" }, { - "@id": "bts:Islowestlevel" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AlignmentWorkflowUrl", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", - "rdfs:label": "AlignmentWorkflowUrl", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:AppliedHardTrimming" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Alignment Workflow Url", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AlignmentWorkflowType", + "@id": "bts:ScRNAseqWorkflowType", "@type": "rdfs:Class", "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "AlignmentWorkflowType", + "rdfs:label": "ScRNAseqWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33500,105 +33791,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BWA" - }, - { - "@id": "bts:BWAwithBQSR" - }, - { - "@id": "bts:BWA-aln" - }, - { - "@id": "bts:BWA-mem" - }, - { - "@id": "bts:BWAwithMarkDuplicatesandBQSR" - }, - { - "@id": "bts:STAR2-Pass" - }, - { - "@id": "bts:STAR2-PassChimeric" - }, - { - "@id": "bts:STAR2-PassGenome" - }, - { - "@id": "bts:STAR2-PassTranscriptome" - }, - { - "@id": "bts:Bowtie" - }, - { - "@id": "bts:Bismark" - }, - { - "@id": "bts:GSNAP" - }, - { - "@id": "bts:BSMAP" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BS-Seeker2" - }, - { - "@id": "bts:BS-Seeker" - }, - { - "@id": "bts:RMAP" - }, - { - "@id": "bts:MethylCoder" - }, - { - "@id": "bts:BRAT-BW" - }, - { - "@id": "bts:Pash" + "@id": "bts:CellRanger" }, { - "@id": "bts:Segemehl" + "@id": "bts:STARsolo" }, { - "@id": "bts:Bisulfighter" + "@id": "bts:HCAOptimus" }, { - "@id": "bts:BatMeth" + "@id": "bts:DropEST" }, { - "@id": "bts:LAST" + "@id": "bts:SEQC" }, { - "@id": "bts:ERNE-BS5" + "@id": "bts:Cufflinks" }, { - "@id": "bts:B-SOLANA" + "@id": "bts:DEXSeq" }, { - "@id": "bts:SOCS-B" + "@id": "bts:HTSeq-FPKM" }, { - "@id": "bts:BWA-meth" + "@id": "bts:Cellannotation" }, { - "@id": "bts:OtherAlignmentWorkflow" + "@id": "bts:Differentiationtrajectoryanalysis" }, { - "@id": "bts:None" + "@id": "bts:Other" } ], - "sms:displayName": "Alignment Workflow Type", + "sms:displayName": "scRNAseq Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IndexFileName", + "@id": "bts:WorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "The name (or part of a name) of a file (of any type). String", - "rdfs:label": "IndexFileName", + "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", + "rdfs:label": "WorkflowVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33607,15 +33841,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Index File Name", + "sms:displayName": "Workflow Version", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageBaseQuality", + "@id": "bts:ScRNAseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Average base quality collected from samtools. Number", - "rdfs:label": "AverageBaseQuality", + "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", + "rdfs:label": "ScRNAseqWorkflowParametersDescription", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33624,15 +33858,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Base Quality", - "sms:required": "sms:false", + "sms:displayName": "scRNAseq Workflow Parameters Description", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageInsertSize", + "@id": "bts:WorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Average insert size collected from samtools. Integer", - "rdfs:label": "AverageInsertSize", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "WorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33641,15 +33875,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Insert Size", - "sms:required": "sms:false", + "sms:displayName": "Workflow Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageReadLength", + "@id": "bts:GenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "Average read length collected from samtools. Integer", - "rdfs:label": "AverageReadLength", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", + "rdfs:label": "GenomicReference", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33658,15 +33892,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Read Length", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Contamination", + "@id": "bts:GenomicReferenceURL", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", - "rdfs:label": "Contamination", + "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", + "rdfs:label": "GenomicReferenceURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33675,15 +33909,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ContaminationError", + "@id": "bts:GenomeAnnotationURL", "@type": "rdfs:Class", - "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", - "rdfs:label": "ContaminationError", + "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", + "rdfs:label": "GenomeAnnotationURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33692,15 +33926,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination Error", - "sms:required": "sms:false", + "sms:displayName": "Genome Annotation URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MeanCoverage", + "@id": "bts:WhitelistCellBarcodeFileLink", "@type": "rdfs:Class", - "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", - "rdfs:label": "MeanCoverage", + "rdfs:comment": "Link to file listing all possible cell barcodes. URL", + "rdfs:label": "WhitelistCellBarcodeFileLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33709,15 +33943,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Coverage", - "sms:required": "sms:false", + "sms:displayName": "Whitelist Cell Barcode File Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIWorkflowLink", + "@id": "bts:CellBarcodeTag", "@type": "rdfs:Class", - "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", - "rdfs:label": "MSIWorkflowLink", + "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", + "rdfs:label": "CellBarcodeTag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33726,15 +33960,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Workflow Link", - "sms:required": "sms:false", + "sms:displayName": "Cell Barcode Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIScore", + "@id": "bts:UMITag", "@type": "rdfs:Class", - "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", - "rdfs:label": "MSIScore", + "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", + "rdfs:label": "UMITag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33743,15 +33977,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Score", - "sms:required": "sms:false", + "sms:displayName": "UMI Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIStatus", + "@id": "bts:AppliedHardTrimming", "@type": "rdfs:Class", - "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", - "rdfs:label": "MSIStatus", + "rdfs:comment": "Was Hard Trimming applied", + "rdfs:label": "AppliedHardTrimming", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33762,27 +33996,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MSI" - }, - { - "@id": "bts:MSI-low" - }, - { - "@id": "bts:MSI-high" + "@id": "bts:Yes-AppliedHardTrimming" }, { - "@id": "bts:MSS" + "@id": "bts:No" } ], - "sms:displayName": "MSI Status", - "sms:required": "sms:false", + "sms:displayName": "Applied Hard Trimming", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PairsOnDiffCHR", + "@id": "bts:ScRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", - "rdfs:label": "PairsOnDiffCHR", + "rdfs:comment": "Gene and Isoform expression files", + "rdfs:label": "ScRNA-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33791,49 +34019,67 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pairs On Diff CHR", + "sms:displayName": "scRNA-seq Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalUniquelyMapped", - "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that map to genome. Integer", - "rdfs:label": "TotalUniquelyMapped", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Uniquely Mapped", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalUnmappedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that did not map to genome. Integer", - "rdfs:label": "TotalUnmappedreads", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Unmapped reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionReadsDuplicated", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", - "rdfs:label": "ProportionReadsDuplicated", + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:LinkedMatrices" + }, + { + "@id": "bts:CellMedianNumberReads" + }, + { + "@id": "bts:CellMedianNumberGenes" + }, + { + "@id": "bts:CellTotal" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:WorkflowVersion" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:DataCategory", + "@type": "rdfs:Class", + "rdfs:comment": "Specific content type of the data file.", + "rdfs:label": "DataCategory", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33842,15 +34088,38 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Duplicated", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:GeneExpression" + }, + { + "@id": "bts:TranscriptExpression" + }, + { + "@id": "bts:ExonExpressionQuantification" + }, + { + "@id": "bts:GeneExpressionQuantification" + }, + { + "@id": "bts:IsoformExpressionQuantification" + }, + { + "@id": "bts:SpliceJunctionQuantification" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Data Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMapped", + "@id": "bts:MatrixType", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", - "rdfs:label": "ProportionReadsMapped", + "rdfs:comment": "Type of data stored in matrix.", + "rdfs:label": "MatrixType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33859,15 +34128,29 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:RawCounts" + }, + { + "@id": "bts:NormalizedCounts" + }, + { + "@id": "bts:ScaledCounts" + }, + { + "@id": "bts:BatchCorrectedCounts" + } + ], + "sms:displayName": "Matrix Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionTargetsNoCoverage", + "@id": "bts:LinkedMatrices", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", - "rdfs:label": "ProportionTargetsNoCoverage", + "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", + "rdfs:label": "LinkedMatrices", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33876,87 +34159,130 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Targets No Coverage", + "sms:displayName": "Linked Matrices", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionBaseMismatch", + "@id": "bts:CellMedianNumberReads", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", - "rdfs:label": "ProportionBaseMismatch", + "rdfs:comment": "Median number of reads per cell. Number", + "rdfs:label": "CellMedianNumberReads", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Base Mismatch", - "sms:required": "sms:false", + "sms:displayName": "Cell Median Number Reads", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ShortReads", + "@id": "bts:CellMedianNumberGenes", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that were too short. Integer", - "rdfs:label": "ShortReads", + "rdfs:comment": "Median number of genes detected per cell. Number", + "rdfs:label": "CellMedianNumberGenes", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Short Reads", - "sms:required": "sms:false", + "sms:displayName": "Cell Median Number Genes", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Islowestlevel", + "@id": "bts:CellTotal", "@type": "rdfs:Class", - "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", - "rdfs:label": "Islowestlevel", + "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", + "rdfs:label": "CellTotal", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel2" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Cell Total", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScRNA-seqLevel4", + "@type": "rdfs:Class", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScRNA-seqLevel4", + "rdfs:subClassOf": [ { - "@id": "bts:Yes-Islowestlevel" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scRNA-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScRNA-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:No" + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" } ], - "sms:displayName": "Is lowest level", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel3", + "@id": "bts:Slide-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq gene expression matrices", - "rdfs:label": "BulkRNA-seqLevel3", + "rdfs:comment": "Raw sequencing files for the Slide-seq assay.", + "rdfs:label": "Slide-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 3", + "sms:displayName": "Slide-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -33970,40 +34296,70 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:PseudoAlignmentUsed" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:DataCategory" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:ExpressionUnits" + "@id": "bts:SpatialRead1" }, { - "@id": "bts:MatrixType" + "@id": "bts:SpatialRead2" }, { - "@id": "bts:FusionGeneDetected" + "@id": "bts:EndBias" }, { - "@id": "bts:FusionGeneIdentity" + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:SpatialBarcodeOffset" + }, + { + "@id": "bts:SpatialBarcodeandUMI" + }, + { + "@id": "bts:SpikeIn" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex" } ], "sms:validationRules": [] }, { - "@id": "bts:PseudoAlignmentUsed", + "@id": "bts:SpatialRead1", "@type": "rdfs:Class", - "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", - "rdfs:label": "PseudoAlignmentUsed", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "SpatialRead1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -34011,24 +34367,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-PseudoAlignmentUsed" + "@id": "bts:CDNA" }, { - "@id": "bts:No" + "@id": "bts:SpatialBarcodeandUMI" } ], - "sms:displayName": "Pseudo Alignment Used", + "sms:displayName": "Spatial Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExpressionUnits", + "@id": "bts:SpatialRead2", "@type": "rdfs:Class", - "rdfs:comment": "How quantities are corrected for gene length", - "rdfs:label": "ExpressionUnits", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "SpatialRead2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -34036,64 +34392,80 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TPM" - }, - { - "@id": "bts:RPKM" - }, - { - "@id": "bts:FPKM" - }, - { - "@id": "bts:Counts" + "@id": "bts:CDNA" }, { - "@id": "bts:Other" - }, + "@id": "bts:SpatialBarcodeandUMI" + } + ], + "sms:displayName": "Spatial Read2", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialBarcodeOffset", + "@type": "rdfs:Class", + "rdfs:comment": "Offset in sequence for spot barcode read (in bp): number", + "rdfs:label": "SpatialBarcodeOffset", + "rdfs:subClassOf": [ { - "@id": "bts:NA" + "@id": "bts:SpatialTranscriptomics" } ], - "sms:displayName": "Expression Units", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Barcode Offset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneDetected", + "@id": "bts:SpatialBarcodeandUMI", "@type": "rdfs:Class", - "rdfs:comment": "Was a fusion gene identified?", - "rdfs:label": "FusionGeneDetected", + "rdfs:comment": "Spot and transcript identifiers", + "rdfs:label": "SpatialBarcodeandUMI", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" + }, + { + "@id": "bts:SpatialRead1" + }, + { + "@id": "bts:SpatialRead2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Spatial Barcode and UMI", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:Yes-FusionGeneDetected" + "@id": "bts:SpatialBarcodeOffset" }, { - "@id": "bts:No" + "@id": "bts:SpatialBarcodeLength" }, { - "@id": "bts:Unknown" + "@id": "bts:UMIBarcodeOffset" + }, + { + "@id": "bts:UMIBarcodeLength" } ], - "sms:displayName": "Fusion Gene Detected", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:FusionGeneIdentity", + "@id": "bts:SpatialLibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "The gene symbols of fused genes.", - "rdfs:label": "FusionGeneIdentity", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "SpatialLibraryConstructionMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -34101,48 +34473,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EWS-FLI" + "@id": "bts:Smart-seq2" }, { - "@id": "bts:EWS-ERG" + "@id": "bts:Smart-SeqV4" }, { - "@id": "bts:SYT-SSX1" + "@id": "bts:10xV1.0" }, { - "@id": "bts:SYT-SSX2" + "@id": "bts:10xV1.1" }, { - "@id": "bts:EWS-WT1" + "@id": "bts:10xV2" }, { - "@id": "bts:OtherFusionGene" + "@id": "bts:10xV3" + }, + { + "@id": "bts:10xV3.1" + }, + { + "@id": "bts:Drop-seq" + }, + { + "@id": "bts:InDropsV2" + }, + { + "@id": "bts:InDropsV3" + }, + { + "@id": "bts:TruDrop" + }, + { + "@id": "bts:NexteraXT" } ], - "sms:displayName": "Fusion Gene Identity", + "sms:displayName": "Spatial Library Construction Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SpatialTranscriptomics", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Transcriptomics", "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] + "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel1", + "@id": "bts:Slide-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing raw files", - "rdfs:label": "BulkWESLevel1", + "rdfs:comment": "Aligned sequencing files and QC for the Slide-seq assay.", + "rdfs:label": "Slide-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 1", + "sms:displayName": "Slide-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Slide-seqLevel1" } ], "sms:requiresDependency": [ @@ -34156,94 +34561,218 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:Slide-seqWorkflowType" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:Slide-seqWorkflowParameterDescription" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:ReadLength" + "@id": "bts:GenomicReference" }, { - "@id": "bts:TargetCaptureKit" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:Checksum" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:MatchedSpatialBarcodeTag" }, { - "@id": "bts:AdapterName" + "@id": "bts:UMITag" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:AppliedHardTrimming" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze the Slide-seq data set. String", + "rdfs:label": "Slide-seqWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Workflow Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqWorkflowParameterDescription", + "@type": "rdfs:Class", + "rdfs:comment": "Parameters used to run the Slide-seq workflow. String", + "rdfs:label": "Slide-seqWorkflowParameterDescription", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Workflow Parameter Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialBarcodeTag", + "@type": "rdfs:Class", + "rdfs:comment": "SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)", + "rdfs:label": "SpatialBarcodeTag", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Barcode Tag", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MatchedSpatialBarcodeTag", + "@type": "rdfs:Class", + "rdfs:comment": "SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)", + "rdfs:label": "MatchedSpatialBarcodeTag", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matched Spatial Barcode Tag", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).", + "rdfs:label": "Slide-seqLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Slide-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:Filename" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:FileFormat" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:RunID" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:DataCategory" }, { - "@id": "bts:LaneNumber" + "@id": "bts:MatrixType" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:Slide-seqWorkflowType" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:Slide-seqWorkflowParameterDescription" }, { - "@id": "bts:TargetDepth" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:BeadsTotal" + }, + { + "@id": "bts:MedianUMICountsperSpot" + }, + { + "@id": "bts:MedianNumberGenesperSpatialSpot" + }, + { + "@id": "bts:Slide-seqBeadFileType" + }, + { + "@id": "bts:Slide-seqFragmentSize" } ], "sms:validationRules": [] }, { - "@id": "bts:TargetCaptureKit", + "@id": "bts:RunID", "@type": "rdfs:Class", - "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", - "rdfs:label": "TargetCaptureKit", + "rdfs:comment": "A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.", + "rdfs:label": "RunID", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Run ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SequencingBatchID", + "@type": "rdfs:Class", + "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", + "rdfs:label": "SequencingBatchID", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34252,167 +34781,387 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, + "sms:displayName": "Sequencing Batch ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BeadsTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Number of sequenced beads. Applies to raw counts matrix only. Integer", + "rdfs:label": "BeadsTotal", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Beads Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedianUMICountsperSpot", + "@type": "rdfs:Class", + "rdfs:comment": "The median number of UMI counts per tissue covered spot.", + "rdfs:label": "MedianUMICountsperSpot", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median UMI Counts per Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:MedianNumberGenesperSpatialSpot", + "@type": "rdfs:Class", + "rdfs:comment": "The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.", + "rdfs:label": "MedianNumberGenesperSpatialSpot", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median Number Genes per Spatial Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:Slide-seqBeadFileType", + "@type": "rdfs:Class", + "rdfs:comment": "The type of Level 3 file submitted as part of the Slide-seq workflow.", + "rdfs:label": "Slide-seqBeadFileType", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, "schema:rangeIncludes": [ { - "@id": "bts:NotApplicable" + "@id": "bts:MatrixFeatures" }, { - "@id": "bts:CustomTargetsFileProvided" + "@id": "bts:MatrixBarcodes" }, { - "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" + "@id": "bts:AllBeadLocations" }, { - "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" + "@id": "bts:AllBeadBarcodes" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" + "@id": "bts:MatchedBeadBarcodes" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" + "@id": "bts:MatchedBeadLocations" }, { - "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Slide-seq Bead File Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqFragmentSize", + "@type": "rdfs:Class", + "rdfs:comment": "Average cDNA length associated with the experiemtn. Integer", + "rdfs:label": "Slide-seqFragmentSize", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Fragment Size", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatrixFeatures", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatrixFeatures", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matrix Features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatrixBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatrixBarcodes", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matrix Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AllBeadLocations", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AllBeadLocations", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "All Bead Locations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AllBeadBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AllBeadBarcodes", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "All Bead Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatchedBeadBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatchedBeadBarcodes", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matched Bead Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatchedBeadLocations", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatchedBeadLocations", + "rdfs:subClassOf": [ + { + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matched Bead Locations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NotApplicable", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NotApplicable", + "rdfs:subClassOf": [ + { + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" + "@id": "bts:SomaticVariantsSampleType" }, { - "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:CustomMSKIMPACTPanel-341Genes" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:CustomMSKIMPACTPanel-410Genes" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:CustomMSKIMPACTPanel-468Genes" + "@id": "bts:PatientColonoscopyPerformedIndicator" }, { - "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + "@id": "bts:ReplicateType" }, { - "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" }, { - "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" + "@id": "bts:ColorectalCancerKRASIndicator" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" + "@id": "bts:ColonPolypOccurenceIndicator" }, { - "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" + "@id": "bts:FamilyHistoryColorectalPolyp" }, { - "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" + "@id": "bts:ColorectalPolypNewIndicator" }, { - "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:FoundationMedicineT5aPanel-322Genes" + "@id": "bts:RefluxTreatmentType" }, { - "@id": "bts:FoundationMedicineT7Panel-429Genes" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" + "@id": "bts:ColorectalCancerTumorBorderConfiguration" }, { - "@id": "bts:NexteraDNAExome" + "@id": "bts:ColorectalPolypShape" }, { - "@id": "bts:NexteraRapidCaptureExomev1.2" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:SeqCapEZHGSCVCRomev2.1" + "@id": "bts:SpecimenLaterality" }, { - "@id": "bts:SeqCapEZHumanExomev2.0" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:SeqCapEZHumanExomev3.0" + "@id": "bts:Slide-seqBeadFileType" }, { - "@id": "bts:SureSelectHumanAllExonv3" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:SureSelectHumanAllExonv4" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:SureSelectHumanAllExonv5" + "@id": "bts:ColorectalPolypAdenomaType" }, { - "@id": "bts:SureSelectHumanAllExonv5+UTR" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:TruSeqAmpliconCancerPanel" + "@id": "bts:CutaneousMelanomaAdditionalFindings" }, { - "@id": "bts:TruSeqExomeEnrichment-62Mb" + "@id": "bts:CauseofDeath" }, { - "@id": "bts:TruSeqRNAExome" + "@id": "bts:TumorGrade" }, { - "@id": "bts:TruSightMyeloidSequencingPanel" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:XGenExomeResearchPanelv1.0" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" + "@id": "bts:TestResult" }, { - "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" + "@id": "bts:StorageMethod" }, { - "@id": "bts:SureSelectHumanAllExonv6" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Unknown" + "@id": "bts:ConcomitantMedicationReceivedType" + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome" + }, + { + "@id": "bts:CancerAssociatedGeneMutations" + }, + { + "@id": "bts:MutationalSignatures" + }, + { + "@id": "bts:PrecancerousConditionType" } ], - "sms:displayName": "Target Capture Kit", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Not Applicable", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel2", + "@id": "bts:BulkRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", - "rdfs:label": "BulkWESLevel2", + "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", + "rdfs:label": "BulkRNA-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34421,11 +35170,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 2", + "sms:displayName": "Bulk RNA-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkWESLevel1" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -34439,159 +35188,200 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:GenomicReference" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:IndexFileName" + "@id": "bts:Micro-regionSeqPlatform" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:ROITag" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:Contamination" + "@id": "bts:ReadLength" }, { - "@id": "bts:ContaminationError" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:AdapterContent" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:Encoding" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:SpikeIn" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:AdapterName" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:QCWorkflowType" + "@id": "bts:LaneNumber" }, { - "@id": "bts:QCWorkflowVersion" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:QCWorkflowLink" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:MSIWorkflowLink" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:MSIScore" + "@id": "bts:TargetDepth" }, { - "@id": "bts:MSIStatus" + "@id": "bts:ToTrimAdapterSequence" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:TranscriptIntegrityNumber" }, { - "@id": "bts:TotalReads" + "@id": "bts:RIN" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:DV200" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:AdapterContent" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Encoding" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:KmerContent" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:ShortReads" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:Islowestlevel" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionCoverage10x", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage10x", - "rdfs:subClassOf": [ - { + "@id": "bts:PerSequenceGCContent" + }, + { + "@id": "bts:PerSequenceQualityScore" + }, + { + "@id": "bts:PerTileSequenceQuality" + }, + { + "@id": "bts:PercentGCContent" + }, + { + "@id": "bts:SequenceDuplicationLevels" + }, + { + "@id": "bts:SequenceLengthDistribution" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:QCWorkflowType" + }, + { + "@id": "bts:QCWorkflowVersion" + }, + { + "@id": "bts:QCWorkflowLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:LibraryLayout", + "@type": "rdfs:Class", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "LibraryLayout", + "rdfs:subClassOf": [ + { "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 10x", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:PairedEnd" + }, + { + "@id": "bts:SingleRead" + }, + { + "@id": "bts:Mid-length" + }, + { + "@id": "bts:LongRead" + } + ], + "sms:displayName": "Library Layout", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage30X", + "@id": "bts:Micro-regionSeqPlatform", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage30X", + "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", + "rdfs:label": "Micro-regionSeqPlatform", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34600,15 +35390,23 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 30X", + "schema:rangeIncludes": [ + { + "@id": "bts:RarecytePick-Seq" + }, + { + "@id": "bts:LaserCaptureMicrodissection" + } + ], + "sms:displayName": "Micro-region Seq Platform", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel3", + "@id": "bts:ROITag", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing called variants", - "rdfs:label": "BulkWESLevel3", + "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", + "rdfs:label": "ROITag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34617,64 +35415,75 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 3", + "sms:displayName": "ROI Tag", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:ReadLength", + "@type": "rdfs:Class", + "rdfs:comment": "The length of the sequencing reads. Can be integer, null", + "rdfs:label": "ReadLength", + "rdfs:subClassOf": [ { - "@id": "bts:BulkWESLevel2" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Read Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LibrarySelectionMethod", + "@type": "rdfs:Class", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "LibrarySelectionMethod", + "rdfs:subClassOf": [ { - "@id": "bts:GenomicReference" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:HybridSelection" }, { - "@id": "bts:GermlineVariantsWorkflowURL" + "@id": "bts:PCR" }, { - "@id": "bts:GermlineVariantsWorkflowType" + "@id": "bts:AffinityEnrichment" }, { - "@id": "bts:SomaticVariantsWorkflowURL" + "@id": "bts:Poly-TEnrichment" }, { - "@id": "bts:SomaticVariantsWorkflowType" + "@id": "bts:Random" }, { - "@id": "bts:SomaticVariantsSampleType" + "@id": "bts:RRNADepletion" }, { - "@id": "bts:StructuralVariantWorkflowURL" + "@id": "bts:MiRNASizeFractionation" }, { - "@id": "bts:StructuralVariantWorkflowType" + "@id": "bts:Other" } ], + "sms:displayName": "Library Selection Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowURL", + "@id": "bts:LibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", - "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34683,15 +35492,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Germline Variants Workflow URL", + "sms:displayName": "Library Preparation Kit Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowType", + "@id": "bts:LibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVendor", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34700,26 +35509,49 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GATK4" - }, + "sms:displayName": "Library Preparation Kit Vendor", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LibraryPreparationKitVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVersion", + "rdfs:subClassOf": [ { - "@id": "bts:OtherGermlineVariantsWorkflowType" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Library Preparation Kit Version", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AdapterName", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the sequencing adapter. String", + "rdfs:label": "AdapterName", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Germline Variants Workflow Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adapter Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowURL", + "@id": "bts:AdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:comment": "Base sequence of the sequencing adapter. String", + "rdfs:label": "AdapterSequence", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34728,15 +35560,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Somatic Variants Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowType", + "@id": "bts:BaseCallerName", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:comment": "Name of the base caller. String", + "rdfs:label": "BaseCallerName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34745,44 +35577,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaVEMan" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:MuTect2" - }, - { - "@id": "bts:MuSE" - }, - { - "@id": "bts:Pindel" - }, - { - "@id": "bts:SomaticSniper" - }, - { - "@id": "bts:VarScan2" - }, - { - "@id": "bts:OtherSomaticVariantsWorkflowType" - }, + "sms:displayName": "Base Caller Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BaseCallerVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Version of the base caller. String", + "rdfs:label": "BaseCallerVersion", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Somatic Variants Workflow Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Base Caller Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsSampleType", + "@id": "bts:FlowCellBarcode", "@type": "rdfs:Class", - "rdfs:comment": "Is the sample case or control in somatic variant analysis", - "rdfs:label": "SomaticVariantsSampleType", + "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", + "rdfs:label": "FlowCellBarcode", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34791,26 +35611,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaseSample" - }, - { - "@id": "bts:ControlSample" - }, + "sms:displayName": "Flow Cell Barcode", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentMaximumLength", + "@type": "rdfs:Class", + "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMaximumLength", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Somatic Variants Sample Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Maximum Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowURL", + "@id": "bts:FragmentMeanLength", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", - "rdfs:label": "StructuralVariantWorkflowURL", + "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentMeanLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34819,15 +35645,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Structural Variant Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Fragment Mean Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowType", + "@id": "bts:FragmentMinimumLength", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "StructuralVariantWorkflowType", + "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMinimumLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -34836,117 +35662,134 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BRASS" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:CNV" - }, - { - "@id": "bts:CNVkit" - }, - { - "@id": "bts:OtherStructuralVariantWorkflowType" - }, + "sms:displayName": "Fragment Minimum Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentStandardDeviationLength", + "@type": "rdfs:Class", + "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentStandardDeviationLength", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Structural Variant Workflow Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Standard Deviation Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLevel1", + "@id": "bts:LaneNumber", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", - "rdfs:label": "MicroarrayLevel1", + "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label": "LaneNumber", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 1", + "sms:displayName": "Lane Number", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:LibraryStrand", + "@type": "rdfs:Class", + "rdfs:comment": "Library stranded-ness.", + "rdfs:label": "LibraryStrand", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NucleicAcidSource" + "@id": "bts:Unstranded" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:FirstStranded" }, { - "@id": "bts:MicroarrayMolecule" + "@id": "bts:SecondStranded" }, { - "@id": "bts:MicroarrayLabel" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Library Strand", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MultiplexBarcode", + "@type": "rdfs:Class", + "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", + "rdfs:label": "MultiplexBarcode", + "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayValueDefinition" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Multiplex Barcode", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SizeSelectionRange", + "@type": "rdfs:Class", + "rdfs:comment": "Range of size selection. String", + "rdfs:label": "SizeSelectionRange", + "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayProtocolAuxiliaryFile" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Size Selection Range", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayPlatformID", + "@id": "bts:TargetDepth", "@type": "rdfs:Class", - "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", - "rdfs:label": "MicroarrayPlatformID", + "rdfs:comment": "The targeted read depth prior to sequencing. Integer", + "rdfs:label": "TargetDepth", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Platform ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match GPL\\d+" - ] + "sms:displayName": "Target Depth", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:MicroarrayMolecule", + "@id": "bts:ToTrimAdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "Microarray is measuring this kind of molecule", - "rdfs:label": "MicroarrayMolecule", + "rdfs:comment": "Does the user suggest adapter trimming?", + "rdfs:label": "ToTrimAdapterSequence", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -34954,142 +35797,157 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DNA" + "@id": "bts:Yes-TrimAdapterSequence" }, { - "@id": "bts:RNA" + "@id": "bts:No" } ], - "sms:displayName": "Microarray Molecule", - "sms:required": "sms:true", + "sms:displayName": "To Trim Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLabel", + "@id": "bts:TranscriptIntegrityNumber", "@type": "rdfs:Class", - "rdfs:comment": "Microarray used this kind of label", - "rdfs:label": "MicroarrayLabel", + "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", + "rdfs:label": "TranscriptIntegrityNumber", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Label", - "sms:required": "sms:true", + "sms:displayName": "Transcript Integrity Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayValueDefinition", + "@id": "bts:RIN", "@type": "rdfs:Class", - "rdfs:comment": "What the provided value signifies", - "rdfs:label": "MicroarrayValueDefinition", + "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", + "rdfs:label": "RIN", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Value Definition", - "sms:required": "sms:true", + "sms:displayName": "RIN", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayProtocolAuxiliaryFile", + "@id": "bts:DV200", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", - "rdfs:label": "MicroarrayProtocolAuxiliaryFile", + "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", + "rdfs:label": "DV200", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Protocol Auxiliary File", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match syn\\d+" - ] + "sms:displayName": "DV200", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLevel2", + "@id": "bts:AdapterContent", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", - "rdfs:label": "MicroarrayLevel2", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "AdapterContent", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:MicroarrayLevel1" - } - ], - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:FAIL" }, { - "@id": "bts:Filename" + "@id": "bts:PASS" }, { - "@id": "bts:FileFormat" + "@id": "bts:WARN" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Unknown" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Adapter Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BasicStatistics", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "BasicStatistics", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:PASS" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:WARN" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:Unknown" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:NotReported" } ], + "sms:displayName": "Basic Statistics", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NormalizationMethod", + "@id": "bts:Encoding", "@type": "rdfs:Class", - "rdfs:comment": "Description of Normalization Process", - "rdfs:label": "NormalizationMethod", + "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", + "rdfs:label": "Encoding", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Normalization Method", + "sms:displayName": "Encoding", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel1", + "@id": "bts:KmerContent", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", - "rdfs:label": "ScATAC-seqLevel1", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "KmerContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35098,109 +35956,35 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:DissociationMethod" - }, - { - "@id": "bts:SingleNucleusBuffer" - }, - { - "@id": "bts:SingleCellIsolationMethod" - }, - { - "@id": "bts:TranspositionReaction" - }, - { - "@id": "bts:ScATACseqLibraryLayout" - }, - { - "@id": "bts:NucleusIdentifier" - }, - { - "@id": "bts:NucleiBarcodeLength" - }, - { - "@id": "bts:NucleiBarcodeRead" - }, - { - "@id": "bts:ScATACseqRead1" - }, - { - "@id": "bts:ScATACseqRead2" - }, - { - "@id": "bts:ScATACseqRead3" - }, - { - "@id": "bts:LibraryConstructionMethod" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:ThresholdforMinimumPassingReads" - }, - { - "@id": "bts:TotalNumberofPassingNuclei" - }, - { - "@id": "bts:MedianFractionofReadsinPeaks" - }, - { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" - }, + "schema:rangeIncludes": [ { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:FAIL" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:PASS" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:WARN" }, { - "@id": "bts:TotalReads" + "@id": "bts:Unknown" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:NotReported" } ], + "sms:displayName": "Kmer Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SingleNucleusBuffer", + "@id": "bts:OverrepresentedSequences", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation buffer", - "rdfs:label": "SingleNucleusBuffer", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "OverrepresentedSequences", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35208,30 +35992,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NIB" + "@id": "bts:FAIL" }, { - "@id": "bts:10x" + "@id": "bts:PASS" }, { - "@id": "bts:Omni" + "@id": "bts:WARN" }, { - "@id": "bts:TST" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Single Nucleus Buffer", - "sms:required": "sms:true", + "sms:displayName": "Overrepresented Sequences", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TranspositionReaction", + "@id": "bts:PerBaseNContent", "@type": "rdfs:Class", - "rdfs:comment": "Name of the transposase, transposon sequences", - "rdfs:label": "TranspositionReaction", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseNContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35239,39 +36026,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Tn5" - }, - { - "@id": "bts:EZ-Tn5" - }, - { - "@id": "bts:Tn5-059" + "@id": "bts:FAIL" }, { - "@id": "bts:NexteraTn5" + "@id": "bts:PASS" }, { - "@id": "bts:Diagenode-unloadedApex-Bio" + "@id": "bts:WARN" }, { - "@id": "bts:Diagenode-loadedApex-Bio" + "@id": "bts:Unknown" }, { - "@id": "bts:In-House" + "@id": "bts:NotReported" } ], - "sms:displayName": "Transposition Reaction", - "sms:required": "sms:true", + "sms:displayName": "Per Base N Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqLibraryLayout", + "@id": "bts:PerBaseSequenceContent", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "ScATACseqLibraryLayout", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35279,21 +36060,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Per Base Sequence Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleusIdentifier", + "@id": "bts:PerBaseSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", - "rdfs:label": "NucleusIdentifier", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceQuality", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35301,64 +36094,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NucleiBarcode" - } - ], - "sms:displayName": "Nucleus Identifier", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiBarcodeLength", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Length", - "rdfs:label": "NucleiBarcodeLength", - "rdfs:subClassOf": [ + "@id": "bts:FAIL" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:PASS" }, { - "@id": "bts:NucleiBarcode" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Barcode Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiBarcodeRead", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Read", - "rdfs:label": "NucleiBarcodeRead", - "rdfs:subClassOf": [ + "@id": "bts:WARN" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Unknown" }, { - "@id": "bts:NucleiBarcode" + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Barcode Read", - "sms:required": "sms:true", + "sms:displayName": "Per Base Sequence Quality", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead1", + "@id": "bts:PerSequenceGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScATACseqRead1", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceGCContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35366,36 +36128,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:FAIL" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:PASS" }, { - "@id": "bts:DNAInsert" + "@id": "bts:WARN" }, { - "@id": "bts:SampleIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:CellBarcode" + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Read1", - "sms:required": "sms:true", + "sms:displayName": "Per Sequence GC Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead2", + "@id": "bts:PerSequenceQualityScore", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScATACseqRead2", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceQualityScore", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35403,33 +36162,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:FAIL" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:PASS" }, { - "@id": "bts:DNAInsert" + "@id": "bts:WARN" }, { - "@id": "bts:SampleIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:CellBarcode" + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Read2", - "sms:required": "sms:true", + "sms:displayName": "Per Sequence Quality Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead3", + "@id": "bts:PerTileSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScATACseqRead3", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerTileSequenceQuality", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -35437,142 +36196,183 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:FAIL" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:PASS" }, { - "@id": "bts:DNAInsert" + "@id": "bts:WARN" }, { - "@id": "bts:SampleIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:CellBarcode" + "@id": "bts:NotReported" } ], - "sms:displayName": "scATACseq Read3", + "sms:displayName": "Per Tile Sequence Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ThresholdforMinimumPassingReads", + "@id": "bts:PercentGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Threshold for calling cells", - "rdfs:label": "ThresholdforMinimumPassingReads", + "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", + "rdfs:label": "PercentGCContent", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Threshold for Minimum Passing Reads", - "sms:required": "sms:true", + "sms:displayName": "Percent GC Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofPassingNuclei", + "@id": "bts:SequenceDuplicationLevels", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei sequenced", - "rdfs:label": "TotalNumberofPassingNuclei", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceDuplicationLevels", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Passing Nuclei", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Duplication Levels", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinPeaks", + "@id": "bts:SequenceLengthDistribution", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in peaks (FRIP)", - "rdfs:label": "MedianFractionofReadsinPeaks", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceLengthDistribution", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Peaks", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], + "sms:displayName": "Sequence Length Distribution", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", + "@id": "bts:TotalReads", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", - "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", + "rdfs:comment": "Total number of reads per sample. Integer", + "rdfs:label": "TotalReads", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "sms:displayName": "Total Reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", + "rdfs:label": "QCWorkflowType", + "rdfs:subClassOf": [ { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianPassingReadPercentage", + "@id": "bts:QCWorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", - "rdfs:label": "MedianPassingReadPercentage", + "rdfs:comment": "Major version for a workflow. String", + "rdfs:label": "QCWorkflowVersion", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Passing Read Percentage", - "sms:required": "sms:true", + "sms:displayName": "QC Workflow Version", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@id": "bts:QCWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Contamination from mitochondrial sequences", - "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:comment": "Link to workflow used. String", + "rdfs:label": "QCWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", - "sms:required": "sms:true", + "sms:displayName": "QC Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel2", + "@id": "bts:BulkRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", - "rdfs:label": "ScATAC-seqLevel2", + "rdfs:comment": "Bulk RNA-seq alignment protocol description", + "rdfs:label": "BulkRNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35581,11 +36381,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 2", + "sms:displayName": "Bulk RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:BulkRNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -35629,37 +36429,40 @@ "@id": "bts:AverageReadLength" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:Contamination" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ContaminationError" }, { - "@id": "bts:TotalReads" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:MapQ30" + "@id": "bts:MSIScore" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:MSIStatus" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:TotalReads" }, { - "@id": "bts:ShortReads" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:ProportionReadsDuplicated" + }, + { + "@id": "bts:ProportionReadsMapped" }, { "@id": "bts:ProportionTargetsNoCoverage" @@ -35668,42 +36471,36 @@ "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" - }, - { - "@id": "bts:Contamination" + "@id": "bts:ShortReads" }, { - "@id": "bts:ContaminationError" + "@id": "bts:Islowestlevel" } ], "sms:validationRules": [] }, { - "@id": "bts:MapQ30", + "@id": "bts:AlignmentWorkflowUrl", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads with Quality >= 30.", - "rdfs:label": "MapQ30", + "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", + "rdfs:label": "AlignmentWorkflowUrl", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MapQ30", - "sms:required": "sms:false", + "sms:displayName": "Alignment Workflow Url", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel3", + "@id": "bts:AlignmentWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files containing peak information for cells", - "rdfs:label": "ScATAC-seqLevel3", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "AlignmentWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35712,797 +36509,638 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScATAC-seqObjectID" - }, - { - "@id": "bts:NCountPeaks" - }, - { - "@id": "bts:NFeaturePeaks" - }, - { - "@id": "bts:TotalRead-Pairs" - }, - { - "@id": "bts:DuplicateRead-Pairs" - }, - { - "@id": "bts:ChimericRead-Pairs" - }, - { - "@id": "bts:UnmappedRead-Pairs" - }, - { - "@id": "bts:LowMapQ" - }, + "schema:rangeIncludes": [ { - "@id": "bts:MitochondrialRead-Pairs" + "@id": "bts:BWA" }, { - "@id": "bts:PassedFilters" + "@id": "bts:BWAwithBQSR" }, { - "@id": "bts:TSSFragments" + "@id": "bts:BWA-aln" }, { - "@id": "bts:DNaseSensitiveRegionFragments" + "@id": "bts:BWA-mem" }, { - "@id": "bts:EnhancerRegionFragments" + "@id": "bts:BWAwithMarkDuplicatesandBQSR" }, { - "@id": "bts:PromoterRegionFragments" + "@id": "bts:STAR2-Pass" }, { - "@id": "bts:OnTargetFragments" + "@id": "bts:STAR2-PassChimeric" }, { - "@id": "bts:BlacklistRegionFragments" + "@id": "bts:STAR2-PassGenome" }, { - "@id": "bts:PeakRegionFragments" + "@id": "bts:STAR2-PassTranscriptome" }, { - "@id": "bts:PeakRegionCutsites" + "@id": "bts:Bowtie" }, { - "@id": "bts:NucleosomeSignal" + "@id": "bts:Bismark" }, { - "@id": "bts:NucleosomePercentile" + "@id": "bts:GSNAP" }, { - "@id": "bts:TSSEnrichment" + "@id": "bts:BSMAP" }, { - "@id": "bts:TSSPercentile" + "@id": "bts:BSmooth" }, { - "@id": "bts:PctReadsinPeaks" + "@id": "bts:BS-Seeker2" }, { - "@id": "bts:BlacklistRatio" + "@id": "bts:BS-Seeker" }, { - "@id": "bts:SeuratClusters" + "@id": "bts:RMAP" }, { - "@id": "bts:NCountRNA" + "@id": "bts:MethylCoder" }, { - "@id": "bts:NFeatureRNA" + "@id": "bts:BRAT-BW" }, { - "@id": "bts:MACS2Seqnames" + "@id": "bts:Pash" }, { - "@id": "bts:MACS2Start" + "@id": "bts:Segemehl" }, { - "@id": "bts:MACS2End" + "@id": "bts:Bisulfighter" }, { - "@id": "bts:MACS2Width" + "@id": "bts:BatMeth" }, { - "@id": "bts:MACS2Strand" + "@id": "bts:LAST" }, { - "@id": "bts:MACS2Name" + "@id": "bts:ERNE-BS5" }, { - "@id": "bts:MACS2Score" + "@id": "bts:B-SOLANA" }, { - "@id": "bts:MACS2FoldChange" + "@id": "bts:SOCS-B" }, { - "@id": "bts:MACS2NegLog10pvalueSummit" + "@id": "bts:BWA-meth" }, { - "@id": "bts:MACS2NegLog10qvalueSummit" + "@id": "bts:OtherAlignmentWorkflow" }, { - "@id": "bts:MACS2RelativeSummitPosition" + "@id": "bts:None" } ], + "sms:displayName": "Alignment Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqObjectID", + "@id": "bts:IndexFileName", "@type": "rdfs:Class", - "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", - "rdfs:label": "ScATAC-seqObjectID", + "rdfs:comment": "The name (or part of a name) of a file (of any type). String", + "rdfs:label": "IndexFileName", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Object ID", - "sms:required": "sms:false", + "sms:displayName": "Index File Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NCountPeaks", + "@id": "bts:AverageBaseQuality", "@type": "rdfs:Class", - "rdfs:comment": "Total number of fragments in peaks", - "rdfs:label": "NCountPeaks", + "rdfs:comment": "Average base quality collected from samtools. Number", + "rdfs:label": "AverageBaseQuality", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nCount Peaks", + "sms:displayName": "Average Base Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NFeaturePeaks", + "@id": "bts:AverageInsertSize", "@type": "rdfs:Class", - "rdfs:comment": "Number of peaks with at least one read", - "rdfs:label": "NFeaturePeaks", + "rdfs:comment": "Average insert size collected from samtools. Integer", + "rdfs:label": "AverageInsertSize", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nFeature Peaks", + "sms:displayName": "Average Insert Size", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalRead-Pairs", + "@id": "bts:AverageReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Total read-pairs", - "rdfs:label": "TotalRead-Pairs", + "rdfs:comment": "Average read length collected from samtools. Integer", + "rdfs:label": "AverageReadLength", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Read-Pairs", + "sms:displayName": "Average Read Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DuplicateRead-Pairs", + "@id": "bts:Contamination", "@type": "rdfs:Class", - "rdfs:comment": "Number of duplicate read-pairs", - "rdfs:label": "DuplicateRead-Pairs", + "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", + "rdfs:label": "Contamination", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Duplicate Read-Pairs", + "sms:displayName": "Contamination", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChimericRead-Pairs", + "@id": "bts:ContaminationError", "@type": "rdfs:Class", - "rdfs:comment": "Number of chimerically mapped read-pairs", - "rdfs:label": "ChimericRead-Pairs", + "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", + "rdfs:label": "ContaminationError", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Chimeric Read-Pairs", + "sms:displayName": "Contamination Error", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UnmappedRead-Pairs", + "@id": "bts:MeanCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs with at least one end not mapped", - "rdfs:label": "UnmappedRead-Pairs", + "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", + "rdfs:label": "MeanCoverage", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Unmapped Read-Pairs", + "sms:displayName": "Mean Coverage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LowMapQ", + "@id": "bts:MSIWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", - "rdfs:label": "LowMapQ", + "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", + "rdfs:label": "MSIWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LowMapQ", + "sms:displayName": "MSI Workflow Link", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MitochondrialRead-Pairs", + "@id": "bts:MSIScore", "@type": "rdfs:Class", - "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", - "rdfs:label": "MitochondrialRead-Pairs", + "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", + "rdfs:label": "MSIScore", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mitochondrial Read-Pairs", + "sms:displayName": "MSI Score", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PassedFilters", + "@id": "bts:MSIStatus", "@type": "rdfs:Class", - "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", - "rdfs:label": "PassedFilters", + "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", + "rdfs:label": "MSIStatus", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Passed Filters", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TSSFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping with TSS regions", - "rdfs:label": "TSSFragments", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "TSS Fragments", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DNaseSensitiveRegionFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", - "rdfs:label": "DNaseSensitiveRegionFragments", - "rdfs:subClassOf": [ + "@id": "bts:MSI" + }, { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DNase Sensitive Region Fragments", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EnhancerRegionFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping enhancer regions", - "rdfs:label": "EnhancerRegionFragments", - "rdfs:subClassOf": [ + "@id": "bts:MSI-low" + }, { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Enhancer Region Fragments", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PromoterRegionFragments", - "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping promoter regions", - "rdfs:label": "PromoterRegionFragments", - "rdfs:subClassOf": [ + "@id": "bts:MSI-high" + }, { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:MSS" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Promoter Region Fragments", + "sms:displayName": "MSI Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OnTargetFragments", + "@id": "bts:PairsOnDiffCHR", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", - "rdfs:label": "OnTargetFragments", + "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", + "rdfs:label": "PairsOnDiffCHR", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "On Target Fragments", + "sms:displayName": "Pairs On Diff CHR", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BlacklistRegionFragments", + "@id": "bts:TotalUniquelyMapped", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping blacklisted regions", - "rdfs:label": "BlacklistRegionFragments", + "rdfs:comment": "Number of reads that map to genome. Integer", + "rdfs:label": "TotalUniquelyMapped", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blacklist Region Fragments", + "sms:displayName": "Total Uniquely Mapped", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeakRegionFragments", + "@id": "bts:TotalUnmappedreads", "@type": "rdfs:Class", - "rdfs:comment": "Number of fragments overlapping peaks", - "rdfs:label": "PeakRegionFragments", + "rdfs:comment": "Number of reads that did not map to genome. Integer", + "rdfs:label": "TotalUnmappedreads", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peak Region Fragments", + "sms:displayName": "Total Unmapped reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeakRegionCutsites", + "@id": "bts:ProportionReadsDuplicated", "@type": "rdfs:Class", - "rdfs:comment": "Number of ends of fragments in peak regions", - "rdfs:label": "PeakRegionCutsites", + "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", + "rdfs:label": "ProportionReadsDuplicated", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peak Region Cutsites", + "sms:displayName": "Proportion Reads Duplicated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleosomeSignal", + "@id": "bts:ProportionReadsMapped", "@type": "rdfs:Class", - "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", - "rdfs:label": "NucleosomeSignal", + "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", + "rdfs:label": "ProportionReadsMapped", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleosome Signal", + "sms:displayName": "Proportion Reads Mapped", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleosomePercentile", + "@id": "bts:ProportionTargetsNoCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Percentile rank of nucleosome score", - "rdfs:label": "NucleosomePercentile", + "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", + "rdfs:label": "ProportionTargetsNoCoverage", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleosome Percentile", + "sms:displayName": "Proportion Targets No Coverage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TSSEnrichment", + "@id": "bts:ProportionBaseMismatch", "@type": "rdfs:Class", - "rdfs:comment": "Transcription start site (TSS) enrichment score", - "rdfs:label": "TSSEnrichment", + "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", + "rdfs:label": "ProportionBaseMismatch", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Enrichment", + "sms:displayName": "Proportion Base Mismatch", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TSSPercentile", + "@id": "bts:ShortReads", "@type": "rdfs:Class", - "rdfs:comment": "Percentile rank of TSS score", - "rdfs:label": "TSSPercentile", + "rdfs:comment": "Number of reads that were too short. Integer", + "rdfs:label": "ShortReads", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TSS Percentile", + "sms:displayName": "Short Reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PctReadsinPeaks", + "@id": "bts:Islowestlevel", "@type": "rdfs:Class", - "rdfs:comment": "Percentage of reads in peaks", - "rdfs:label": "PctReadsinPeaks", + "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", + "rdfs:label": "Islowestlevel", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:ScRNA-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pct Reads in Peaks", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BlacklistRatio", - "@type": "rdfs:Class", - "rdfs:comment": "Ratio of reads in blacklist regions", - "rdfs:label": "BlacklistRatio", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blacklist Ratio", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SeuratClusters", - "@type": "rdfs:Class", - "rdfs:comment": "Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm", - "rdfs:label": "SeuratClusters", - "rdfs:subClassOf": [ + "@id": "bts:Yes-Islowestlevel" + }, { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Seurat Clusters", + "sms:displayName": "Is lowest level", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NCountRNA", + "@id": "bts:BulkRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Total number of fragments in genes", - "rdfs:label": "NCountRNA", + "rdfs:comment": "Bulk RNA-seq gene expression matrices", + "rdfs:label": "BulkRNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nCount RNA", + "sms:displayName": "Bulk RNA-seq Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NFeatureRNA", - "@type": "rdfs:Class", - "rdfs:comment": "Number of genes detected in cell", - "rdfs:label": "NFeatureRNA", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:BulkRNA-seqLevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "nFeature RNA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Seqnames", - "@type": "rdfs:Class", - "rdfs:comment": "Chromosome id", - "rdfs:label": "MACS2Seqnames", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Seqnames", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Start", - "@type": "rdfs:Class", - "rdfs:comment": "Genomic starting position in MACS2", - "rdfs:label": "MACS2Start", - "rdfs:subClassOf": [ + "@id": "bts:Component" + }, { - "@id": "bts:ScATAC-seqLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Start", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2End", - "@type": "rdfs:Class", - "rdfs:comment": "Genomic ending position in MACS2", - "rdfs:label": "MACS2End", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:PseudoAlignmentUsed" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:ExpressionUnits" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:FusionGeneDetected" + }, + { + "@id": "bts:FusionGeneIdentity" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 End", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MACS2Width", + "@id": "bts:PseudoAlignmentUsed", "@type": "rdfs:Class", - "rdfs:comment": "Width of the peak in bases in MACS2", - "rdfs:label": "MACS2Width", + "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", + "rdfs:label": "PseudoAlignmentUsed", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Width", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Strand", - "@type": "rdfs:Class", - "rdfs:comment": "DNA stand aligned with in MACS2", - "rdfs:label": "MACS2Strand", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Yes-PseudoAlignmentUsed" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Strand", - "sms:required": "sms:false", + "sms:displayName": "Pseudo Alignment Used", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2Name", + "@id": "bts:ExpressionUnits", "@type": "rdfs:Class", - "rdfs:comment": "Name of the peak in MACS2", - "rdfs:label": "MACS2Name", + "rdfs:comment": "How quantities are corrected for gene length", + "rdfs:label": "ExpressionUnits", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2Score", - "@type": "rdfs:Class", - "rdfs:comment": "Peak score (proportional to q-value) in MACS2", - "rdfs:label": "MACS2Score", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:TPM" + }, + { + "@id": "bts:RPKM" + }, + { + "@id": "bts:FPKM" + }, + { + "@id": "bts:Counts" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:NA" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Score", - "sms:required": "sms:false", + "sms:displayName": "Expression Units", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MACS2FoldChange", + "@id": "bts:FusionGeneDetected", "@type": "rdfs:Class", - "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", - "rdfs:label": "MACS2FoldChange", + "rdfs:comment": "Was a fusion gene identified?", + "rdfs:label": "FusionGeneDetected", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Fold Change", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2NegLog10pvalueSummit", - "@type": "rdfs:Class", - "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", - "rdfs:label": "MACS2NegLog10pvalueSummit", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Yes-FusionGeneDetected" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Neg Log10 pvalue Summit", + "sms:displayName": "Fusion Gene Detected", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MACS2NegLog10qvalueSummit", + "@id": "bts:FusionGeneIdentity", "@type": "rdfs:Class", - "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", - "rdfs:label": "MACS2NegLog10qvalueSummit", + "rdfs:comment": "The gene symbols of fused genes.", + "rdfs:label": "FusionGeneIdentity", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MACS2 Neg Log10 qvalue Summit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MACS2RelativeSummitPosition", - "@type": "rdfs:Class", - "rdfs:comment": "Position of the peak summit related to the start position in MACS2", - "rdfs:label": "MACS2RelativeSummitPosition", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:EWS-FLI" + }, + { + "@id": "bts:EWS-ERG" + }, + { + "@id": "bts:SYT-SSX1" + }, + { + "@id": "bts:SYT-SSX2" + }, + { + "@id": "bts:EWS-WT1" + }, + { + "@id": "bts:OtherFusionGene" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MACS2 Relative Summit Position", + "sms:displayName": "Fusion Gene Identity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:ScmC-seqLevel1", + "@id": "bts:BulkWESLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw scmC-seq data.", - "rdfs:label": "ScmC-seqLevel1", + "rdfs:comment": "Bulk Whole Exome Sequencing raw files", + "rdfs:label": "BulkWESLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36511,7 +37149,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scmC-seq Level 1", + "sms:displayName": "Bulk WES Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -36535,123 +37173,91 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:ScmCseqRead1" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:ScmCseqRead2" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:ScmCseqRead3" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:SingleCellIsolationMethod" + "@id": "bts:ReadLength" }, { - "@id": "bts:SingleNucleusBuffer" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:SingleNucleusCapture" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:BisulfiteConversion" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:NucleusIdentifier" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:AdapterName" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:MedianFractionofReadsinPeaks" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:PeaksCallingSoftware" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:ThresholdforMinimumPassingReads" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:TotalNumberofPassingNuclei" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:TotalReads" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScmCseqRead1", - "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScmCseqRead1", - "rdfs:subClassOf": [ + "@id": "bts:FragmentStandardDeviationLength" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LaneNumber" + }, { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "scmCseq Read1", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScmCseqRead2", - "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScmCseqRead2", - "rdfs:subClassOf": [ + "@id": "bts:LibraryPreparationDaysfromIndex" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SizeSelectionRange" + }, { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:TargetDepth" }, { - "@id": "bts:CDNA" + "@id": "bts:ToTrimAdapterSequence" } ], - "sms:displayName": "scmCseq Read2", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScmCseqRead3", + "@id": "bts:TargetCaptureKit", "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScmCseqRead3", + "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", + "rdfs:label": "TargetCaptureKit", "rdfs:subClassOf": [ { - "@id": "bts:ScmC-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -36659,199 +37265,165 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:NotApplicable" }, { - "@id": "bts:CDNA" - } - ], - "sms:displayName": "scmCseq Read3", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SingleNucleusCapture", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation method", - "rdfs:label": "SingleNucleusCapture", - "rdfs:subClassOf": [ + "@id": "bts:CustomTargetsFileProvided" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" + }, { - "@id": "bts:Plates" + "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" }, { - "@id": "bts:10x" + "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" }, { - "@id": "bts:Droplet" - } - ], - "sms:displayName": "Single Nucleus Capture", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BisulfiteConversion", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the kit used in bisulfite conversion.", - "rdfs:label": "BisulfiteConversion", - "rdfs:subClassOf": [ + "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" + }, { - "@id": "bts:BulkMethylation-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" + }, { - "@id": "bts:ZimoEZDNAMethylationKit" + "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" }, { - "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" + "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" }, { - "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" + "@id": "bts:CustomMSKIMPACTPanel-341Genes" }, { - "@id": "bts:NEBNextEnzymaticMethyl-seqKit" + "@id": "bts:CustomMSKIMPACTPanel-410Genes" }, { - "@id": "bts:AgilentSureSelectXTMethyl-Seq" - } - ], - "sms:displayName": "Bisulfite Conversion", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PeaksCallingSoftware", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name of peaks calling tool", - "rdfs:label": "PeaksCallingSoftware", - "rdfs:subClassOf": [ + "@id": "bts:CustomMSKIMPACTPanel-468Genes" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Peaks Calling Software", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScmC-seqLevel2", - "@type": "rdfs:Class", - "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", - "rdfs:label": "ScmC-seqLevel2", - "rdfs:subClassOf": [ + "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scmC-seq Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + }, { - "@id": "bts:ScmC-seqLevel1" - } - ], - "sms:requiresDependency": [ + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + }, { - "@id": "bts:Component" + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" }, { - "@id": "bts:Filename" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" }, { - "@id": "bts:FileFormat" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" }, { - "@id": "bts:AlignmentWorkflowUrl" + "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" }, { - "@id": "bts:GenomicReference" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" }, { - "@id": "bts:IndexFileName" + "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" }, { - "@id": "bts:Contamination" + "@id": "bts:FoundationMedicineT5aPanel-322Genes" }, { - "@id": "bts:ContaminationError" + "@id": "bts:FoundationMedicineT7Panel-429Genes" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" }, { - "@id": "bts:TotalReads" + "@id": "bts:NexteraDNAExome" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:NexteraRapidCaptureExomev1.2" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:SeqCapEZHGSCVCRomev2.1" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:SeqCapEZHumanExomev2.0" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:SeqCapEZHumanExomev3.0" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:SureSelectHumanAllExonv3" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:SureSelectHumanAllExonv4" }, { - "@id": "bts:ShortReads" + "@id": "bts:SureSelectHumanAllExonv5" + }, + { + "@id": "bts:SureSelectHumanAllExonv5+UTR" + }, + { + "@id": "bts:TruSeqAmpliconCancerPanel" + }, + { + "@id": "bts:TruSeqExomeEnrichment-62Mb" + }, + { + "@id": "bts:TruSeqRNAExome" + }, + { + "@id": "bts:TruSightMyeloidSequencingPanel" + }, + { + "@id": "bts:XGenExomeResearchPanelv1.0" + }, + { + "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" + }, + { + "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" + }, + { + "@id": "bts:SureSelectHumanAllExonv6" + }, + { + "@id": "bts:Unknown" } ], + "sms:displayName": "Target Capture Kit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel4", + "@id": "bts:BulkWESLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScATAC-seqLevel4", + "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", + "rdfs:label": "BulkWESLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36860,11 +37432,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 4", + "sms:displayName": "Bulk WES Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel3" + "@id": "bts:BulkWESLevel1" } ], "sms:requiresDependency": [ @@ -36884,221 +37456,170 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ScATACseqWorkflowType" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:ScATACseqWorkflowParametersDescription" + "@id": "bts:GenomicReference" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:WorkflowLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScATACseqWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:IndexFileName" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowParametersDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", - "rdfs:label": "ScATACseqWorkflowParametersDescription", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Parameters Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScDNA-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Single-cell DNA-seq", - "rdfs:label": "ScDNA-seqLevel1", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scDNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:SequencingBatchID" - }, - { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:NucleicAcidSource" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:ReadLength" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:Contamination" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:ContaminationError" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:AdapterName" + "@id": "bts:AdapterContent" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:Encoding" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:PerSequenceGCContent" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:PerSequenceQualityScore" }, { - "@id": "bts:LaneNumber" + "@id": "bts:PerTileSequenceQuality" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:PercentGCContent" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:SequenceDuplicationLevels" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:SequenceLengthDistribution" }, { - "@id": "bts:TargetDepth" + "@id": "bts:QCWorkflowType" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:QCWorkflowVersion" }, { - "@id": "bts:AdapterContent" + "@id": "bts:QCWorkflowLink" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:Encoding" + "@id": "bts:MSIScore" }, { - "@id": "bts:KmerContent" + "@id": "bts:MSIStatus" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:TotalReads" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:ShortReads" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:TotalReads" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:QCWorkflowType" - }, + "@id": "bts:Islowestlevel" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionCoverage10x", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage10x", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowVersion" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion Coverage 10x", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionCoverage30X", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage30X", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowLink" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion Coverage 30X", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScDNA-seqLevel2", + "@id": "bts:BulkWESLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", - "rdfs:label": "ScDNA-seqLevel2", + "rdfs:comment": "Bulk Whole Exome Sequencing called variants", + "rdfs:label": "BulkWESLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37107,11 +37628,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scDNA-seq Level 2", + "sms:displayName": "Bulk WES Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScDNA-seqLevel1" + "@id": "bts:BulkWESLevel2" } ], "sms:requiresDependency": [ @@ -37130,12 +37651,6 @@ { "@id": "bts:HTANDataFileID" }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, { "@id": "bts:GenomicReference" }, @@ -37143,73 +37658,170 @@ "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:IndexFileName" + "@id": "bts:GermlineVariantsWorkflowURL" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:GermlineVariantsWorkflowType" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:SomaticVariantsWorkflowURL" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:SomaticVariantsWorkflowType" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:SomaticVariantsSampleType" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:StructuralVariantWorkflowURL" }, { - "@id": "bts:TotalReads" - }, + "@id": "bts:StructuralVariantWorkflowType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:GermlineVariantsWorkflowURL", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", + "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:subClassOf": [ { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Germline Variants Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:GermlineVariantsWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GATK4" }, { - "@id": "bts:MapQ30" + "@id": "bts:OtherGermlineVariantsWorkflowType" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:None" + } + ], + "sms:displayName": "Germline Variants Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsWorkflowURL", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Somatic Variants Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CaVEMan" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:GATK4" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:MuTect2" }, { - "@id": "bts:ShortReads" + "@id": "bts:MuSE" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:Pindel" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:SomaticSniper" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:VarScan2" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:OtherSomaticVariantsWorkflowType" }, { - "@id": "bts:ProportionMitochondrialReads" + "@id": "bts:None" + } + ], + "sms:displayName": "Somatic Variants Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsSampleType", + "@type": "rdfs:Class", + "rdfs:comment": "Is the sample case or control in somatic variant analysis", + "rdfs:label": "SomaticVariantsSampleType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CaseSample" }, { - "@id": "bts:Contamination" + "@id": "bts:ControlSample" }, { - "@id": "bts:ContaminationError" + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Somatic Variants Sample Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionMitochondrialReads", + "@id": "bts:StructuralVariantWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of reads mapping to mitochondria.", - "rdfs:label": "ProportionMitochondrialReads", + "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", + "rdfs:label": "StructuralVariantWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37218,15 +37830,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Mitochondrial Reads", - "sms:required": "sms:false", + "sms:displayName": "Structural Variant Workflow URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel1", + "@id": "bts:StructuralVariantWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", - "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "StructuralVariantWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37235,7 +37847,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 1", + "schema:rangeIncludes": [ + { + "@id": "bts:BRASS" + }, + { + "@id": "bts:GATK4" + }, + { + "@id": "bts:CNV" + }, + { + "@id": "bts:CNVkit" + }, + { + "@id": "bts:OtherStructuralVariantWorkflowType" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Structural Variant Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", + "rdfs:label": "MicroarrayLevel1", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -37253,40 +37902,62 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:BisulfiteConversion" + "@id": "bts:MicroarrayPlatformID" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:MicroarrayMolecule" }, { - "@id": "bts:ReplicateType" + "@id": "bts:MicroarrayLabel" }, { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:MicroarrayValueDefinition" }, { - "@id": "bts:TotalDNAInput" + "@id": "bts:MicroarrayProtocolAuxiliaryFile" } ], "sms:validationRules": [] }, { - "@id": "bts:ReplicateType", + "@id": "bts:MicroarrayPlatformID", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", - "rdfs:label": "ReplicateType", + "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", + "rdfs:label": "MicroarrayPlatformID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Platform ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match GPL\\d+" + ] + }, + { + "@id": "bts:MicroarrayMolecule", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray is measuring this kind of molecule", + "rdfs:label": "MicroarrayMolecule", + "rdfs:subClassOf": [ + { + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { @@ -37294,77 +37965,142 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Technicalreplicate" + "@id": "bts:DNA" }, { - "@id": "bts:Biologicalreplicate" - }, + "@id": "bts:RNA" + } + ], + "sms:displayName": "Microarray Molecule", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayLabel", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray used this kind of label", + "rdfs:label": "MicroarrayLabel", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:MicroarrayLevel1" } ], - "sms:displayName": "Replicate Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Label", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationAssayType", + "@id": "bts:MicroarrayValueDefinition", "@type": "rdfs:Class", - "rdfs:comment": "Assay types normally determine genomic coverage", - "rdfs:label": "BulkMethylationAssayType", + "rdfs:comment": "What the provided value signifies", + "rdfs:label": "MicroarrayValueDefinition", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Microarray Value Definition", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayProtocolAuxiliaryFile", + "@type": "rdfs:Class", + "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", + "rdfs:label": "MicroarrayProtocolAuxiliaryFile", + "rdfs:subClassOf": [ { - "@id": "bts:Wholegenome" - }, + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Protocol Auxiliary File", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match syn\\d+" + ] + }, + { + "@id": "bts:MicroarrayLevel2", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", + "rdfs:label": "MicroarrayLevel2", + "rdfs:subClassOf": [ { - "@id": "bts:TargetedGenome" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:BeadchipArray" + "@id": "bts:MicroarrayLevel1" } ], - "sms:displayName": "Bulk Methylation Assay Type", - "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:TargetedGenome" + "@id": "bts:Component" }, { - "@id": "bts:BeadchipArray" + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:MicroarrayPlatformID" + }, + { + "@id": "bts:NormalizationMethod" } ], "sms:validationRules": [] }, { - "@id": "bts:TotalDNAInput", + "@id": "bts:NormalizationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", - "rdfs:label": "TotalDNAInput", + "rdfs:comment": "Description of Normalization Process", + "rdfs:label": "NormalizationMethod", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:RPPALevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total DNA Input", + "sms:displayName": "Normalization Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel2", + "@id": "bts:ScATAC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", - "rdfs:label": "BulkMethylation-seqLevel2", + "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", + "rdfs:label": "ScATAC-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -37373,12 +38109,9 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 2", + "sms:displayName": "scATAC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ - { - "@id": "bts:BulkMethylation-seqLevel1" - }, { "@id": "bts:Biospecimen" } @@ -37394,97 +38127,91 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:Trimmer" - }, - { - "@id": "bts:BulkMethylationGenomicReference" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:IndexFileName" + "@id": "bts:SingleNucleusBuffer" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:DuplicateRemovalSoftware" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:ScATACseqLibraryLayout" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:NucleusIdentifier" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:NucleiBarcodeLength" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:NucleiBarcodeRead" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:ScATACseqRead1" }, { - "@id": "bts:Contamination" + "@id": "bts:ScATACseqRead2" }, { - "@id": "bts:ContaminationError" + "@id": "bts:ScATACseqRead3" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:LibraryConstructionMethod" }, { - "@id": "bts:TotalReads" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:ThresholdforMinimumPassingReads" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:TotalNumberofPassingNuclei" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:MedianFractionofReadsinPeaks" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:MedianPassingReadPercentage" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" }, { - "@id": "bts:ShortReads" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X" + "@id": "bts:TotalReads" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:ProtocolLink" } ], "sms:validationRules": [] }, { - "@id": "bts:Trimmer", + "@id": "bts:SingleNucleusBuffer", "@type": "rdfs:Class", - "rdfs:comment": "Software used for trimming", - "rdfs:label": "Trimmer", + "rdfs:comment": "Nuclei isolation buffer", + "rdfs:label": "SingleNucleusBuffer", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37492,51 +38219,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FASTXtoolkit" + "@id": "bts:NIB" }, { - "@id": "bts:SolexaQA" + "@id": "bts:10x" }, { - "@id": "bts:Btrim" + "@id": "bts:Omni" }, { - "@id": "bts:Cutadapt" - }, + "@id": "bts:TST" + } + ], + "sms:displayName": "Single Nucleus Buffer", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TranspositionReaction", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the transposase, transposon sequences", + "rdfs:label": "TranspositionReaction", + "rdfs:subClassOf": [ { - "@id": "bts:Kraken" + "@id": "bts:ScATAC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Tn5" }, { - "@id": "bts:PRINSEQ" + "@id": "bts:EZ-Tn5" }, { - "@id": "bts:Adapterremoval" + "@id": "bts:Tn5-059" }, { - "@id": "bts:TrimGalore!" + "@id": "bts:NexteraTn5" }, { - "@id": "bts:ConDeTri" + "@id": "bts:Diagenode-unloadedApex-Bio" }, { - "@id": "bts:ERNE-FILTER" + "@id": "bts:Diagenode-loadedApex-Bio" }, { - "@id": "bts:Trimmo-matic" + "@id": "bts:In-House" } ], - "sms:displayName": "Trimmer", + "sms:displayName": "Transposition Reaction", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationGenomicReference", + "@id": "bts:ScATACseqLibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "The human genome reference used in the alignment of reads", - "rdfs:label": "BulkMethylationGenomicReference", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "ScATACseqLibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37544,27 +38290,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HG19" - }, - { - "@id": "bts:HG38" - }, - { - "@id": "bts:T2TCHM13" + "@id": "bts:ScATACseqPairedEnd" } ], - "sms:displayName": "Bulk Methylation Genomic Reference", + "sms:displayName": "scATACseq Library Layout", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DuplicateRemovalSoftware", + "@id": "bts:NucleusIdentifier", "@type": "rdfs:Class", - "rdfs:comment": "Software used for remove duplicate reads", - "rdfs:label": "DuplicateRemovalSoftware", + "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", + "rdfs:label": "NucleusIdentifier", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37572,107 +38312,101 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Samtoolssort" - }, - { - "@id": "bts:PicardMarkDuplicates" + "@id": "bts:NucleiBarcode" } ], - "sms:displayName": "Duplicate Removal Software", + "sms:displayName": "Nucleus Identifier", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X", + "@id": "bts:NucleiBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", - "rdfs:label": "ProportionofMinimumCpGCoverage10X", + "rdfs:comment": "Nuclei Barcode Length", + "rdfs:label": "NucleiBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NucleiBarcode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion of Minimum CpG Coverage 10X", - "sms:required": "sms:false", + "sms:displayName": "Nuclei Barcode Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel3", + "@id": "bts:NucleiBarcodeRead", "@type": "rdfs:Class", - "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", - "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:comment": "Nuclei Barcode Read", + "rdfs:label": "NucleiBarcodeRead", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NucleiBarcode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "Nuclei Barcode Read", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATACseqRead1", + "@type": "rdfs:Class", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScATACseqRead1", + "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:Biospecimen" + "@id": "bts:ScATACseqPairedEnd" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:DMCCallingTool" - }, - { - "@id": "bts:DMCCallingWorkflowURL" - }, - { - "@id": "bts:DMRCallingTool" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DMRCallingWorkflowURL" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:PUC19methylationratio" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Lambdamethylationratio" + "@id": "bts:DNAInsert" }, { - "@id": "bts:DMCdatafileformat" + "@id": "bts:SampleIndex" }, { - "@id": "bts:DMRdatafileFormat" + "@id": "bts:CellBarcode" } ], + "sms:displayName": "scATACseq Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMCCallingTool", + "@id": "bts:ScATACseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMCCallingTool", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScATACseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:ScATACseqPairedEnd" } ], "schema:isPartOf": { @@ -37680,67 +38414,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" - }, - { - "@id": "bts:MethylSig" - }, - { - "@id": "bts:DSS" - }, - { - "@id": "bts:MOABS" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:DSS-single" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Metilene" + "@id": "bts:DNAInsert" }, { - "@id": "bts:MACAU" + "@id": "bts:SampleIndex" }, { - "@id": "bts:MethylDackel" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "DMC Calling Tool", + "sms:displayName": "scATACseq Read2", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMCCallingWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMCCallingWorkflowURL", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DMC Calling Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] - }, - { - "@id": "bts:DMRCallingTool", + "@id": "bts:ScATACseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMRCallingTool", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScATACseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -37748,158 +38448,155 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" - }, - { - "@id": "bts:MethylSig" - }, - { - "@id": "bts:DSS" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:MOABS" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:DSS-single" + "@id": "bts:DNAInsert" }, { - "@id": "bts:Metilene" + "@id": "bts:SampleIndex" }, { - "@id": "bts:MACAU" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "DMR Calling Tool", - "sms:required": "sms:true", + "sms:displayName": "scATACseq Read3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMRCallingWorkflowURL", + "@id": "bts:ThresholdforMinimumPassingReads", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMRCallingWorkflowURL", + "rdfs:comment": "Threshold for calling cells", + "rdfs:label": "ThresholdforMinimumPassingReads", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DMR Calling Workflow URL", + "sms:displayName": "Threshold for Minimum Passing Reads", "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] + "sms:validationRules": [] }, { - "@id": "bts:PUC19methylationratio", + "@id": "bts:TotalNumberofPassingNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", - "rdfs:label": "PUC19methylationratio", + "rdfs:comment": "Number of nuclei sequenced", + "rdfs:label": "TotalNumberofPassingNuclei", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "pUC19 methylation ratio", + "sms:displayName": "Total Number of Passing Nuclei", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Lambdamethylationratio", + "@id": "bts:MedianFractionofReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", - "rdfs:label": "Lambdamethylationratio", + "rdfs:comment": "Median fraction of reads in peaks (FRIP)", + "rdfs:label": "MedianFractionofReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lambda methylation ratio", + "sms:displayName": "Median Fraction of Reads in Peaks", "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PeaksCallingSoftware" + } + ], "sms:validationRules": [] }, { - "@id": "bts:DMCdatafileformat", + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files", - "rdfs:label": "DMCdatafileformat", + "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, + "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:BedGraph" + "@id": "bts:PeaksCallingSoftware" } ], - "sms:displayName": "DMC data file format", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMRdatafileFormat", + "@id": "bts:MedianPassingReadPercentage", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files.", - "rdfs:label": "DMRdatafileFormat", + "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", + "rdfs:label": "MedianPassingReadPercentage", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, + "sms:displayName": "Median Passing Read Percentage", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@type": "rdfs:Class", + "rdfs:comment": "Contamination from mitochondrial sequences", + "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:subClassOf": [ { - "@id": "bts:BedGraph" + "@id": "bts:ScATAC-seqLevel1" } ], - "sms:displayName": "DMR data file Format", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel1", + "@id": "bts:ScATAC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Raw imaging data", - "rdfs:label": "ImagingLevel1", + "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", + "rdfs:label": "ScATAC-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 1", + "sms:displayName": "scATAC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScATAC-seqLevel1" } ], "sms:requiresDependency": [ @@ -37913,242 +38610,124 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:GenomicReference" }, { - "@id": "bts:CommitSHA" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:Pre-processingCompleted" + "@id": "bts:IndexFileName" }, { - "@id": "bts:Pre-processingRequired" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:Comment" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingAssayType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of imaging assay", - "rdfs:label": "ImagingAssayType", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:H&E" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:CyCIF" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:T-CyCIF" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:IHC" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:MIHC" + "@id": "bts:TotalReads" }, { - "@id": "bts:MxIF" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:SABER" + "@id": "bts:MapQ30" }, { - "@id": "bts:IMC" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:CODEX" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:GeoMX-DSP" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:MIBI" + "@id": "bts:ShortReads" }, { - "@id": "bts:MERFISH" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:ExSeq" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:RareCyteOrion" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Imaging Assay Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SoftwareandVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Name of software used to generate expression values. String", - "rdfs:label": "SoftwareandVersion", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Software and Version", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CommitSHA", - "@type": "rdfs:Class", - "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", - "rdfs:label": "CommitSHA", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Commit SHA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pre-processingCompleted", - "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingCompleted", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:Channel/CycleRegistration" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:TMAde-arraying" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" }, { - "@id": "bts:None" + "@id": "bts:Contamination" }, { - "@id": "bts:Other" + "@id": "bts:ContaminationError" } ], - "sms:displayName": "Pre-processing Completed", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingRequired", + "@id": "bts:MapQ30", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingRequired", + "rdfs:comment": "Number of reads with Quality >= 30.", + "rdfs:label": "MapQ30", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Pre-processing Required", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Comment", - "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Comment", + "sms:displayName": "MapQ30", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel2", + "@id": "bts:ScATAC-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Raw and pre-processed image data", - "rdfs:label": "ImagingLevel2", + "rdfs:comment": "Processed data files containing peak information for cells", + "rdfs:label": "ScATAC-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 2", + "sms:displayName": "scATAC-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel1" + "@id": "bts:ScATAC-seqLevel2" } ], "sms:requiresDependency": [ @@ -38162,1022 +38741,792 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" + "@id": "bts:ScATAC-seqObjectID" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:NCountPeaks" }, { - "@id": "bts:Microscope" + "@id": "bts:NFeaturePeaks" }, { - "@id": "bts:Objective" + "@id": "bts:TotalRead-Pairs" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:DuplicateRead-Pairs" }, { - "@id": "bts:LensNA" + "@id": "bts:ChimericRead-Pairs" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:UnmappedRead-Pairs" }, { - "@id": "bts:WorkingDistanceUnit" + "@id": "bts:LowMapQ" }, { - "@id": "bts:Immersion" + "@id": "bts:MitochondrialRead-Pairs" }, { - "@id": "bts:Pyramid" + "@id": "bts:PassedFilters" }, { - "@id": "bts:Zstack" + "@id": "bts:TSSFragments" }, { - "@id": "bts:Tseries" + "@id": "bts:DNaseSensitiveRegionFragments" }, { - "@id": "bts:PassedQC" + "@id": "bts:EnhancerRegionFragments" }, { - "@id": "bts:Comment" + "@id": "bts:PromoterRegionFragments" }, { - "@id": "bts:FOVnumber" + "@id": "bts:OnTargetFragments" }, { - "@id": "bts:FOVX" + "@id": "bts:BlacklistRegionFragments" }, { - "@id": "bts:FOVXUnit" + "@id": "bts:PeakRegionFragments" }, { - "@id": "bts:FOVY" + "@id": "bts:PeakRegionCutsites" }, { - "@id": "bts:FOVYUnit" + "@id": "bts:NucleosomeSignal" }, { - "@id": "bts:FrameAveraging" + "@id": "bts:NucleosomePercentile" }, { - "@id": "bts:ImageID" + "@id": "bts:TSSEnrichment" }, { - "@id": "bts:DimensionOrder" + "@id": "bts:TSSPercentile" }, { - "@id": "bts:PhysicalSizeX" + "@id": "bts:PctReadsinPeaks" }, { - "@id": "bts:PhysicalSizeXUnit" + "@id": "bts:BlacklistRatio" }, { - "@id": "bts:PhysicalSizeY" + "@id": "bts:SeuratClusters" }, { - "@id": "bts:PhysicalSizeYUnit" + "@id": "bts:NCountRNA" }, { - "@id": "bts:PhysicalSizeZ" + "@id": "bts:NFeatureRNA" }, { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:MACS2Seqnames" }, { - "@id": "bts:PixelsBigEndian" + "@id": "bts:MACS2Start" }, { - "@id": "bts:PlaneCount" + "@id": "bts:MACS2End" }, { - "@id": "bts:SizeC" + "@id": "bts:MACS2Width" }, { - "@id": "bts:SizeT" + "@id": "bts:MACS2Strand" }, { - "@id": "bts:SizeX" + "@id": "bts:MACS2Name" }, { - "@id": "bts:SizeY" + "@id": "bts:MACS2Score" }, { - "@id": "bts:SizeZ" + "@id": "bts:MACS2FoldChange" }, { - "@id": "bts:PixelType" + "@id": "bts:MACS2NegLog10pvalueSummit" }, { - "@id": "bts:MERFISHPositionsFile" + "@id": "bts:MACS2NegLog10qvalueSummit" }, { - "@id": "bts:MERFISHCodebookFile" + "@id": "bts:MACS2RelativeSummitPosition" } ], "sms:validationRules": [] }, { - "@id": "bts:ChannelMetadataFilename", + "@id": "bts:ScATAC-seqObjectID", "@type": "rdfs:Class", - "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label": "ChannelMetadataFilename", + "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", + "rdfs:label": "ScATAC-seqObjectID", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ScATAC-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Metadata Filename", - "sms:required": "sms:true", + "sms:displayName": "scATAC-seq Object ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Microscope", + "@id": "bts:NCountPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", + "rdfs:comment": "Total number of fragments in peaks", + "rdfs:label": "NCountPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", + "sms:displayName": "nCount Peaks", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Objective", + "@id": "bts:NFeaturePeaks", "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", + "rdfs:comment": "Number of peaks with at least one read", + "rdfs:label": "NFeaturePeaks", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Objective", + "sms:displayName": "nFeature Peaks", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NominalMagnification", + "@id": "bts:TotalRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", + "rdfs:comment": "Total read-pairs", + "rdfs:label": "TotalRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "Total Read-Pairs", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:LensNA", + "@id": "bts:DuplicateRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", - "rdfs:label": "LensNA", + "rdfs:comment": "Number of duplicate read-pairs", + "rdfs:label": "DuplicateRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LensNA", + "sms:displayName": "Duplicate Read-Pairs", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:WorkingDistance", + "@id": "bts:ChimericRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", + "rdfs:comment": "Number of chimerically mapped read-pairs", + "rdfs:label": "ChimericRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "WorkingDistance", + "sms:displayName": "Chimeric Read-Pairs", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:WorkingDistanceUnit" - } - ], "sms:validationRules": [] }, { - "@id": "bts:WorkingDistanceUnit", + "@id": "bts:UnmappedRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", + "rdfs:comment": "Number of read-pairs with at least one end not mapped", + "rdfs:label": "UnmappedRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", + "sms:displayName": "Unmapped Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Immersion", + "@id": "bts:LowMapQ", "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", + "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", + "rdfs:label": "LowMapQ", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Air" - }, - { - "@id": "bts:Oil" - }, - { - "@id": "bts:Water" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", + "sms:displayName": "LowMapQ", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pyramid", + "@id": "bts:MitochondrialRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", + "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", + "rdfs:label": "MitochondrialRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", + "sms:displayName": "Mitochondrial Read-Pairs", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zstack", + "@id": "bts:PassedFilters", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", + "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", + "rdfs:label": "PassedFilters", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Zstack", - "sms:required": "sms:true", + "sms:displayName": "Passed Filters", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tseries", + "@id": "bts:TSSFragments", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", + "rdfs:comment": "Number of fragments overlapping with TSS regions", + "rdfs:label": "TSSFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Tseries", - "sms:required": "sms:true", + "sms:displayName": "TSS Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PassedQC", + "@id": "bts:DNaseSensitiveRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", + "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", + "rdfs:label": "DNaseSensitiveRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", + "sms:displayName": "DNase Sensitive Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVnumber", + "@id": "bts:EnhancerRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", + "rdfs:comment": "Number of fragments overlapping enhancer regions", + "rdfs:label": "EnhancerRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOV number", + "sms:displayName": "Enhancer Region Fragments", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVX", + "@id": "bts:PromoterRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", + "rdfs:comment": "Number of fragments overlapping promoter regions", + "rdfs:label": "PromoterRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVX", + "sms:displayName": "Promoter Region Fragments", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVXUnit", + "@id": "bts:OnTargetFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", + "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", + "rdfs:label": "OnTargetFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", + "sms:displayName": "On Target Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVY", + "@id": "bts:BlacklistRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", + "rdfs:comment": "Number of fragments overlapping blacklisted regions", + "rdfs:label": "BlacklistRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVY", + "sms:displayName": "Blacklist Region Fragments", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVYUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVYUnit", + "@id": "bts:PeakRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", + "rdfs:comment": "Number of fragments overlapping peaks", + "rdfs:label": "PeakRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVYUnit", + "sms:displayName": "Peak Region Fragments", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FrameAveraging", + "@id": "bts:PeakRegionCutsites", "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label": "FrameAveraging", + "rdfs:comment": "Number of ends of fragments in peak regions", + "rdfs:label": "PeakRegionCutsites", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Frame Averaging", + "sms:displayName": "Peak Region Cutsites", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageID", + "@id": "bts:NucleosomeSignal", "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", + "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", + "rdfs:label": "NucleosomeSignal", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", + "sms:displayName": "Nucleosome Signal", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DimensionOrder", + "@id": "bts:NucleosomePercentile", "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", + "rdfs:comment": "Percentile rank of nucleosome score", + "rdfs:label": "NucleosomePercentile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:XYZCT" - }, - { - "@id": "bts:XYZTC" - }, - { - "@id": "bts:XYCTZ" - }, - { - "@id": "bts:XYCZT" - }, - { - "@id": "bts:XYTZC" - }, - { - "@id": "bts:ZYX" - } - ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", + "sms:displayName": "Nucleosome Percentile", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeX", + "@id": "bts:TSSEnrichment", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeX", + "rdfs:comment": "Transcription start site (TSS) enrichment score", + "rdfs:label": "TSSEnrichment", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeXUnit" - } - ], + "sms:displayName": "TSS Enrichment", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeXUnit", + "@id": "bts:TSSPercentile", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", + "rdfs:comment": "Percentile rank of TSS score", + "rdfs:label": "TSSPercentile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", + "sms:displayName": "TSS Percentile", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeY", + "@id": "bts:PctReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeY", + "rdfs:comment": "Percentage of reads in peaks", + "rdfs:label": "PctReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeYUnit" - } - ], + "sms:displayName": "Pct Reads in Peaks", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:BlacklistRatio", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "Ratio of reads in blacklist regions", + "rdfs:label": "BlacklistRatio", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", + "sms:displayName": "Blacklist Ratio", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZ", + "@id": "bts:SeuratClusters", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeZ", + "rdfs:comment": "Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm", + "rdfs:label": "SeuratClusters", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeZ", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeZUnit" - } - ], + "sms:displayName": "Seurat Clusters", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZUnit", + "@id": "bts:NCountRNA", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeZUnit", + "rdfs:comment": "Total number of fragments in genes", + "rdfs:label": "NCountRNA", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeZUnit", - "sms:required": "sms:true", + "sms:displayName": "nCount RNA", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PixelsBigEndian", + "@id": "bts:NFeatureRNA", "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", + "rdfs:comment": "Number of genes detected in cell", + "rdfs:label": "NFeatureRNA", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, + "sms:displayName": "nFeature RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Seqnames", + "@type": "rdfs:Class", + "rdfs:comment": "Chromosome id", + "rdfs:label": "MACS2Seqnames", + "rdfs:subClassOf": [ { - "@id": "bts:False" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "Pixels BigEndian", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Seqnames", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PlaneCount", + "@id": "bts:MACS2Start", "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", - "rdfs:label": "PlaneCount", + "rdfs:comment": "Genomic starting position in MACS2", + "rdfs:label": "MACS2Start", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PlaneCount", - "sms:required": "sms:true", + "sms:displayName": "MACS2 Start", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeC", + "@id": "bts:MACS2End", "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", + "rdfs:comment": "Genomic ending position in MACS2", + "rdfs:label": "MACS2End", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeC", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 End", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeT", + "@id": "bts:MACS2Width", "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", + "rdfs:comment": "Width of the peak in bases in MACS2", + "rdfs:label": "MACS2Width", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeT", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Width", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeX", + "@id": "bts:MACS2Strand", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", + "rdfs:comment": "DNA stand aligned with in MACS2", + "rdfs:label": "MACS2Strand", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeX", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Strand", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeY", + "@id": "bts:MACS2Name", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeY", + "rdfs:comment": "Name of the peak in MACS2", + "rdfs:label": "MACS2Name", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeY", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Name", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SizeZ", + "@id": "bts:MACS2Score", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeZ", + "rdfs:comment": "Peak score (proportional to q-value) in MACS2", + "rdfs:label": "MACS2Score", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeZ", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:displayName": "MACS2 Score", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:PixelType", + "@id": "bts:MACS2FoldChange", "@type": "rdfs:Class", - "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", - "rdfs:label": "PixelType", + "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", + "rdfs:label": "MACS2FoldChange", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Int8" - }, - { - "@id": "bts:Int16" - }, - { - "@id": "bts:Int32" - }, - { - "@id": "bts:Uint8" - }, - { - "@id": "bts:Uint16" - }, - { - "@id": "bts:Uint32" - }, - { - "@id": "bts:Float" - }, - { - "@id": "bts:Double" - }, + "sms:displayName": "MACS2 Fold Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2NegLog10pvalueSummit", + "@type": "rdfs:Class", + "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10pvalueSummit", + "rdfs:subClassOf": [ { - "@id": "bts:Bit" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "PixelType", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Neg Log10 pvalue Summit", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHPositionsFile", + "@id": "bts:MACS2NegLog10qvalueSummit", "@type": "rdfs:Class", - "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", - "rdfs:label": "MERFISHPositionsFile", + "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10qvalueSummit", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Positions File", + "sms:displayName": "MACS2 Neg Log10 qvalue Summit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHCodebookFile", + "@id": "bts:MACS2RelativeSummitPosition", "@type": "rdfs:Class", - "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", - "rdfs:label": "MERFISHCodebookFile", + "rdfs:comment": "Position of the peak summit related to the start position in MACS2", + "rdfs:label": "MACS2RelativeSummitPosition", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Codebook File", + "sms:displayName": "MACS2 Relative Summit Position", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Segmentation", + "@id": "bts:ScmC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Object segmentations", - "rdfs:label": "ImagingLevel3Segmentation", + "rdfs:comment": "Files contain raw scmC-seq data.", + "rdfs:label": "ScmC-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Segmentation", + "sms:displayName": "scmC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -39191,40 +39540,79 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:Parameterfile" + "@id": "bts:ScmCseqRead1" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:ScmCseqRead2" }, { - "@id": "bts:CommitSHA" + "@id": "bts:ScmCseqRead3" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:NumberofObjects" + "@id": "bts:SingleNucleusBuffer" + }, + { + "@id": "bts:SingleNucleusCapture" + }, + { + "@id": "bts:BisulfiteConversion" + }, + { + "@id": "bts:LibraryLayout" + }, + { + "@id": "bts:NucleusIdentifier" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:MedianFractionofReadsinPeaks" + }, + { + "@id": "bts:MedianPassingReadPercentage" + }, + { + "@id": "bts:PeaksCallingSoftware" + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:ThresholdforMinimumPassingReads" + }, + { + "@id": "bts:TotalNumberofPassingNuclei" + }, + { + "@id": "bts:TotalReads" } ], "sms:validationRules": [] }, { - "@id": "bts:ImagingSegmentationDataType", + "@id": "bts:ScmCseqRead1", "@type": "rdfs:Class", - "rdfs:comment": "Specifies how the segmentation is stored", - "rdfs:label": "ImagingSegmentationDataType", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScmCseqRead1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -39232,50 +39620,49 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Mask" - }, - { - "@id": "bts:Outline" - }, - { - "@id": "bts:Polygon" - }, - { - "@id": "bts:ProbabilityMap" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:Point" + "@id": "bts:CDNA" } ], - "sms:displayName": "Imaging Segmentation Data Type", + "sms:displayName": "scmCseq Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Parameterfile", + "@id": "bts:ScmCseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", - "rdfs:label": "Parameterfile", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScmCseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Parameter file", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingObjectClass", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read2", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScmCseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "Defines the structure that the mask delineates", - "rdfs:label": "ImagingObjectClass", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScmCseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -39283,70 +39670,113 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Nucleus" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:Cytoplasm" + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read3", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SingleNucleusCapture", + "@type": "rdfs:Class", + "rdfs:comment": "Nuclei isolation method", + "rdfs:label": "SingleNucleusCapture", + "rdfs:subClassOf": [ + { + "@id": "bts:ScmC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Plates" }, { - "@id": "bts:Plasmamembrane" + "@id": "bts:10x" }, { - "@id": "bts:Wholecell" + "@id": "bts:Droplet" + } + ], + "sms:displayName": "Single Nucleus Capture", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BisulfiteConversion", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the kit used in bisulfite conversion.", + "rdfs:label": "BisulfiteConversion", + "rdfs:subClassOf": [ + { + "@id": "bts:BulkMethylation-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ZimoEZDNAMethylationKit" }, { - "@id": "bts:Spot" + "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" }, { - "@id": "bts:ImagingObjectClassOther" + "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" + }, + { + "@id": "bts:NEBNextEnzymaticMethyl-seqKit" + }, + { + "@id": "bts:AgilentSureSelectXTMethyl-Seq" } ], - "sms:displayName": "Imaging Object Class", + "sms:displayName": "Bisulfite Conversion", "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] + "sms:validationRules": [] }, { - "@id": "bts:NumberofObjects", + "@id": "bts:PeaksCallingSoftware", "@type": "rdfs:Class", - "rdfs:comment": "The number of objects (eg cells) described", - "rdfs:label": "NumberofObjects", + "rdfs:comment": "Generic name of peaks calling tool", + "rdfs:label": "PeaksCallingSoftware", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Objects", + "sms:displayName": "Peaks Calling Software", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Image", + "@id": "bts:ScmC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Quality controlled imaging data", - "rdfs:label": "ImagingLevel3Image", + "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", + "rdfs:label": "ScmC-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Image", + "sms:displayName": "scmC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ImagingLevel2" + "@id": "bts:ScmC-seqLevel1" } ], "sms:requiresDependency": [ @@ -39360,203 +39790,339 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANParentChannelMetadataID" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:GenomicReference" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:IndexFileName" }, { - "@id": "bts:Microscope" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:Objective" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:LensNA" + "@id": "bts:Contamination" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:ContaminationError" }, { - "@id": "bts:Immersion" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:Pyramid" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:Zstack" + "@id": "bts:TotalReads" }, { - "@id": "bts:Tseries" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PassedQC" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:Comment" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:FOVnumber" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:FOVX" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:FOVY" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:FrameAveraging" + "@id": "bts:ShortReads" } ], "sms:validationRules": [] }, { - "@id": "bts:HTANParentChannelMetadataID", + "@id": "bts:ScATAC-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID for a level 3 channels table.", - "rdfs:label": "HTANParentChannelMetadataID", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScATAC-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel4" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent Channel Metadata ID", + "sms:displayName": "scATAC-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScATAC-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScATACseqWorkflowType" + }, + { + "@id": "bts:ScATACseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ScATACseqWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScATACseqWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATACseq Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Channels", + "@id": "bts:ScATACseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Channel-level Metadata Attributes", - "rdfs:label": "ImagingLevel3Channels", + "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", + "rdfs:label": "ScATACseqWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Channels", + "sms:displayName": "scATACseq Workflow Parameters Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScDNA-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Single-cell DNA-seq", + "rdfs:label": "ScDNA-seqLevel1", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scDNA-seq Level 1", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], "sms:requiresDependency": [ { - "@id": "bts:HTANChannelMetadataID" + "@id": "bts:Component" }, { - "@id": "bts:ChannelID" + "@id": "bts:Filename" }, { - "@id": "bts:ChannelName" + "@id": "bts:FileFormat" }, { - "@id": "bts:ChannelPassedQC" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CycleNumber" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SubCycleNumber" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:AntibodyRole" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:TargetName" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:AntibodyName" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:RRIDidentifier" + "@id": "bts:ReadLength" }, { - "@id": "bts:Fluorophore" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:Clone" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:Lot" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:Vendor" + "@id": "bts:AdapterName" }, { - "@id": "bts:CatalogNumber" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:ExcitationWavelength" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:EmissionWavelength" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:ExcitationBandwidth" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:EmissionBandwidth" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:MetalIsotopeMass" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:OligoBarcodeUpperStrand" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:OligoBarcodeLowerStrand" + "@id": "bts:LaneNumber" }, { - "@id": "bts:Dilution" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:Concentration" + "@id": "bts:MultiplexBarcode" + }, + { + "@id": "bts:SizeSelectionRange" + }, + { + "@id": "bts:TargetDepth" + }, + { + "@id": "bts:ToTrimAdapterSequence" + }, + { + "@id": "bts:AdapterContent" + }, + { + "@id": "bts:BasicStatistics" + }, + { + "@id": "bts:Encoding" + }, + { + "@id": "bts:KmerContent" + }, + { + "@id": "bts:OverrepresentedSequences" + }, + { + "@id": "bts:PerBaseNContent" + }, + { + "@id": "bts:PerBaseSequenceContent" + }, + { + "@id": "bts:PerBaseSequenceQuality" + }, + { + "@id": "bts:PerSequenceGCContent" + }, + { + "@id": "bts:PerSequenceQualityScore" + }, + { + "@id": "bts:PerTileSequenceQuality" + }, + { + "@id": "bts:PercentGCContent" + }, + { + "@id": "bts:SequenceDuplicationLevels" + }, + { + "@id": "bts:SequenceLengthDistribution" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:QCWorkflowType" + }, + { + "@id": "bts:QCWorkflowVersion" + }, + { + "@id": "bts:QCWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", + "@id": "bts:ScDNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", + "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", + "rdfs:label": "ScDNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", + "sms:displayName": "scDNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScDNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -39566,123 +40132,172 @@ { "@id": "bts:Filename" }, - { - "@id": "bts:RunID" - }, { "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:GenomicReference" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:IndexFileName" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:EndBias" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:CaptureArea" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:TotalReads" }, { - "@id": "bts:SlideVersion" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:SlideID" + "@id": "bts:MapQ30" }, { - "@id": "bts:ImageRe-orientation" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:PermeabilizationTime" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:RIN" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:DV200" + "@id": "bts:ShortReads" + }, + { + "@id": "bts:ProportionCoverage10x" + }, + { + "@id": "bts:ProportionCoverage30X" + }, + { + "@id": "bts:ProportionTargetsNoCoverage" + }, + { + "@id": "bts:ProportionBaseMismatch" + }, + { + "@id": "bts:ProportionMitochondrialReads" + }, + { + "@id": "bts:Contamination" + }, + { + "@id": "bts:ContaminationError" } ], "sms:validationRules": [] }, { - "@id": "bts:CaptureArea", + "@id": "bts:ProportionMitochondrialReads", "@type": "rdfs:Class", - "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", - "rdfs:label": "CaptureArea", + "rdfs:comment": "Proportion of reads mapping to mitochondria.", + "rdfs:label": "ProportionMitochondrialReads", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Proportion Mitochondrial Reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", + "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:A" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:B" + "@id": "bts:Filename" }, { - "@id": "bts:C" + "@id": "bts:FileFormat" }, { - "@id": "bts:D" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:A1" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:B1" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:C1" + "@id": "bts:BisulfiteConversion" }, { - "@id": "bts:D1" + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:ReplicateType" + }, + { + "@id": "bts:BulkMethylationAssayType" + }, + { + "@id": "bts:TotalDNAInput" } ], - "sms:displayName": "Capture Area", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlideVersion", + "@id": "bts:ReplicateType", "@type": "rdfs:Class", - "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "rdfs:label": "SlideVersion", + "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", + "rdfs:label": "ReplicateType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -39690,99 +40305,93 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:V1" - }, - { - "@id": "bts:V2" + "@id": "bts:Technicalreplicate" }, { - "@id": "bts:V3" + "@id": "bts:Biologicalreplicate" }, { - "@id": "bts:V4" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Slide Version", - "sms:required": "sms:false", + "sms:displayName": "Replicate Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SlideID", + "@id": "bts:BulkMethylationAssayType", "@type": "rdfs:Class", - "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", - "rdfs:label": "SlideID", + "rdfs:comment": "Assay types normally determine genomic coverage", + "rdfs:label": "BulkMethylationAssayType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImageRe-orientation", - "@type": "rdfs:Class", - "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", - "rdfs:label": "ImageRe-orientation", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Wholegenome" + }, + { + "@id": "bts:TargetedGenome" + }, + { + "@id": "bts:BeadchipArray" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:displayName": "Bulk Methylation Assay Type", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:TRUE" + "@id": "bts:TargetedGenome" }, { - "@id": "bts:FALSE" + "@id": "bts:BeadchipArray" } ], - "sms:displayName": "Image Re-orientation", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PermeabilizationTime", + "@id": "bts:TotalDNAInput", "@type": "rdfs:Class", - "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", - "rdfs:label": "PermeabilizationTime", + "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", + "rdfs:label": "TotalDNAInput", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylationAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Permeabilization Time", + "sms:displayName": "Total DNA Input", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "@id": "bts:BulkMethylation-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", + "rdfs:label": "BulkMethylation-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", + "sms:displayName": "Bulk Methylation-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:BulkMethylation-seqLevel1" + }, + { + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -39795,9 +40404,6 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:Checksum" - }, { "@id": "bts:HTANParentDataFileID" }, @@ -39805,132 +40411,91 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:UMITag" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:WhitelistSpatialBarcodeFileLink" + "@id": "bts:Trimmer" }, { - "@id": "bts:SpatialBarcodeTag" + "@id": "bts:BulkMethylationGenomicReference" }, { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:IndexFileName" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:GenomicReference" + "@id": "bts:DuplicateRemovalSoftware" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:RunID" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:CaptureArea" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:WhitelistSpatialBarcodeFileLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", - "rdfs:label": "WhitelistSpatialBarcodeFileLink", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Whitelist Spatial Barcode File Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", - "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Contamination" + }, { - "@id": "bts:Component" + "@id": "bts:ContaminationError" }, { - "@id": "bts:Filename" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:FileFormat" + "@id": "bts:TotalReads" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:RunID" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:VisiumFileType" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:SlideID" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:CaptureArea" + "@id": "bts:ShortReads" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:ProportionofMinimumCpGCoverage10X" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:ProportionCoverage30X" } ], "sms:validationRules": [] }, { - "@id": "bts:VisiumFileType", + "@id": "bts:Trimmer", "@type": "rdfs:Class", - "rdfs:comment": "The file type generated for the visium experiment.", - "rdfs:label": "VisiumFileType", + "rdfs:comment": "Software used for trimming", + "rdfs:label": "Trimmer", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { @@ -39938,79 +40503,134 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Referencepng" + "@id": "bts:FASTXtoolkit" }, { - "@id": "bts:Referencejpg" + "@id": "bts:SolexaQA" }, { - "@id": "bts:Jsonscalefactors" + "@id": "bts:Btrim" }, { - "@id": "bts:Probedatasetcsv" + "@id": "bts:Cutadapt" }, { - "@id": "bts:Qcresulthtml" + "@id": "bts:Kraken" }, { - "@id": "bts:Filteredmex" + "@id": "bts:PRINSEQ" }, { - "@id": "bts:Unfilteredmex" + "@id": "bts:Adapterremoval" }, { - "@id": "bts:TissuePositions" + "@id": "bts:TrimGalore!" }, { - "@id": "bts:Barcodes" + "@id": "bts:ConDeTri" }, { - "@id": "bts:Features" + "@id": "bts:ERNE-FILTER" }, { - "@id": "bts:Fiducialimagepng" - }, + "@id": "bts:Trimmo-matic" + } + ], + "sms:displayName": "Trimmer", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylationGenomicReference", + "@type": "rdfs:Class", + "rdfs:comment": "The human genome reference used in the alignment of reads", + "rdfs:label": "BulkMethylationGenomicReference", + "rdfs:subClassOf": [ { - "@id": "bts:Fiducialimagejpg" - }, + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Detectedimagepng" + "@id": "bts:HG19" }, { - "@id": "bts:Detectedjpg" + "@id": "bts:HG38" }, { - "@id": "bts:Highresimage" + "@id": "bts:T2TCHM13" + } + ], + "sms:displayName": "Bulk Methylation Genomic Reference", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DuplicateRemovalSoftware", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for remove duplicate reads", + "rdfs:label": "DuplicateRemovalSoftware", + "rdfs:subClassOf": [ + { + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Samtoolssort" }, { - "@id": "bts:Lowresimage" + "@id": "bts:PicardMarkDuplicates" } ], - "sms:displayName": "Visium File Type", + "sms:displayName": "Duplicate Removal Software", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "@id": "bts:ProportionofMinimumCpGCoverage10X", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", + "rdfs:label": "ProportionofMinimumCpGCoverage10X", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", + "sms:displayName": "Proportion of Minimum CpG Coverage 10X", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", + "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + "@id": "bts:BulkMethylation-seqLevel2" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -40023,9 +40643,6 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:HTANParentBiospecimenID" - }, { "@id": "bts:HTANParentDataFileID" }, @@ -40033,1259 +40650,1698 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:RunID" - }, - { - "@id": "bts:VisiumFileType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:CaptureArea" + "@id": "bts:DMCCallingTool" }, { - "@id": "bts:Spotsundertissue" + "@id": "bts:DMCCallingWorkflowURL" }, { - "@id": "bts:MeanReadsperSpatialSpot" + "@id": "bts:DMRCallingTool" }, { - "@id": "bts:MedianNumberGenesperSpatialSpot" + "@id": "bts:DMRCallingWorkflowURL" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:PUC19methylationratio" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Lambdamethylationratio" }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome" + "@id": "bts:DMCdatafileformat" }, { - "@id": "bts:MedianUMICountsperSpot" + "@id": "bts:DMRdatafileFormat" } ], "sms:validationRules": [] }, { - "@id": "bts:Spotsundertissue", + "@id": "bts:DMCCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "The number of barcodes associated with a spot under tissue.", - "rdfs:label": "Spotsundertissue", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMCCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spots under tissue", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MeanReadsperSpatialSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", - "rdfs:label": "MeanReadsperSpatialSpot", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mean Reads per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:SequencingSaturation", - "@type": "rdfs:Class", - "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", - "rdfs:label": "SequencingSaturation", - "rdfs:subClassOf": [ + "@id": "bts:MethylKit" + }, { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BSmooth" + }, + { + "@id": "bts:BiSeq" + }, + { + "@id": "bts:MethylSig" + }, + { + "@id": "bts:DSS" + }, + { + "@id": "bts:MOABS" + }, + { + "@id": "bts:DSS-single" + }, + { + "@id": "bts:Metilene" + }, + { + "@id": "bts:MACAU" + }, + { + "@id": "bts:MethylDackel" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Saturation", + "sms:displayName": "DMC Calling Tool", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome", + "@id": "bts:DMCCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", - "rdfs:label": "ProportionReadsMappedtoTranscriptome", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMCCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped to Transcriptome", + "sms:displayName": "DMC Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "@id": "bts:DMRCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMRCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, + "schema:rangeIncludes": [ { - "@id": "bts:FileFormat" + "@id": "bts:MethylKit" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:BSmooth" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:BiSeq" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:MethylSig" }, { - "@id": "bts:RunID" + "@id": "bts:DSS" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:MOABS" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:DSS-single" }, { - "@id": "bts:VisiumWorkflowType" + "@id": "bts:Metilene" }, { - "@id": "bts:VisiumWorkflowParametersDescription" + "@id": "bts:MACAU" } ], + "sms:displayName": "DMR Calling Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:VisiumWorkflowType", + "@id": "bts:DMRCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", - "rdfs:label": "VisiumWorkflowType", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMRCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Visium Workflow Type", + "sms:displayName": "DMR Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:VisiumWorkflowParametersDescription", + "@id": "bts:PUC19methylationratio", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow..", - "rdfs:label": "VisiumWorkflowParametersDescription", + "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", + "rdfs:label": "PUC19methylationratio", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Visium Workflow Parameters Description", + "sms:displayName": "pUC19 methylation ratio", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Referencepng", + "@id": "bts:Lambdamethylationratio", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencepng", + "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", + "rdfs:label": "Lambdamethylationratio", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "reference png", - "sms:required": "sms:false", + "sms:displayName": "Lambda methylation ratio", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Referencejpg", + "@id": "bts:DMCdatafileformat", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencejpg", + "rdfs:comment": "Format of the data files", + "rdfs:label": "DMCdatafileformat", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "reference jpg", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:BED" + }, + { + "@id": "bts:BedGraph" + } + ], + "sms:displayName": "DMC data file format", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Jsonscalefactors", + "@id": "bts:DMRdatafileFormat", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Jsonscalefactors", + "rdfs:comment": "Format of the data files.", + "rdfs:label": "DMRdatafileFormat", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "json scale factors", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:BED" + }, + { + "@id": "bts:BedGraph" + } + ], + "sms:displayName": "DMR data file Format", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:Probedatasetcsv", + "@id": "bts:ImagingLevel1", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Probedatasetcsv", + "rdfs:comment": "Raw imaging data", + "rdfs:label": "ImagingLevel1", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "probe dataset csv", + "sms:displayName": "Imaging Level 1", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:Pre-processingCompleted" + }, + { + "@id": "bts:Pre-processingRequired" + }, + { + "@id": "bts:Comment" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Qcresulthtml", + "@id": "bts:ImagingAssayType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Qcresulthtml", + "rdfs:comment": "Type of imaging assay", + "rdfs:label": "ImagingAssayType", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "qc result html", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:H&E" + }, + { + "@id": "bts:CyCIF" + }, + { + "@id": "bts:T-CyCIF" + }, + { + "@id": "bts:IHC" + }, + { + "@id": "bts:MIHC" + }, + { + "@id": "bts:MxIF" + }, + { + "@id": "bts:SABER" + }, + { + "@id": "bts:IMC" + }, + { + "@id": "bts:CODEX" + }, + { + "@id": "bts:GeoMX-DSP" + }, + { + "@id": "bts:MIBI" + }, + { + "@id": "bts:MERFISH" + }, + { + "@id": "bts:ExSeq" + }, + { + "@id": "bts:RareCyteOrion" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Imaging Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Filteredmex", + "@id": "bts:SoftwareandVersion", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Filteredmex", + "rdfs:comment": "Name of software used to generate expression values. String", + "rdfs:label": "SoftwareandVersion", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "filtered mex", - "sms:required": "sms:false", + "sms:displayName": "Software and Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Unfilteredmex", + "@id": "bts:CommitSHA", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Unfilteredmex", + "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", + "rdfs:label": "CommitSHA", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "unfiltered mex", + "sms:displayName": "Commit SHA", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TissuePositions", + "@id": "bts:Pre-processingCompleted", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TissuePositions", + "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingCompleted", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tissue_positions", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Illuminationcorrection" + }, + { + "@id": "bts:TileStitching" + }, + { + "@id": "bts:Channel/CycleRegistration" + }, + { + "@id": "bts:TMAde-arraying" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Pre-processing Completed", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Barcodes", + "@id": "bts:Pre-processingRequired", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Barcodes", + "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingRequired", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "barcodes", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Illuminationcorrection" + }, + { + "@id": "bts:TileStitching" + }, + { + "@id": "bts:Channel/CycleRegistration" + }, + { + "@id": "bts:TMAde-arraying" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Pre-processing Required", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Features", + "@id": "bts:Comment", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Features", + "rdfs:comment": "Free text field (generally for QC comment)", + "rdfs:label": "Comment", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "features", + "sms:displayName": "Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fiducialimagepng", + "@id": "bts:ImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fiducialimagepng", + "rdfs:comment": "Raw and pre-processed image data", + "rdfs:label": "ImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "fiducial image png", + "sms:displayName": "Imaging Level 2", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ChannelMetadataFilename" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:Microscope" + }, + { + "@id": "bts:Objective" + }, + { + "@id": "bts:NominalMagnification" + }, + { + "@id": "bts:LensNA" + }, + { + "@id": "bts:WorkingDistance" + }, + { + "@id": "bts:WorkingDistanceUnit" + }, + { + "@id": "bts:Immersion" + }, + { + "@id": "bts:Pyramid" + }, + { + "@id": "bts:Zstack" + }, + { + "@id": "bts:Tseries" + }, + { + "@id": "bts:PassedQC" + }, + { + "@id": "bts:Comment" + }, + { + "@id": "bts:FOVnumber" + }, + { + "@id": "bts:FOVX" + }, + { + "@id": "bts:FOVXUnit" + }, + { + "@id": "bts:FOVY" + }, + { + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:FrameAveraging" + }, + { + "@id": "bts:ImageID" + }, + { + "@id": "bts:DimensionOrder" + }, + { + "@id": "bts:PhysicalSizeX" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeY" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZ" + }, + { + "@id": "bts:PhysicalSizeZUnit" + }, + { + "@id": "bts:PixelsBigEndian" + }, + { + "@id": "bts:PlaneCount" + }, + { + "@id": "bts:SizeC" + }, + { + "@id": "bts:SizeT" + }, + { + "@id": "bts:SizeX" + }, + { + "@id": "bts:SizeY" + }, + { + "@id": "bts:SizeZ" + }, + { + "@id": "bts:PixelType" + }, + { + "@id": "bts:MERFISHPositionsFile" + }, + { + "@id": "bts:MERFISHCodebookFile" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Fiducialimagejpg", + "@id": "bts:ChannelMetadataFilename", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Fiducialimagejpg", + "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label": "ChannelMetadataFilename", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "fiducial image jpg", - "sms:required": "sms:false", + "sms:displayName": "Channel Metadata Filename", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Detectedimagepng", + "@id": "bts:Microscope", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Detectedimagepng", + "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", + "rdfs:label": "Microscope", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "detected image png", - "sms:required": "sms:false", + "sms:displayName": "Microscope", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Detectedjpg", + "@id": "bts:Objective", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Detectedjpg", + "rdfs:comment": "Objective", + "rdfs:label": "Objective", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "detected jpg", + "sms:displayName": "Objective", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Highresimage", + "@id": "bts:NominalMagnification", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Highresimage", + "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", + "rdfs:label": "NominalMagnification", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "high res image", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "NominalMagnification", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Lowresimage", + "@id": "bts:LensNA", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Lowresimage", + "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label": "LensNA", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "low res image", + "sms:displayName": "LensNA", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:A", + "@id": "bts:WorkingDistance", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "A", + "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", + "rdfs:label": "WorkingDistance", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "A", + "sms:displayName": "WorkingDistance", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:WorkingDistanceUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:B", + "@id": "bts:WorkingDistanceUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "B", + "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" - }, - { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "B", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:C", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "C", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Cm" }, { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "C", + "sms:displayName": "WorkingDistanceUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:D", + "@id": "bts:Immersion", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "D", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "D", + "schema:rangeIncludes": [ + { + "@id": "bts:Air" + }, + { + "@id": "bts:Oil" + }, + { + "@id": "bts:Water" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Immersion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:A1", + "@id": "bts:Pyramid", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "A1", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "A1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Pyramid", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:B1", + "@id": "bts:Zstack", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "B1", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "B1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Zstack", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:C1", + "@id": "bts:Tseries", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "C1", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "C1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Tseries", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:D1", + "@id": "bts:PassedQC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "D1", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "D1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelsQC" + } + ], + "sms:displayName": "Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:V1", + "@id": "bts:FOVnumber", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V1", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V1", + "sms:displayName": "FOV number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:V2", + "@id": "bts:FOVX", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V2", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V2", + "sms:displayName": "FOVX", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:requiresDependency": [ + { + "@id": "bts:FOVXUnit" + } + ], + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:V3", + "@id": "bts:FOVXUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V3", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V3", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVXUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:V4", + "@id": "bts:FOVY", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V4", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V4", + "sms:displayName": "FOVY", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:requiresDependency": [ + { + "@id": "bts:FOVYUnit" + } + ], + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:TRUE", + "@id": "bts:FOVYUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TRUE", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", "rdfs:subClassOf": [ { - "@id": "bts:ImageRe-orientation" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TRUE", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVYUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FALSE", + "@id": "bts:FrameAveraging", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "FALSE", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", "rdfs:subClassOf": [ { - "@id": "bts:ImageRe-orientation" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FALSE", + "sms:displayName": "Frame Averaging", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeLength", + "@id": "bts:ImageID", "@type": "rdfs:Class", - "rdfs:comment": "Length of spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeLength", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode Length", + "sms:displayName": "Image ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CDNA", + "@id": "bts:DimensionOrder", "@type": "rdfs:Class", - "rdfs:comment": "Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase", - "rdfs:label": "CDNA", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SpatialRead1" + "@id": "bts:XYZCT" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:XYZTC" }, { - "@id": "bts:ScmCseqRead1" + "@id": "bts:XYCTZ" }, { - "@id": "bts:ScmCseqRead2" + "@id": "bts:XYCZT" }, { - "@id": "bts:ScmCseqRead3" + "@id": "bts:XYTZC" }, { - "@id": "bts:Read1" - }, + "@id": "bts:ZYX" + } + ], + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeX", + "rdfs:subClassOf": [ { - "@id": "bts:Read2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cDNA", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:CDNAOffset" - }, - { - "@id": "bts:CDNALength" + "@id": "bts:PhysicalSizeXUnit" } ], "sms:validationRules": [] }, { - "@id": "bts:Smart-seq2", + "@id": "bts:PhysicalSizeXUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Smart-seq2", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Smart-seq2", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Smart-SeqV4", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Smart-SeqV4", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Cm" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Smart-SeqV4", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeXUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xV1.0", + "@id": "bts:PhysicalSizeY", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV1.0", + "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeY", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV1.0", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeYUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:10xV1.1", + "@id": "bts:PhysicalSizeYUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV1.1", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV1.1", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV2", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV2", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Cm" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV2", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xV3", + "@id": "bts:PhysicalSizeZ", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeZ", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV3", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeZ", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeZUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:10xV3.1", + "@id": "bts:PhysicalSizeZUnit", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3.1", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeZUnit", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV3.1", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Drop-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Drop-seq", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Cm" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Drop-seq", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeZUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InDropsV2", + "@id": "bts:PixelsBigEndian", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV2", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "inDropsV2", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:True" + }, + { + "@id": "bts:False" + } + ], + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InDropsV3", + "@id": "bts:PlaneCount", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV3", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "inDropsV3", - "sms:required": "sms:false", + "sms:displayName": "PlaneCount", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TruDrop", + "@id": "bts:SizeC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TruDrop", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TruDrop", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeC", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:NexteraXT", + "@id": "bts:SizeT", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NexteraXT", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nextera XT", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeT", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:UMIBarcodeOffset", + "@id": "bts:SizeX", "@type": "rdfs:Class", - "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", - "rdfs:label": "UMIBarcodeOffset", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Offset", + "sms:displayName": "SizeX", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:UMIBarcodeLength", + "@id": "bts:SizeY", "@type": "rdfs:Class", - "rdfs:comment": "Length of UMI barcode read (in bp): number", - "rdfs:label": "UMIBarcodeLength", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Length", + "sms:displayName": "SizeY", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "@id": "bts:SizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, + "sms:displayName": "SizeZ", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:PixelType", + "@type": "rdfs:Class", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", + "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Imaging" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HTANDataFileID" + "@id": "bts:Int8" }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile" + "@id": "bts:Int16" }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform" + "@id": "bts:Int32" }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod" + "@id": "bts:Uint8" }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName" + "@id": "bts:Uint16" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor" + "@id": "bts:Uint32" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion" + "@id": "bts:Float" }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile" + "@id": "bts:Double" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Bit" } ], + "sms:displayName": "PixelType", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile", + "@id": "bts:MERFISHPositionsFile", "@type": "rdfs:Class", - "rdfs:comment": "The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxDSPPKCFile", + "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", + "rdfs:label": "MERFISHPositionsFile", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP PKC File", - "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] + "sms:displayName": "MERFISH Positions File", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform", + "@id": "bts:MERFISHCodebookFile", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "GeoMxDSPNGSSequencingPlatform", + "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", + "rdfs:label": "MERFISHCodebookFile", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Sequencing Platform", + "sms:displayName": "MERFISH Codebook File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", + "@id": "bts:ImagingLevel3Segmentation", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "GeoMxDSPNGSLibrarySelectionMethod", + "rdfs:comment": "Object segmentations", + "rdfs:label": "ImagingLevel3Segmentation", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Selection Method", + "sms:displayName": "Imaging Level 3 Segmentation", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingSegmentationDataType" + }, + { + "@id": "bts:Parameterfile" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:ImagingObjectClass" + }, + { + "@id": "bts:NumberofObjects" + } + ], "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName", + "@id": "bts:ImagingSegmentationDataType", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPNGSLibraryPreparationKitName", + "rdfs:comment": "Specifies how the segmentation is stored", + "rdfs:label": "ImagingSegmentationDataType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Preparation Kit Name", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Mask" + }, + { + "@id": "bts:Outline" + }, + { + "@id": "bts:Polygon" + }, + { + "@id": "bts:ProbabilityMap" + }, + { + "@id": "bts:Point" + } + ], + "sms:displayName": "Imaging Segmentation Data Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor", + "@id": "bts:Parameterfile", "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPLibraryPreparationKitVendor", + "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", + "rdfs:label": "Parameterfile", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Library Preparation Kit Vendor", + "sms:displayName": "Parameter file", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion", + "@id": "bts:ImagingObjectClass", "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPLibraryPreparationKitVersion", + "rdfs:comment": "Defines the structure that the mask delineates", + "rdfs:label": "ImagingObjectClass", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Library Preparation Kit Version", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:Nucleus" + }, + { + "@id": "bts:Cytoplasm" + }, + { + "@id": "bts:Plasmamembrane" + }, + { + "@id": "bts:Wholecell" + }, + { + "@id": "bts:Spot" + }, + { + "@id": "bts:ImagingObjectClassOther" + } + ], + "sms:displayName": "Imaging Object Class", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile", + "@id": "bts:NumberofObjects", "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxLabWorksheetFile", + "rdfs:comment": "The number of objects (eg cells) described", + "rdfs:label": "NumberofObjects", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File", - "sms:required": "sms:false", + "sms:displayName": "Number of Objects", + "sms:required": "sms:true", "sms:validationRules": [ - "list", - "regex match syn\\d+" + "int" ] }, { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "@id": "bts:ImagingLevel3Image", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", - "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "rdfs:comment": "Quality controlled imaging data", + "rdfs:label": "ImagingLevel3Image", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -41294,68 +42350,117 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", + "sms:displayName": "Imaging Level 3 Image", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ImagingLevel2" + } + ], "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, { "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Scanname" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:ROIname" + "@id": "bts:HTANParentChannelMetadataID" }, { - "@id": "bts:Segmentname" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Tags" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:QCstatus" + "@id": "bts:Microscope" }, { - "@id": "bts:ScanHeight" + "@id": "bts:Objective" }, { - "@id": "bts:ScanWidth" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:LensNA" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:BindingDensity" + "@id": "bts:Immersion" }, { - "@id": "bts:Positivenormfactor" + "@id": "bts:Pyramid" }, { - "@id": "bts:Surfacearea" + "@id": "bts:Zstack" }, { - "@id": "bts:Nucleicount" + "@id": "bts:Tseries" }, { - "@id": "bts:TissueStain" + "@id": "bts:PassedQC" + }, + { + "@id": "bts:Comment" + }, + { + "@id": "bts:FOVnumber" + }, + { + "@id": "bts:FOVX" + }, + { + "@id": "bts:FOVY" + }, + { + "@id": "bts:FrameAveraging" } ], "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "@id": "bts:HTANParentChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", - "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "rdfs:comment": "HTAN ID for a level 3 channels table.", + "rdfs:label": "HTANParentChannelMetadataID", + "rdfs:subClassOf": [ + { + "@id": "bts:ImagingLevel4" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Channel Metadata ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingLevel3Channels", + "@type": "rdfs:Class", + "rdfs:comment": "Channel-level Metadata Attributes", + "rdfs:label": "ImagingLevel3Channels", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -41364,83 +42469,185 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", + "sms:displayName": "Imaging Level 3 Channels", "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANChannelMetadataID" }, { - "@id": "bts:Scanname" + "@id": "bts:ChannelID" }, { - "@id": "bts:Slidename" + "@id": "bts:ChannelName" }, { - "@id": "bts:ROIname" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:Segmentname" + "@id": "bts:CycleNumber" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:SubCycleNumber" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:AntibodyRole" }, { - "@id": "bts:Tags" + "@id": "bts:TargetName" }, { - "@id": "bts:ScanHeight" + "@id": "bts:AntibodyName" }, { - "@id": "bts:ScanWidth" + "@id": "bts:RRIDidentifier" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:Fluorophore" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:Clone" }, { - "@id": "bts:Surfacearea" + "@id": "bts:Lot" }, { - "@id": "bts:Nucleicount" + "@id": "bts:Vendor" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:MapQ30" + "@id": "bts:ExcitationWavelength" }, { - "@id": "bts:Rawreads" + "@id": "bts:EmissionWavelength" }, { - "@id": "bts:Stitchedreads" + "@id": "bts:ExcitationBandwidth" }, { - "@id": "bts:Alignedreads" + "@id": "bts:EmissionBandwidth" }, { - "@id": "bts:Deduplicatedreads" + "@id": "bts:MetalIsotopeElement" }, { - "@id": "bts:InSituNegativemedian" + "@id": "bts:MetalIsotopeMass" }, { - "@id": "bts:Biologicalprobemedian" + "@id": "bts:OligoBarcodeUpperStrand" + }, + { + "@id": "bts:OligoBarcodeLowerStrand" + }, + { + "@id": "bts:Dilution" + }, + { + "@id": "bts:Concentration" } ], "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPAssayType", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The assay type which was used for the GeoMx DSP pipeline.", - "rdfs:label": "GeoMxDSPAssayType", + "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ReadIndicator" + }, + { + "@id": "bts:SpatialRead1" + }, + { + "@id": "bts:SpatialRead2" + }, + { + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:EndBias" + }, + { + "@id": "bts:ReverseTranscriptionPrimer" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SlideVersion" + }, + { + "@id": "bts:SlideID" + }, + { + "@id": "bts:ImageRe-orientation" + }, + { + "@id": "bts:PermeabilizationTime" + }, + { + "@id": "bts:RIN" + }, + { + "@id": "bts:DV200" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CaptureArea", + "@type": "rdfs:Class", + "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", + "rdfs:label": "CaptureArea", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41451,95 +42658,129 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RNAnCounter" + "@id": "bts:A" }, { - "@id": "bts:ProteinnCounter" + "@id": "bts:B" }, { - "@id": "bts:ProteinNGS" + "@id": "bts:C" }, { - "@id": "bts:RNANGS" + "@id": "bts:D" + }, + { + "@id": "bts:A1" + }, + { + "@id": "bts:B1" + }, + { + "@id": "bts:C1" + }, + { + "@id": "bts:D1" } ], - "sms:displayName": "GeoMx DSP Assay Type", - "sms:required": "sms:true", + "sms:displayName": "Capture Area", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RNAnCounter", + "@id": "bts:SlideVersion", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNAnCounter", + "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "rdfs:label": "SlideVersion", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RNA nCounter", + "schema:rangeIncludes": [ + { + "@id": "bts:V1" + }, + { + "@id": "bts:V2" + }, + { + "@id": "bts:V3" + }, + { + "@id": "bts:V4" + } + ], + "sms:displayName": "Slide Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProteinnCounter", + "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProteinnCounter", + "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", + "rdfs:label": "SlideID", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protein nCounter", + "sms:displayName": "Slide ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProteinNGS", + "@id": "bts:ImageRe-orientation", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProteinNGS", + "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", + "rdfs:label": "ImageRe-orientation", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protein NGS", + "schema:rangeIncludes": [ + { + "@id": "bts:TRUE" + }, + { + "@id": "bts:FALSE" + } + ], + "sms:displayName": "Image Re-orientation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RNANGS", + "@id": "bts:PermeabilizationTime", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNANGS", + "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", + "rdfs:label": "PermeabilizationTime", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RNA NGS", + "sms:displayName": "Permeabilization Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41548,20 +42789,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" - }, - { - "@id": "bts:ImagingLevel2" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -41575,46 +42807,58 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Checksum" + }, + { + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:UMITag" }, { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" + "@id": "bts:WhitelistSpatialBarcodeFileLink" }, { - "@id": "bts:GeoMxDSPUniqueProbeCount" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:GeoMxDSPUniqueTargetCount" + "@id": "bts:AppliedHardTrimming" }, { - "@id": "bts:GeoMxDSPGenomicReference" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:MatrixType" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:GeoMxDSPWorkflowType" + "@id": "bts:GenomicReference" }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:GeoMxDSPWorkflowLink" + "@id": "bts:GenomeAnnotationURL" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:CaptureArea" } ], "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "@id": "bts:WhitelistSpatialBarcodeFileLink", "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", - "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", + "rdfs:label": "WhitelistSpatialBarcodeFileLink", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41623,18 +42867,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", + "sms:displayName": "Whitelist Spatial Barcode File Link", "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPUniqueProbeCount", + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique probes reported.", - "rdfs:label": "GeoMxDSPUniqueProbeCount", + "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41643,17 +42884,61 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Unique Probe Count", + "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:VisiumFileType" + }, + { + "@id": "bts:SlideID" + }, + { + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPUniqueTargetCount", + "@id": "bts:VisiumFileType", "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique genes reported.", - "rdfs:label": "GeoMxDSPUniqueTargetCount", + "rdfs:comment": "The file type generated for the visium experiment.", + "rdfs:label": "VisiumFileType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41662,17 +42947,65 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Unique Target Count", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "schema:rangeIncludes": [ + { + "@id": "bts:Referencepng" + }, + { + "@id": "bts:Referencejpg" + }, + { + "@id": "bts:Jsonscalefactors" + }, + { + "@id": "bts:Probedatasetcsv" + }, + { + "@id": "bts:Qcresulthtml" + }, + { + "@id": "bts:Filteredmex" + }, + { + "@id": "bts:Unfilteredmex" + }, + { + "@id": "bts:TissuePositions" + }, + { + "@id": "bts:Barcodes" + }, + { + "@id": "bts:Features" + }, + { + "@id": "bts:Fiducialimagepng" + }, + { + "@id": "bts:Fiducialimagejpg" + }, + { + "@id": "bts:Detectedimagepng" + }, + { + "@id": "bts:Detectedjpg" + }, + { + "@id": "bts:Highresimage" + }, + { + "@id": "bts:Lowresimage" + } + ], + "sms:displayName": "Visium File Type", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPGenomicReference", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", - "rdfs:label": "GeoMxDSPGenomicReference", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41681,17 +43014,79 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Genomic Reference", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:VisiumFileType" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:CaptureArea" + }, + { + "@id": "bts:Spotsundertissue" + }, + { + "@id": "bts:MeanReadsperSpatialSpot" + }, + { + "@id": "bts:MedianNumberGenesperSpatialSpot" + }, + { + "@id": "bts:SequencingSaturation" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:ProportionReadsMappedtoTranscriptome" + }, + { + "@id": "bts:MedianUMICountsperSpot" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowType", + "@id": "bts:Spotsundertissue", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", - "rdfs:label": "GeoMxDSPWorkflowType", + "rdfs:comment": "The number of barcodes associated with a spot under tissue.", + "rdfs:label": "Spotsundertissue", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41700,15 +43095,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Spots under tissue", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription", + "@id": "bts:MeanReadsperSpatialSpot", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", - "rdfs:label": "GeoMxDSPWorkflowParameterDescription", + "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", + "rdfs:label": "MeanReadsperSpatialSpot", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41717,15 +43114,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Parameter Description", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Mean Reads per Spatial Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:GeoMxDSPWorkflowLink", + "@id": "bts:SequencingSaturation", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "GeoMxDSPWorkflowLink", + "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", + "rdfs:label": "SequencingSaturation", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -41734,746 +43133,995 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Link", - "sms:required": "sms:false", + "sms:displayName": "Sequencing Saturation", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Scanname", + "@id": "bts:ProportionReadsMappedtoTranscriptome", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", - "rdfs:label": "Scanname", + "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", + "rdfs:label": "ProportionReadsMappedtoTranscriptome", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan name", + "sms:displayName": "Proportion Reads Mapped to Transcriptome", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIname", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", - "rdfs:label": "ROIname", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI name", - "sms:required": "sms:true", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:RunID" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:VisiumWorkflowType" + }, + { + "@id": "bts:VisiumWorkflowParametersDescription" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Segmentname", + "@id": "bts:VisiumWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Name given to segment at time of generation", - "rdfs:label": "Segmentname", + "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", + "rdfs:label": "VisiumWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Segment name", + "sms:displayName": "Visium Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIXCoordinate", + "@id": "bts:VisiumWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "X location within the image", - "rdfs:label": "ROIXCoordinate", + "rdfs:comment": "Parameters used to run the workflow..", + "rdfs:label": "VisiumWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI X Coordinate", + "sms:displayName": "Visium Workflow Parameters Description", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIYCoordinate", + "@id": "bts:Referencepng", "@type": "rdfs:Class", - "rdfs:comment": "Y location within the image", - "rdfs:label": "ROIYCoordinate", + "rdfs:comment": "TBD", + "rdfs:label": "Referencepng", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI Y Coordinate", - "sms:required": "sms:true", + "sms:displayName": "reference png", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tags", + "@id": "bts:Referencejpg", "@type": "rdfs:Class", - "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", - "rdfs:label": "Tags", + "rdfs:comment": "TBD", + "rdfs:label": "Referencejpg", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tags", - "sms:required": "sms:true", + "sms:displayName": "reference jpg", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:QCstatus", + "@id": "bts:Jsonscalefactors", "@type": "rdfs:Class", - "rdfs:comment": "ROI quality control flag as reported by the application", - "rdfs:label": "QCstatus", + "rdfs:comment": "TBD", + "rdfs:label": "Jsonscalefactors", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC status", + "sms:displayName": "json scale factors", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanHeight", + "@id": "bts:Probedatasetcsv", "@type": "rdfs:Class", - "rdfs:comment": "Height of the scan for GeoMx Analysis", - "rdfs:label": "ScanHeight", + "rdfs:comment": "TBD", + "rdfs:label": "Probedatasetcsv", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Height", - "sms:required": "sms:true", + "sms:displayName": "probe dataset csv", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanWidth", + "@id": "bts:Qcresulthtml", "@type": "rdfs:Class", - "rdfs:comment": "Width of the scan for GeoMx Analysis", - "rdfs:label": "ScanWidth", + "rdfs:comment": "TBD", + "rdfs:label": "Qcresulthtml", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Width", - "sms:required": "sms:true", + "sms:displayName": "qc result html", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetX", + "@id": "bts:Filteredmex", "@type": "rdfs:Class", - "rdfs:comment": "Offset X of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetX", + "rdfs:comment": "TBD", + "rdfs:label": "Filteredmex", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset X", - "sms:required": "sms:true", + "sms:displayName": "filtered mex", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetY", + "@id": "bts:Unfilteredmex", "@type": "rdfs:Class", - "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetY", + "rdfs:comment": "TBD", + "rdfs:label": "Unfilteredmex", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset Y", - "sms:required": "sms:true", + "sms:displayName": "unfiltered mex", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BindingDensity", + "@id": "bts:TissuePositions", "@type": "rdfs:Class", - "rdfs:comment": "The binding density as reported by the application", - "rdfs:label": "BindingDensity", + "rdfs:comment": "TBD", + "rdfs:label": "TissuePositions", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Binding Density", + "sms:displayName": "tissue_positions", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Positivenormfactor", + "@id": "bts:Barcodes", "@type": "rdfs:Class", - "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", - "rdfs:label": "Positivenormfactor", + "rdfs:comment": "TBD", + "rdfs:label": "Barcodes", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:VisiumFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Positive norm factor", + "sms:displayName": "barcodes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Surfacearea", + "@id": "bts:Features", "@type": "rdfs:Class", - "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. 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"@id": "bts:Sequencing" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Aligned Read Length", - "sms:required": "sms:true", + "sms:displayName": "TruDrop", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tool", + "@id": "bts:NexteraXT", "@type": "rdfs:Class", - "rdfs:comment": "Were any software or computational tools generated for this content", - "rdfs:label": "Tool", + "rdfs:comment": "TBD", + "rdfs:label": "NexteraXT", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, + "sms:displayName": "Nextera XT", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:UMIBarcodeOffset", + "@type": "rdfs:Class", + "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", + "rdfs:label": "UMIBarcodeOffset", + "rdfs:subClassOf": [ { - "@id": "bts:No" + "@id": "bts:ScRNA-seqLevel1" } ], - "sms:displayName": "Tool", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "UMI Barcode Offset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Resolution", + "@id": "bts:UMIBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", - "rdfs:label": "Resolution", + "rdfs:comment": "Length of UMI barcode read (in bp): number", + "rdfs:label": "UMIBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Resolution", + "sms:displayName": "UMI Barcode Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HI-C-seqLevel3", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Summary data for the HI-C-seq assay.", - "rdfs:label": "HI-C-seqLevel3", + "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. 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Specific model of the sequencing instrument.", + "rdfs:label": "GeoMxDSPNGSSequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loop Window", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like ", - " regex search -?\\d+" - ] + "sms:displayName": "GeoMx DSP NGS Sequencing Platform", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:StripeWindow", + "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant architectural stripes. 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String", + "rdfs:label": "GeoMxDSPLibraryPreparationKitVersion", "rdfs:subClassOf": [ { - "@id": "bts:BiotinEnrichment" - }, - { - "@id": "bts:ChannelPassedQC" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "GeoMx DSP Library Preparation Kit Version", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SynapseIDofGeoMxLabWorksheetFile", + "@type": "rdfs:Class", + "rdfs:comment": "Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. 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"@id": "bts:Other", + "@id": "bts:RNANGS", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Other", + "rdfs:label": "RNANGS", "rdfs:subClassOf": [ { - "@id": "bts:StripeCalling" - }, - { - "@id": "bts:LoopCalling" - }, - { - "@id": "bts:HistologyAssessmentBy" - }, - { - "@id": "bts:HistologyAssessmentMedium" - }, - { - "@id": "bts:AlcoholType" - }, - { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" - }, - { - "@id": "bts:BreastCancerGenomicTestPerformed" - }, - { - "@id": "bts:DataCollectionMode" - }, - { - "@id": "bts:Immersion" - }, - { - "@id": "bts:TypeofTobaccoUsed" - }, - { - "@id": "bts:PrecancerousConditionType" - }, - { - "@id": "bts:COVID19ComplicationsSeverity" - }, - { - "@id": "bts:ClassificationofTumor" - }, - { - "@id": "bts:BreastCarcinomaDetectionMethodType" - }, - { - "@id": "bts:PriorInvasiveBreastDisease" - }, - { - "@id": "bts:BreastCarcinomaSurgicalProcedureName" - }, - { - "@id": "bts:OvarianCancerSurgicalOutcome" - }, - { - "@id": "bts:MSScanMode" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:ExpressionUnits" - }, - { - "@id": "bts:SlideChargeType" - }, - { - "@id": "bts:FiducialMarker" - }, - { - "@id": "bts:ReasonTreatmentEnded" - }, - { - "@id": "bts:LabTestsforMMRStatus" - }, - { - "@id": "bts:BreastCarcinomaHistologyCategory" - }, - { - "@id": "bts:GliomaSpecificMetastasisSites" - }, - { - "@id": "bts:AdditonalFindingsUninvolvedProstate" - }, - { - "@id": "bts:SlicingMethod" - }, - { - "@id": "bts:ImmunosuppressiveTreatmentType" - }, - { - "@id": "bts:LungCancerDetectionMethodType" - }, - { - "@id": "bts:ColorectalCancerDetectionMethodType" - }, - { - "@id": "bts:BreastBiopsyProcedureFindingType" - }, - { - "@id": "bts:BreastCancerAssessmentTests" - }, - { - "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" - }, - { - "@id": "bts:SarcomaTumorExtensionType" - }, - { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" - }, - { - "@id": "bts:Pre-processingCompleted" - }, - { - "@id": "bts:Pre-processingRequired" - }, - { - "@id": "bts:MSSource" - }, - { - "@id": "bts:Race" - }, - { - "@id": "bts:DataCategory" - }, - { - "@id": "bts:ExtentofTumorResection" - }, - { - "@id": "bts:ColorectalPolypType" - }, - { - "@id": "bts:BreastCarcinomaERStainingIntensity" - }, - { - "@id": "bts:BreastCarcinomaPRStainingIntensity" - }, - { - "@id": "bts:SarcomaSubtype" - }, - { - "@id": "bts:LibrarySelectionMethod" - }, - { - "@id": "bts:CutaneousMelanomaAdditionalFindings" - }, - { - "@id": "bts:DiabetesTreatmentType" - }, - { - "@id": "bts:OvarianCancerHistologicSubtype" - }, - { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" - }, - { - "@id": "bts:ProstateCarcinomaHistologicType" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:MolecularAnalysisMethod" - }, - { - "@id": "bts:LungAdjacentHistologyType" - }, - { - "@id": "bts:VariantType" - }, - { - "@id": "bts:LungCancerParticipantProcedureHistory" - }, - { - "@id": "bts:MethodofDiagnosis" - }, - { - "@id": "bts:FixativeType" - }, - { - "@id": "bts:HPVPositiveType" - }, - { - "@id": "bts:ConcomitantMedicationReceivedType" - }, - { - "@id": "bts:TreatmentType" - }, - { - "@id": "bts:CurrentLungCancerSymptoms" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:MutationalSignatures" - }, - { - "@id": "bts:LungCancerHarboringGenomicAberrations" - }, - { - "@id": "bts:RelationshipType" - }, - { - "@id": "bts:LungTopography" - }, - { - "@id": "bts:Comorbidity" - }, - { - "@id": "bts:PriorSitesofRadiation" - }, - { - "@id": "bts:License" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "other", + "sms:displayName": "RNA NGS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HiCCUPS", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HiCCUPS", + "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "rdfs:subClassOf": [ { - "@id": "bts:LoopCalling" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiCCUPS", + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Cooltools", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cooltools", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:LoopCalling" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cooltools", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingLevel4", - "@type": "rdfs:Class", - "rdfs:comment": "Derived imaging data: Object-by-feature array", - "rdfs:label": "ImagingLevel4", - "rdfs:subClassOf": [ + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" + }, { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:ImagingLevel2" + }, { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "sms:requiresDependency": [ @@ -43285,210 +44586,104 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:HTANParentChannelMetadataID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:GeoMxDSPAssayType" }, { - "@id": "bts:Parameterfile" + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:GeoMxDSPUniqueProbeCount" }, { - "@id": "bts:CommitSHA" + "@id": "bts:GeoMxDSPUniqueTargetCount" }, { - "@id": "bts:NumberofObjects" + "@id": "bts:GeoMxDSPGenomicReference" }, { - "@id": "bts:NumberofFeatures" + "@id": "bts:MatrixType" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:GeoMxDSPWorkflowType" }, { - "@id": "bts:ImagingSummaryStatistic" + "@id": "bts:GeoMxDSPWorkflowParameterDescription" + }, + { + "@id": "bts:GeoMxDSPWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:NumberofFeatures", + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", "@type": "rdfs:Class", - "rdfs:comment": "The number of features (eg channels) described", - "rdfs:label": "NumberofFeatures", + "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", + "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Features", + "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", "sms:required": "sms:true", "sms:validationRules": [ - "int" + "list", + "regex match syn\\d+" ] }, { - "@id": "bts:ImagingSummaryStatistic", + "@id": "bts:GeoMxDSPUniqueProbeCount", "@type": "rdfs:Class", - "rdfs:comment": "Function used to summarize object/feature intensity", - "rdfs:label": "ImagingSummaryStatistic", + "rdfs:comment": "Total number of unique probes reported.", + "rdfs:label": "GeoMxDSPUniqueProbeCount", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Mean" - }, - { - "@id": "bts:Median" - }, - { - "@id": "bts:NotSpecified" - } - ], - "sms:displayName": "Imaging Summary Statistic", + "sms:displayName": "GeoMx DSP Unique Probe Count", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:SRRSImagingLevel2", + "@id": "bts:GeoMxDSPUniqueTargetCount", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN raw and pre-processed image data", - "rdfs:label": "SRRSImagingLevel2", + "rdfs:comment": "Total number of unique genes reported.", + "rdfs:label": "GeoMxDSPUniqueTargetCount", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Imaging Level 2", + "sms:displayName": "GeoMx DSP Unique Target Count", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:Microscope" - }, - { - "@id": "bts:Objective" - }, - { - "@id": "bts:NominalMagnification" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:FrameAveraging" - }, - { - "@id": "bts:ImageID" - }, - { - "@id": "bts:DimensionOrder" - }, - { - "@id": "bts:PhysicalSizeX" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeY" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PixelsBigEndian" - }, - { - "@id": "bts:PlaneCount" - }, - { - "@id": "bts:SizeC" - }, - { - "@id": "bts:SizeT" - }, - { - "@id": "bts:SizeX" - }, - { - "@id": "bts:SizeY" - }, - { - "@id": "bts:SizeZ" - }, - { - "@id": "bts:PixelType" - } - ], - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:10XGenomicsXeniumISSExperiment", + "@id": "bts:GeoMxDSPGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment", - "rdfs:label": "10XGenomicsXeniumISSExperiment", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", + "rdfs:label": "GeoMxDSPGenomicReference", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43497,82 +44692,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10X Genomics Xenium ISS Experiment", + "sms:displayName": "GeoMx DSP Genomic Reference", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:XeniumBundleContents" - }, - { - "@id": "bts:SlideID" - }, - { - "@id": "bts:ROIname" - }, - { - "@id": "bts:PanelName" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:TotalNumberofCells" - }, - { - "@id": "bts:TotalNumberofTargets" - }, - { - "@id": "bts:Surfacearea" - }, - { - "@id": "bts:ExperimentIFChannels" - }, - { - "@id": "bts:TranscriptsperCell" - }, - { - "@id": "bts:PercentofTranscriptswithinCells" - }, - { - "@id": "bts:DecodedTranscripts" - }, - { - "@id": "bts:XeniumIFimageHTANFileID" - }, - { - "@id": "bts:XeniumHEimageHTANFileID" - } - ], - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:XeniumBundleContents", + "@id": "bts:GeoMxDSPWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "A comma separated list of filenames within the Xenium bundle zip file", - "rdfs:label": "XeniumBundleContents", + "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", + "rdfs:label": "GeoMxDSPWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43581,15 +44711,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium Bundle Contents", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PanelName", + "@id": "bts:GeoMxDSPWorkflowParameterDescription", "@type": "rdfs:Class", - "rdfs:comment": "The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))", - "rdfs:label": "PanelName", + "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", + "rdfs:label": "GeoMxDSPWorkflowParameterDescription", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43598,15 +44728,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Panel Name", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Parameter Description", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofCells", + "@id": "bts:GeoMxDSPWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "The total number of cells analyzed on the flow cell", - "rdfs:label": "TotalNumberofCells", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "GeoMxDSPWorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43615,546 +44745,439 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Cells", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofTargets", + "@id": "bts:Scanname", "@type": "rdfs:Class", - "rdfs:comment": "Refers to the target of an assay. Can be genes/transcripts or probes", - "rdfs:label": "TotalNumberofTargets", + "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", + "rdfs:label": "Scanname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Targets", + "sms:displayName": "Scan name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExperimentIFChannels", + "@id": "bts:ROIname", "@type": "rdfs:Class", - "rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)", - "rdfs:label": "ExperimentIFChannels", + "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", + "rdfs:label": "ROIname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Experiment IF Channels", + "sms:displayName": "ROI name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TranscriptsperCell", + "@id": "bts:Segmentname", "@type": "rdfs:Class", - "rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide", - "rdfs:label": "TranscriptsperCell", + "rdfs:comment": "Name given to segment at time of generation", + "rdfs:label": "Segmentname", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcripts per Cell", + "sms:displayName": "Segment name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentofTranscriptswithinCells", + "@id": "bts:ROIXCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of transcripts assigned to assayed cells", - "rdfs:label": "PercentofTranscriptswithinCells", + "rdfs:comment": "X location within the image", + "rdfs:label": "ROIXCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent of Transcripts within Cells", + "sms:displayName": "ROI X Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DecodedTranscripts", + "@id": "bts:ROIYCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).", - "rdfs:label": "DecodedTranscripts", + "rdfs:comment": "Y location within the image", + "rdfs:label": "ROIYCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Decoded Transcripts", + "sms:displayName": "ROI Y Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:XeniumIFimageHTANFileID", + "@id": "bts:Tags", "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumIFimageHTANFileID", + "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", + "rdfs:label": "Tags", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium IF image HTAN File ID", - "sms:required": "sms:false", + "sms:displayName": "Tags", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:XeniumHEimageHTANFileID", + "@id": "bts:QCstatus", "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumHEimageHTANFileID", + "rdfs:comment": "ROI quality control flag as reported by the application", + "rdfs:label": "QCstatus", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium HE image HTAN File ID", + "sms:displayName": "QC status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPALevel2", + "@id": "bts:ScanHeight", "@type": "rdfs:Class", - "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", - "rdfs:label": "RPPALevel2", + "rdfs:comment": "Height of the scan for GeoMx Analysis", + "rdfs:label": "ScanHeight", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANRPPAAntibodyTable" - }, - { - "@id": "bts:AssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - } - ], + "sms:displayName": "Scan Height", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HTANRPPAAntibodyTable", + "@id": "bts:ScanWidth", "@type": "rdfs:Class", - "rdfs:comment": "A table containing antibody level metadata for RPPA", - "rdfs:label": "HTANRPPAAntibodyTable", + "rdfs:comment": "Width of the scan for GeoMx Analysis", + "rdfs:label": "ScanWidth", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table", + "sms:displayName": "Scan Width", "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:HTANRPPAAntibodyTableID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:AbNameReportedonDataset" - }, - { - "@id": "bts:GENCODEGeneSymbolTarget" - }, - { - "@id": "bts:UNIPROTProteinIDTarget" - }, - { - "@id": "bts:PhosphoproteinFlag" - }, - { - "@id": "bts:Vendor" - }, - { - "@id": "bts:CatalogNumber" - }, - { - "@id": "bts:InternalAbID" - }, - { - "@id": "bts:Species" - }, - { - "@id": "bts:RPPADilution" - }, - { - "@id": "bts:PhosphoSite" - }, - { - "@id": "bts:RPPAValidationStatus" - }, - { - "@id": "bts:Clone" - }, - { - "@id": "bts:Clonality" - }, - { - "@id": "bts:AntibodyNotes" - } - ], "sms:validationRules": [] }, { - "@id": "bts:HTANRPPAAntibodyTableID", + "@id": "bts:ScanOffsetX", "@type": "rdfs:Class", - "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", - "rdfs:label": "HTANRPPAAntibodyTableID", + "rdfs:comment": "Offset X of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetX", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table ID", + "sms:displayName": "Scan Offset X", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AbNameReportedonDataset", + "@id": "bts:ScanOffsetY", "@type": "rdfs:Class", - "rdfs:comment": "The antibody name.", - "rdfs:label": "AbNameReportedonDataset", + "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetY", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ab Name Reported on Dataset", + "sms:displayName": "Scan Offset Y", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GENCODEGeneSymbolTarget", + "@id": "bts:BindingDensity", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", - "rdfs:label": "GENCODEGeneSymbolTarget", + "rdfs:comment": "The binding density as reported by the application", + "rdfs:label": "BindingDensity", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GENCODE Gene Symbol Target", - "sms:required": "sms:true", + "sms:displayName": "Binding Density", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UNIPROTProteinIDTarget", + "@id": "bts:Positivenormfactor", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", - "rdfs:label": "UNIPROTProteinIDTarget", + "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", + "rdfs:label": "Positivenormfactor", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UNIPROT Protein ID Target", - "sms:required": "sms:true", + "sms:displayName": "Positive norm factor", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhosphoproteinFlag", + "@id": "bts:Surfacearea", "@type": "rdfs:Class", - "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", - "rdfs:label": "PhosphoproteinFlag", + "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", + "rdfs:label": "Surfacearea", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Phosphoprotein Flag", + "sms:displayName": "Surface area", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Vendor", + "@id": "bts:Nucleicount", "@type": "rdfs:Class", - "rdfs:comment": "Vendor", - "rdfs:label": "Vendor", + "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", + "rdfs:label": "Nucleicount", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Vendor", - "sms:required": "sms:false", + "sms:displayName": "Nuclei count", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CatalogNumber", + "@id": "bts:TissueStain", "@type": "rdfs:Class", - "rdfs:comment": "Catalog Number", - "rdfs:label": "CatalogNumber", + "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", + "rdfs:label": "TissueStain", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Catalog Number", + "sms:displayName": "Tissue Stain", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InternalAbID", + "@id": "bts:Slidename", "@type": "rdfs:Class", - "rdfs:comment": "Internal lab ID for an antibody.", - "rdfs:label": "InternalAbID", + "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", + "rdfs:label": "Slidename", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Internal Ab ID", - "sms:required": "sms:true", + "sms:displayName": "Slide name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Species", + "@id": "bts:Rawreads", "@type": "rdfs:Class", - "rdfs:comment": "Host animal.", - "rdfs:label": "Species", + "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", + "rdfs:label": "Rawreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Mouse" - }, - { - "@id": "bts:Rabbit" - }, - { - "@id": "bts:Goat" - } - ], - "sms:displayName": "Species", - "sms:required": "sms:true", + "sms:displayName": "Raw reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPADilution", + "@id": "bts:Stitchedreads", "@type": "rdfs:Class", - "rdfs:comment": "The dilution ratio.", - "rdfs:label": "RPPADilution", + "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", + "rdfs:label": "Stitchedreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Dilution", + "sms:displayName": "Stitched reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhosphoSite", + "@id": "bts:Alignedreads", "@type": "rdfs:Class", - "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", - "rdfs:label": "PhosphoSite", + "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", + "rdfs:label": "Alignedreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Phospho Site", + "sms:displayName": "Aligned reads", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:PhosphoproteinFlag" - } - ], "sms:validationRules": [] }, { - "@id": "bts:RPPAValidationStatus", + "@id": "bts:Deduplicatedreads", "@type": "rdfs:Class", - "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", - "rdfs:label": "RPPAValidationStatus", + "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", + "rdfs:label": "Deduplicatedreads", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Valid" - }, - { - "@id": "bts:UsewithCaution" - }, - { - "@id": "bts:UnderEvaluation" - }, - { - "@id": "bts:UsedforQC" - } - ], - "sms:displayName": "RPPA Validation Status", + "sms:displayName": "Deduplicated reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clone", + "@id": "bts:InSituNegativemedian", "@type": "rdfs:Class", - "rdfs:comment": "Clone", - "rdfs:label": "Clone", + "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", + "rdfs:label": "InSituNegativemedian", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Clone", + "sms:displayName": "In Situ Negative median", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AntibodyNotes", + "@id": "bts:Biologicalprobemedian", "@type": "rdfs:Class", - "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", - "rdfs:label": "AntibodyNotes", + "rdfs:comment": "Is the median count from all probes except the negative control probes. A measure of signal to background for each segment", + "rdfs:label": "Biologicalprobemedian", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody Notes", + "sms:displayName": "Biological probe median", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPALevel3", + "@id": "bts:HI-C-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", - "rdfs:label": "RPPALevel3", + "rdfs:comment": "Unaligned sequence data", + "rdfs:label": "HI-C-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 3", + "sms:displayName": "HI-C-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -44165,6 +45188,12 @@ { "@id": "bts:Component" }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, { "@id": "bts:Filename" }, @@ -44172,209 +45201,238 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:GenomicReference" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:AssayType" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:CrosslinkingCondtion" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:DNADigestionCondition" + }, + { + "@id": "bts:NucleiPermeabilizationMethod" + }, + { + "@id": "bts:LigationCondition" + }, + { + "@id": "bts:BiotinEnrichment" + }, + { + "@id": "bts:DNAInputAmount" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:ProtocolLink" } ], "sms:validationRules": [] }, { - "@id": "bts:RPPALevel4", + "@id": "bts:CrosslinkingCondtion", "@type": "rdfs:Class", - "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", - "rdfs:label": "RPPALevel4", + "rdfs:comment": "Detailed condition for DNA crosslinking", + "rdfs:label": "CrosslinkingCondtion", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "Crosslinking Condtion", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DNADigestionCondition", + "@type": "rdfs:Class", + "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", + "rdfs:label": "DNADigestionCondition", + "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:Sequencing" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DNA Digestion Condition", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleiPermeabilizationMethod", + "@type": "rdfs:Class", + "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", + "rdfs:label": "NucleiPermeabilizationMethod", + "rdfs:subClassOf": [ { - 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Use either synapse_path or entity_Id", - "rdfs:label": "MSInstrumentMetadataFile", + "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", + "rdfs:label": "XeniumHEimageHTANFileID", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MS Instrument Metadata File", + "sms:displayName": "Xenium HE image HTAN File ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryLevel2", + "@id": "bts:RPPALevel2", "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2", - "rdfs:label": "MassSpectrometryLevel2", + "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", + "rdfs:label": "RPPALevel2", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -45137,11 +46535,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Level 2", + "sms:displayName": "RPPA Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -45155,7 +46553,7 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:HTANParticipantID" }, { "@id": "bts:HTANParentBiospecimenID" @@ -45164,52 +46562,41 @@ "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:MSAssayCategory" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:HTANRPPAAntibodyTable" }, { - "@id": "bts:MassSpectrometryAuxiliaryFile" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MSAssayCategory", - "@type": "rdfs:Class", - "rdfs:comment": "Type of Mass Spectrometry performed.", - "rdfs:label": "MSAssayCategory", - "rdfs:subClassOf": [ + "@id": "bts:AssayType" + }, { - "@id": "bts:MassSpectrometryLevel2" + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MS Assay Category", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryAuxiliaryFile", + "@id": "bts:HTANRPPAAntibodyTable", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).", - "rdfs:label": "MassSpectrometryAuxiliaryFile", + "rdfs:comment": "A table containing antibody level metadata for RPPA", + "rdfs:label": "HTANRPPAAntibodyTable", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:RPPALevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Auxiliary File", - "sms:required": "sms:false", + "sms:displayName": "HTAN RPPA Antibody Table", + "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:Component" + "@id": "bts:HTANRPPAAntibodyTableID" }, { "@id": "bts:Filename" @@ -45218,175 +46605,126 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:AbNameReportedonDataset" }, { - "@id": "bts:HTANDataFileID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MassSpectrometryLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3", - "rdfs:label": "MassSpectrometryLevel3", - "rdfs:subClassOf": [ + "@id": "bts:GENCODEGeneSymbolTarget" + }, { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Spectrometry Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:UNIPROTProteinIDTarget" + }, { - "@id": "bts:MassSpectrometryLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:PhosphoproteinFlag" + }, { - "@id": "bts:Component" + "@id": "bts:Vendor" }, { - "@id": "bts:Filename" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:FileFormat" + "@id": "bts:InternalAbID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Species" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:RPPADilution" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:PhosphoSite" }, { - "@id": "bts:MSAssayCategory" + "@id": "bts:RPPAValidationStatus" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Clone" }, { - "@id": "bts:MassSpectrometryAuxiliaryFile" + "@id": "bts:Clonality" + }, + { + "@id": "bts:AntibodyNotes" } ], "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometryLevel4", + "@id": "bts:HTANRPPAAntibodyTableID", "@type": "rdfs:Class", - "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4", - "rdfs:label": "MassSpectrometryLevel4", + "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", + "rdfs:label": "HTANRPPAAntibodyTableID", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:MassSpectrometryLevel3" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:MSAssayCategory" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:MassSpectrometryAuxiliaryFile" - } - ], + "sms:displayName": "HTAN RPPA Antibody Table ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HTANChannelMetadataID", + "@id": "bts:AbNameReportedonDataset", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID for this channel metadata table (same for all rows)", - "rdfs:label": "HTANChannelMetadataID", + "rdfs:comment": "The antibody name.", + "rdfs:label": "AbNameReportedonDataset", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Channel Metadata ID", + "sms:displayName": "Ab Name Reported on Dataset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelID", + "@id": "bts:GENCODEGeneSymbolTarget", "@type": "rdfs:Class", - "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')", - "rdfs:label": "ChannelID", + "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", + "rdfs:label": "GENCODEGeneSymbolTarget", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel ID", + "sms:displayName": "GENCODE Gene Symbol Target", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelName", + "@id": "bts:UNIPROTProteinIDTarget", "@type": "rdfs:Class", - "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", - "rdfs:label": "ChannelName", + "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", + "rdfs:label": "UNIPROTProteinIDTarget", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Name", + "sms:displayName": "UNIPROT Protein ID Target", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelPassedQC", + "@id": "bts:PhosphoproteinFlag", "@type": "rdfs:Class", - "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", - "rdfs:label": "ChannelPassedQC", + "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", + "rdfs:label": "PhosphoproteinFlag", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -45394,21 +46732,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:True" }, { - "@id": "bts:No-ChannelFailedQC" + "@id": "bts:False" } ], - "sms:displayName": "Channel Passed QC", + "sms:displayName": "Phosphoprotein Flag", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CycleNumber", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", - "rdfs:label": "CycleNumber", + "rdfs:comment": "Vendor", + "rdfs:label": "Vendor", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel3Channels" @@ -45417,17 +46755,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cycle Number", + "sms:displayName": "Vendor", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SubCycleNumber", + "@id": "bts:CatalogNumber", "@type": "rdfs:Class", - "rdfs:comment": "Sub cycle number", - "rdfs:label": "SubCycleNumber", + "rdfs:comment": "Catalog Number", + "rdfs:label": "CatalogNumber", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel3Channels" @@ -45436,112 +46772,130 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sub Cycle Number", + "sms:displayName": "Catalog Number", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:AntibodyRole", + "@id": "bts:InternalAbID", "@type": "rdfs:Class", - "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", - "rdfs:label": "AntibodyRole", + "rdfs:comment": "Internal lab ID for an antibody.", + "rdfs:label": "InternalAbID", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Primary" - }, - { - "@id": "bts:Secondary" - } - ], - "sms:displayName": "Antibody Role", + "sms:displayName": "Internal Ab ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TargetName", + "@id": "bts:Species", "@type": "rdfs:Class", - "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", - "rdfs:label": "TargetName", + "rdfs:comment": "Host animal.", + "rdfs:label": "Species", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Target Name", + "schema:rangeIncludes": [ + { + "@id": "bts:Mouse" + }, + { + "@id": "bts:Rabbit" + }, + { + "@id": "bts:Goat" + } + ], + "sms:displayName": "Species", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AntibodyName", + "@id": "bts:RPPADilution", "@type": "rdfs:Class", - "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", - "rdfs:label": "AntibodyName", + "rdfs:comment": "The dilution ratio.", + "rdfs:label": "RPPADilution", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody Name", - "sms:required": "sms:true", + "sms:displayName": "RPPA Dilution", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RRIDidentifier", + "@id": "bts:PhosphoSite", "@type": "rdfs:Class", - "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", - "rdfs:label": "RRIDidentifier", + "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", + "rdfs:label": "PhosphoSite", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RRID identifier", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match AB_\\d+" - ] + "sms:displayName": "Phospho Site", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:PhosphoproteinFlag" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:Fluorophore", + "@id": "bts:RPPAValidationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", - "rdfs:label": "Fluorophore", + "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", + "rdfs:label": "RPPAValidationStatus", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fluorophore", + "schema:rangeIncludes": [ + { + "@id": "bts:Valid" + }, + { + "@id": "bts:UsewithCaution" + }, + { + "@id": "bts:UnderEvaluation" + }, + { + "@id": "bts:UsedforQC" + } + ], + "sms:displayName": "RPPA Validation Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lot", + "@id": "bts:Clone", "@type": "rdfs:Class", - "rdfs:comment": "Lot number from vendor", - "rdfs:label": "Lot", + "rdfs:comment": "Clone", + "rdfs:label": "Clone", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel3Channels" @@ -45550,578 +46904,659 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lot", + "sms:displayName": "Clone", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExcitationWavelength", + "@id": "bts:AntibodyNotes", "@type": "rdfs:Class", - "rdfs:comment": "Center/peak of the excitation spectrum (nm)", - "rdfs:label": "ExcitationWavelength", + "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", + "rdfs:label": "AntibodyNotes", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Excitation Wavelength", + "sms:displayName": "Antibody Notes", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:EmissionWavelength", + "@id": "bts:RPPALevel3", "@type": "rdfs:Class", - "rdfs:comment": "Center/peak of the emission spectrum (nm)", - "rdfs:label": "EmissionWavelength", + "rdfs:comment": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", + "rdfs:label": "RPPALevel3", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Emission Wavelength", + "sms:displayName": "RPPA Level 3", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:NormalizationMethod" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:ExcitationBandwidth", + "@id": "bts:RPPALevel4", "@type": "rdfs:Class", - "rdfs:comment": "Nominal width of excitation spectrum (nm)", - "rdfs:label": "ExcitationBandwidth", + "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", + "rdfs:label": "RPPALevel4", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Excitation Bandwidth", + "sms:displayName": "RPPA Level 4", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:requiresComponent": [ + { + "@id": "bts:RPPALevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" + }, + { + "@id": "bts:BatchCorrectionMethod" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:EmissionBandwidth", + "@id": "bts:BatchCorrectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Nominal width of emission spectrum (nm)", - "rdfs:label": "EmissionBandwidth", + "rdfs:comment": "Method that was used to batch correct Level 3 data", + "rdfs:label": "BatchCorrectionMethod", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:RPPALevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Emission Bandwidth", + "sms:displayName": "Batch Correction Method", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:MetalIsotopeElement", + "@id": "bts:NanostringCosMxSMIExperiment", "@type": "rdfs:Class", - "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", - "rdfs:label": "MetalIsotopeElement", + "rdfs:comment": "RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)", + "rdfs:label": "NanostringCosMxSMIExperiment", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Nanostring CosMx SMI Experiment", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:H" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:He" + "@id": "bts:Component" }, { - "@id": "bts:Li" + "@id": "bts:Filename" }, { - "@id": "bts:Be" + "@id": "bts:FileFormat" }, { - "@id": "bts:B" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:C" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:N" + "@id": "bts:CosMxBundleContents" }, { - "@id": "bts:O" + "@id": "bts:SlideID" }, { - "@id": "bts:F" + "@id": "bts:CosMxAssayType" }, { - "@id": "bts:Ne" + "@id": "bts:PanelName" }, { - "@id": "bts:Na" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Mg" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:Al" + "@id": "bts:TotalNumberofCells" }, { - "@id": "bts:Si" + "@id": "bts:TotalNumberofTargets" }, { - "@id": "bts:P" + "@id": "bts:NumberofFOVs" }, { - "@id": "bts:S" + "@id": "bts:Surfacearea" }, { - "@id": "bts:Cl" + "@id": "bts:ExperimentIFChannels" }, { - "@id": "bts:Ar" + "@id": "bts:TranscriptsperCell" }, { - "@id": "bts:K" + "@id": "bts:PercentofTranscriptswithinCells" }, { - "@id": "bts:Ca" + "@id": "bts:MeanTotalTranscriptsperArea" }, { - "@id": "bts:Sc" + "@id": "bts:UniqueGenes" }, { - "@id": "bts:Ti" - }, + "@id": "bts:TotalNegativeProbeCounts" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CosMxBundleContents", + "@type": "rdfs:Class", + "rdfs:comment": "A comma separated list of filenames within the CosMx bundle zip file", + "rdfs:label": "CosMxBundleContents", + "rdfs:subClassOf": [ { - "@id": "bts:V" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CosMx Bundle Contents", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CosMxAssayType", + "@type": "rdfs:Class", + "rdfs:comment": "The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay", + "rdfs:label": "CosMxAssayType", + "rdfs:subClassOf": [ { - "@id": "bts:Cr" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Mn" + "@id": "bts:RNA" }, { - "@id": "bts:Fe" - }, + "@id": "bts:Protein" + } + ], + "sms:displayName": "CosMx Assay Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NumberofFOVs", + "@type": "rdfs:Class", + "rdfs:comment": "The total number of FOVs recorded for the sample on a single flow cell", + "rdfs:label": "NumberofFOVs", + "rdfs:subClassOf": [ { - "@id": "bts:Co" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Number of FOVs", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MeanTotalTranscriptsperArea", + "@type": "rdfs:Class", + "rdfs:comment": "The mean total transcripts per um3", + "rdfs:label": "MeanTotalTranscriptsperArea", + "rdfs:subClassOf": [ { - 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RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteType", + "rdfs:subClassOf": [ { - "@id": "bts:Rf" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Db" + "@id": "bts:CfDNAAnalyte" }, { - "@id": "bts:Sg" + "@id": "bts:DNAAnalyte" }, { - "@id": "bts:Bh" + "@id": "bts:RNAAnalyte" }, { - "@id": "bts:Hs" + "@id": "bts:TotalRNAAnalyte" }, { - "@id": "bts:Mt" + "@id": "bts:TissueBlockAnalyte" }, { - "@id": "bts:Ds" + "@id": "bts:TissueSectionAnalyte" }, { - "@id": "bts:Rg" + "@id": "bts:PBMCsorPlasmaorSerumAnalyte" }, { - "@id": "bts:Cn" + "@id": "bts:CDNALibrariesAnalyte" }, { - "@id": "bts:Nh" + "@id": "bts:PBMCs" }, { - "@id": "bts:Fl" + "@id": "bts:Plasma" }, { - "@id": "bts:Mc" + "@id": "bts:SerumAnalyte" }, { - "@id": "bts:Lv" + "@id": "bts:Lipid" }, { - "@id": "bts:Ts" + "@id": "bts:Protein" }, { - "@id": "bts:Og" - } - ], - "sms:displayName": "Metal Isotope Element", - "sms:required": "sms:false", - "sms:validationRules": [ - "str" - ] - }, - { - "@id": "bts:MetalIsotopeMass", - "@type": "rdfs:Class", - "rdfs:comment": "Element mass number", - "rdfs:label": "MetalIsotopeMass", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Metal Isotope Mass", - "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:OligoBarcodeUpperStrand", - "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Upper Strand", - "rdfs:label": "OligoBarcodeUpperStrand", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:Metabolite" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Oligo Barcode Upper Strand", - "sms:required": "sms:false", + "sms:displayName": "Analyte Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OligoBarcodeLowerStrand", + "@id": "bts:MS-basedTargeted", "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Lower Strand", - "rdfs:label": "OligoBarcodeLowerStrand", + "rdfs:comment": "Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.", + "rdfs:label": "MS-basedTargeted", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oligo Barcode Lower Strand", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Dilution", - "@type": "rdfs:Class", - "rdfs:comment": "Dilution (eg 1:1000)", - "rdfs:label": "Dilution", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Dilution", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Concentration", - "@type": "rdfs:Class", - "rdfs:comment": "Concentration (eg 10ug/mL)", - "rdfs:label": "Concentration", - "rdfs:subClassOf": [ + "@id": "bts:Targeted" + }, { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:Untargeted" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Concentration", - "sms:required": "sms:false", + "sms:displayName": "MS-based Targeted", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:No-ChannelFailedQC", + "@id": "bts:MSInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "Channel failed QC", - "rdfs:label": "No-ChannelFailedQC", + "rdfs:comment": "An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.", + "rdfs:label": "MSInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ChannelPassedQC" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "No - Channel Failed QC", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:ChannelQCFailureType" - } - ], + "sms:displayName": "MS Instrument Vendor and Model", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelQCFailureType", + "@id": "bts:MSSource", "@type": "rdfs:Class", - "rdfs:comment": "Reason the channel failed QC", - "rdfs:label": "ChannelQCFailureType", + "rdfs:comment": "The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)", + "rdfs:label": "MSSource", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -46129,1002 +47564,1529 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Off-targetstaining" + "@id": "bts:MALDI" }, { - "@id": "bts:Auto-fluoresence" + "@id": "bts:MALDI-2" }, { - "@id": "bts:Stainingartefacet" + "@id": "bts:DESI" }, { - "@id": "bts:Imagingartefact" + "@id": "bts:SIMS" }, { - "@id": "bts:Other/multiplechannelQCfaliuretypes" + "@id": "bts:NESI" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Channel QC Failure Type", - "sms:required": "sms:false", + "sms:displayName": "MS Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Off-targetstaining", + "@id": "bts:Polarity", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Off-targetstaining", + "rdfs:comment": "The polarity of the mass analysis (positive or negative ion modes)", + "rdfs:label": "Polarity", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Off-target staining", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Auto-fluoresence", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Auto-fluoresence", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:Positive" + }, + { + "@id": "bts:Negative" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Auto-fluoresence", - "sms:required": "sms:false", + "sms:displayName": "Polarity", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Stainingartefacet", + "@id": "bts:MassRangeLowValue", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Stainingartefacet", + "rdfs:comment": "The low value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeLowValue", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Staining artefacet", - "sms:required": "sms:false", + "sms:displayName": "Mass Range Low Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Imagingartefact", + "@id": "bts:MassRangeHighValue", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Imagingartefact", + "rdfs:comment": "The high value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeHighValue", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging artefact", - "sms:required": "sms:false", + "sms:displayName": "Mass Range High Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Other/multiplechannelQCfaliuretypes", + "@id": "bts:DataCollectionMode", "@type": "rdfs:Class", - "rdfs:comment": "QC failure type not speficied", - "rdfs:label": "Other/multiplechannelQCfaliuretypes", + "rdfs:comment": "Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", + "rdfs:label": "DataCollectionMode", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other/multiple channel QC faliure types", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:ChannelQCFailureComment" + "@id": "bts:DDA" + }, + { + "@id": "bts:DIA" + }, + { + "@id": "bts:Other" } ], + "sms:displayName": "Data Collection Mode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ChannelQCFailureComment", + "@id": "bts:MSScanMode", "@type": "rdfs:Class", - "rdfs:comment": "Custom comment on channel QC faliure", - "rdfs:label": "ChannelQCFailureComment", + "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", + "rdfs:label": "MSScanMode", "rdfs:subClassOf": [ { - 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"sms:displayName": "Zn", + "sms:displayName": "Lot", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ga", + "@id": "bts:ExcitationWavelength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ga", + "rdfs:comment": "Center/peak of the excitation spectrum (nm)", + "rdfs:label": "ExcitationWavelength", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ga", + "sms:displayName": "Excitation Wavelength", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Ge", + "@id": "bts:EmissionWavelength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ge", + "rdfs:comment": "Center/peak of the emission spectrum (nm)", + "rdfs:label": "EmissionWavelength", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - 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"sms:displayName": "Se", + "sms:displayName": "Emission Bandwidth", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Br", + "@id": "bts:MetalIsotopeElement", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Br", + "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", + "rdfs:label": "MetalIsotopeElement", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Br", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:H" + }, + { + "@id": "bts:He" + }, + { + "@id": "bts:Li" + }, + { + "@id": "bts:Be" + }, + { + "@id": "bts:B" + }, + { + "@id": "bts:C" + }, + { + "@id": "bts:N" + }, + { + "@id": "bts:O" + }, + { + "@id": "bts:F" + }, + { + "@id": "bts:Ne" + }, + { + "@id": "bts:Na" + }, + { + "@id": "bts:Mg" + }, + { + "@id": "bts:Al" + }, + { + "@id": "bts:Si" + }, + { + "@id": "bts:P" + }, + { + "@id": "bts:S" + }, + { + "@id": "bts:Cl" + }, + { + "@id": "bts:Ar" + }, + { + "@id": "bts:K" + }, + { + "@id": "bts:Ca" + }, + { + "@id": "bts:Sc" + }, + { + "@id": "bts:Ti" + }, + { + "@id": "bts:V" + }, + { + "@id": "bts:Cr" + }, + { + "@id": "bts:Mn" + }, + { + "@id": "bts:Fe" + }, + { + "@id": "bts:Co" + }, + { + "@id": "bts:Ni" + }, + { + "@id": "bts:Cu" + }, + { + "@id": "bts:Zn" + }, + { + "@id": "bts:Ga" + }, + { + "@id": "bts:Ge" + }, + { + "@id": "bts:As" + }, + { + "@id": "bts:Se" + }, + { + "@id": "bts:Br" + }, + { + "@id": "bts:Kr" + }, + { + "@id": "bts:Rb" + }, + { + "@id": "bts:Sr" + }, + { + "@id": "bts:Y" + }, + { + "@id": "bts:Zr" + }, + { + "@id": "bts:Nb" + }, + { + "@id": "bts:Mo" + }, + { + "@id": "bts:Tc" + }, + { + "@id": "bts:Ru" + }, + { + "@id": "bts:Rh" + }, + { + "@id": "bts:Pd" + }, + { + "@id": "bts:Ag" + }, + { + "@id": "bts:Cd" + }, + { + "@id": "bts:In" + }, + { + "@id": "bts:Sn" + }, + { + "@id": "bts:Sb" + }, + { + "@id": "bts:Te" + }, + { + "@id": "bts:I" + }, + { + "@id": "bts:Xe" + }, + { + "@id": "bts:Cs" + }, + { + "@id": "bts:Ba" + }, + { + "@id": "bts:La" + }, + { + "@id": "bts:Ce" + }, + { + "@id": "bts:Pr" + }, + { + "@id": "bts:Nd" + }, + { + "@id": "bts:Pm" + }, + { + "@id": "bts:Sm" + }, + { + "@id": "bts:Eu" + }, + { + "@id": "bts:Gd" + }, + { + "@id": "bts:Tb" + }, + { + "@id": "bts:Dy" + }, + { + "@id": "bts:Ho" + }, + { + "@id": "bts:Er" + }, + { + "@id": "bts:Tm" + }, + { + "@id": "bts:Yb" + }, + { + "@id": "bts:Lu" + }, + { + "@id": "bts:Hf" + }, + { + "@id": "bts:Ta" + }, + { + "@id": "bts:W" + }, + { + "@id": "bts:Re" + }, + { + "@id": "bts:Os" + }, + { + "@id": "bts:Ir" + }, + { + "@id": "bts:Pt" + }, + { + "@id": "bts:Au" + }, + { + "@id": "bts:Hg" + }, + { + "@id": "bts:Tl" + }, + { + "@id": "bts:Pb" + }, + { + "@id": "bts:Bi" + }, + { + "@id": "bts:Po" + }, + { + "@id": "bts:At" + }, + { + "@id": "bts:Rn" + }, + { + "@id": "bts:Fr" + }, + { + "@id": "bts:Ra" + }, + { + "@id": "bts:Ac" + }, + { + "@id": "bts:Th" + }, + { + "@id": "bts:Pa" + }, + { + "@id": "bts:U" + }, + { + "@id": "bts:Np" + }, + { + "@id": "bts:Pu" + }, + { + "@id": "bts:Am" + }, + { + "@id": "bts:Bk" + }, + { + "@id": "bts:Cf" + }, + { + "@id": "bts:Es" + }, + { + "@id": "bts:Fm" + }, + { + "@id": "bts:Md" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Lr" + }, + { + "@id": "bts:Rf" + }, + { + "@id": "bts:Db" + }, + { + "@id": "bts:Sg" + }, + { + "@id": "bts:Bh" + }, + { + "@id": "bts:Hs" + }, + { + "@id": "bts:Mt" + }, + { + "@id": "bts:Ds" + }, + { + "@id": "bts:Rg" + }, + { + "@id": "bts:Cn" + }, + { + "@id": "bts:Nh" + }, + { + "@id": "bts:Fl" + }, + { + "@id": "bts:Mc" + }, + { + "@id": "bts:Lv" + }, + { + "@id": "bts:Ts" + }, + { + "@id": "bts:Og" + } + ], + "sms:displayName": "Metal Isotope Element", + "sms:required": "sms:false", + "sms:validationRules": [ + "str" + ] }, { - "@id": "bts:Kr", + "@id": "bts:MetalIsotopeMass", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Kr", + "rdfs:comment": "Element mass number", + "rdfs:label": "MetalIsotopeMass", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Kr", + "sms:displayName": "Metal Isotope Mass", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:Rb", + "@id": "bts:OligoBarcodeUpperStrand", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Rb", + "rdfs:comment": "Oligo Barcode - Upper Strand", + "rdfs:label": "OligoBarcodeUpperStrand", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rb", + "sms:displayName": "Oligo Barcode Upper Strand", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sr", + "@id": "bts:OligoBarcodeLowerStrand", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Sr", + "rdfs:comment": "Oligo Barcode - Lower Strand", + "rdfs:label": "OligoBarcodeLowerStrand", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sr", + "sms:displayName": "Oligo Barcode Lower Strand", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Y", + "@id": "bts:Dilution", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Y", + "rdfs:comment": "Dilution (eg 1:1000)", + "rdfs:label": "Dilution", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Y", + "sms:displayName": "Dilution", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zr", + "@id": "bts:Concentration", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Zr", + "rdfs:comment": "Concentration (eg 10ug/mL)", + "rdfs:label": "Concentration", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Zr", + "sms:displayName": "Concentration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nb", + "@id": "bts:No-ChannelFailedQC", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Nb", + "rdfs:comment": "Channel failed QC", + "rdfs:label": "No-ChannelFailedQC", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ChannelPassedQC" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nb", + "sms:displayName": "No - Channel Failed QC", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ChannelQCFailureType" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Mo", + "@id": "bts:ChannelQCFailureType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Mo", + "rdfs:comment": "Reason the channel failed QC", + "rdfs:label": "ChannelQCFailureType", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mo", + "schema:rangeIncludes": [ + { + "@id": "bts:Off-targetstaining" + }, + { + "@id": "bts:Auto-fluoresence" + }, + { + "@id": "bts:Stainingartefacet" + }, + { + "@id": "bts:Imagingartefact" + }, + { + "@id": "bts:Other/multiplechannelQCfaliuretypes" + } + ], + "sms:displayName": "Channel QC Failure Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tc", + "@id": "bts:Off-targetstaining", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tc", + "rdfs:label": "Off-targetstaining", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tc", + "sms:displayName": "Off-target staining", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ru", + "@id": "bts:Auto-fluoresence", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ru", + "rdfs:label": "Auto-fluoresence", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ru", + "sms:displayName": "Auto-fluoresence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rh", + "@id": "bts:Stainingartefacet", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rh", + "rdfs:label": "Stainingartefacet", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rh", + "sms:displayName": "Staining artefacet", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pd", + "@id": "bts:Imagingartefact", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pd", + "rdfs:label": "Imagingartefact", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pd", + "sms:displayName": "Imaging artefact", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ag", + "@id": "bts:Other/multiplechannelQCfaliuretypes", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Ag", + "rdfs:comment": "QC failure type not speficied", + "rdfs:label": "Other/multiplechannelQCfaliuretypes", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ag", + "sms:displayName": "Other/multiple channel QC faliure types", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ChannelQCFailureComment" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Cd", + "@id": "bts:ChannelQCFailureComment", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cd", + "rdfs:comment": "Custom comment on channel QC faliure", + "rdfs:label": "ChannelQCFailureComment", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cd", + "sms:displayName": "Channel QC Failure Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:In", + "@id": "bts:Primary", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "In", + "rdfs:label": "Primary", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AntibodyRole" + }, + { + "@id": "bts:ClassificationofTumor" + }, + { + "@id": "bts:TumorTissueType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "In", + "sms:displayName": "Primary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sn", + "@id": "bts:Secondary", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sn", + "rdfs:label": "Secondary", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AntibodyRole" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sn", + "sms:displayName": "Secondary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sb", + "@id": "bts:H", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sb", + "rdfs:label": "H", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47133,15 +49095,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sb", + "sms:displayName": "H", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Te", + "@id": "bts:He", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Te", + "rdfs:label": "He", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47150,25 +49112,16 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Te", + "sms:displayName": "He", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:I", + "@id": "bts:Li", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "I", + "rdfs:label": "Li", "rdfs:subClassOf": [ - { - "@id": "bts:ISSStage" - }, - { - "@id": "bts:MelanomaSpecimenClarkLevelValue" - }, - { - "@id": "bts:FitzpatrickSkinTone" - }, { "@id": "bts:MetalIsotopeElement" } @@ -47176,15 +49129,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "I", + "sms:displayName": "Li", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Xe", + "@id": "bts:Be", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Xe", + "rdfs:label": "Be", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47193,15 +49146,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xe", + "sms:displayName": "Be", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cs", + "@id": "bts:N", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cs", + "rdfs:label": "N", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47210,15 +49163,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cs", + "sms:displayName": "N", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ba", + "@id": "bts:O", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ba", + "rdfs:label": "O", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47227,15 +49180,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ba", + "sms:displayName": "O", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:La", + "@id": "bts:F", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "La", + "rdfs:label": "F", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47244,15 +49197,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "La", + "sms:displayName": "F", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ce", + "@id": "bts:Ne", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ce", + "rdfs:label": "Ne", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47261,15 +49214,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ce", + "sms:displayName": "Ne", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pr", + "@id": "bts:Na", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pr", + "rdfs:label": "Na", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47278,15 +49231,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pr", + "sms:displayName": "Na", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nd", + "@id": "bts:Mg", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nd", + "rdfs:label": "Mg", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47295,15 +49248,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nd", + "sms:displayName": "Mg", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pm", + "@id": "bts:Al", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pm", + "rdfs:label": "Al", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47312,15 +49265,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pm", + "sms:displayName": "Al", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sm", + "@id": "bts:Si", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sm", + "rdfs:label": "Si", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47329,15 +49282,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sm", + "sms:displayName": "Si", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Eu", + "@id": "bts:P", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Eu", + "rdfs:label": "P", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47346,15 +49299,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Eu", + "sms:displayName": "P", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Gd", + "@id": "bts:S", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Gd", + "rdfs:label": "S", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47363,15 +49316,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gd", + "sms:displayName": "S", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tb", + "@id": "bts:Cl", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tb", + "rdfs:label": "Cl", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47380,15 +49333,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tb", + "sms:displayName": "Cl", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Dy", + "@id": "bts:Ar", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Dy", + "rdfs:label": "Ar", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47397,15 +49350,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dy", + "sms:displayName": "Ar", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ho", + "@id": "bts:K", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ho", + "rdfs:label": "K", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47414,15 +49367,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ho", + "sms:displayName": "K", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Er", + "@id": "bts:Ca", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Er", + "rdfs:label": "Ca", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47431,15 +49384,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Er", + "sms:displayName": "Ca", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tm", + "@id": "bts:Sc", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tm", + "rdfs:label": "Sc", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47448,15 +49401,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tm", + "sms:displayName": "Sc", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yb", + "@id": "bts:Ti", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Yb", + "rdfs:label": "Ti", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47465,16 +49418,22 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yb", + "sms:displayName": "Ti", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lu", + "@id": "bts:V", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lu", + "rdfs:label": "V", "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaSpecimenClarkLevelValue" + }, + { + "@id": "bts:FitzpatrickSkinTone" + }, { "@id": "bts:MetalIsotopeElement" } @@ -47482,15 +49441,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lu", + "sms:displayName": "V", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hf", + "@id": "bts:Cr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hf", + "rdfs:label": "Cr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47499,22 +49458,16 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hf", + "sms:displayName": "Cr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ta", + "@id": "bts:Mn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ta", + "rdfs:label": "Mn", "rdfs:subClassOf": [ - { - "@id": "bts:AJCCClinicalT" - }, - { - "@id": "bts:AJCCPathologicT" - }, { "@id": "bts:MetalIsotopeElement" } @@ -47522,15 +49475,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ta", + "sms:displayName": "Mn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:W", + "@id": "bts:Fe", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "W", + "rdfs:label": "Fe", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47539,15 +49492,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "W", + "sms:displayName": "Fe", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Re", + "@id": "bts:Co", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Re", + "rdfs:label": "Co", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47556,15 +49509,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Re", + "sms:displayName": "Co", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Os", + "@id": "bts:Ni", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Os", + "rdfs:label": "Ni", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47573,15 +49526,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Os", + "sms:displayName": "Ni", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ir", + "@id": "bts:Cu", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ir", + "rdfs:label": "Cu", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47590,15 +49543,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ir", + "sms:displayName": "Cu", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pt", + "@id": "bts:Zn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pt", + "rdfs:label": "Zn", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47607,15 +49560,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pt", + "sms:displayName": "Zn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Au", + "@id": "bts:Ga", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Au", + "rdfs:label": "Ga", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47624,15 +49577,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Au", + "sms:displayName": "Ga", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hg", + "@id": "bts:Ge", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hg", + "rdfs:label": "Ge", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47641,15 +49594,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hg", + "sms:displayName": "Ge", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tl", + "@id": "bts:As", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tl", + "rdfs:label": "As", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47658,15 +49611,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tl", + "sms:displayName": "As", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pb", + "@id": "bts:Se", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pb", + "rdfs:label": "Se", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47675,15 +49628,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pb", + "sms:displayName": "Se", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bi", + "@id": "bts:Br", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bi", + "rdfs:label": "Br", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47692,15 +49645,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bi", + "sms:displayName": "Br", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Po", + "@id": "bts:Kr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Po", + "rdfs:label": "Kr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47709,15 +49662,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Po", + "sms:displayName": "Kr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:At", + "@id": "bts:Rb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "At", + "rdfs:label": "Rb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47726,15 +49679,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "At", + "sms:displayName": "Rb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rn", + "@id": "bts:Sr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rn", + "rdfs:label": "Sr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47743,15 +49696,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rn", + "sms:displayName": "Sr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fr", + "@id": "bts:Y", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Fr", + "rdfs:label": "Y", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47760,15 +49713,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fr", + "sms:displayName": "Y", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ra", + "@id": "bts:Zr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ra", + "rdfs:label": "Zr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47777,15 +49730,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ra", + "sms:displayName": "Zr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ac", + "@id": "bts:Nb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ac", + "rdfs:label": "Nb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47794,15 +49747,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ac", + "sms:displayName": "Nb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Th", + "@id": "bts:Mo", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Th", + "rdfs:label": "Mo", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47811,15 +49764,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Th", + "sms:displayName": "Mo", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pa", + "@id": "bts:Tc", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pa", + "rdfs:label": "Tc", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47828,15 +49781,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pa", + "sms:displayName": "Tc", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:U", + "@id": "bts:Ru", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "U", + "rdfs:label": "Ru", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47845,15 +49798,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "U", + "sms:displayName": "Ru", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Np", + "@id": "bts:Rh", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Np", + "rdfs:label": "Rh", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47862,15 +49815,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Np", + "sms:displayName": "Rh", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pu", + "@id": "bts:Pd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pu", + "rdfs:label": "Pd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47879,15 +49832,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pu", + "sms:displayName": "Pd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bk", + "@id": "bts:Ag", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bk", + "rdfs:label": "Ag", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47896,15 +49849,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bk", + "sms:displayName": "Ag", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cf", + "@id": "bts:Cd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cf", + "rdfs:label": "Cd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47913,15 +49866,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cf", + "sms:displayName": "Cd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Es", + "@id": "bts:In", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Es", + "rdfs:label": "In", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47930,15 +49883,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Es", + "sms:displayName": "In", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fm", + "@id": "bts:Sn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Fm", + "rdfs:label": "Sn", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47947,15 +49900,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fm", + "sms:displayName": "Sn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lr", + "@id": "bts:Sb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lr", + "rdfs:label": "Sb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47964,15 +49917,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lr", + "sms:displayName": "Sb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rf", + "@id": "bts:Te", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rf", + "rdfs:label": "Te", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -47981,16 +49934,25 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rf", + "sms:displayName": "Te", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Db", + "@id": "bts:I", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Db", + "rdfs:label": "I", "rdfs:subClassOf": [ + { + "@id": "bts:ISSStage" + }, + { + "@id": "bts:MelanomaSpecimenClarkLevelValue" + }, + { + "@id": "bts:FitzpatrickSkinTone" + }, { "@id": "bts:MetalIsotopeElement" } @@ -47998,15 +49960,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Db", + "sms:displayName": "I", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sg", + "@id": "bts:Xe", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sg", + "rdfs:label": "Xe", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48015,15 +49977,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sg", + "sms:displayName": "Xe", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bh", + "@id": "bts:Cs", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bh", + "rdfs:label": "Cs", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48032,15 +49994,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bh", + "sms:displayName": "Cs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hs", + "@id": "bts:Ba", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hs", + "rdfs:label": "Ba", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48049,15 +50011,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hs", + "sms:displayName": "Ba", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mt", + "@id": "bts:La", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mt", + "rdfs:label": "La", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48066,15 +50028,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mt", + "sms:displayName": "La", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ds", + "@id": "bts:Ce", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ds", + "rdfs:label": "Ce", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48083,15 +50045,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ds", + "sms:displayName": "Ce", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rg", + "@id": "bts:Pr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rg", + "rdfs:label": "Pr", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48100,15 +50062,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rg", + "sms:displayName": "Pr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cn", + "@id": "bts:Nd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cn", + "rdfs:label": "Nd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48117,15 +50079,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cn", + "sms:displayName": "Nd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nh", + "@id": "bts:Pm", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nh", + "rdfs:label": "Pm", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48134,15 +50096,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nh", + "sms:displayName": "Pm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Fl", + "@id": "bts:Sm", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Fl", + "rdfs:label": "Sm", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48151,15 +50113,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fl", + "sms:displayName": "Sm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mc", + "@id": "bts:Eu", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mc", + "rdfs:label": "Eu", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48168,15 +50130,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mc", + "sms:displayName": "Eu", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lv", + "@id": "bts:Gd", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lv", + "rdfs:label": "Gd", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48185,15 +50147,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lv", + "sms:displayName": "Gd", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ts", + "@id": "bts:Tb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ts", + "rdfs:label": "Tb", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48202,15 +50164,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ts", + "sms:displayName": "Tb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Og", + "@id": "bts:Dy", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Og", + "rdfs:label": "Dy", "rdfs:subClassOf": [ { "@id": "bts:MetalIsotopeElement" @@ -48219,4070 +50181,2951 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Og", + "sms:displayName": "Dy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:H&E", + "@id": "bts:Ho", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "H&E", + "rdfs:label": "Ho", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "H&E", + "sms:displayName": "Ho", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CyCIF", + "@id": "bts:Er", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CyCIF", + "rdfs:label": "Er", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CyCIF", + "sms:displayName": "Er", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:T-CyCIF", + "@id": "bts:Tm", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "T-CyCIF", + "rdfs:label": "Tm", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "t-CyCIF", + "sms:displayName": "Tm", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IHC", + "@id": "bts:Yb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "IHC", + "rdfs:label": "Yb", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IHC", + "sms:displayName": "Yb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MIHC", + "@id": "bts:Lu", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MIHC", + "rdfs:label": "Lu", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mIHC", + "sms:displayName": "Lu", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MxIF", + "@id": "bts:Hf", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MxIF", + "rdfs:label": "Hf", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MxIF", + "sms:displayName": "Hf", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SABER", + "@id": "bts:Ta", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "SABER", + "rdfs:label": "Ta", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:AJCCClinicalT" + }, + { + "@id": "bts:AJCCPathologicT" + }, + { + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SABER", + "sms:displayName": "Ta", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IMC", + "@id": "bts:W", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "IMC", + "rdfs:label": "W", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IMC", + "sms:displayName": "W", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CODEX", + "@id": "bts:Re", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CODEX", + "rdfs:label": "Re", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CODEX", + "sms:displayName": "Re", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMX-DSP", + "@id": "bts:Os", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "GeoMX-DSP", + "rdfs:label": "Os", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMX-DSP", + "sms:displayName": "Os", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MIBI", + "@id": "bts:Ir", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MIBI", + "rdfs:label": "Ir", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MIBI", + "sms:displayName": "Ir", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISH", + "@id": "bts:Pt", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MERFISH", + "rdfs:label": "Pt", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH", + "sms:displayName": "Pt", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExSeq", + "@id": "bts:Au", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ExSeq", + "rdfs:label": "Au", "rdfs:subClassOf": [ { - "@id": "bts:DataType" - }, - { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq", + "sms:displayName": "Au", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RareCyteOrion", + "@id": "bts:Hg", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "RareCyteOrion", + "rdfs:label": "Hg", "rdfs:subClassOf": [ { - "@id": "bts:ImagingAssayType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RareCyte Orion", + "sms:displayName": "Hg", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Imaging", + "@id": "bts:Tl", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Imaging", + "rdfs:label": "Tl", "rdfs:subClassOf": [ { - "@id": "bts:DataType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging", + "sms:displayName": "Tl", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cm", + "@id": "bts:Pb", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cm", + "rdfs:label": "Pb", "rdfs:subClassOf": [ { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZUnit" - }, - { - "@id": "bts:DimensionsUnit" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cm", + "sms:displayName": "Pb", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mm", + "@id": "bts:Bi", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mm", + "rdfs:label": "Bi", "rdfs:subClassOf": [ { - "@id": "bts:DimensionsUnit" - }, - { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mm", + "sms:displayName": "Bi", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Μm", + "@id": "bts:Po", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Μm", + "rdfs:label": "Po", "rdfs:subClassOf": [ { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "µm", + "sms:displayName": "Po", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nm", + "@id": "bts:At", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nm", + "rdfs:label": "At", "rdfs:subClassOf": [ { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nm", + "sms:displayName": "At", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Å", + "@id": "bts:Rn", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Å", + "rdfs:label": "Rn", "rdfs:subClassOf": [ { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Å", + "sms:displayName": "Rn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Air", + "@id": "bts:Fr", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Air", + "rdfs:label": "Fr", "rdfs:subClassOf": [ { - "@id": "bts:Immersion" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Air", + "sms:displayName": "Fr", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Oil", + "@id": "bts:Ra", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Oil", + "rdfs:label": "Ra", "rdfs:subClassOf": [ { - "@id": "bts:Immersion" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oil", + "sms:displayName": "Ra", "sms:required": "sms:false", "sms:validationRules": [] }, { - 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"@id": "bts:HereditaryCancerPredispositionSyndrome" - }, + "@id": "bts:ScRNA-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Empty Well Barcode", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:WellIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays", + "rdfs:label": "WellIndex", + "rdfs:subClassOf": [ { - "@id": "bts:CancerAssociatedGeneMutations" - }, + "@id": "bts:ScRNA-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MutationalSignatures" + "@id": "bts:Yes" }, { - "@id": "bts:LungCancerHarboringGenomicAberrations" - }, + "@id": "bts:No" + } + ], + "sms:displayName": "Well Index", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:3Prime", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "3Prime", + "rdfs:subClassOf": [ { - "@id": "bts:LaboratoryTest" - }, + "@id": "bts:EndBias" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "3 Prime", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:5Prime", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "5Prime", + "rdfs:subClassOf": [ { - "@id": "bts:RelationshipPrimaryDiagnosis" - }, + "@id": "bts:EndBias" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "5 Prime", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FullLengthTranscript", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FullLengthTranscript", + "rdfs:subClassOf": [ { - "@id": "bts:TreatmentType" - }, + "@id": "bts:EndBias" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Full Length Transcript", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Oligo-dT", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Oligo-dT", + "rdfs:subClassOf": [ { - "@id": "bts:LungTopography" - }, + "@id": "bts:ReverseTranscriptionPrimer" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Oligo-dT", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Poly-dT", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Poly-dT", + "rdfs:subClassOf": [ { - "@id": "bts:RiskFactor" - }, + "@id": "bts:ReverseTranscriptionPrimer" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Poly-dT", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Featurebarcoding", + "@type": "rdfs:Class", + "rdfs:comment": "A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc]", + "rdfs:label": "Featurebarcoding", + "rdfs:subClassOf": [ { - "@id": "bts:RelationshipType" + "@id": "bts:ScRNA-seqLevel1" }, { - "@id": "bts:Comorbidity" - }, + "@id": "bts:ReverseTranscriptionPrimer" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Feature barcoding", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:PriorSitesofRadiation" - }, + "@id": "bts:FeatureReferenceId" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:FeatureReferenceId", + "@type": "rdfs:Class", + "rdfs:comment": "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", + "rdfs:label": "FeatureReferenceId", + "rdfs:subClassOf": [ { - "@id": "bts:TopographyCode" - }, + "@id": "bts:ScRNA-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Feature Reference Id", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ERCC", + "@type": "rdfs:Class", + "rdfs:comment": "The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization", + "rdfs:label": "ERCC", + "rdfs:subClassOf": [ { - "@id": "bts:ProgressionorRecurrenceAnatomicSite" - }, + "@id": "bts:SpikeIn" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ERCC", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:TreatmentAnatomicSite" - }, + "@id": "bts:SpikeInConcentration" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:OtherSpikeIn", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "OtherSpikeIn", + "rdfs:subClassOf": [ { - "@id": "bts:SiteofResectionorBiopsy" - }, + "@id": "bts:SpikeIn" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Other Spike In", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NoSpikeIn", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NoSpikeIn", + "rdfs:subClassOf": [ { - "@id": "bts:TissueorOrganofOrigin" - }, + "@id": "bts:SpikeIn" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "No Spike In", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PhiX", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "PhiX", + "rdfs:subClassOf": [ { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:SpikeIn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Not Reported", + "sms:displayName": "PhiX", "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:SpikeInConcentration", + "@type": "rdfs:Class", + "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", + "rdfs:label": "SpikeInConcentration", + "rdfs:subClassOf": [ + { + "@id": "bts:ERCC" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spike In Concentration", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:NIB", "@type": "rdfs:Class", @@ -53337,23 +54180,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:RRNADepletion", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RRNADepletion", - "rdfs:subClassOf": [ - { - "@id": "bts:LibrarySelectionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "rRNA Depletion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:MiRNASizeFractionation", "@type": "rdfs:Class", @@ -141596,23 +142422,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Publication", - "@type": "rdfs:Class", - "rdfs:comment": "An empty parent attribute for publications", - "rdfs:label": "Publication", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Publication", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:PublicationManifest", "@type": "rdfs:Class", @@ -148972,312 +149781,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xVisiumSpatialTranscriptomics", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkMethylation-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkMethylation-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk Methylation-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkRNA-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkRNA-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk RNA-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkWES", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkWES", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk WES", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ElectronMicroscopy", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ElectronMicroscopy", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Electron Microscopy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HI-C-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HI-C-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HI-C-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RPPA", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RPPA", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RPPA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MassSpectrometry", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MassSpectrometry", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mass Spectrometry", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomics", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSImaging", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SRRSImaging", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Imaging", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Slide-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATAC-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScATAC-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATAC-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScDNA-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScDNA-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scDNA-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScRNA-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ScRNA-seq", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scRNA-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AccessoryManifest", - "@type": "rdfs:Class", - "rdfs:comment": "Accessory specific attributes", - "rdfs:label": "AccessoryManifest", - "rdfs:subClassOf": [ - { - "@id": "bts:Accessory" - }, - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Accessory Manifest", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:DatasetName" - }, - { - "@id": "bts:AccessorySynapseID" - }, - { - "@id": "bts:AccessoryDescription" - }, - { - "@id": "bts:DataType" - }, - { - "@id": "bts:HTANCenterID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:Accessory-associatedHTANParentDataFileID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:OtherDataTypeSpecified", - "@type": "rdfs:Class", - "rdfs:comment": "Other types of data associated with the content.", - "rdfs:label": "OtherDataTypeSpecified", - "rdfs:subClassOf": [ - { - "@id": "bts:Publication" - }, - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Data Type Specified", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] - }, { "@id": "bts:Accessory", "@type": "rdfs:Class", From 4c2ddd75eeb27d3589b56153115351f12dea3f69 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Mon, 3 Jun 2024 20:00:03 +0100 Subject: [PATCH 11/14] Delete JSON to unblock action. Action will regenerate. --- HTAN.model.jsonld | 151884 ------------------------------------------- 1 file changed, 151884 deletions(-) delete mode 100644 HTAN.model.jsonld diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld deleted file mode 100644 index af28a7e0..00000000 --- a/HTAN.model.jsonld +++ /dev/null @@ -1,151884 +0,0 @@ -{ - "@context": { - "bts": "http://schema.biothings.io/", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "schema": "http://schema.org/", - "xsd": "http://www.w3.org/2001/XMLSchema#" - }, - "@graph": [ - { - "@id": "bts:Assay", - "@type": "rdfs:Class", - "rdfs:comment": "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]", - "rdfs:label": "Assay", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Assay", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Device", - "@type": "rdfs:Class", - "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", - "rdfs:label": "Device", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Device", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Sequencing", - "@type": "rdfs:Class", - "rdfs:comment": "Module for next generation sequencing assays", - "rdfs:label": "Sequencing", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Component", - "@type": "rdfs:Class", - "rdfs:comment": "Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.", - "rdfs:label": "Component", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Component", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Patient", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN patient", - "rdfs:label": "Patient", - "rdfs:subClassOf": [ - { - "@id": "bts:IndividualOrganism" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Patient", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Demographics" - }, - { - "@id": "bts:FamilyHistory" - }, - { - "@id": "bts:Exposure" - }, - { - "@id": "bts:FollowUp" - }, - { - "@id": "bts:Diagnosis" - }, - { - "@id": "bts:Therapy" - }, - { - "@id": "bts:MolecularTest" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParticipantID", - 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Parent could be another biospecimen or a research participant.", - "rdfs:label": "HTANParentID", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentDataFileID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", - "rdfs:label": "HTANParentDataFileID", - "rdfs:subClassOf": [ - { - "@id": "bts:File" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Data File ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Tier 2 Cancer Data", - "rdfs:label": "ClinicalDataTier2", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:SentinelLymphNodeCount" - }, - { - "@id": "bts:SentinelNodePositiveAssessmentCount" - }, - { - "@id": "bts:TumorExtranodalExtensionIndicator" - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:OtherBiopsyResectionSite" - }, - { - "@id": "bts:ExtentofTumorResection" - }, - { - "@id": "bts:PriorSitesofRadiation" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:ConcomitantMedicationReceivedType" - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator" - }, - { - "@id": "bts:COVID19OccurrenceIndicator" - }, - { - "@id": "bts:COVID19CurrentStatus" - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator" - }, - { - "@id": "bts:COVID19AntibodyTesting" - }, - { - "@id": "bts:COVID19ComplicationsSeverity" - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup" - }, - { - "@id": "bts:Ecigvapeuse" - }, - { - "@id": "bts:Ecigvape30dayusenum" - }, - { - "@id": "bts:Ecigvapetimesperday" - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears" - }, - { - "@id": "bts:Chewingtobaccodailyusecount" - }, - { - "@id": "bts:Secondhandsmokeexposureyears" - }, - { - "@id": "bts:KnownGeneticPredispositionMutation" - }, - { - "@id": "bts:HereditaryCancerPredispositionSyndrome" - }, - { - "@id": "bts:CancerAssociatedGeneMutations" - }, - { - "@id": "bts:MutationalSignatures" - }, - { - "@id": "bts:MismatchRepairSystemStatus" - }, - { - "@id": "bts:LabTestsforMMRStatus" - }, - { - "@id": "bts:ModeofCancerDetection" - }, - { - "@id": "bts:EducationLevel" - }, - { - "@id": "bts:CountryofBirth" - }, - { - "@id": "bts:MedicallyUnderservedArea" - }, - { - "@id": "bts:RuralvsUrban" - }, - { - "@id": "bts:CancerIncidence" - }, - { - "@id": "bts:CancerIncidenceLocation" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TimepointLabel", - "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StartDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", - "rdfs:label": "StartDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Start Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:StopDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", - "rdfs:label": "StopDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Stop Days from Index", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:SentinelLymphNodeCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric count of sentinel lymph nodes.", - "rdfs:label": "SentinelLymphNodeCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sentinel Lymph Node Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SentinelNodePositiveAssessmentCount", - "@type": "rdfs:Class", - "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", - "rdfs:label": "SentinelNodePositiveAssessmentCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sentinel Node Positive Assessment Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorExtranodalExtensionIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", - "rdfs:label": "TumorExtranodalExtensionIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:NO" - }, - { - "@id": "bts:YES" - }, - { - "@id": "bts:Nosourcedocumentation" - }, - { - "@id": "bts:Notapplicable" - }, - { - "@id": "bts:Notsampledordissected" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Present-extensive" - }, - { - "@id": "bts:Present-minimal" - }, - { - "@id": "bts:UNKNOWN" - }, - { - "@id": "bts:Unspecified" - } - ], - "sms:displayName": "Tumor Extranodal Extension Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", - "rdfs:label": "SatelliteMetastasisPresentIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Satellite Metastasis Present Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherBiopsyResectionSite", - "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", - "rdfs:label": "OtherBiopsyResectionSite", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Biopsy Resection Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ExtentofTumorResection", - "@type": "rdfs:Class", - "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", - "rdfs:label": "ExtentofTumorResection", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:GrossTotalResection" - }, - { - "@id": "bts:OpenBiopsy" - }, - { - "@id": "bts:SubtotalResection" - }, - { - "@id": "bts:ExtensiveSubtotal" - }, - { - "@id": "bts:Minor" - }, - { - "@id": "bts:Optimaldebulking" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Partialdebulking" - }, - { - "@id": "bts:Segmental" - }, - { - "@id": "bts:Suboptimal" - }, - { - "@id": "bts:Suboptimaldebulking" - }, - { - "@id": "bts:NTR" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Extent of Tumor Resection", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PriorSitesofRadiation", - "@type": "rdfs:Class", - "rdfs:comment": "The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.", - "rdfs:label": "PriorSitesofRadiation", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Abdomentotal" - }, - { - "@id": "bts:AbdominalWall" - }, - { - "@id": "bts:Acetabulum" - }, - { - "@id": "bts:Adenoid" - }, - { - "@id": "bts:Adipose" - }, - { - "@id": "bts:Adrenal" - }, - { - "@id": "bts:AlveolarRidge" - }, - { - "@id": "bts:AmnioticFluid" - }, - { - "@id": "bts:AmpullaofVater" - }, - { - "@id": "bts:AnalSphincter" - }, - { - "@id": "bts:Ankle" - }, - { - "@id": "bts:Anorectum" - }, - { - "@id": "bts:AntecubitalFossa" - }, - { - "@id": "bts:Antrum" - }, - { - "@id": "bts:Anus" - }, - { - "@id": "bts:Aorta" - }, - { - "@id": "bts:AorticBody" - }, - { - "@id": "bts:Appendix" - }, - { - "@id": "bts:AqueousFluid" - }, - { - "@id": "bts:Arm" - }, - { - "@id": "bts:Artery" - }, - { - "@id": "bts:AscendingColon" - }, - { - "@id": "bts:AscendingColonHepaticFlexure" - }, - { - "@id": "bts:Ascites" - }, - { - "@id": "bts:AuditoryCanal" - }, - { - "@id": "bts:AutonomicNervousSystem" - }, - { - "@id": "bts:Axilla" - }, - { - "@id": "bts:Back" - }, - { - "@id": "bts:BileDuct" - }, - { - "@id": "bts:Bladder" - }, - { - "@id": "bts:Blood" - }, - { - "@id": "bts:BloodVessel" - }, - { - "@id": "bts:Bodytotal" - }, - { - "@id": "bts:Bone" - }, - { - "@id": "bts:BoneMarrow" - }, - { - "@id": "bts:Bonenon-spine" - }, - { - "@id": "bts:Bowel" - }, - { - "@id": "bts:Brain" - }, - { - "@id": "bts:BrainStem" - }, - { - "@id": "bts:Breast" - }, - { - "@id": "bts:BroadLigament" - }, - { - "@id": "bts:Bronchiole" - }, - { - "@id": "bts:Bronchus" - }, - { - "@id": "bts:Brow" - }, - { - "@id": "bts:BuccalCavity" - }, - { - "@id": "bts:BuccalMucosa" - }, - { - "@id": "bts:Buttock" - }, - { - "@id": "bts:Calf" - }, - { - "@id": "bts:Capillary" - }, - { - "@id": "bts:Cardia" - }, - { - "@id": "bts:Carina" - }, - { - "@id": "bts:CarotidArtery" - }, - { - "@id": "bts:CarotidBody" - }, - { - "@id": "bts:Cartilage" - }, - { - "@id": "bts:Cecum" - }, - { - "@id": "bts:Cell-Line" - }, - { - "@id": "bts:CentralNervousSystem" - }, - { - "@id": "bts:Cerebellum" - }, - { - "@id": "bts:CerebralCortex" - }, - { - "@id": "bts:CerebrospinalFluid" - }, - { - "@id": "bts:Cerebrum" - }, - { - "@id": "bts:CervicalSpine" - }, - { - "@id": "bts:Cervix" - }, - { - "@id": "bts:Chest" - }, - { - "@id": "bts:ChestWall" - }, - { - "@id": "bts:Chin" - }, - { - "@id": "bts:Clavicle" - }, - { - "@id": "bts:Clitoris" - }, - { - "@id": "bts:Colon" - }, - { - "@id": "bts:ColonMucosaOnly" - }, - { - "@id": "bts:CommonDuct" - }, - { - "@id": "bts:Conjunctiva" - }, - { - "@id": "bts:ConnectiveTissue" - }, - { - "@id": "bts:Dermal" - }, - { - "@id": "bts:DescendingColon" - }, - { - "@id": "bts:Diaphragm" - }, - { - "@id": "bts:DistantSite" - }, - { - "@id": "bts:Duodenum" - }, - { - "@id": "bts:Ear" - }, - { - "@id": "bts:EarCanal" - }, - { - "@id": "bts:EarPinna(External)" - }, - { - "@id": "bts:Elbow" - }, - { - "@id": "bts:EndocrineGland" - }, - { - "@id": "bts:Epididymis" - }, - { - "@id": "bts:EpiduralSpace" - }, - { - "@id": "bts:Epitrochlear" - }, - { - "@id": "bts:EsophagogastricJunction" - }, - { - "@id": "bts:Esophagus" - }, - { - "@id": "bts:EsophagusMucosaOnly" - }, - { - "@id": "bts:Eye" - }, - { - "@id": "bts:FallopianTube" - }, - { - "@id": "bts:FemoralArtery" - }, - { - "@id": "bts:FemoralVein" - }, - { - "@id": "bts:Femur" - }, - { - "@id": "bts:Fibroblasts" - }, - { - "@id": "bts:Fibula" - }, - { - "@id": "bts:Finger" - }, - { - "@id": "bts:FloorofMouth" - }, - { - "@id": "bts:Fluid" - }, - { - "@id": "bts:Foot" - }, - { - "@id": "bts:Forearm" - }, - { - "@id": "bts:Forehead" - }, - { - "@id": "bts:Foreskin" - }, - { - "@id": "bts:FrontalCortex" - }, - { - "@id": "bts:FrontalLobe" - }, - { - "@id": "bts:FundusofStomach" - }, - { - "@id": "bts:Gallbladder" - }, - { - "@id": "bts:Ganglia" - }, - { - "@id": "bts:GastroesophagealJunction" - }, - { - "@id": "bts:GastrointestinalTract" - }, - { - "@id": "bts:GastrointestinalIntestine" - }, - { - "@id": "bts:GenitourinaryNOS" - }, - { - "@id": "bts:Groin" - }, - { - "@id": "bts:Gum" - }, - { - "@id": "bts:Hand" - }, - { - "@id": "bts:HardPalate" - }, - { - "@id": "bts:HeadFaceOrNeckNos" - }, - { - "@id": "bts:HeadandNeck" - }, - { - "@id": "bts:Heart" - }, - { - "@id": "bts:Hepatic" - }, - { - "@id": "bts:HepaticDuct" - }, - { - "@id": "bts:HepaticVein" - }, - { - "@id": "bts:Hilar" - }, - { - "@id": "bts:Hip" - }, - { - "@id": "bts:Hippocampus" - }, - { - "@id": "bts:Humerus" - }, - { - "@id": "bts:Hypopharynx" - }, - { - "@id": "bts:IleocecalValve" - }, - { - "@id": "bts:Ileum" - }, - { - "@id": "bts:Ilium" - }, - { - "@id": "bts:IndexFinger" - }, - { - "@id": "bts:Ischium" - }, - { - "@id": "bts:IsletCells" - }, - { - "@id": "bts:Jaw" - }, - { - "@id": "bts:Jejunum" - }, - { - "@id": "bts:Joint" - }, - { - "@id": "bts:Kidney" - }, - { - "@id": "bts:Knee" - }, - { - "@id": "bts:LacrimalGland" - }, - { - "@id": "bts:LargeBowel" - }, - { - "@id": "bts:Laryngopharynx" - }, - { - "@id": "bts:Larynx" - }, - { - "@id": "bts:Leg" - }, - { - "@id": "bts:Leptomeninges" - }, - { - "@id": "bts:Ligament" - }, - { - "@id": "bts:Lip" - }, - { - "@id": "bts:Liver" - }, - { - "@id": "bts:LumbarSpine" - }, - { - "@id": "bts:Lung" - }, - { - "@id": "bts:LymphNode" - }, - { - "@id": "bts:LymphNode(s)Axilla" - }, - { - "@id": "bts:LymphNode(s)Cervical" - }, - { - "@id": "bts:LymphNode(s)Distant" - }, - { - "@id": "bts:LymphNode(s)Epitrochlear" - }, - { - "@id": "bts:LymphNode(s)Femoral" - }, - { - "@id": "bts:LymphNode(s)Hilar" - }, - { - "@id": "bts:LymphNode(s)Iliac-Common" - }, - { - "@id": "bts:LymphNode(s)Iliac-External" - }, - { - "@id": "bts:LymphNode(s)Inguinal" - }, - { - "@id": "bts:LymphNode(s)InternalMammary" - }, - { - "@id": "bts:LymphNode(s)Mammary" - }, - { - "@id": "bts:LymphNode(s)Mediastinal" - }, - { - "@id": "bts:LymphNode(s)Mesenteric" - }, - { - "@id": "bts:LymphNode(s)Occipital" - }, - { - "@id": "bts:LymphNode(s)Paraaortic" - }, - { - "@id": "bts:LymphNode(s)Parotid" - }, - { - "@id": "bts:LymphNode(s)Pelvic" - }, - { - "@id": "bts:LymphNode(s)Popliteal" - }, - { - "@id": "bts:LymphNode(s)Regional" - }, - { - "@id": "bts:LymphNode(s)Retroperitoneal" - }, - { - "@id": "bts:LymphNode(s)Scalene" - }, - { - "@id": "bts:LymphNode(s)Splenic" - }, - { - "@id": "bts:LymphNode(s)Subclavicular" - }, - { - "@id": "bts:LymphNode(s)Submandibular" - }, - { - "@id": "bts:LymphNode(s)Supraclavicular" - }, - { - "@id": "bts:Mandible" - }, - { - "@id": "bts:Mantle" - }, - { - "@id": "bts:Maxilla" - }, - { - "@id": "bts:MediastinalSoftTissue" - }, - { - "@id": "bts:Mediastinum" - }, - { - "@id": "bts:Mesentery" - }, - { - "@id": "bts:Mesothelium" - }, - { - "@id": "bts:MiddleFinger" - }, - { - "@id": "bts:Mitochondria" - }, - { - "@id": "bts:Muscle" - }, - { - "@id": "bts:Nails" - }, - { - "@id": "bts:NasalCavity" - }, - { - "@id": "bts:NasalSoftTissue" - }, - { - "@id": "bts:Nasopharynx" - }, - { - "@id": "bts:Neck" - }, - { - "@id": "bts:Nerve" - }, - { - "@id": "bts:Nerve(s)Cranial" - }, - { - "@id": "bts:OccipitalCortex" - }, - { - "@id": "bts:OcularOrbits" - }, - { - "@id": "bts:Omentum" - }, - { - "@id": "bts:OralCavity" - }, - { - "@id": "bts:OralCavityMucosaOnly" - }, - { - "@id": "bts:Oropharynx" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Ovary" - }, - { - "@id": "bts:Palate" - }, - { - "@id": "bts:Pancreas" - }, - { - "@id": "bts:Parametrium" - }, - { - "@id": "bts:ParaspinalGanglion" - }, - { - "@id": "bts:Parathyroid" - }, - { - "@id": "bts:ParotidGland" - }, - { - "@id": "bts:Patella" - }, - { - "@id": "bts:Pelvis" - }, - { - "@id": "bts:Penis" - }, - { - "@id": "bts:Pericardium" - }, - { - "@id": "bts:PeriorbitalSoftTissue" - }, - { - "@id": "bts:PeritonealCavity" - }, - { - "@id": "bts:Peritoneum" - }, - { - "@id": "bts:Pharynx" - }, - { - "@id": "bts:Pineal" - }, - { - "@id": "bts:PinealGland" - }, - { - "@id": "bts:PituitaryGland" - }, - { - "@id": "bts:Placenta" - }, - { - "@id": "bts:Pleura" - }, - { - "@id": "bts:PoplitealFossa" - }, - { - "@id": "bts:Pouch" - }, - { - "@id": "bts:PrimaryTumorField" - }, - { - "@id": "bts:Primarytumorsite" - }, - { - "@id": "bts:Prostate" - }, - { - "@id": "bts:ProstateBed" - }, - { - "@id": "bts:ProstateSeminalVesiclesandLymphNodes" - }, - { - "@id": "bts:Pylorus" - }, - { - "@id": "bts:RectosigmoidJunction" - }, - { - "@id": "bts:Rectum" - }, - { - "@id": "bts:RegionalSite" - }, - { - "@id": "bts:Retina" - }, - { - "@id": "bts:Retro-OrbitalRegion" - }, - { - "@id": "bts:Retroperitoneum" - }, - { - "@id": "bts:Rib" - }, - { - "@id": "bts:RingFinger" - }, - { - "@id": "bts:RoundLigament" - }, - { - "@id": "bts:Sacrum" - }, - { - "@id": "bts:SalivaryGland" - }, - { - "@id": "bts:Scalp" - }, - { - "@id": "bts:Scapula" - }, - { - "@id": "bts:SciaticNerve" - }, - { - "@id": "bts:Scrotum" - }, - { - "@id": "bts:SeminalVesicle" - }, - { - "@id": "bts:Shoulder" - }, - { - "@id": "bts:SigmoidColon" - }, - { - "@id": "bts:Sinus" - }, - { - "@id": "bts:Sinus(es)Maxillary" - }, - { - "@id": "bts:SkeletalMuscle" - }, - { - "@id": "bts:Skin" - }, - { - "@id": "bts:Skinlowerextremitylocal" - }, - { - "@id": "bts:Skintotal" - }, - { - "@id": "bts:Skintrunklocal" - }, - { - "@id": "bts:Skinupperextremitylocal" - }, - { - "@id": "bts:Skull" - }, - { - "@id": "bts:SmallBowel" - }, - { - "@id": "bts:SmallBowelMucosaOnly" - }, - { - "@id": "bts:SmallFinger" - }, - { - "@id": "bts:SoftTissue" - }, - { - "@id": "bts:SpinalColumn" - }, - { - "@id": "bts:SpinalCord" - }, - { - "@id": "bts:Spine" - }, - { - "@id": "bts:Spleen" - }, - { - "@id": "bts:SplenicFlexure" - }, - { - "@id": "bts:Sternum" - }, - { - "@id": "bts:Stomach" - }, - { - "@id": "bts:StomachMucosaOnly" - }, - { - "@id": "bts:SubcutaneousTissue" - }, - { - "@id": "bts:Synovium" - }, - { - "@id": "bts:TemporalCortex" - }, - { - "@id": "bts:Tendon" - }, - { - "@id": "bts:Testis" - }, - { - "@id": "bts:Thigh" - }, - { - "@id": "bts:ThoracicSpine" - }, - { - "@id": "bts:Thorax" - }, - { - "@id": "bts:Throat" - }, - { - "@id": "bts:Thumb" - }, - { - "@id": "bts:Thymus" - }, - { - "@id": "bts:Thyroid" - }, - { - "@id": "bts:Tibia" - }, - { - "@id": "bts:Tongue" - }, - { - "@id": "bts:Tonsil" - }, - { - "@id": "bts:Tonsil(Pharyngeal)" - }, - { - "@id": "bts:Trachea/MajorBronchi" - }, - { - "@id": "bts:TransverseColon" - }, - { - "@id": "bts:Trunk" - }, - { - "@id": "bts:UmbilicalCord" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Ureter" - }, - { - "@id": "bts:Urethra" - }, - { - "@id": "bts:UrinaryTract" - }, - { - "@id": "bts:Uterus" - }, - { - "@id": "bts:Uvula" - }, - { - "@id": "bts:Vagina" - }, - { - "@id": "bts:VasDeferens" - }, - { - "@id": "bts:Vein" - }, - { - "@id": "bts:Venous" - }, - { - "@id": "bts:Vertebra" - }, - { - "@id": "bts:Vulva" - }, - { - "@id": "bts:WhiteBloodCells" - }, - { - "@id": "bts:Wrist" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Prior Sites of Radiation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Immunosuppression", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not immunosuppressive therapy was administered.", - "rdfs:label": "Immunosuppression", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "Immunosuppression", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ConcomitantMedicationReceivedType", - "@type": "rdfs:Class", - "rdfs:comment": "An enumerated list of the type of concomitant medication received by the patient.", - "rdfs:label": "ConcomitantMedicationReceivedType", - "rdfs:subClassOf": [ - { - "@id": "bts:Therapy" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Anticoagulantagents" - }, - { - "@id": "bts:Anticonvulsant" - }, - { - "@id": "bts:Antifungal" - }, - { - "@id": "bts:Antiplateletagents" - }, - { - "@id": "bts:Antidepressants-ModerateCYP2D6inhibitors" - }, - { - "@id": "bts:Antidepressants-StrongCYP2D6inhibitors" - }, - { - "@id": "bts:Antidepressants-weakCYP2D2inhibitorsornon-inhibitors" - }, - { - "@id": "bts:Anxiolyticsorsedatives" - }, - { - "@id": "bts:Aspirin" - }, - { - "@id": "bts:Bisphosphonatesfortreatment/preventionofboneloss" - }, - { - "@id": "bts:Corticosteroid" - }, - { - "@id": "bts:COX-2inhibitor" - }, - { - "@id": "bts:Decadron" - }, - { - "@id": "bts:Diabetes-Insulin" - }, - { - "@id": "bts:Diabetes-Metformincontainingagents" - }, - { - "@id": "bts:Growthfactor" - }, - { - "@id": "bts:Intravaginalestrogenpreparations" - }, - { - "@id": "bts:Lipid-loweringdrugs" - }, - { - "@id": "bts:Non-prescriptionsupplementsformemory" - }, - { - "@id": "bts:Non-prescriptionsupplementsforreliefofhotflashes" - }, - { - "@id": "bts:Non-steroidalanti-inflammatoryagents" - }, - { - "@id": "bts:Opioids" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Prescriptionmedicationsformemory" - }, - { - "@id": "bts:Prescriptionmedicationsforreliefofhotflashes" - }, - { - "@id": "bts:Prophylacticantiplatelettherapy" - }, - { - "@id": "bts:Tricyclicantidepressants" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Concomitant Medication Received Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", - "rdfs:label": "FamilyMemberVitalStatusIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:VitalStatusAlive" - }, - { - "@id": "bts:VitalStatusDead" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Family Member Vital Status Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19OccurrenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", - "rdfs:label": "COVID19OccurrenceIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Occurrence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CurrentStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", - "rdfs:label": "COVID19CurrentStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Patientcurrentlyhassymptoms" - }, - { - "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" - }, - { - "@id": "bts:PatientneverhadanysymptomsofCOVID-19" - }, - { - "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" - }, - { - "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" - }, - { - "@id": "bts:Statusunknownduetootherreasons" - } - ], - "sms:displayName": "COVID19 Current Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", - "rdfs:label": "COVID19PositiveLabTestIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Positive Lab Test Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19AntibodyTesting", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", - "rdfs:label": "COVID19AntibodyTesting", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:SARS-CoV-2IgMantibodypositive" - }, - { - "@id": "bts:SARS-CoV-2IgGantibodypositive" - }, - { - "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" - }, - { - "@id": "bts:SARS-CoV-2IgMantibodynegative" - }, - { - "@id": "bts:SARS-CoV-2IgGantibodynegative" - }, - { - "@id": "bts:SARS-CoV-2IgG/IgMantibodynegative" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Antibody Testing", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19ComplicationsSeverity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.", - "rdfs:label": "COVID19ComplicationsSeverity", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cardiaccomplications" - }, - { - "@id": "bts:Pulmonarycomplications" - }, - { - "@id": "bts:Systemiccomplications" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "COVID19 Complications Severity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder", - "rdfs:label": "COVID19CancerTreatmentFollowup", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "COVID19 Cancer Treatment Followup", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapeuse", - "@type": "rdfs:Class", - "rdfs:comment": "Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)", - "rdfs:label": "Ecigvapeuse", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Current" - }, - { - "@id": "bts:Former" - }, - { - "@id": "bts:Never" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ecig vape use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvape30dayusenum", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days e-cigarettes or vaping device was used in the last 30 days", - "rdfs:label": "Ecigvape30dayusenum", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape 30 day use num", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapetimesperday", - "@type": "rdfs:Class", - "rdfs:comment": "e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)", - "rdfs:label": "Ecigvapetimesperday", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape times per day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", - "rdfs:label": "Typeofsmokeexposurecumulativeyears", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Type of smoke exposure cumulative years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chewingtobaccodailyusecount", - "@type": "rdfs:Class", - "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", - "rdfs:label": "Chewingtobaccodailyusecount", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Chewing tobacco daily use count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Secondhandsmokeexposureyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's exposure to second-hand cigarette smoke", - "rdfs:label": "Secondhandsmokeexposureyears", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second hand smoke exposure years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KnownGeneticPredispositionMutation", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", - "rdfs:label": "KnownGeneticPredispositionMutation", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Known Genetic Predisposition Mutation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HereditaryCancerPredispositionSyndrome", - "@type": "rdfs:Class", - "rdfs:comment": "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", - "rdfs:label": "HereditaryCancerPredispositionSyndrome", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alpha-1antitrypsin" - }, - { - "@id": "bts:Attenuatedfamilialadenomatouspolyposis" - }, - { - "@id": "bts:BAP1mutantdisease" - }, - { - "@id": "bts:Beckwith-Wiedemann" - }, - { - "@id": "bts:Biliarydisorder" - }, - { - "@id": "bts:Birt-Hogg-Dubesyndrome" - }, - { - "@id": "bts:Carneycomplex" - }, - { - "@id": "bts:Cirrhosisunknownetiology" - }, - { - "@id": "bts:Constitutionalmismatchrepairdeficiency" - }, - { - "@id": "bts:Familialadenomatouspolyposis" - }, - { - "@id": "bts:Familialgastrointestinalstromaltumor" - }, - { - "@id": "bts:Familialpancreaticcancer" - }, - { - "@id": "bts:Familialprostatecancer" - }, - { - "@id": "bts:Familialrenalcancer" - }, - { - "@id": "bts:Fanconianemia" - }, - { - "@id": "bts:GlycogenStorageDisease" - }, - { - "@id": "bts:Gorlinsyndrome" - }, - { - "@id": "bts:Hereditarybreast–ovariancancersyndrome" - 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}, - { - "@id": "bts:Ukraine" - }, - { - "@id": "bts:UnitedArabEmirates" - }, - { - "@id": "bts:UnitedKingdom" - }, - { - "@id": "bts:UnitedStates" - }, - { - "@id": "bts:Uruguay" - }, - { - "@id": "bts:Uzbekistan" - }, - { - "@id": "bts:Vanuatu" - }, - { - "@id": "bts:Venezuela" - }, - { - "@id": "bts:Vietnam" - }, - { - "@id": "bts:VirginIslandsBritish" - }, - { - "@id": "bts:VirginIslandsU.S." - }, - { - "@id": "bts:WallisandFutuna" - }, - { - "@id": "bts:WesternSahara" - }, - { - "@id": "bts:Yemen" - }, - { - "@id": "bts:Zambia" - }, - { - "@id": "bts:Zimbabwe" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Country of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedArea", - "@type": "rdfs:Class", - "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", - "rdfs:label": "MedicallyUnderservedArea", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:MedicallyUnderservedArea-Yes" - }, - { - "@id": "bts:MedicallyUnderservedArea-No" - }, - { - "@id": "bts:MedicallyUnderservedArea-Unknown" - } - ], - "sms:displayName": "Medically Underserved Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RuralvsUrban", - "@type": "rdfs:Class", - "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", - "rdfs:label": "RuralvsUrban", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:UrbanPopulation(population>50000)" - }, - { - "@id": "bts:UrbanCluster(population2500-50000)" - }, - { - "@id": "bts:RuralPopulation(population<2500)" - } - ], - "sms:displayName": "Rural vs Urban", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidence", - "@type": "rdfs:Class", - "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", - "rdfs:label": "CancerIncidence", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidenceLocation", - "@type": "rdfs:Class", - "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", - "rdfs:label": "CancerIncidenceLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Cancer related clinical data specific to SRRS", - "rdfs:label": "SRRSClinicalDataTier2", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:EducationLevel" - }, - { - "@id": "bts:CountryofBirth" - }, - { - "@id": "bts:MedicallyUnderservedArea" - }, - { - "@id": "bts:RuralvsUrban" - }, - { - "@id": "bts:CancerIncidence" - }, - { - "@id": "bts:CancerIncidenceLocation" - }, - { - "@id": "bts:Ethnicity" - }, - { - "@id": "bts:Gender" - }, - { - "@id": "bts:Race" - }, - { - "@id": "bts:VitalStatus" - }, - { - "@id": "bts:AgeatDiagnosis" - }, - { - "@id": "bts:DaystoLastFollowup" - }, - { - "@id": "bts:DaystoLastKnownDiseaseStatus" - }, - { - "@id": "bts:DaystoRecurrence" - }, - { - "@id": "bts:LastKnownDiseaseStatus" - }, - { - "@id": "bts:Morphology" - }, - { - "@id": "bts:PrimaryDiagnosis" - }, - { - "@id": "bts:ProgressionorRecurrence" - }, - { - "@id": "bts:SiteofResectionorBiopsy" - }, - { - "@id": "bts:TissueorOrganofOrigin" - }, - { - "@id": "bts:NCIAtlasCancerSite" - }, - { - "@id": "bts:TumorGrade" - }, - { - "@id": "bts:PackYearsSmoked" - }, - { - "@id": "bts:YearsSmoked" - }, - { - "@id": "bts:DaystoFollowUp" - }, - { - "@id": "bts:GeneSymbol" - }, - { - "@id": "bts:MolecularAnalysisMethod" - }, - { - "@id": "bts:TestResult" - }, - { - "@id": "bts:TreatmentType" - }, - { - "@id": "bts:TumorLargestDimensionDiameter" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Ethnicity", - "@type": "rdfs:Class", - "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", - "rdfs:label": "Ethnicity", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Hispanicorlatino" - }, - { - "@id": "bts:Nothispanicorlatino" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Ethnicity", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Gender", - "@type": "rdfs:Class", - "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", - "rdfs:label": "Gender", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Female" - }, - { - "@id": "bts:Male" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Unspecified" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Gender", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Race", - "@type": "rdfs:Class", - "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", - "rdfs:label": "Race", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:White" - }, - { - "@id": "bts:Americanindianoralaskanative" - }, - { - "@id": "bts:Blackorafricanamerican" - }, - { - "@id": "bts:Asian" - }, - { - "@id": "bts:Nativehawaiianorotherpacificislander" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Race", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VitalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alive" - }, - { - "@id": "bts:Dead" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vital Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", - "rdfs:label": "AgeatDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Age at Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoLastFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastFollowup", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Follow up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoLastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastKnownDiseaseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoRecurrence", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:LastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", - "rdfs:label": "LastKnownDiseaseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Distantmetrecurrence/progression" - }, - { - "@id": "bts:Loco-regionalrecurrence/progression" - }, - { - "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" - }, - { - "@id": "bts:Tumorfree" - }, - { - "@id": "bts:Unknowntumorstatus" - }, - { - "@id": "bts:Withtumor" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Morphology", - "@type": "rdfs:Class", - "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", - "rdfs:label": "Morphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Morphology", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PrimaryDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "PrimaryDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Acinarcellcarcinoma" - }, - { - "@id": "bts:Acutebasophilicleukaemia" - }, - { - "@id": "bts:AcuteleukemiaBurkitttype" - }, - { - "@id": "bts:AcuteleukemiaNOS" - }, - { - "@id": "bts:Acutelymphaticleukemia" - }, - { - "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" - }, - { - "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" - }, - { - "@id": "bts:AcutelymphoblasticleukemiaNOS" - }, - { - "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" - }, - { - "@id": "bts:Acutelymphocyticleukemia" - }, - { - "@id": "bts:Acutelymphoidleukemia" - }, - { - "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" - }, - { - "@id": "bts:AcutemyeloidleukemiaMLL" - }, - { - "@id": "bts:AcutemyeloidleukemiaNOS" - }, - { - "@id": "bts:Acutemyelomonocyticleukemia" - }, - { - "@id": "bts:AcutepromyelocyticleukemiaNOS" - }, - { - "@id": "bts:Adenocarcinoidtumor" - }, - { - "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" - }, - { - "@id": "bts:AdenocarcinomainapolypNOS" - }, - { - "@id": "bts:Adenocarcinomainadenomatouspolyp" - }, - { - "@id": "bts:Adenocarcinomainpolypoidadenoma" - }, - { - "@id": "bts:AdenocarcinomainsituinapolypNOS" - }, - { - "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" - }, - { - "@id": "bts:Adenocarcinomainsituintubularadenoma" - }, - { - "@id": "bts:Adenocarcinomainsitumucinous" - }, - { - "@id": "bts:Adenocarcinomainsitunon-mucinous" - }, - { - "@id": "bts:AdenocarcinomainsituNOS" - }, - { - "@id": "bts:Adenocarcinomaintubularadenoma" - }, - { - "@id": "bts:Adenocarcinomainvillousadenoma" - }, - { - "@id": "bts:Adenocarcinomaofanalducts" - }, - { - "@id": "bts:Adenocarcinomaofanalglands" - }, - { - "@id": "bts:Adenocarcinomadiffusetype" - }, - { - "@id": "bts:Adenocarcinomaendocervicaltype" - }, - { - "@id": "bts:Adenocarcinomaintestinaltype" - }, - { - "@id": "bts:AdenocarcinomametastaticNOS" - }, - { - "@id": "bts:AdenocarcinomaNOS" - }, - { - "@id": "bts:Adenocarcinomapancreatobiliarytype" - }, - { - "@id": "bts:Adultrhabdomyoma" - }, - { - "@id": "bts:AdultT-celllymphoma" - }, - { - "@id": "bts:AdultT-celllymphoma/leukemia" - }, - { - "@id": "bts:Astrocytomaanaplastic" - }, - { - "@id": "bts:Astrocytomalowgrade" - }, - { - "@id": "bts:AstrocytomaNOS" - }, - { - "@id": "bts:BcelllymphomaNOS" - }, - { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" - }, - { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" - }, - { - "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" - }, - { - "@id": "bts:B-ALL" - }, - { - "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" - }, - { - "@id": "bts:Basalcelladenocarcinoma" - }, - { - "@id": "bts:Basalcelladenoma" - }, - { - "@id": "bts:BasalcellcarcinomaNOS" - }, - { - "@id": "bts:Basalcellepithelioma" - }, - { - "@id": "bts:Basalcelltumor" - }, - { - "@id": "bts:Basophiladenocarcinoma" - }, - { - "@id": "bts:Basophiladenoma" - }, - { - "@id": "bts:Basophilcarcinoma" - }, - { - "@id": "bts:Bileductadenocarcinoma" - }, - { - "@id": "bts:Bileductadenoma" - }, - { - "@id": "bts:Bileductcarcinoma" - }, - { - "@id": "bts:Bileductcystadenocarcinoma" - }, - { - "@id": "bts:Bileductcystadenoma" - }, - { - "@id": "bts:Bronchialadenomacarcinoid" - }, - { - "@id": "bts:Bronchialadenomacylindroid" - }, - { - "@id": "bts:BronchialadenomaNOS" - }, - { - "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" - }, - { - "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" - }, - { - "@id": "bts:Bronchio-alveolarcarcinomamucinous" - }, - { - "@id": "bts:Bronchiolaradenocarcinoma" - }, - { - "@id": "bts:Bronchiolarcarcinoma" - }, - { - "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" - }, - { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" - }, - { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" - }, - { - "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" - }, - { - "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" - }, - { - "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" - }, - { - "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" - }, - { - "@id": "bts:Burkittcellleukemia" - }, - { - "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" - }, - { - "@id": "bts:Burkitttumor" - }, - { - "@id": "bts:Burkitt-likelymphoma" - }, - { - "@id": "bts:C-ALL" - }, - { - "@id": "bts:Cancer" - }, - { - "@id": "bts:Capillaryhemangioma" - }, - { - "@id": "bts:Capillarylymphangioma" - }, - { - "@id": "bts:CarcinomainapolypNOS" - }, - { - "@id": "bts:Carcinomainadenomatouspolyp" - }, - { - "@id": "bts:Carcinomainpleomorphicadenoma" - }, - { - "@id": "bts:CarcinomainsituinapolypNOS" - }, - { - "@id": "bts:Carcinomainsituinadenomatouspolyp" - }, - { - "@id": "bts:CarcinomainsituNOS" - }, - { - "@id": "bts:CarcinomaanaplasticNOS" - }, - { - "@id": "bts:Carcinomadiffusetype" - }, - { - "@id": "bts:Carcinomaintestinaltype" - }, - { - "@id": "bts:CarcinomametastaticNOS" - }, - { - "@id": "bts:CarcinomaNOS" - }, - { - "@id": "bts:CarcinosarcomaNOS" - }, - { - "@id": "bts:CarcinomaundifferentiatedNOS" - }, - { - "@id": "bts:CementomaNOS" - }, - { - "@id": "bts:Centralneuroblastoma" - }, - { - "@id": "bts:Centralneurocytoma" - }, - { - "@id": "bts:Cerebellarliponeurocytoma" - }, - { - "@id": "bts:CerebellarsarcomaNOS" - }, - { - "@id": "bts:CervicalintraepithelialneoplasiagradeIII" - 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}, - { - "@id": "bts:Hepatoidcarcinoma" - }, - { - "@id": "bts:HodgkindiseaseNOS" - }, - { - "@id": "bts:Hodgkingranuloma" - }, - { - "@id": "bts:HodgkinlymphomamixedcellularityNOS" - }, - { - "@id": "bts:HodgkinlymphomanodularsclerosisNOS" - }, - { - "@id": "bts:HodgkinlymphomaNOS" - }, - { - "@id": "bts:HodgkinparagranulomaNOS" - }, - { - "@id": "bts:Hodgkinsarcoma" - }, - { - "@id": "bts:InfiltratingbasalcellcarcinomaNOS" - }, - { - "@id": "bts:InfiltratingductcarcinomaNOS" - }, - { - "@id": "bts:Infiltratingductandcolloidcarcinoma" - }, - { - "@id": "bts:Infiltratingductandcribriformcarcinoma" - }, - { - "@id": "bts:Inflammatoryadenocarcinoma" - }, - { - "@id": "bts:Inflammatorycarcinoma" - }, - { - "@id": "bts:Interstitialcelltumorbenign" - }, - { - "@id": "bts:Interstitialcelltumormalignant" - }, - { - "@id": "bts:InterstitialcelltumorNOS" - }, - { - "@id": "bts:Intracysticpapilloma" - }, - { - "@id": "bts:Intradermalnevus" - }, - { - "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" - }, - { - "@id": "bts:Intraductalandlobularcarcinoma" - }, - { - "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" - }, - { - "@id": "bts:Intraductalcarcinomaclinging" - }, - { - "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" - }, - { - "@id": "bts:IntraductalcarcinomaNOS" - }, - { - "@id": "bts:Intraductalcarcinomasolidtype" - }, - { - "@id": "bts:Intraductalmicropapillarycarcinoma" - }, - { - "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" - }, - { - "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" - }, - { - "@id": "bts:Intraductalpapillarycarcinoma" - }, - { - "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" - }, - { - "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" - }, - { - "@id": "bts:Intraductaltubulopapillaryneoplasm" - }, - { - "@id": "bts:IntraepidermalcarcinomaNOS" - }, - { - "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" - }, - { - "@id": "bts:IntravascularB-celllymphoma" - }, - { - "@id": "bts:Juvenilemyelomonocyticleukemia" - }, - { - "@id": "bts:Kaposisarcoma" - }, - { - "@id": "bts:LargecellcarcinomaNOS" - }, - { - "@id": "bts:Liposarcomadifferentiated" - }, - { - "@id": "bts:LiposarcomaNOS" - }, - { - "@id": "bts:Liposarcomawelldifferentiated" - }, - { - "@id": "bts:Livercelladenoma" - }, - { - "@id": "bts:Livercellcarcinoma" - }, - { - "@id": "bts:Lobularadenocarcinoma" - }, - { - "@id": "bts:Lobularandductalcarcinoma" - }, - { - "@id": "bts:LobularcarcinomainsituNOS" - }, - { - "@id": "bts:Lobularcarcinomanoninfiltrating" - }, - { - "@id": "bts:LobularcarcinomaNOS" - }, - { - "@id": "bts:LymphaticleukemicNOS" - }, - { - "@id": "bts:LymphoblasticleukemiaNOS" - }, - { - "@id": "bts:Lymphoblastoma" - }, - { - "@id": "bts:LymphocyticleukemiaNOS" - }, - { - "@id": "bts:LymphomaNOS" - }, - { - "@id": "bts:Malignancy" - }, - { - "@id": "bts:MalignantlymphomadiffuseNOS" - }, - { - "@id": "bts:MalignantlymphomaHodgkin" - }, - { - "@id": "bts:MalignantlymphomaimmunoblasticNOS" - }, - { - "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" - }, - { - "@id": "bts:MalignantlymphomalargeB-cellNOS" - }, - { - "@id": "bts:MalignantlymphomalargecellNOS" - }, - { - "@id": "bts:MalignantlymphomalymphoblasticNOS" - }, - { - "@id": "bts:MalignantlymphomalymphocyticdiffuseNOS" - }, - { - "@id": "bts:MalignantlymphomalymphocyticnodularNOS" - }, - { - "@id": "bts:MalignantlymphomalymphocyticNOS" - }, - { - "@id": "bts:Malignantlymphomamixedcelltypediffuse" - }, - { - "@id": "bts:Malignantlymphomamixedcelltypefollicular" - }, - { - "@id": "bts:Malignantlymphomamixedcelltypenodular" - }, - { - "@id": "bts:MalignantlymphomanodularNOS" - }, - { - "@id": "bts:Malignantlymphomanon-HodgkinNOS" - }, - { - "@id": "bts:MalignantlymphomaNOS" - }, - { - "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" - }, - { - "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" - }, - { - "@id": "bts:Malignantmelanomaingiantpigmentednevus" - }, - { - "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" - }, - { - "@id": "bts:Malignantmelanomainjunctionalnevus" - }, - { - "@id": "bts:Malignantmelanomainprecancerousmelanosis" - }, - { - "@id": "bts:MalignantmelanomaNOS" - }, - { - "@id": "bts:Malignantmelanomaregressing" - }, - { - "@id": "bts:Mammarycarcinomainsitu" - }, - { - "@id": "bts:Medullaryadenocarcinoma" - }, - { - "@id": "bts:MedullarycarcinomaNOS" - }, - { - "@id": "bts:Medullaryosteosarcoma" - }, - { - "@id": "bts:MedulloblastomaNOS" - }, - { - "@id": "bts:Melanoameloblastoma" - }, - { - "@id": "bts:Melanocyticnevus" - }, - { - "@id": "bts:Melanocytomaeyeball" - }, - { - "@id": "bts:MelanocytomaNOS" - }, - { - "@id": "bts:Melanomainsitu" - }, - { - "@id": "bts:Melanomamalignantofsoftparts" - }, - { - "@id": "bts:MelanomaNOS" - }, - { - "@id": "bts:Melanoticmedulloblastoma" - }, - { - "@id": "bts:MelanoticMPNST" - }, - { - "@id": "bts:Melanoticneuroectodermaltumor" - }, - { - "@id": "bts:Melanoticneurofibroma" - }, - { - "@id": "bts:Melanoticprogonoma" - }, - { - "@id": "bts:MelanoticpsammomatousMPNST" - }, - { - "@id": "bts:Melanoticschwannoma" - }, - { - "@id": "bts:Meningealmelanocytoma" - }, - { - "@id": "bts:Meningealmelanoma" - }, - { - "@id": "bts:Meningiomaanaplastic" - }, - { - "@id": "bts:Meningiomamalignant" - }, - { - "@id": "bts:MeningiomaNOS" - }, - { - "@id": "bts:MicropapillarycarcinomaNOS" - }, - { - "@id": "bts:Mixedadenocarcinomaandepidermoidcarcinoma" - }, - { - "@id": "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" - }, - { - "@id": "bts:Mixedmedullary-follicularcarcinoma" - }, - { - "@id": "bts:Mixedmedullary-papillarycarcinoma" - }, - { - "@id": "bts:Mixedpancreaticendocrineandexocrinetumormalignant" - }, - { - "@id": "bts:Mixedpinealtumor" - }, - { - "@id": "bts:Mixedsmallcellcarcinoma" - }, - { - "@id": "bts:Mixedsquamouscellandglandularpapilloma" - }, - { - "@id": "bts:MixedtumormalignantNOS" - }, - { - "@id": "bts:MixedtumorNOS" - }, - { - "@id": "bts:MonocyticleukemiaNOS" - }, - { - "@id": "bts:Mucosal-associatedlymphoidtissuelymphoma" - }, - { - "@id": "bts:Mucousadenocarcinoma" - }, - { - "@id": "bts:Multiplemyeloma" - }, - { - "@id": "bts:MyelocyticleukemiaNOS" - }, - { - "@id": "bts:MyeloidleukemiaNOS" - }, - { - "@id": "bts:MyelomaNOS" - }, - { - "@id": "bts:Myoepithelioma" - }, - { - "@id": "bts:Neoplasmbenign" - }, - { - "@id": "bts:Neoplasmmalignant" - }, - { - "@id": "bts:Neoplasmmalignantuncertainwhetherprimaryormetastatic" - }, - { - "@id": "bts:Neoplasmmetastatic" - }, - { - "@id": "bts:NeoplasmNOS" - }, - { - "@id": "bts:Neoplasmsecondary" - }, - { - "@id": "bts:Neoplasmuncertainwhetherbenignormalignant" - }, - { - "@id": "bts:NephroblastomaNOS" - }, - { - "@id": "bts:NeuroblastomaNOS" - }, - { - "@id": "bts:NeuroendocrinecarcinomaNOS" - }, - { - "@id": "bts:NeuroepitheliomaNOS" - }, - { - "@id": "bts:NeurofibromaNOS" - }, - { - "@id": "bts:NeurofibromatosisNOS" - }, - { - "@id": "bts:Neurofibrosarcoma" - }, - { - "@id": "bts:Neurosarcoma" - }, - { - "@id": "bts:NevusNOS" - }, - { - "@id": "bts:Non-HodgkinlymphomaNOS" - }, - { - "@id": "bts:Non-invasivelowgradeserouscarcinoma" - }, - { - "@id": "bts:Non-lymphocyticleukemiaNOS" - }, - { - "@id": "bts:Non-smallcellcarcinoma" - }, - { - "@id": "bts:Nonpigmentednevus" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:Oatcellcarcinoma" - }, - { - "@id": "bts:Osteoblastomamalignant" - }, - { - "@id": "bts:OsteoblastomaNOS" - }, - { - "@id": "bts:OsteosarcomaNOS" - }, - { - "@id": "bts:Pagetdiseaseandinfiltratingductcarcinomaofbreast" - }, - { - "@id": "bts:Pagetdiseaseandintraductalcarcinomaofbreast" - }, - { - "@id": "bts:Pagetdiseaseofbreast" - }, - { - "@id": "bts:Pagetdiseaseextramammary" - }, - { - "@id": "bts:Pagetdiseasemammary" - }, - { - "@id": "bts:Pagetoidreticulosis" - }, - { - "@id": "bts:Pancreaticendocrinetumorbenign" - }, - { - "@id": "bts:Pancreaticendocrinetumormalignant" - }, - { - "@id": "bts:Pancreaticendocrinetumornonfunctioning" - }, - { - "@id": "bts:PancreaticendocrinetumorNOS" - }, - { - "@id": "bts:Pancreaticmicroadenoma" - }, - { - "@id": "bts:Pancreatobiliaryneoplasmnon-invasive" - }, - { - "@id": "bts:Pancreatobiliary-typecarcinoma" - }, - { - "@id": "bts:Pancreatoblastoma" - }, - { - "@id": "bts:Papillaryadenocarcinomafollicularvariant" - }, - { - "@id": "bts:PapillaryadenocarcinomaNOS" - }, - { - "@id": "bts:Papillaryadenofibroma" - }, - { - "@id": "bts:PapillaryadenomaNOS" - }, - { - "@id": "bts:Papillaryandfollicularcarcinoma" - }, - { - "@id": "bts:Papillarycarcinomainsitu" - }, - { - "@id": "bts:PapillarycarcinomaNOS" - }, - { - "@id": "bts:PapillarycystadenomaNOS" - }, - { - "@id": "bts:Papillaryepidermoidcarcinoma" - }, - { - "@id": "bts:Papillaryglioneuronaltumor" - }, - { - "@id": "bts:Papillarymeningioma" - }, - { - "@id": "bts:Papillarymicrocarcinoma" - }, - { - "@id": "bts:Papillaryrenalcellcarcinoma" - }, - { - "@id": "bts:Papillaryserousadenocarcinoma" - }, - { - "@id": "bts:Papillaryserouscystadenocarcinoma" - }, - { - "@id": "bts:PapillaryserouscystadenomaNOS" - }, - { - "@id": "bts:Papillarysquamouscellcarcinoma" - }, - { - "@id": "bts:Papillarysquamouscellcarcinomainsitu" - }, - { - "@id": "bts:Papillarytransitionalcellcarcinoma" - }, - { - "@id": "bts:Papillarytumorofthepinealregion" - }, - { - "@id": "bts:Papillaryurothelialcarcinoma" - }, - { - "@id": "bts:Papillomaofbladder" - }, - { - "@id": "bts:PapillomaNOS" - }, - { - "@id": "bts:Papillomatosisglandular" - }, - { - "@id": "bts:PapillomatosisNOS" - }, - { - "@id": "bts:Papillotubularadenocarcinoma" - }, - { - "@id": "bts:Papillotubularadenoma" - }, - { - "@id": "bts:Paragangliomabenign" - }, - { - "@id": "bts:Paragangliomamalignant" - }, - { - "@id": "bts:ParagangliomaNOS" - }, - { - "@id": "bts:PeripheralT-celllymphomalargecell" - }, - { - "@id": "bts:PeripheralT-celllymphomaNOS" - }, - { - "@id": "bts:Pigmentedadenoma" - }, - { - "@id": "bts:Pigmentedbasalcellcarcinoma" - }, - { - "@id": "bts:PigmentednevusNOS" - }, - { - "@id": "bts:PituitaryadenomaNOS" - }, - { - "@id": "bts:PituitarycarcinomaNOS" - }, - { - "@id": "bts:Pleomorphicadenoma" - }, - { - "@id": "bts:Pleomorphiccarcinoma" - }, - { - "@id": "bts:Pleomorphiclipoma" - }, - { - "@id": "bts:Pleomorphicliposarcoma" - }, - { - "@id": "bts:Pleomorphiclobularcarcinoma" - }, - { - "@id": "bts:Pleomorphiclobularcarcinomainsitu" - }, - { - "@id": "bts:PrecancerousmelanosisNOS" - }, - { - "@id": "bts:PrecursorB-celllymphoblasticleukemia" - }, - { - "@id": "bts:PrecursorB-celllymphoblasticlymphoma" - }, - { - "@id": "bts:PrecursorcelllymphoblasticleukemiaNOS" - }, - { - "@id": "bts:PrecursorT-celllymphoblasticleukemia" - }, - { - "@id": "bts:PrecursorT-celllymphoblasticlymphoma" - }, - { - "@id": "bts:Preleukemia" - }, - { - "@id": "bts:Preleukemicsyndrome" - }, - { - "@id": "bts:Primaryamyloidosis" - }, - { - "@id": "bts:Pro-BALL" - }, - { - "@id": "bts:Pro-TALL" - }, - { - "@id": "bts:ProstaticintraepithelialneoplasiagradeIII" - }, - { - "@id": "bts:Pulmonaryadenomatosis" - }, - { - "@id": "bts:Pulmonaryarteryintimalsarcoma" - }, - { - "@id": "bts:Pulmonaryblastoma" - }, - { - "@id": "bts:Renalcarcinomacollectingducttype" - }, - { - "@id": "bts:Renalcelladenocarcinoma" - }, - { - "@id": "bts:Renalcellcarcinomachromophobetype" - }, - { - "@id": "bts:RenalcellcarcinomaNOS" - }, - { - "@id": "bts:Renalcellcarcinomasarcomatoid" - }, - { - "@id": "bts:Renalcellcarcinomaspindlecell" - }, - { - "@id": "bts:Renalcellcarcinomaunclassified" - }, - { - "@id": "bts:Renalmedullarycarcinoma" - }, - { - "@id": "bts:Rhabdoidmeningioma" - }, - { - "@id": "bts:Rhabdoidsarcoma" - }, - { - "@id": "bts:RhabdoidtumorNOS" - }, - { - "@id": "bts:RhabdomyomaNOS" - }, - { - "@id": "bts:Rhabdomyosarcomawithganglionicdifferentiation" - }, - { - "@id": "bts:RhabdomyosarcomaNOS" - }, - { - "@id": "bts:Rhabdosarcoma" - }, - { - "@id": "bts:Rodentulcer" - }, - { - "@id": "bts:SarcomaNOS" - }, - { - "@id": "bts:Sclerosinghemangioma" - }, - { - "@id": "bts:Sclerosinghepaticcarcinoma" - }, - { - "@id": "bts:Secondarycarcinoma" - }, - { - "@id": "bts:Secretorycarcinomaofbreast" - }, - { - "@id": "bts:SerouscystadenocarcinomaNOS" - }, - { - "@id": "bts:Seroussurfacepapillarycarcinoma" - }, - { - "@id": "bts:High-gradeserouscarcinoma" - }, - { - "@id": "bts:Skinappendagecarcinoma" - }, - { - "@id": "bts:SmallcellcarcinomaNOS" - }, - { - "@id": "bts:Smallcellneuroendocrinecarcinoma" - }, - { - "@id": "bts:Smallcellosteosarcoma" - }, - { - "@id": "bts:Smallcellsarcoma" - }, - { - "@id": "bts:Smallcongenitalnevus" - }, - { - "@id": "bts:SpindlecellcarcinomaNOS" - }, - { - "@id": "bts:SpindlecellmelanomaNOS" - }, - { - "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" - }, - { - "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" - }, - { - "@id": "bts:Spleniclymphomawithvillouslymphocytes" - }, - { - "@id": "bts:SplenicmarginalzoneB-celllymphoma" - }, - { - "@id": "bts:SplenicmarginalzonelymphomaNOS" - }, - { - "@id": "bts:SquamouscellcarcinomainsituNOS" - }, - { - "@id": "bts:Squamouscellcarcinomaadenoid" - }, - { - "@id": "bts:Squamouscellcarcinomaclearcelltype" - }, - { - "@id": "bts:SquamouscellcarcinomaNOS" - }, - { - "@id": "bts:Tlymphoblasticleukemia/lymphoma" - }, - { - "@id": "bts:T-celllargegranularlymphocyticleukemia" - }, - { - "@id": "bts:T-celllargegranularlymphocytosis" - }, - { - "@id": "bts:T-celllymphomaNOS" - }, - { - "@id": "bts:TeratomamalignantNOS" - }, - { - "@id": "bts:TeratomaNOS" - }, - { - "@id": "bts:Therapyrelatedmyeloidneoplasm" - }, - { - "@id": "bts:Transitionalcarcinoma" - }, - { - "@id": "bts:Transitionalcellcarcinoma" - }, - { - "@id": "bts:Transitionalcellcarcinomainsitu" - }, - { - "@id": "bts:Tubularadenocarcinoma" - }, - { - "@id": "bts:TubularadenomaNOS" - }, - { - "@id": "bts:Tubularandroblastomawithlipidstorage" - }, - { - "@id": "bts:TubularandroblastomaNOS" - }, - { - "@id": "bts:Tubularcarcinoid" - }, - { - "@id": "bts:Tubularcarcinoma" - }, - { - "@id": "bts:Tubulo-papillaryadenoma" - }, - { - "@id": "bts:Tubulocysticrenalcellcarcinoma" - }, - { - "@id": "bts:Tubulolobularcarcinoma" - }, - { - "@id": "bts:Tubulopapillaryadenocarcinoma" - }, - { - "@id": "bts:TubulovillousadenomaNOS" - }, - { - "@id": "bts:Tumorcellsbenign" - }, - { - "@id": "bts:Tumorcellsmalignant" - }, - { - "@id": "bts:TumorcellsNOS" - }, - { - "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" - }, - { - "@id": "bts:Tumorembolus" - }, - { - "@id": "bts:Tumorbenign" - }, - { - "@id": "bts:TumormalignantNOS" - }, - { - "@id": "bts:Tumormetastatic" - }, - { - "@id": "bts:TumorNOS" - }, - { - "@id": "bts:Tumorsecondary" - }, - { - "@id": "bts:Tumorletbenign" - }, - { - "@id": "bts:Typicalcarcinoid" - }, - { - "@id": "bts:Unclassifiedtumorbenign" - }, - { - "@id": "bts:Unclassifiedtumorborderlinemalignancy" - }, - { - "@id": "bts:Unclassifiedtumormalignant" - }, - { - "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" - }, - { - "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" - }, - { - "@id": "bts:Undifferentiatedepithelioidsarcoma" - }, - { - "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" - }, - { - "@id": "bts:Undifferentiatedleukaemia" - }, - { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" - }, - { - "@id": "bts:Undifferentiatedroundcellsarcoma" - }, - { - "@id": "bts:Undifferentiatedsarcoma" - }, - { - "@id": "bts:Undifferentiatedspindlecellsarcoma" - }, - { - "@id": "bts:Undifferentiateduterinesarcoma" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Primary Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProgressionorRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", - "rdfs:label": "ProgressionorRecurrence", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-ProgressionorRecurrence" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Progression or Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteofResectionorBiopsy", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "SiteofResectionorBiopsy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" - }, - { - "@id": "bts:Abdominalesophagus" - }, - { - "@id": "bts:AccessorysinusNOS" - }, - { - "@id": "bts:Acousticnerve" - }, - { - "@id": "bts:AdrenalglandNOS" - }, - { - "@id": "bts:AmpullaofVater" - }, - { - "@id": "bts:Analcanal" - }, - { - "@id": "bts:Anterior2/3oftongueNOS" - }, - { - "@id": "bts:Anteriorfloorofmouth" - }, - { - "@id": "bts:Anteriormediastinum" - }, - { - "@id": "bts:Anteriorsurfaceofepiglottis" - }, - { - "@id": "bts:Anteriorwallofbladder" - }, - { - "@id": "bts:Anteriorwallofnasopharynx" - }, - { - "@id": "bts:AnusNOS" - }, - { - "@id": "bts:Aorticbodyandotherparaganglia" - }, - { - "@id": "bts:Appendix" - }, - { - "@id": "bts:Ascendingcolon" - }, - { - "@id": "bts:AutonomicnervoussystemNOS" - }, - { - "@id": "bts:Axillarytailofbreast" - }, - { - "@id": "bts:BaseoftongueNOS" - }, - { - "@id": "bts:Bladderneck" - }, - { - "@id": "bts:BladderNOS" - }, - { - "@id": "bts:Blood" - }, - { - "@id": "bts:Bodyofpancreas" - }, - { - "@id": "bts:Bodyofpenis" - }, - { - "@id": "bts:Bodyofstomach" - }, - { - "@id": "bts:Bonemarrow" - }, - { - "@id": "bts:BoneoflimbNOS" - }, - { - "@id": "bts:BoneNOS" - }, - { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" - }, - { - "@id": "bts:Borderoftongue" - }, - { - "@id": "bts:Brainstem" - }, - { - "@id": "bts:BrainNOS" - }, - { - "@id": "bts:Branchialcleft" - }, - { - "@id": "bts:BreastNOS" - }, - { - "@id": "bts:Broadligament" - }, - { - "@id": "bts:CardiaNOS" - }, - { - "@id": "bts:Carotidbody" - }, - { - "@id": "bts:Caudaequina" - }, - { - "@id": "bts:Cecum" - }, - { - "@id": "bts:Centralportionofbreast" - }, - { - "@id": "bts:CerebellumNOS" - }, - { - "@id": "bts:Cerebralmeninges" - }, - { - "@id": "bts:Cerebrum" - }, - { - "@id": "bts:Cervicalesophagus" - }, - { - "@id": "bts:Cervixuteri" - }, - { - "@id": "bts:Choroid" - }, - { - "@id": "bts:Ciliarybody" - }, - { - "@id": "bts:Cloacogeniczone" - }, - { - "@id": "bts:ColonNOS" - }, - { - "@id": "bts:Commissureoflip" - }, - { - "@id": "bts:Conjunctiva" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" - }, - { - "@id": "bts:CorneaNOS" - }, - { - "@id": "bts:Corpusuteri" - }, - { - "@id": "bts:Cortexofadrenalgland" - }, - { - "@id": "bts:CranialnerveNOS" - }, - { - "@id": "bts:Craniopharyngealduct" - }, - { - "@id": "bts:Descendedtestis" - }, - { - "@id": "bts:Descendingcolon" - }, - { - "@id": "bts:Domeofbladder" - }, - { - "@id": "bts:DorsalsurfaceoftongueNOS" - }, - { - "@id": "bts:Duodenum" - }, - { - "@id": "bts:Endocervix" - }, - { - "@id": "bts:EndocrineglandNOS" - }, - { - "@id": "bts:Endometrium" - }, - { - "@id": "bts:Epididymis" - }, - { - "@id": "bts:EsophagusNOS" - }, - { - "@id": "bts:Ethmoidsinus" - }, - { - "@id": "bts:Exocervix" - }, - { - "@id": "bts:Externalear" - }, - { - "@id": "bts:ExternallipNOS" - }, - { - "@id": "bts:Externallowerlip" - }, - { - "@id": "bts:Externalupperlip" - }, - { - "@id": "bts:Extrahepaticbileduct" - }, - { - "@id": "bts:EyeNOS" - }, - { - "@id": "bts:Eyelid" - }, - { - "@id": "bts:Fallopiantube" - }, - { - "@id": "bts:FemalegenitaltractNOS" - }, - { - "@id": "bts:FloorofmouthNOS" - }, - { - "@id": "bts:Frontallobe" - }, - { - "@id": "bts:Frontalsinus" - }, - { - "@id": "bts:Fundusofstomach" - }, - { - "@id": "bts:Fundusuteri" - }, - { - "@id": "bts:Gallbladder" - }, - { - "@id": "bts:Gastricantrum" - }, - { - "@id": "bts:GastrointestinaltractNOS" - }, - { - "@id": "bts:Glanspenis" - }, - { - "@id": "bts:Glottis" - }, - { - "@id": "bts:GreatercurvatureofstomachNOS" - }, - { - "@id": "bts:GumNOS" - }, - { - "@id": "bts:Hardpalate" - }, - { - "@id": "bts:Headofpancreas" - }, - { - "@id": "bts:HeadfaceorneckNOS" - }, - { - "@id": "bts:Heart" - }, - { - "@id": "bts:HematopoieticsystemNOS" - }, - { - "@id": "bts:Hepaticflexureofcolon" - }, - { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" - }, - { - "@id": "bts:HypopharynxNOS" - }, - { - "@id": "bts:Ileum" - }, - { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" - }, - { - "@id": "bts:IntestinaltractNOS" - }, - { - "@id": "bts:Intra-abdominallymphnodes" - }, - { - "@id": "bts:Intrahepaticbileduct" - }, - { - "@id": "bts:Intrathoraciclymphnodes" - }, - { - "@id": "bts:IsletsofLangerhans" - }, - { - "@id": "bts:Isthmusuteri" - }, - { - "@id": "bts:Jejunum" - }, - { - "@id": "bts:KidneyNOS" - }, - { - "@id": "bts:Labiummajus" - }, - { - "@id": "bts:Labiumminus" - }, - { - "@id": "bts:Lacrimalgland" - }, - { - "@id": "bts:Laryngealcartilage" - }, - { - "@id": "bts:LarynxNOS" - }, - { - "@id": "bts:Lateralfloorofmouth" - }, - { - "@id": "bts:Lateralwallofbladder" - }, - { - "@id": "bts:Lateralwallofnasopharynx" - }, - { - "@id": "bts:Lateralwalloforopharynx" - }, - { - "@id": "bts:LessercurvatureofstomachNOS" - }, - { - "@id": "bts:Lingualtonsil" - }, - { - "@id": "bts:LipNOS" - }, - { - "@id": "bts:Liver" - }, - { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" - }, - { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" - }, - { - "@id": "bts:Lowergum" - }, - { - "@id": "bts:LowerlimbNOS" - }, - { - "@id": "bts:Lowerlobelung" - }, - { - "@id": "bts:Lowerthirdofesophagus" - }, - { - "@id": "bts:Lower-innerquadrantofbreast" - }, - { - "@id": "bts:Lower-outerquadrantofbreast" - }, - { - "@id": "bts:LungNOS" - }, - { - "@id": "bts:LymphnodeNOS" - }, - { - "@id": "bts:Lymphnodesofaxillaorarm" - }, - { - "@id": "bts:Lymphnodesofheadfaceandneck" - }, - { - "@id": "bts:Lymphnodesofinguinalregionorleg" - }, - { - "@id": "bts:Lymphnodesofmultipleregions" - }, - { - "@id": "bts:Mainbronchus" - }, - { - "@id": "bts:MajorsalivaryglandNOS" - }, - { - "@id": "bts:MalegenitalorgansNOS" - }, - { - "@id": "bts:Mandible" - }, - { - "@id": "bts:Maxillarysinus" - }, - { - "@id": "bts:Meckeldiverticulum" - }, - { - "@id": "bts:MediastinumNOS" - }, - { - "@id": "bts:Medullaofadrenalgland" - }, - { - "@id": "bts:MeningesNOS" - }, - { - "@id": "bts:Middleear" - }, - { - "@id": "bts:Middlelobelung" - }, - { - "@id": "bts:Middlethirdofesophagus" - }, - { - "@id": "bts:MouthNOS" - }, - { - "@id": "bts:MucosaoflipNOS" - }, - { - "@id": "bts:Mucosaoflowerlip" - }, - { - "@id": "bts:Mucosaofupperlip" - }, - { - "@id": "bts:Myometrium" - }, - { - "@id": "bts:Nasalcavity" - }, - { - "@id": "bts:NasopharynxNOS" - }, - { - "@id": "bts:NervoussystemNOS" - }, - { - "@id": "bts:Nipple" - }, - { - "@id": "bts:Occipitallobe" - }, - { - "@id": "bts:Olfactorynerve" - }, - { - "@id": "bts:Opticnerve" - }, - { - "@id": "bts:OrbitNOS" - }, - { - "@id": "bts:OropharynxNOS" - }, - { - "@id": "bts:Otherill-definedsites" - }, - { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" - }, - { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" - }, - { - "@id": "bts:Otherspecifiedpartsofpancreas" - }, - { - "@id": "bts:Ovary" - }, - { - "@id": "bts:Overlappinglesionofaccessorysinuses" - }, - { - "@id": "bts:Overlappinglesionofbladder" - }, - { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" - }, - { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" - }, - { - "@id": "bts:Overlappinglesionofbrain" - }, - { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" - }, - { - "@id": "bts:Overlappinglesionofbreast" - }, - { - "@id": "bts:Overlappinglesionofcervixuteri" - }, - { - "@id": "bts:Overlappinglesionofcolon" - }, - { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" - }, - { - "@id": "bts:Overlappinglesionofcorpusuteri" - }, - { - "@id": "bts:Overlappinglesionofdigestivesystem" - }, - { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" - }, - { - "@id": "bts:Overlappinglesionofesophagus" - }, - { - "@id": "bts:Overlappinglesionofeyeandadnexa" - }, - { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" - }, - { - "@id": "bts:Overlappinglesionoffloorofmouth" - }, - { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" - }, - { - "@id": "bts:Overlappinglesionofhypopharynx" - }, - { - "@id": "bts:Overlappinglesionofill-definedsites" - }, - { - "@id": "bts:Overlappinglesionoflarynx" - }, - { - "@id": "bts:Overlappinglesionoflip" - }, - { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" - }, - { - "@id": "bts:Overlappinglesionoflung" - }, - { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" - }, - { - "@id": "bts:Overlappinglesionofmalegenitalorgans" - }, - { - "@id": "bts:Overlappinglesionofnasopharynx" - }, - { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" - }, - { - "@id": "bts:Overlappinglesionofpalate" - }, - { - "@id": "bts:Overlappinglesionofpancreas" - }, - { - "@id": "bts:Overlappinglesionofpenis" - }, - { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" - }, - { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" - }, - { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" - }, - { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" - }, - { - "@id": "bts:Overlappinglesionofskin" - }, - { - "@id": "bts:Overlappinglesionofsmallintestine" - }, - { - "@id": "bts:Overlappinglesionofstomach" - }, - { - "@id": "bts:Overlappinglesionoftongue" - }, - { - "@id": "bts:Overlappinglesionoftonsil" - }, - { - "@id": "bts:Overlappinglesionofurinaryorgans" - }, - { - "@id": "bts:Overlappinglesionofvulva" - }, - { - "@id": "bts:Overlappinglesionsoforopharynx" - }, - { - "@id": "bts:PalateNOS" - }, - { - "@id": "bts:PancreasNOS" - }, - { - "@id": "bts:Pancreaticduct" - }, - { - "@id": "bts:Parametrium" - }, - { - "@id": "bts:Paraspinal" - }, - { - "@id": "bts:Parathyroidgland" - }, - { - "@id": "bts:Paraurethralgland" - }, - { - "@id": "bts:Parietallobe" - }, - { - "@id": "bts:Parotidgland" - }, - { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" - }, - { - "@id": "bts:Pelviclymphnodes" - }, - { - "@id": "bts:PelvisNOS" - }, - { - "@id": "bts:PenisNOS" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" - }, - { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" - }, - { - "@id": "bts:PeritoneumNOS" - }, - { - "@id": "bts:PharynxNOS" - }, - { - "@id": "bts:Pinealgland" - }, - { - "@id": "bts:Pituitarygland" - }, - { - "@id": "bts:Placenta" - }, - { - "@id": "bts:PleuraNOS" - }, - { - "@id": "bts:Postcricoidregion" - }, - { - "@id": "bts:Posteriormediastinum" - }, - { - "@id": "bts:Posteriorwallofbladder" - }, - { - "@id": "bts:Posteriorwallofhypopharynx" - }, - { - "@id": "bts:Posteriorwallofnasopharynx" - }, - { - "@id": "bts:Posteriorwalloforopharynx" - }, - { - "@id": "bts:Prepuce" - }, - { - "@id": "bts:Prostategland" - }, - { - "@id": "bts:Pylorus" - }, - { - "@id": "bts:Pyriformsinus" - }, - { - "@id": "bts:Rectosigmoidjunction" - }, - { - "@id": "bts:RectumNOS" - }, - { - "@id": "bts:Renalpelvis" - }, - { - "@id": "bts:ReticuloendothelialsystemNOS" - }, - { - "@id": "bts:Retina" - }, - { - "@id": "bts:Retromolararea" - }, - { - "@id": "bts:Retroperitoneum" - }, - { - "@id": "bts:Ribsternumclavicleandassociatedjoints" - }, - { - "@id": "bts:Roundligament" - }, - { - "@id": "bts:ScrotumNOS" - }, - { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" - }, - { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" - }, - { - "@id": "bts:Sigmoidcolon" - }, - { - "@id": "bts:SkinoflipNOS" - }, - { - "@id": "bts:Skinoflowerlimbandhip" - }, - { - "@id": "bts:Skinofotherandunspecifiedpartsofface" - }, - { - "@id": "bts:Skinofscalpandneck" - }, - { - "@id": "bts:Skinoftrunk" - }, - { - "@id": "bts:Skinofupperlimbandshoulder" - }, - { - "@id": "bts:SkinNOS" - }, - { - "@id": "bts:SmallintestineNOS" - }, - { - "@id": "bts:SoftpalateNOS" - }, - { - "@id": "bts:Specifiedpartsofperitoneum" - }, - { - "@id": "bts:Spermaticcord" - }, - { - "@id": "bts:Sphenoidsinus" - }, - { - "@id": "bts:Spinalcord" - }, - { - "@id": "bts:Spinalmeninges" - }, - { - "@id": "bts:Spleen" - }, - { - "@id": "bts:Splenicflexureofcolon" - }, - { - "@id": "bts:StomachNOS" - }, - { - "@id": "bts:Subglottis" - }, - { - "@id": "bts:Sublingualgland" - }, - { - "@id": "bts:Submandibulargland" - }, - { - "@id": "bts:Superiorwallofnasopharynx" - }, - { - "@id": "bts:Supraglottis" - }, - { - "@id": "bts:Tailofpancreas" - }, - { - "@id": "bts:Temporallobe" - }, - { - "@id": "bts:TestisNOS" - }, - { - "@id": "bts:Thoracicesophagus" - }, - { - "@id": "bts:ThoraxNOS" - }, - { - "@id": "bts:Thymus" - }, - { - "@id": "bts:Thyroidgland" - }, - { - "@id": "bts:TongueNOS" - }, - { - "@id": "bts:TonsilNOS" - }, - { - "@id": "bts:Tonsillarfossa" - }, - { - "@id": "bts:Tonsillarpillar" - }, - { - "@id": "bts:Trachea" - }, - { - "@id": "bts:Transversecolon" - }, - { - "@id": "bts:Trigoneofbladder" - }, - { - "@id": "bts:Undescendedtestis" - }, - { - "@id": "bts:Unknownprimarysite" - }, - { - "@id": "bts:Uppergum" - }, - { - "@id": "bts:UpperlimbNOS" - }, - { - "@id": "bts:Upperlobelung" - }, - { - "@id": "bts:UpperrespiratorytractNOS" - }, - { - "@id": "bts:Upperthirdofesophagus" - }, - { - "@id": "bts:Upper-innerquadrantofbreast" - }, - { - "@id": "bts:Upper-outerquadrantofbreast" - }, - { - "@id": "bts:Urachus" - }, - { - "@id": "bts:Ureter" - }, - { - "@id": "bts:Uretericorifice" - }, - { - "@id": "bts:Urethra" - }, - { - "@id": "bts:UrinarysystemNOS" - }, - { - "@id": "bts:Uterineadnexa" - }, - { - "@id": "bts:UterusNOS" - }, - { - "@id": "bts:Uvula" - }, - { - "@id": "bts:VaginaNOS" - }, - { - "@id": "bts:Vallecula" - }, - { - "@id": "bts:VentralsurfaceoftongueNOS" - }, - { - "@id": "bts:VentricleNOS" - }, - { - "@id": "bts:Vertebralcolumn" - }, - { - "@id": "bts:Vestibuleofmouth" - }, - { - "@id": "bts:VulvaNOS" - }, - { - "@id": "bts:Waldeyerring" - }, - { - "@id": "bts:BiliarytractNOS" - }, - { - "@id": "bts:Cheekmucosa" - }, - { - "@id": "bts:Clitoris" - }, - { - "@id": "bts:Overlappinglesionofbiliarytract" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Site of Resection or Biopsy", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TissueorOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "TissueorOrganofOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" - }, - { - "@id": "bts:Abdominalesophagus" - }, - { - "@id": "bts:AccessorysinusNOS" - }, - { - "@id": "bts:Acousticnerve" - }, - { - "@id": "bts:AdrenalglandNOS" - }, - { - "@id": "bts:AmpullaofVater" - }, - { - "@id": "bts:Analcanal" - }, - { - "@id": "bts:Anterior2/3oftongueNOS" - }, - { - "@id": "bts:Anteriorfloorofmouth" - }, - { - "@id": "bts:Anteriormediastinum" - }, - { - "@id": "bts:Anteriorsurfaceofepiglottis" - }, - { - "@id": "bts:Anteriorwallofbladder" - }, - { - "@id": "bts:Anteriorwallofnasopharynx" - }, - { - "@id": "bts:AnusNOS" - }, - { - "@id": "bts:Aorticbodyandotherparaganglia" - }, - { - "@id": "bts:Appendix" - }, - { - "@id": "bts:Ascendingcolon" - }, - { - "@id": "bts:AutonomicnervoussystemNOS" - }, - { - "@id": "bts:Axillarytailofbreast" - }, - { - "@id": "bts:BaseoftongueNOS" - }, - { - "@id": "bts:Bladderneck" - }, - { - "@id": "bts:BladderNOS" - }, - { - "@id": "bts:Blood" - }, - { - "@id": "bts:Bodyofpancreas" - }, - { - "@id": "bts:Bodyofpenis" - }, - { - "@id": "bts:Bodyofstomach" - }, - { - "@id": "bts:Bonemarrow" - }, - { - "@id": "bts:BoneoflimbNOS" - }, - { - "@id": "bts:BoneNOS" - }, - { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" - }, - { - "@id": "bts:Borderoftongue" - }, - { - "@id": "bts:Brainstem" - }, - { - "@id": "bts:BrainNOS" - }, - { - "@id": "bts:Branchialcleft" - }, - { - "@id": "bts:BreastNOS" - }, - { - "@id": "bts:Broadligament" - }, - { - "@id": "bts:CardiaNOS" - }, - { - "@id": "bts:Carotidbody" - }, - { - "@id": "bts:Caudaequina" - }, - { - "@id": "bts:Cecum" - }, - { - "@id": "bts:Centralportionofbreast" - }, - { - "@id": "bts:CerebellumNOS" - }, - { - "@id": "bts:Cerebralmeninges" - }, - { - "@id": "bts:Cerebrum" - }, - { - "@id": "bts:Cervicalesophagus" - }, - { - "@id": "bts:Cervixuteri" - }, - { - "@id": "bts:Choroid" - }, - { - "@id": "bts:Ciliarybody" - }, - { - "@id": "bts:Cloacogeniczone" - }, - { - "@id": "bts:ColonNOS" - }, - { - "@id": "bts:Commissureoflip" - }, - { - "@id": "bts:Conjunctiva" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" - }, - { - "@id": "bts:CorneaNOS" - }, - { - "@id": "bts:Corpusuteri" - }, - { - "@id": "bts:Cortexofadrenalgland" - }, - { - "@id": "bts:CranialnerveNOS" - }, - { - "@id": "bts:Craniopharyngealduct" - }, - { - "@id": "bts:Descendedtestis" - }, - { - "@id": "bts:Descendingcolon" - }, - { - "@id": "bts:Domeofbladder" - }, - { - "@id": "bts:DorsalsurfaceoftongueNOS" - }, - { - "@id": "bts:Duodenum" - }, - { - "@id": "bts:Endocervix" - }, - { - "@id": "bts:EndocrineglandNOS" - }, - { - "@id": "bts:Endometrium" - }, - { - "@id": "bts:Epididymis" - }, - { - "@id": "bts:EsophagusNOS" - }, - { - "@id": "bts:Ethmoidsinus" - }, - { - "@id": "bts:Exocervix" - }, - { - "@id": "bts:Externalear" - }, - { - "@id": "bts:ExternallipNOS" - }, - { - "@id": "bts:Externallowerlip" - }, - { - "@id": "bts:Externalupperlip" - }, - { - "@id": "bts:Extrahepaticbileduct" - }, - { - "@id": "bts:EyeNOS" - }, - { - "@id": "bts:Eyelid" - }, - { - "@id": "bts:Fallopiantube" - }, - { - "@id": "bts:FemalegenitaltractNOS" - }, - { - "@id": "bts:FloorofmouthNOS" - }, - { - "@id": "bts:Frontallobe" - }, - { - "@id": "bts:Frontalsinus" - }, - { - "@id": "bts:Fundusofstomach" - }, - { - "@id": "bts:Fundusuteri" - }, - { - "@id": "bts:Gallbladder" - }, - { - "@id": "bts:Gastricantrum" - }, - { - "@id": "bts:GastrointestinaltractNOS" - }, - { - "@id": "bts:Glanspenis" - }, - { - "@id": "bts:Glottis" - }, - { - "@id": "bts:GreatercurvatureofstomachNOS" - }, - { - "@id": "bts:GumNOS" - }, - { - "@id": "bts:Hardpalate" - }, - { - "@id": "bts:Headofpancreas" - }, - { - "@id": "bts:HeadfaceorneckNOS" - }, - { - "@id": "bts:Heart" - }, - { - "@id": "bts:HematopoieticsystemNOS" - }, - { - "@id": "bts:Hepaticflexureofcolon" - }, - { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" - }, - { - "@id": "bts:HypopharynxNOS" - }, - { - "@id": "bts:Ileum" - }, - { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" - }, - { - "@id": "bts:IntestinaltractNOS" - }, - { - "@id": "bts:Intra-abdominallymphnodes" - }, - { - "@id": "bts:Intrahepaticbileduct" - }, - { - "@id": "bts:Intrathoraciclymphnodes" - }, - { - "@id": "bts:IsletsofLangerhans" - }, - { - "@id": "bts:Isthmusuteri" - }, - { - "@id": "bts:Jejunum" - }, - { - "@id": "bts:KidneyNOS" - }, - { - "@id": "bts:Labiummajus" - }, - { - "@id": "bts:Labiumminus" - }, - { - "@id": "bts:Lacrimalgland" - }, - { - "@id": "bts:Laryngealcartilage" - }, - { - "@id": "bts:LarynxNOS" - }, - { - "@id": "bts:Lateralfloorofmouth" - }, - { - "@id": "bts:Lateralwallofbladder" - }, - { - "@id": "bts:Lateralwallofnasopharynx" - }, - { - "@id": "bts:Lateralwalloforopharynx" - }, - { - "@id": "bts:LessercurvatureofstomachNOS" - }, - { - "@id": "bts:Lingualtonsil" - }, - { - "@id": "bts:LipNOS" - }, - { - "@id": "bts:Liver" - }, - { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" - }, - { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" - }, - { - "@id": "bts:Lowergum" - }, - { - "@id": "bts:LowerlimbNOS" - }, - { - "@id": "bts:Lowerlobelung" - }, - { - "@id": "bts:Lowerthirdofesophagus" - }, - { - "@id": "bts:Lower-innerquadrantofbreast" - }, - { - "@id": "bts:Lower-outerquadrantofbreast" - }, - { - "@id": "bts:LungNOS" - }, - { - "@id": "bts:LymphnodeNOS" - }, - { - "@id": "bts:Lymphnodesofaxillaorarm" - }, - { - "@id": "bts:Lymphnodesofheadfaceandneck" - }, - { - "@id": "bts:Lymphnodesofinguinalregionorleg" - }, - { - "@id": "bts:Lymphnodesofmultipleregions" - }, - { - "@id": "bts:Mainbronchus" - }, - { - "@id": "bts:MajorsalivaryglandNOS" - }, - { - "@id": "bts:MalegenitalorgansNOS" - }, - { - "@id": "bts:Mandible" - }, - { - "@id": "bts:Maxillarysinus" - }, - { - "@id": "bts:Meckeldiverticulum" - }, - { - "@id": "bts:MediastinumNOS" - }, - { - "@id": "bts:Medullaofadrenalgland" - }, - { - "@id": "bts:MeningesNOS" - }, - { - "@id": "bts:Middleear" - }, - { - "@id": "bts:Middlelobelung" - }, - { - "@id": "bts:Middlethirdofesophagus" - }, - { - "@id": "bts:MouthNOS" - }, - { - "@id": "bts:MucosaoflipNOS" - }, - { - "@id": "bts:Mucosaoflowerlip" - }, - { - "@id": "bts:Mucosaofupperlip" - }, - { - "@id": "bts:Myometrium" - }, - { - "@id": "bts:Nasalcavity" - }, - { - "@id": "bts:NasopharynxNOS" - }, - { - "@id": "bts:NervoussystemNOS" - }, - { - "@id": "bts:Nipple" - }, - { - "@id": "bts:Occipitallobe" - }, - { - "@id": "bts:Olfactorynerve" - }, - { - "@id": "bts:Opticnerve" - }, - { - "@id": "bts:OrbitNOS" - }, - { - "@id": "bts:OropharynxNOS" - }, - { - "@id": "bts:Otherill-definedsites" - }, - { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" - }, - { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" - }, - { - "@id": "bts:Otherspecifiedpartsofpancreas" - }, - { - "@id": "bts:Ovary" - }, - { - "@id": "bts:Overlappinglesionofaccessorysinuses" - }, - { - "@id": "bts:Overlappinglesionofbladder" - }, - { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" - }, - { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" - }, - { - "@id": "bts:Overlappinglesionofbrain" - }, - { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" - }, - { - "@id": "bts:Overlappinglesionofbreast" - }, - { - "@id": "bts:Overlappinglesionofcervixuteri" - }, - { - "@id": "bts:Overlappinglesionofcolon" - }, - { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" - }, - { - "@id": "bts:Overlappinglesionofcorpusuteri" - }, - { - "@id": "bts:Overlappinglesionofdigestivesystem" - }, - { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" - }, - { - "@id": "bts:Overlappinglesionofesophagus" - }, - { - "@id": "bts:Overlappinglesionofeyeandadnexa" - }, - { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" - }, - { - "@id": "bts:Overlappinglesionoffloorofmouth" - }, - { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" - }, - { - "@id": "bts:Overlappinglesionofhypopharynx" - }, - { - "@id": "bts:Overlappinglesionofill-definedsites" - }, - { - "@id": "bts:Overlappinglesionoflarynx" - }, - { - "@id": "bts:Overlappinglesionoflip" - }, - { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" - }, - { - "@id": "bts:Overlappinglesionoflung" - }, - { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" - }, - { - "@id": "bts:Overlappinglesionofmalegenitalorgans" - }, - { - "@id": "bts:Overlappinglesionofnasopharynx" - }, - { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" - }, - { - "@id": "bts:Overlappinglesionofpalate" - }, - { - "@id": "bts:Overlappinglesionofpancreas" - }, - { - "@id": "bts:Overlappinglesionofpenis" - }, - { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" - }, - { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" - }, - { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" - }, - { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" - }, - { - "@id": "bts:Overlappinglesionofskin" - }, - { - "@id": "bts:Overlappinglesionofsmallintestine" - }, - { - "@id": "bts:Overlappinglesionofstomach" - }, - { - "@id": "bts:Overlappinglesionoftongue" - }, - { - "@id": "bts:Overlappinglesionoftonsil" - }, - { - "@id": "bts:Overlappinglesionofurinaryorgans" - }, - { - "@id": "bts:Overlappinglesionofvulva" - }, - { - "@id": "bts:Overlappinglesionsoforopharynx" - }, - { - "@id": "bts:PalateNOS" - }, - { - "@id": "bts:PancreasNOS" - }, - { - "@id": "bts:Pancreaticduct" - }, - { - "@id": "bts:Parametrium" - }, - { - "@id": "bts:Paraspinal" - }, - { - "@id": "bts:Parathyroidgland" - }, - { - "@id": "bts:Paraurethralgland" - }, - { - "@id": "bts:Parietallobe" - }, - { - "@id": "bts:Parotidgland" - }, - { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" - }, - { - "@id": "bts:Pelviclymphnodes" - }, - { - "@id": "bts:PelvisNOS" - }, - { - "@id": "bts:PenisNOS" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" - }, - { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" - }, - { - "@id": "bts:PeritoneumNOS" - }, - { - "@id": "bts:PharynxNOS" - }, - { - "@id": "bts:Pinealgland" - }, - { - "@id": "bts:Pituitarygland" - }, - { - "@id": "bts:Placenta" - }, - { - "@id": "bts:PleuraNOS" - }, - { - "@id": "bts:Postcricoidregion" - }, - { - "@id": "bts:Posteriormediastinum" - }, - { - "@id": "bts:Posteriorwallofbladder" - }, - { - "@id": "bts:Posteriorwallofhypopharynx" - }, - { - "@id": "bts:Posteriorwallofnasopharynx" - }, - { - "@id": "bts:Posteriorwalloforopharynx" - }, - { - "@id": "bts:Prepuce" - }, - { - "@id": "bts:Prostategland" - }, - { - "@id": "bts:Pylorus" - }, - { - "@id": "bts:Pyriformsinus" - }, - { - "@id": "bts:Rectosigmoidjunction" - }, - { - "@id": "bts:RectumNOS" - }, - { - "@id": "bts:Renalpelvis" - }, - { - "@id": "bts:ReticuloendothelialsystemNOS" - }, - { - "@id": "bts:Retina" - }, - { - "@id": "bts:Retromolararea" - }, - { - "@id": "bts:Retroperitoneum" - }, - { - "@id": "bts:Ribsternumclavicleandassociatedjoints" - }, - { - "@id": "bts:Roundligament" - }, - { - "@id": "bts:ScrotumNOS" - }, - { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" - }, - { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" - }, - { - "@id": "bts:Sigmoidcolon" - }, - { - "@id": "bts:SkinoflipNOS" - }, - { - "@id": "bts:Skinoflowerlimbandhip" - }, - { - "@id": "bts:Skinofotherandunspecifiedpartsofface" - }, - { - "@id": "bts:Skinofscalpandneck" - }, - { - "@id": "bts:Skinoftrunk" - }, - { - "@id": "bts:Skinofupperlimbandshoulder" - }, - { - "@id": "bts:SkinNOS" - }, - { - "@id": "bts:SmallintestineNOS" - }, - { - "@id": "bts:SoftpalateNOS" - }, - { - "@id": "bts:Specifiedpartsofperitoneum" - }, - { - "@id": "bts:Spermaticcord" - 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If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. 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{ - "@id": "bts:ImmediateFamilyHistoryOvarianCancer", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beforeage50" - }, - { - "@id": "bts:Notbeforeage50" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Ovarian Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", - 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"@type": "rdfs:Class", - "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. 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{ - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Cancer KRAS Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColonPolypOccurenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "ColonPolypOccurenceIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colon Polyp Occurence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyHistoryColorectalPolyp", - 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"@type": "rdfs:Class", - "rdfs:comment": "Size of the polyp removed in cm", - "rdfs:label": "SizeofPolypRemoved", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size of Polyp Removed", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypCount", - "@type": "rdfs:Class", - "rdfs:comment": "The total number of polyps detected", - "rdfs:label": "ColorectalPolypCount", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Polyp Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of polyp found in the participant", - "rdfs:label": "ColorectalPolypType", - "rdfs:subClassOf": [ - { - "@id": "bts:ColorectalCancerTier3" - 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}, - { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" - }, - { - "@id": "bts:BreastBiopsyProcedureFindingType" - }, - { - "@id": "bts:BreastQuadrantSite" - }, - { - "@id": "bts:BreastCancerAssessmentTests" - }, - { - "@id": "bts:BreastCancerGenomicTestPerformed" - }, - { - "@id": "bts:MammaprintRiskGroup" - }, - { - "@id": "bts:OncotypeRiskGroup" - }, - { - "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" - }, - { - "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" - }, - { - "@id": "bts:BreastCancerAllredEstrogenReceptorScore" - }, - { - "@id": "bts:PriorInvasiveBreastDisease" - }, - { - "@id": "bts:BreastCarcinomaERStatusPercentageValue" - }, - { - "@id": "bts:BreastCarcinomaPRStatusPercentageValue" - }, - { - "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" - }, - { - "@id": "bts:BreastCarcinomaCentromere17CopyNumber" - }, - { - "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" - }, - { - "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" - }, - { - "@id": "bts:BreastCarcinomaSurgicalProcedureName" - }, - { - "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" - }, - { - "@id": "bts:BreastCarcinomaHER2Status" - }, - { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" - }, - { - "@id": "bts:BreastCarcinomaERStainingIntensity" - }, - { - "@id": "bts:BreastCarcinomaPRStainingIntensity" - }, - { - "@id": "bts:OncotypeScore" - }, - { - "@id": "bts:BreastImagingPerformedType" - }, - { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" - }, - { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" - }, - { - "@id": "bts:BIRADSMammographyBreastDensityCategory" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", - "rdfs:label": "BreastCarcinomaDetectionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - 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}, - { - "@id": "bts:Invasivemixedductalandlobularcarcinoma" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Breast Carcinoma Histology Category", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", - "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", - "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alveolartype" - }, - { - "@id": "bts:Classicaltype" - }, - { - "@id": "bts:Datanotavailable" - }, - { - "@id": "bts:Pleomorphictype" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", - "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for the most common type of invasive breast carcinoma.", - "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Classicaltype" - }, - { - "@id": "bts:Invasivecarcinoma-typecannotbedetermined" - }, - { - "@id": "bts:Invasivecribriformcarcinoma" - }, - { - "@id": "bts:Invasivemicropapillarycarcinoma" - }, - { - "@id": "bts:Invasivepapillarycarcinoma" - }, - { - "@id": "bts:Invasivetubularcarcinoma" - }, - { - "@id": "bts:Medullarycarcinoma" - }, - { - "@id": "bts:Mucinouscarcinoma" - }, - { - "@id": "bts:Tubulolobularcarcinoma" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Invasive Ductal Breast Carcinoma Histologic Category", - "sms:required": "sms:false", - 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"rdfs:label": "BreastQuadrantSite", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Upperouterquadrant" - }, - { - "@id": "bts:Lowerouterquadrant" - }, - { - "@id": "bts:Upperinnerquadrant" - }, - { - "@id": "bts:Lowerinnerquadrant" - }, - { - "@id": "bts:Central" - }, - { - "@id": "bts:Nipple" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Breast Quadrant Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerAssessmentTests", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", - "rdfs:label": "BreastCancerAssessmentTests", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - 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If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoBirth", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Birth", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:CountryofResidence", - "@type": "rdfs:Class", - "rdfs:comment": "Country of Residence at enrollment", - "rdfs:label": "CountryofResidence", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Afghanistan" - }, - { - "@id": "bts:Albania" - }, - { - "@id": "bts:Algeria" - }, - { - "@id": "bts:Andorra" - }, - { - "@id": "bts:Angola" - }, - { - "@id": "bts:Anguilla" - }, - { - "@id": "bts:AntiguaandBarbuda" - }, - { - "@id": "bts:Argentina" - }, - { - "@id": "bts:Armenia" - }, - { - "@id": "bts:Aruba" - }, - { - "@id": "bts:Australia" - }, - { - "@id": "bts:Austria" - }, - { - "@id": "bts:Azerbaijan" - }, - { - "@id": "bts:Bahamas" - }, - { - "@id": "bts:Bahrain" - }, - { - "@id": "bts:Bangladesh" - }, - { - "@id": "bts:Barbados" - }, - { - "@id": "bts:Belarus" - }, - { - "@id": "bts:Belgium" - }, - { - "@id": "bts:Belize" - }, - { - "@id": "bts:Benin" - }, - { - "@id": "bts:Bermuda" - }, - { - "@id": "bts:Bhutan" - }, - { - "@id": "bts:Bolivia" - }, - { - "@id": "bts:BosniaandHerzegovina" - }, - { - "@id": "bts:Botswana" - }, - { - "@id": "bts:Brazil" - }, - { - "@id": "bts:Brunei" - }, - { - "@id": "bts:Bulgaria" - }, - { - "@id": "bts:BurkinaFaso" - }, - { - "@id": "bts:Burundi" - }, - { - "@id": "bts:Cambodia" - }, - { - "@id": "bts:Cameroon" - }, - { - "@id": "bts:Canada" - }, - { - "@id": "bts:CapeVerde" - }, - { - "@id": "bts:CaymanIslands" - }, - { - "@id": "bts:CentralAfricanRepublic" - }, - { - "@id": "bts:Chad" - }, - { - "@id": "bts:Chile" - }, - { - "@id": "bts:China" - }, - { - "@id": "bts:Colombia" - }, - { - "@id": "bts:Comoros" - }, - { - "@id": "bts:Congo" - }, - { - "@id": "bts:CookIslands" - }, - { - "@id": "bts:CostaRica" - }, - { - "@id": "bts:Coted'Ivoire" - }, - { - "@id": "bts:Croatia" - }, - { - "@id": "bts:Cuba" - }, - { - "@id": "bts:Curacao" - }, - { - "@id": "bts:Cyprus" - }, - { - "@id": "bts:CzechRepublic(Czechia)" - }, - { - "@id": "bts:DemocraticRepublicoftheCongo" - }, - { - "@id": "bts:Denmark" - }, - { - "@id": "bts:Djibouti" - }, - { - "@id": "bts:Dominica" - }, - { - "@id": "bts:DominicanRepublic" - }, - { - "@id": "bts:Ecuador" - }, - { - "@id": "bts:Egypt" - }, - { - "@id": "bts:ElSalvador" - }, - { - "@id": "bts:EquatorialGuinea" - }, - { - "@id": "bts:Eritrea" - }, - { - "@id": "bts:Estonia" - }, - { - "@id": "bts:Eswatini" - }, - { - "@id": "bts:Ethiopia" - }, - { - "@id": "bts:FalklandIslands(Malvinas)" - }, - { - "@id": "bts:FaroeIslands" - }, - { - "@id": "bts:FederatedStatesofMicronesia" - }, - { - "@id": "bts:Fiji" - }, - { - "@id": "bts:Finland" - }, - { - "@id": "bts:France" - }, - { - "@id": "bts:FrenchGuiana" - }, - { - "@id": "bts:FrenchPolynesia" - }, - { - "@id": "bts:Gabon" - }, - { - "@id": "bts:Gambia" - }, - { - "@id": "bts:Georgia" - }, - { - "@id": "bts:Germany" - }, - { - "@id": "bts:Ghana" - }, - { - "@id": "bts:Gibraltar" - }, - { - "@id": "bts:Greece" - }, - { - "@id": "bts:Greenland" - }, - { - "@id": "bts:Grenada" - }, - { - "@id": "bts:Guadeloupe" - }, - { - "@id": "bts:Guam" - }, - { - "@id": "bts:Guatemala" - }, - { - "@id": "bts:Guernsey" - }, - { - "@id": "bts:Guinea" - }, - { - "@id": "bts:Guinea-Bissau" - }, - { - "@id": "bts:Guyana" - }, - { - "@id": "bts:Haiti" - }, - { - "@id": "bts:HolySee" - }, - { - "@id": "bts:Honduras" - }, - { - "@id": "bts:HongKong" - }, - { - "@id": "bts:Hungary" - }, - { - "@id": "bts:Iceland" - }, - { - "@id": "bts:India" - }, - { - "@id": "bts:Indonesia" - }, - { - "@id": "bts:Iran" - }, - { - "@id": "bts:Iraq" - }, - { - "@id": "bts:Ireland" - }, - { - "@id": "bts:IsleofMan" - }, - { - "@id": "bts:Israel" - }, - { - "@id": "bts:Italy" - }, - { - "@id": "bts:Jamaica" - }, - { - "@id": "bts:Japan" - }, - { - "@id": "bts:Jersey" - }, - { - "@id": "bts:Jordan" - }, - { - "@id": "bts:Kazakhstan" - }, - { - "@id": "bts:Kenya" - }, - { - "@id": "bts:Kiribati" - }, - { - "@id": "bts:Kosovo" - }, - { - "@id": "bts:Kuwait" - }, - { - "@id": "bts:Kyrgyzstan" - }, - { - "@id": "bts:Laos" - }, - { - "@id": "bts:Latvia" - }, - { - "@id": "bts:Lebanon" - }, - { - "@id": "bts:Lesotho" - }, - { - "@id": "bts:Liberia" - }, - { - "@id": "bts:Libya" - }, - { - "@id": "bts:Liechtenstein" - }, - { - "@id": "bts:Lithuania" - }, - { - "@id": "bts:Luxembourg" - }, - { - "@id": "bts:Macau" - }, - { - "@id": "bts:Madagascar" - }, - { - "@id": "bts:Malawi" - }, - { - "@id": "bts:Malaysia" - }, - { - "@id": "bts:Maldives" - }, - { - "@id": "bts:Mali" - }, - { - "@id": "bts:Malta" - }, - { - "@id": "bts:MarshallIslands" - }, - { - "@id": "bts:Martinique" - }, - { - "@id": "bts:Mauritania" - }, - { - "@id": "bts:Mauritius" - }, - { - "@id": "bts:Mayotte" - }, - { - "@id": "bts:Mexico" - }, - { - "@id": "bts:Moldova" - }, - { - "@id": "bts:Monaco" - }, - { - "@id": "bts:Mongolia" - }, - { - "@id": "bts:Montenegro" - }, - { - "@id": "bts:Montserrat" - }, - { - "@id": "bts:Morocco" - }, - { - "@id": "bts:Mozambique" - }, - { - "@id": "bts:Myanmar" - }, - { - "@id": "bts:Namibia" - }, - { - "@id": "bts:Nauru" - }, - { - "@id": "bts:Nepal" - }, - { - "@id": "bts:Netherlands" - }, - { - "@id": "bts:NewCaledonia" - }, - { - "@id": "bts:NewZealand" - }, - { - "@id": "bts:Nicaragua" - }, - { - "@id": "bts:Niger" - }, - { - "@id": "bts:Nigeria" - }, - { - "@id": "bts:Niue" - }, - { - "@id": "bts:NorthKorea" - }, - { - "@id": "bts:NorthMacedonia" - }, - { - "@id": "bts:NorthernMarianaIslands" - }, - { - "@id": "bts:Norway" - }, - { - "@id": "bts:Oman" - }, - { - "@id": "bts:Pakistan" - }, - { - "@id": "bts:Palau" - }, - { - "@id": "bts:Panama" - }, - { - "@id": "bts:PapuaNewGuinea" - }, - { - "@id": "bts:Paraguay" - }, - { - "@id": "bts:Peru" - }, - { - "@id": "bts:Philippines" - }, - { - "@id": "bts:Poland" - }, - { - "@id": "bts:Portugal" - }, - { - "@id": "bts:PuertoRico" - }, - { - "@id": "bts:Qatar" - }, - { - "@id": "bts:Reunion" - }, - { - "@id": "bts:Romania" - }, - { - "@id": "bts:Russia" - }, - { - "@id": "bts:Rwanda" - }, - { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" - }, - { - "@id": "bts:SaintKittsandNevis" - }, - { - "@id": "bts:SaintLucia" - }, - { - "@id": "bts:SaintPierreandMiquelon" - }, - { - "@id": "bts:SaintVincentandtheGrenadines" - }, - { - "@id": "bts:Samoa" - }, - { - "@id": "bts:SanMarino" - }, - { - "@id": "bts:SaoTomeandPrincipe" - }, - { - "@id": "bts:SaudiArabia" - }, - { - "@id": "bts:Senegal" - }, - { - "@id": "bts:Serbia" - }, - { - "@id": "bts:Seychelles" - }, - { - "@id": "bts:SierraLeone" - }, - { - "@id": "bts:Singapore" - }, - { - "@id": "bts:Slovakia" - }, - { - "@id": "bts:Slovenia" - }, - { - "@id": "bts:SolomonIslands" - }, - { - "@id": "bts:Somalia" - }, - { - "@id": "bts:SouthAfrica" - }, - { - "@id": "bts:SouthKorea" - }, - { - "@id": "bts:SouthSudan" - }, - { - "@id": "bts:Spain" - }, - { - "@id": "bts:SriLanka" - }, - { - "@id": "bts:StateofPalestine" - }, - { - "@id": "bts:Sudan" - }, - { - "@id": "bts:Suriname" - }, - { - "@id": "bts:Svalbard&JanMayenIslands" - }, - { - "@id": "bts:Sweden" - }, - { - "@id": "bts:Switzerland" - }, - { - "@id": "bts:Syria" - }, - { - "@id": "bts:Taiwan" - }, - { - "@id": "bts:Tajikistan" - }, - { - "@id": "bts:Tanzania" - }, - { - "@id": "bts:Thailand" - }, - { - "@id": "bts:Timor-Leste" - }, - { - "@id": "bts:Togo" - }, - { - "@id": "bts:Tokelau" - }, - { - "@id": "bts:Tonga" - }, - { - "@id": "bts:TrinidadandTobago" - }, - { - "@id": "bts:Tunisia" - }, - { - "@id": "bts:Turkey" - }, - { - "@id": "bts:Turkmenistan" - }, - { - "@id": "bts:Tuvalu" - }, - { - "@id": "bts:Uganda" - }, - { - "@id": "bts:Ukraine" - }, - { - "@id": "bts:UnitedArabEmirates" - }, - { - "@id": "bts:UnitedKingdom" - }, - { - "@id": "bts:UnitedStates" - }, - { - "@id": "bts:Uruguay" - }, - { - "@id": "bts:Uzbekistan" - }, - { - "@id": "bts:Vanuatu" - }, - { - "@id": "bts:Venezuela" - }, - { - "@id": "bts:Vietnam" - }, - { - "@id": "bts:VirginIslandsBritish" - }, - { - "@id": "bts:VirginIslandsU.S." - }, - { - "@id": "bts:WallisandFutuna" - }, - { - "@id": "bts:WesternSahara" - }, - { - "@id": "bts:Yemen" - }, - { - "@id": "bts:Zambia" - }, - { - "@id": "bts:Zimbabwe" - } - ], - "sms:displayName": "Country of Residence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeIsObfuscated", - "@type": "rdfs:Class", - "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "rdfs:label": "AgeIsObfuscated", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Age Is Obfuscated", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:YearOfBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label": "YearOfBirth", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Year Of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OccupationDurationYears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Occupation Duration Years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PrematureAtBirth", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Premature At Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WeeksGestationatBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weeks Gestation at Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RelativewithCancerHistory", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-CancerHistoryRelative" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relative with Cancer History", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokingExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-SmokingExposure" - }, - { - "@id": "bts:No-SmokingExposure" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AlcoholExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-AlcoholExposure" - }, - { - "@id": "bts:No-AlcoholExposure" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AsbestosExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Asbestos Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CoalDustExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Coal Dust Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RadonExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Radon Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RespirableCrystallineSilicaExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Respirable Crystalline Silica Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdverseEvent", - "@type": "rdfs:Class", - "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", - "rdfs:label": "AdverseEvent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdominalDistension" - }, - { - "@id": "bts:AbdominalInfection" - }, - { - "@id": "bts:AbdominalPain" - }, - { - "@id": "bts:AbdominalSoftTissueNecrosis" - }, - { - "@id": "bts:AbducensNerveDisorder" - }, - { - "@id": "bts:AccessoryNerveDisorder" - }, - { - "@id": "bts:Acidosis" - }, - { - "@id": "bts:AcousticNerveDisorderNOS" - }, - { - "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" - }, - { - "@id": "bts:AcuteCoronarySyndrome" - }, - { - "@id": "bts:AcuteKidneyInjury" - }, - { - "@id": "bts:AdrenalInsufficiency" - }, - { - "@id": "bts:AdultRespiratoryDistressSyndrome" - }, - { - "@id": "bts:Agitation" - }, - { - "@id": "bts:Akathisia" - }, - { - "@id": "bts:AlanineAminotransferaseIncreased" - }, - { - "@id": "bts:AlcoholIntolerance" - }, - { - "@id": "bts:AlkalinePhosphataseIncreased" - }, - { - "@id": "bts:Alkalosis" - }, - { - "@id": "bts:AllergicReaction" - }, - { - "@id": "bts:AllergicRhinitis" - }, - { - "@id": "bts:Alopecia" - }, - { - "@id": "bts:Amnesia" - }, - { - "@id": "bts:AnalFistula" - }, - { - "@id": "bts:AnalHemorrhage" - }, - { - "@id": "bts:AnalMucositis" - }, - { - "@id": "bts:AnalNecrosis" - }, - { - "@id": "bts:AnalPain" - }, - { - "@id": "bts:AnalStenosis" - }, - { - "@id": "bts:AnalUlcer" - }, - { - "@id": "bts:Anaphylaxis" - }, - { - "@id": "bts:Anemia" - }, - { - "@id": "bts:AnkleFracture" - }, - { - "@id": "bts:AnorectalInfection" - }, - { - "@id": "bts:Anorexia" - }, - { - "@id": "bts:Anorgasmia" - }, - { - "@id": "bts:Anxiety" - }, - { - "@id": "bts:AorticInjury" - }, - { - "@id": "bts:AorticValveDisease" - }, - { - "@id": "bts:Aphonia" - }, - { - "@id": "bts:Apnea" - }, - { - "@id": "bts:Appendicitis" - }, - { - "@id": "bts:AppendicitisPerforated" - }, - { - "@id": "bts:Arachnoiditis" - }, - { - "@id": "bts:ArterialInjury" - }, - { - "@id": "bts:ArteritisInfective" - 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}, - { - "@id": "bts:LocalizedEdema" - }, - { - "@id": "bts:Lordosis" - }, - { - "@id": "bts:LowerGastrointestinalHemorrhage" - }, - { - "@id": "bts:LungInfection" - }, - { - "@id": "bts:LymphGlandInfection" - }, - { - "@id": "bts:LymphLeakage" - }, - { - "@id": "bts:LymphNodePain" - }, - { - "@id": "bts:Lymphedema" - }, - { - "@id": "bts:Lymphocele" - }, - { - "@id": "bts:LymphocyteCountDecreased" - }, - { - "@id": "bts:LymphocyteCountIncreased" - }, - { - "@id": "bts:Malabsorption" - }, - { - "@id": "bts:Malaise" - }, - { - "@id": "bts:Mania" - }, - { - "@id": "bts:MediastinalHemorrhage" - }, - { - "@id": "bts:MediastinalInfection" - }, - { - "@id": "bts:MemoryImpairment" - }, - { - "@id": "bts:Meningismus" - }, - { - "@id": "bts:Meningitis" - }, - { - "@id": "bts:Menopause" - }, - { - "@id": "bts:Menorrhagia" - }, - { - "@id": "bts:MetabolismandNutritionDisordersOther" - }, - { - "@id": "bts:MiddleEarInflammation" - }, - { - "@id": "bts:MitralValveDisease" - }, - { - "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" - 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}, - { - "@id": "bts:Radiculitis" - }, - { - "@id": "bts:RashAcneiform" - }, - { - "@id": "bts:RashMaculo-Papular" - }, - { - "@id": "bts:RashPustular" - }, - { - "@id": "bts:RectalAnastomoticLeak" - }, - { - "@id": "bts:RectalFistula" - }, - { - "@id": "bts:RectalHemorrhage" - }, - { - "@id": "bts:RectalMucositis" - }, - { - "@id": "bts:RectalNecrosis" - }, - { - "@id": "bts:RectalObstruction" - }, - { - "@id": "bts:RectalPain" - }, - { - "@id": "bts:RectalPerforation" - }, - { - "@id": "bts:RectalStenosis" - }, - { - "@id": "bts:RectalUlcer" - }, - { - "@id": "bts:RecurrentLaryngealNervePalsy" - }, - { - "@id": "bts:RenalandUrinaryDisordersOther" - }, - { - "@id": "bts:RenalCalculi" - }, - { - "@id": "bts:RenalColic" - }, - { - "@id": "bts:RenalHemorrhage" - }, - { - "@id": "bts:ReproductiveSystemandBreastDisordersOther" - }, - { - "@id": "bts:RespiratoryFailure" - }, - { - "@id": "bts:Respiratory" - }, - { - "@id": "bts:ThoracicandMediastinalDisordersOther" - }, - { - "@id": "bts:Restlessness" - }, - { - "@id": "bts:RestrictiveCardiomyopathy" - }, - { - "@id": "bts:RetinalDetachment" - }, - { - "@id": "bts:RetinalTear" - }, - { - "@id": "bts:RetinalVascularDisorder" - }, - { - "@id": "bts:RetinoicAcidSyndrome" - }, - { - "@id": "bts:Retinopathy" - }, - { - "@id": "bts:RetroperitonealHemorrhage" - }, - { - "@id": "bts:ReversiblePosteriorLeukoencephalopathySyndrome" - }, - { - "@id": "bts:RhinitisInfective" - }, - { - "@id": "bts:RightVentricularDysfunction" - }, - { - "@id": "bts:SalivaryDuctInflammation" - }, - { - "@id": "bts:SalivaryGlandFistula" - }, - { - "@id": "bts:SalivaryGlandInfection" - }, - { - "@id": "bts:ScalpPain" - }, - { - "@id": "bts:ScleralDisorder" - }, - { - "@id": "bts:Scoliosis" - }, - { - "@id": "bts:ScrotalInfection" - }, - { - "@id": "bts:ScrotalPain" - }, - { - "@id": "bts:Seizure" - }, - { - "@id": "bts:Sepsis" - }, - { - "@id": "bts:Seroma" - }, - { - "@id": "bts:SerumAmylaseIncreased" - }, - { - "@id": "bts:SerumSickness" - }, - { - "@id": "bts:SickSinusSyndrome" - }, - { - "@id": "bts:SinusBradycardia" - }, - { - "@id": "bts:SinusDisorder" - }, - { - "@id": "bts:SinusPain" - }, - { - "@id": "bts:SinusTachycardia" - }, - { - "@id": "bts:Sinusitis" - }, - { - "@id": "bts:SkinandSubcutaneousTissueDisordersOther" - }, - { - "@id": "bts:SkinAtrophy" - }, - { - "@id": "bts:SkinHyperpigmentation" - }, - { - "@id": "bts:SkinHypopigmentation" - }, - { - "@id": "bts:SkinInduration" - }, - { - "@id": "bts:SkinInfection" - }, - { - "@id": "bts:SkinUlceration" - }, - { - "@id": "bts:SleepApnea" - }, - { - "@id": "bts:SmallIntestinalAnastomoticLeak" - }, - { - "@id": "bts:SmallIntestinalMucositis" - }, - { - "@id": "bts:SmallIntestinalObstruction" - }, - { - "@id": "bts:SmallIntestinalPerforation" - }, - { - "@id": "bts:SmallIntestinalStenosis" - }, - { - "@id": "bts:SmallIntestineInfection" - }, - { - "@id": "bts:SmallIntestineUlcer" - }, - { - "@id": "bts:Sneezing" - }, - { - "@id": "bts:SocialCircumstancesOther" - }, - { - "@id": "bts:SoftTissueInfection" - }, - { - "@id": "bts:SoftTissueNecrosisLowerLimb" - }, - { - "@id": "bts:SoftTissueNecrosisUpperLimb" - }, - { - "@id": "bts:Somnolence" - }, - { - "@id": "bts:SoreThroat" - }, - { - "@id": "bts:Spasticity" - }, - { - "@id": "bts:SpermaticCordAnastomoticLeak" - }, - { - "@id": "bts:SpermaticCordHemorrhage" - }, - { - "@id": "bts:SpermaticCordObstruction" - }, - { - "@id": "bts:SpinalFracture" - }, - { - "@id": "bts:SpleenDisorder" - }, - { - "@id": "bts:SplenicInfection" - }, - { - "@id": "bts:StenosisofGastrointestinalStoma" - }, - { - "@id": "bts:Stevens-JohnsonSyndrome" - }, - { - "@id": "bts:StomaSiteInfection" - }, - { - "@id": "bts:StomachPain" - }, - { - "@id": "bts:StomalUlcer" - }, - { - "@id": "bts:Stridor" - }, - { - "@id": "bts:Stroke" - }, - { - "@id": "bts:SuddenDeathNOS" - }, - { - "@id": "bts:SuicidalIdeation" - }, - { - "@id": "bts:SuicideAttempt" - }, - { - "@id": "bts:SuperficialSoftTissueFibrosis" - }, - { - "@id": "bts:SuperficialThrombophlebitis" - }, - { - "@id": "bts:SuperiorVenaCavaSyndrome" - }, - { - "@id": "bts:SupraventricularTachycardia" - }, - { - "@id": "bts:SurgicalandMedicalProceduresOther" - }, - { - "@id": "bts:Syncope" - }, - { - "@id": "bts:Telangiectasia" - }, - { - "@id": "bts:TesticularDisorder" - }, - { - "@id": "bts:TesticularHemorrhage" - }, - { - "@id": "bts:TesticularPain" - }, - { - "@id": "bts:ThromboembolicEvent" - }, - { - "@id": "bts:ThromboticThrombocytopenicPurpura" - }, - { - "@id": "bts:Tinnitus" - }, - { - "@id": "bts:ToothDevelopmentDisorder" - }, - { - "@id": "bts:ToothDiscoloration" - }, - { - "@id": "bts:ToothInfection" - }, - { - "@id": "bts:Toothache" - }, - { - "@id": "bts:ToxicEpidermalNecrolysis" - }, - { - "@id": "bts:TrachealFistula" - }, - { - "@id": "bts:TrachealHemorrhage" - }, - { - "@id": "bts:TrachealMucositis" - }, - { - "@id": "bts:TrachealObstruction" - }, - { - "@id": "bts:TrachealStenosis" - }, - { - "@id": "bts:Tracheitis" - }, - { - "@id": "bts:TracheostomySiteBleeding" - }, - { - "@id": "bts:TransientIschemicAttacks" - }, - { - "@id": "bts:TreatmentRelatedSecondaryMalignancy" - }, - { - "@id": "bts:Tremor" - }, - { - "@id": "bts:TricuspidValveDisease" - }, - { - "@id": "bts:TrigeminalNerveDisorder" - }, - { - "@id": "bts:Trismus" - }, - { - "@id": "bts:TumorLysisSyndrome" - }, - { - "@id": "bts:TumorPain" - }, - { - "@id": "bts:Typhlitis" - }, - { - "@id": "bts:UnequalLimbLength" - }, - { - "@id": "bts:UnintendedPregnancy" - }, - { - "@id": "bts:UpperGastrointestinalHemorrhage" - }, - { - "@id": "bts:UpperRespiratoryInfection" - }, - { - "@id": "bts:UretericAnastomoticLeak" - }, - { - "@id": "bts:UrethralAnastomoticLeak" - }, - { - "@id": "bts:UrethralInfection" - }, - { - "@id": "bts:UrinaryFistula" - }, - { - "@id": "bts:UrinaryFrequency" - }, - { - "@id": "bts:UrinaryIncontinence" - }, - { - "@id": "bts:UrinaryRetention" - }, - { - "@id": "bts:UrinaryTractInfection" - }, - { - "@id": "bts:UrinaryTractObstruction" - }, - { - "@id": "bts:UrinaryTractPain" - }, - { - "@id": "bts:UrinaryUrgency" - }, - { - "@id": "bts:UrineDiscoloration" - }, - { - "@id": "bts:UrineOutputDecreased" - }, - { - "@id": "bts:UrostomyLeak" - }, - { - "@id": "bts:UrostomyObstruction" - }, - { - "@id": "bts:UrostomySiteBleeding" - }, - { - "@id": "bts:UrostomyStenosis" - }, - { - "@id": "bts:Urticaria" - }, - { - "@id": "bts:UterineAnastomoticLeak" - }, - { - "@id": "bts:UterineFistula" - }, - { - "@id": "bts:UterineHemorrhage" - }, - { - "@id": "bts:UterineInfection" - }, - { - "@id": "bts:UterineObstruction" - }, - { - "@id": "bts:UterinePain" - }, - { - "@id": "bts:UterinePerforation" - }, - { - "@id": "bts:Uveitis" - }, - { - "@id": "bts:VaginalAnastomoticLeak" - }, - { - "@id": "bts:VaginalDischarge" - }, - { - "@id": "bts:VaginalDryness" - }, - { - "@id": "bts:VaginalFistula" - }, - { - "@id": "bts:VaginalHemorrhage" - }, - { - "@id": "bts:VaginalInfection" - }, - { - "@id": "bts:VaginalInflammation" - }, - { - "@id": "bts:VaginalObstruction" - }, - { - "@id": "bts:VaginalPain" - }, - { - "@id": "bts:VaginalPerforation" - }, - { - "@id": "bts:VaginalStricture" - }, - { - "@id": "bts:Vaginismus" - }, - { - "@id": "bts:VagusNerveDisorder" - }, - { - "@id": "bts:VasDeferensAnastomoticLeak" - }, - { - "@id": "bts:VascularAccessComplication" - }, - { - "@id": "bts:VascularDisordersOther" - }, - { - "@id": "bts:Vasculitis" - }, - { - "@id": "bts:VasovagalReaction" - }, - { - "@id": "bts:VenousInjury" - }, - { - "@id": "bts:VentricularArrhythmia" - }, - { - "@id": "bts:VentricularFibrillation" - }, - { - "@id": "bts:VentricularTachycardia" - }, - { - "@id": "bts:Vertigo" - }, - { - "@id": "bts:VestibularDisorder" - }, - { - "@id": "bts:Virilization" - }, - { - "@id": "bts:VisceralArterialIschemia" - }, - { - "@id": "bts:VitalCapacityAbnormal" - }, - { - "@id": "bts:VitreousHemorrhage" - }, - { - "@id": "bts:VoiceAlteration" - }, - { - "@id": "bts:Vomiting" - }, - { - "@id": "bts:VulvalInfection" - }, - { - "@id": "bts:WateringEyes" - }, - { - "@id": "bts:WeightGain" - }, - { - "@id": "bts:WeightLoss" - }, - { - "@id": "bts:Wheezing" - }, - { - "@id": "bts:WhiteBloodCellDecreased" - }, - { - "@id": "bts:Wolff-Parkinson-WhiteSyndrome" - }, - { - "@id": "bts:WoundComplication" - }, - { - "@id": "bts:WoundDehiscence" - }, - { - "@id": "bts:WoundInfection" - }, - { - "@id": "bts:WristFracture" - } - ], - "sms:displayName": "Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BarrettsEsophagusGobletCellsPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", - "rdfs:label": "BarrettsEsophagusGobletCellsPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Barretts Esophagus Goblet Cells Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BMI", - "@type": "rdfs:Class", - "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", - "rdfs:label": "BMI", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "BMI", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CauseofResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", - "rdfs:label": "CauseofResponse", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cause of Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Comorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", - "rdfs:label": "Comorbidity", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AcuteRenalFailure" - }, - { - "@id": "bts:Adenocarcinoma" - }, - { - "@id": "bts:AdrenocorticalInsufficiency" - }, - { - "@id": "bts:AdenomatousPolyposisColi" - }, - { - "@id": "bts:Allergies" - }, - { - "@id": "bts:Alpha-1Antitrypsin" - }, - { - "@id": "bts:Anemia" - }, - { - "@id": "bts:Anxiety" - }, - { - "@id": "bts:Arrhythmia" - }, - { - "@id": "bts:Arthritis" - }, - { - "@id": "bts:Asthma" - }, - { - "@id": "bts:AtrialFibrillation" - }, - { - "@id": "bts:AvascularNecrosis" - }, - { - "@id": "bts:Barrett'sEsophagus" - }, - { - "@id": "bts:BasalCellCarcinoma" - }, - { - "@id": "bts:Beckwith-Wiedemann" - }, - { - "@id": "bts:Behcet'sDisease" - }, - { - "@id": "bts:BiliaryDisorder" - }, - { - "@id": "bts:BloodClots" - }, - { - "@id": "bts:BoneFracture(s)" - }, - { - "@id": "bts:Bronchitis" - }, - { - "@id": "bts:CalciumChannelBlockers" - 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{ - "@id": "bts:DVT/PE" - }, - { - "@id": "bts:Dyslipidemia" - }, - { - "@id": "bts:Epilepsy" - }, - { - "@id": "bts:Eczema" - }, - { - "@id": "bts:Epstein-BarrVirus" - }, - { - "@id": "bts:FamilialAdenomatousPolyposis" - }, - { - "@id": "bts:FanconiAnemia" - }, - { - "@id": "bts:Fibrosis" - }, - { - "@id": "bts:GastroesophagealRefluxDisease" - }, - { - "@id": "bts:GERD" - }, - { - "@id": "bts:Glaucoma" - }, - { - "@id": "bts:GlycogenStorageDisease" - }, - { - "@id": "bts:Gout" - }, - { - "@id": "bts:GonadalDysfunction" - }, - { - "@id": "bts:GorlinSyndrome" - }, - { - "@id": "bts:H.pyloriInfection" - }, - { - "@id": "bts:Hashimoto'sThyroiditis" - }, - { - "@id": "bts:Headache" - }, - { - "@id": "bts:HeartDisease" - }, - { - "@id": "bts:Hemihypertrophy" - }, - { - "@id": "bts:HemorrhagicCystitis" - }, - { - "@id": "bts:Hepatitis" - }, - { - "@id": "bts:HepatitisAInfection" - }, - { - "@id": "bts:HepatitisBInfection" - }, - { - "@id": "bts:HepatitisCInfection" - }, - { - "@id": "bts:ChronicHepatitis" - }, - { - "@id": "bts:HereditaryNon-polyposisColonCancer" - }, - { - "@id": "bts:Herpes" - }, - { - "@id": "bts:HighGradeLiverDysplasticNodule" - }, - { - "@id": "bts:HIV/AIDS" - }, - { - "@id": "bts:HumanPapillomavirusInfection" - }, - { - "@id": "bts:HUS/TTP" - }, - { - "@id": "bts:Hypercholesterolemia" - }, - { - "@id": "bts:Hypercalcemia" - }, - { - "@id": "bts:Hyperglycemia" - }, - { - "@id": "bts:Hyperlipidemia" - }, - { - "@id": "bts:Hypertension" - }, - { - "@id": "bts:Hypospadias" - }, - { - "@id": "bts:Hypothyroidism" - }, - { - "@id": "bts:InflammatoryBowelDisease" - }, - { - "@id": "bts:InsulinControlledDiabetes" - }, - { - "@id": "bts:InterstitialPneumontisorARDS" - }, - { - "@id": "bts:IntraductalPapillaryMucinousNeoplasm" - }, - { - "@id": "bts:IronOverload" - }, - { - "@id": "bts:IschemicHeartDisease" - }, - { - "@id": "bts:ITP" - }, - { - "@id": "bts:JointReplacement" - }, - { - "@id": "bts:KidneyDisease" - }, - { - "@id": "bts:LiverCirrhosis(LiverDisease)" - }, - { - "@id": "bts:LiverToxicity(Non-Infectious)" - }, - { - "@id": "bts:Li-FraumeniSyndrome" - }, - { - "@id": "bts:LowGradeLiverDysplasticNodule" - }, - { - "@id": "bts:Lupus" - }, - { - "@id": "bts:LynchSyndrome" - }, - { - "@id": "bts:MAI" - }, - { - "@id": "bts:MyastheniaGravis" - }, - { - "@id": "bts:MyocardialInfarction" - }, - { - "@id": "bts:NeuroendocrineTumor" - }, - { - "@id": "bts:NonalcoholicSteatohepatitis" - }, - { - "@id": "bts:Obesity" - }, - { - "@id": "bts:Organtransplant(site)" - }, - { - "@id": "bts:Osteoarthritis" - }, - { - "@id": "bts:OsteoporosisorOsteopenia" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:OtherCancerWithin5Years" - }, - { - "@id": "bts:OtherNonmalignantSystemicDisease" - }, - { - "@id": "bts:OtherPulmonaryComplications" - }, - { - "@id": "bts:Pancreatitis" - }, - { - "@id": "bts:Pain(Various)" - }, - { - "@id": "bts:PepticUlcer(Ulcer)" - }, - { - "@id": "bts:PeripheralNeuropathy" - }, - { - "@id": "bts:PeripheralVascularDisease" - }, - { - "@id": "bts:Peutz-JeghersDisease" - }, - { - "@id": "bts:PregnancyinPatientorPartner" - }, - { - "@id": "bts:PrimarySclerosingCholangitis" - }, - { - "@id": "bts:Psoriasis" - }, - { - "@id": "bts:PulmonaryFibrosis" - }, - { - "@id": "bts:PulmonaryHemorrhage" - }, - { - "@id": "bts:RenalFailure(RequiringDialysis)" - }, - { - "@id": "bts:RenalDialysis" - }, - { - "@id": "bts:RenalInsufficiency" - }, - { - "@id": "bts:RheumatologicDisease" - }, - { - "@id": "bts:RheumatoidArthritis" - }, - { - "@id": "bts:Rubinstein-TaybiSyndrome" - }, - { - "@id": "bts:Sarcoidosis" - }, - { - "@id": "bts:Seizure" - }, - { - "@id": "bts:Sleepapnea" - }, - { - "@id": "bts:Smoking" - }, - { - "@id": "bts:Steatosis" - }, - { - "@id": "bts:Stroke" - }, - { - "@id": "bts:TransientIschemicAttack" - }, - { - "@id": "bts:Tuberculosis" - }, - { - "@id": "bts:TurcotSyndrome" - }, - { - "@id": "bts:Tyrosinemia" - }, - { - "@id": "bts:UlcerativeColitis" - }, - { - "@id": "bts:WagrSyndrome" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity", - 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If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoAdverseEvent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoComorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoComorbidity", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DiabetesTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", - "rdfs:label": "DiabetesTreatmentType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alpha-GlucosidaseInhibitor" - }, - { - "@id": "bts:Biguanide" - }, - { - "@id": "bts:Diet" - }, - { - "@id": "bts:InjectedInsulin" - }, - { - "@id": "bts:Insulin" - }, - { - "@id": "bts:OralHypoglycemic" - }, - { - "@id": "bts:Sulfonylurea" - }, - { - 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}, - { - "@id": "bts:MX-MixedResponse" - }, - { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" - }, - { - "@id": "bts:NPB-NoPalliativeBenefit" - }, - { - "@id": "bts:NR-NoResponse" - }, - { - "@id": "bts:PA-PalliativeTherapy" - }, - { - "@id": "bts:PB-PalliativeBenefit" - }, - { - "@id": "bts:PD-ProgressiveDisease" - }, - { - "@id": "bts:PDM-PersistentDistantMetastasis" - }, - { - "@id": "bts:PLD-PersistentLocoregionalDisease" - }, - { - "@id": "bts:PPD-Pseudoprogression" - }, - { - "@id": "bts:PR-PartialResponse" - }, - { - "@id": "bts:PSR-Pseudoresponse" - }, - { - "@id": "bts:RD-ResponsiveDisease" - }, - { - "@id": "bts:RP-Response" - }, - { - "@id": "bts:RPD-RadiographicProgressiveDisease" - }, - { - "@id": "bts:SCR-StringentCompleteResponse" - }, - { - "@id": "bts:SD-StableDisease" - }, - { - "@id": "bts:SPD-SurgicalProgression" - }, - { - "@id": "bts:TE-TooEarly" - }, - { - "@id": "bts:TF-TumorFree" - }, - { - "@id": "bts:VGPR-VeryGoodPartialResponse" - }, - { - "@id": "bts:WT-WithTumor" - 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}, - "schema:rangeIncludes": [ - { - "@id": "bts:\"0\"" - }, - { - "@id": "bts:\"1\"" - }, - { - "@id": "bts:\"2\"" - }, - { - "@id": "bts:\"3\"" - }, - { - "@id": "bts:\"4\"" - }, - { - "@id": "bts:\"5\"" - }, - { - "@id": "bts:\"0.0\"" - }, - { - "@id": "bts:\"1.0\"" - }, - { - "@id": "bts:\"2.0\"" - }, - { - "@id": "bts:\"3.0\"" - }, - { - "@id": "bts:\"4.0\"" - }, - { - "@id": "bts:\"5.0\"" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "ECOG Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", - "rdfs:label": "FEV1FVCPostBronchPercent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 FVC Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", - "rdfs:label": "FEV1FVCPreBronchPercent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV 1 FVC Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", - "rdfs:label": "FEV1RefPostBronchPercent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", - "rdfs:label": "FEV1RefPreBronchPercent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Height", - "@type": "rdfs:Class", - "rdfs:comment": "The height of the patient in centimeters.", - "rdfs:label": "Height", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Height", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "HepatitisSustainedVirologicalResponse", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hepatitis Sustained Virological Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HPVPositiveType", - "@type": "rdfs:Class", - "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", - "rdfs:label": "HPVPositiveType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:\"16\"" - }, - { - "@id": "bts:\"18\"" - }, - { - "@id": "bts:\"26\"" - }, - { - "@id": "bts:\"31\"" - }, - { - "@id": "bts:\"33\"" - }, - { - "@id": "bts:\"35\"" - }, - { - "@id": "bts:\"39\"" - }, - { - "@id": "bts:\"45\"" - }, - { - "@id": "bts:\"51\"" - }, - { - "@id": "bts:\"52\"" - }, - { - "@id": "bts:\"53\"" - }, - { - "@id": "bts:\"56\"" - }, - { - "@id": "bts:\"58\"" - }, - { - "@id": "bts:\"59\"" - }, - { - "@id": "bts:\"63\"" - }, - { - "@id": "bts:\"66\"" - }, - { - "@id": "bts:\"68\"" - }, - { - "@id": "bts:\"70\"" - }, - { - "@id": "bts:\"73\"" - }, - { - "@id": "bts:\"82\"" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "HPV Positive Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KarnofskyPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", - "rdfs:label": "KarnofskyPerformanceStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:\"0\"" - }, - { - "@id": "bts:\"10\"" - }, - { - "@id": "bts:\"20\"" - }, - { - "@id": "bts:\"30\"" - }, - { - "@id": "bts:\"40\"" - }, - { - "@id": "bts:\"50\"" - }, - { - "@id": "bts:\"60\"" - }, - { - "@id": "bts:\"70\"" - }, - { - "@id": "bts:\"80\"" - }, - { - "@id": "bts:\"90\"" - }, - { - "@id": "bts:\"100\"" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Karnofsky Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MenopauseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's menopause status.", - "rdfs:label": "MenopauseStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Premenopausal" - }, - { - "@id": "bts:Perimenopausal" - }, - { - "@id": "bts:Postmenopausal" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Menopause Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreatitisOnsetYear", - "@type": "rdfs:Class", - "rdfs:comment": "Date of onset of pancreatitis.", - "rdfs:label": "PancreatitisOnsetYear", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pancreatitis Onset Year", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:RefluxTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", - "rdfs:label": "RefluxTreatmentType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Antacids" - }, - { - "@id": "bts:H2Blockers" - }, - { - "@id": "bts:MedicallyTreated" - }, - { - "@id": "bts:NoTreatment" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:ProtonPumpInhibitors" - }, - { - "@id": "bts:SurgicallyTreated" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Reflux Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RiskFactor", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactor", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AlcoholConsumption" - }, - { - "@id": "bts:AlcoholicLiverDisease" - }, - { - "@id": "bts:AllergyAnimalNOS" - }, - { - "@id": "bts:AllergyAnt" - }, - { - "@id": "bts:AllergyBee" - }, - { - "@id": "bts:AllergyCat" - }, - { - "@id": "bts:AllergyDairyorLactose" - }, - { - "@id": "bts:AllergyDog" - }, - { - "@id": "bts:AllergyEggs" - }, - { - "@id": "bts:AllergyFoodNOS" - }, - { - "@id": "bts:AllergyFruit" - }, - { - "@id": "bts:AllergyMeat" - }, - { - "@id": "bts:AllergyMoldorDust" - }, - { - "@id": "bts:AllergyNuts" - }, - { - "@id": "bts:AllergyProcessedFoods" - }, - { - "@id": "bts:AllergySeafood" - }, - { - "@id": "bts:AllergyWasp" - }, - { - "@id": "bts:Alpha-1AntitrypsinDeficiency" - }, - { - "@id": "bts:AutoimmuneAtrophicChronicGastritis" - }, - { - "@id": "bts:Barrett'sEsophagus" - }, - { - "@id": "bts:Beckwith-Wiedemann" - }, - { - "@id": "bts:Behcet'sDisease" - }, - { - "@id": "bts:Cancer" - }, - { - "@id": "bts:Cholelithiasis" - }, - { - "@id": "bts:ChronicHepatitis" - }, - { - "@id": "bts:Cirrhosis" - }, - { - "@id": "bts:ColonPolyps" - }, - { - "@id": "bts:Commonvariableimmunedeficiency(CVID)" - }, - { - "@id": "bts:Denys-DrashSyndrome" - }, - { - "@id": "bts:DiabetesNOS" - }, - { - "@id": "bts:DiabetesTypeI" - }, - { - "@id": "bts:DiabetesTypeII" - }, - { - "@id": "bts:Diet" - }, - { - "@id": "bts:Diverticulitis" - }, - { - "@id": "bts:Endometriosis" - }, - { - "@id": "bts:Endosalpingiosis" - }, - { - "@id": "bts:Eczema" - }, - { - "@id": "bts:Epstein-BarrVirus" - }, - { - "@id": "bts:FamilialAdenomatousPolyposis" - }, - { - "@id": "bts:FanconiAnemia" - }, - { - "@id": "bts:Fibrosis" - }, - { - "@id": "bts:GastricPolyp(s)" - }, - { - "@id": "bts:Gilbert'sSyndrome" - }, - { - "@id": "bts:GorlinSyndrome" - }, - { - "@id": "bts:Hashimoto'sThyroiditis" - }, - { - "@id": "bts:HayFever" - }, - { - "@id": "bts:Headache" - }, - { - "@id": "bts:HelicobacterPylori-AssociatedGastritis" - }, - { - "@id": "bts:HematologicDisorderNOS" - }, - { - "@id": "bts:Hemihypertrophy" - }, - { - "@id": "bts:Hemochromatosis" - }, - { - "@id": "bts:HepaticEncephalopathy" - }, - { - "@id": "bts:HepatitisBInfection" - }, - { - "@id": "bts:HepatitisCInfection" - }, - { - "@id": "bts:HepatitisNOS" - }, - { - "@id": "bts:HighGradeDysplasia" - }, - { - "@id": "bts:HIV" - }, - { - "@id": "bts:HumanPapillomavirusInfection" - }, - { - "@id": "bts:Hypospadias" - }, - { - "@id": "bts:IntestinalMetaplasia" - }, - { - "@id": "bts:IronOverload" - }, - { - "@id": "bts:Li-FraumeniSyndrome" - }, - { - "@id": "bts:LowGradeDysplasia" - }, - { - "@id": "bts:LymphocyticThyroiditis" - }, - { - "@id": "bts:LynchSyndrome" - }, - { - "@id": "bts:MyastheniaGravis" - }, - { - "@id": "bts:NonalcoholicFattyLiverDisease" - }, - { - "@id": "bts:NonalcoholicSteatohepatitis" - }, - { - "@id": "bts:Obesity" - }, - { - "@id": "bts:OralContraceptives" - }, - { - "@id": "bts:Pancreatitis" - }, - { - "@id": "bts:ParasiticDiseaseofBiliaryTract" - }, - { - "@id": "bts:PrimarySclerosingCholangitis" - }, - { - "@id": "bts:RecurrentPyogenicCholangitis" - }, - { - "@id": "bts:RefluxDisease" - }, - { - "@id": "bts:RheumatoidArthritis" - }, - { - "@id": "bts:Rubinstein-TaybiSyndrome" - }, - { - "@id": "bts:Sarcoidosis" - }, - { - "@id": "bts:Seizure" - }, - { - "@id": "bts:SensoryChanges" - }, - { - "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" - }, - { - "@id": "bts:Steatosis" - }, - { - "@id": "bts:Tattoo" - }, - { - "@id": "bts:ThyroidNodularHyperplasia" - }, - { - "@id": "bts:TobaccoNOS" - }, - { - "@id": "bts:TobaccoSmokeless" - }, - { - "@id": "bts:TobaccoSmoking" - }, - { - "@id": "bts:TurcotSyndrome" - }, - { - "@id": "bts:UndescendedTestis" - }, - { - "@id": "bts:VisionChanges" - }, - { - "@id": "bts:WagrSyndrome" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Risk Factor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RiskFactorTreatment", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactorTreatment", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Risk Factor Treatment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ViralHepatitisSerologies", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", - "rdfs:label": "ViralHepatitisSerologies", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:HBVCoreAntibody" - }, - { - "@id": "bts:HBVDNA" - }, - { - "@id": "bts:HBVGenotype" - }, - { - "@id": "bts:HBVSurfaceAntibody" - }, - { - "@id": "bts:HCVGenotype" - }, - { - "@id": "bts:HepatitisBSurfaceAntigen" - }, - { - "@id": "bts:HepatitisCAntibody" - }, - { - "@id": "bts:HepatitisCVirusRNA" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Viral Hepatitis Serologies", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Weight", - "@type": "rdfs:Class", - "rdfs:comment": "The weight of the patient measured in kilograms.", - "rdfs:label": "Weight", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdverseEventGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "AdverseEventGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Grade1" - }, - { - "@id": "bts:Grade2" - }, - { - "@id": "bts:Grade3" - }, - { - "@id": "bts:Grade4" - }, - { - "@id": "bts:Grade5" - } - ], - "sms:displayName": "Adverse Event Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AIDSRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", - "rdfs:label": "AIDSRiskFactors", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Candidiasis" - }, - { - "@id": "bts:Coccidioidomycosis" - }, - { - "@id": "bts:Cryptococcosis" - }, - { - "@id": "bts:Cytomegalovirus" - }, - { - "@id": "bts:Encephalopathy" - }, - { - "@id": "bts:HerpesSimplexVirus" - }, - { - "@id": "bts:Histoplasmosis" - }, - { - "@id": "bts:Isosporiasis" - }, - { - "@id": "bts:MycobacteriumaviumComplex" - }, - { - "@id": "bts:Mycobacteriumtuberculosis" - }, - { - "@id": "bts:Mycobacterium" - }, - { - "@id": "bts:NOS" - }, - { - "@id": "bts:Nocardiosis" - }, - { - "@id": "bts:PneumocystisPneumonia" - }, - { - "@id": "bts:Pneumonia" - }, - { - "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" - }, - { - "@id": "bts:SalmonellaSepticemia" - }, - { - "@id": "bts:Toxoplasmosis" - }, - { - "@id": "bts:WastingSyndrome" - } - ], - "sms:displayName": "AIDS Risk Factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BodySurfaceArea", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", - "rdfs:label": "BodySurfaceArea", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Body Surface Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CD4Count", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", - "rdfs:label": "CD4Count", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "CD4 Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CDCHIVRiskFactors", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", - "rdfs:label": "CDCHIVRiskFactors", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Hemophiliac" - }, - { - "@id": "bts:HeterosexualContact" - }, - { - "@id": "bts:HomosexualContact" - }, - { - "@id": "bts:IntravenousDrugUser" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:TransfusionRecipient" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "CDC HIV Risk Factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoImaging", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoImaging", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Imaging", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:EvidenceofRecurrenceType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", - "rdfs:label": "EvidenceofRecurrenceType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BiopsywithHistologicConfirmation" - }, - { - "@id": "bts:ConvincingImageSource" - }, - { - "@id": "bts:PositiveBiomarkers" - } - ], - "sms:displayName": "Evidence of Recurrence Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HAARTTreatmentIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", - "rdfs:label": "HAARTTreatmentIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "HAART Treatment Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HIVViralLoad", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", - "rdfs:label": "HIVViralLoad", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HIV Viral Load", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HormonalContraceptiveUse", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", - "rdfs:label": "HormonalContraceptiveUse", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CurrentUser" - }, - { - "@id": "bts:FormerUser" - }, - { - "@id": "bts:NeverUsed" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hormonal Contraceptive Use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HysterectomyMarginsInvolved", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", - "rdfs:label": "HysterectomyMarginsInvolved", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bladder" - }, - { - "@id": "bts:MacroscopicParametrium" - }, - { - "@id": "bts:MicroscopicParametrium" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Vagina" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hysterectomy Margins Involved", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HysterectomyType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", - "rdfs:label": "HysterectomyType", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:HysterectomyNOS" - }, - { - "@id": "bts:Notperformed" - }, - { - "@id": "bts:RadicalHysterectomy" - }, - { - "@id": "bts:SimpleHysterectomy" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Hysterectomy Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingResult", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", - "rdfs:label": "ImagingResult", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Positive" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:Negative" - }, - { - "@id": "bts:NotPerformed" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Imaging Result", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", - 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}, - { - "@id": "bts:Bone" - }, - { - "@id": "bts:BoneMarrow" - }, - { - "@id": "bts:Brain" - }, - { - "@id": "bts:CerebrospinalFluid" - }, - { - "@id": "bts:CentralNervousSystem" - }, - { - "@id": "bts:Colon" - }, - { - "@id": "bts:DistantNodes" - }, - { - "@id": "bts:DistantOrgan" - }, - { - "@id": "bts:Groin" - }, - { - "@id": "bts:Kidney" - }, - { - "@id": "bts:Liver" - }, - { - "@id": "bts:Lung" - }, - { - "@id": "bts:LymphNode" - }, - { - "@id": "bts:Axillary" - }, - { - "@id": "bts:Inguinal" - }, - { - "@id": "bts:LymphNodeNOS" - }, - { - "@id": "bts:Mediastinum" - }, - { - "@id": "bts:Omentum" - }, - { - "@id": "bts:Ovary" - }, - { - "@id": "bts:Pelvis" - }, - { - "@id": "bts:PeritonealCavity" - }, - { - "@id": "bts:Peritoneum" - }, - { - "@id": "bts:Pleura" - }, - { - "@id": "bts:Scalp" - }, - { - "@id": "bts:Skin" - }, - { - "@id": "bts:SmallIntestine" - }, - { - "@id": "bts:SoftTissue" - }, - { - "@id": "bts:SpinalCord" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Metastasis at Diagnosis Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FirstSymptomPriortoDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", - "rdfs:label": "FirstSymptomPriortoDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AlteredMentalStatus" - }, - { - "@id": "bts:Headaches" - }, - { - "@id": "bts:MotororMovementChanges" - }, - { - "@id": "bts:Seizures" - }, - { - "@id": "bts:SensoryChanges" - }, - { - "@id": "bts:VisualChanges" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "First Symptom Prior to Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:PercentTumorInvasion", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Tumor Invasion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ResidualDisease", - "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - }, - { - "@id": "bts:InitialDiseaseStatus" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:R0" - }, - { - "@id": "bts:R1" - }, - { - "@id": "bts:R2" - }, - { - "@id": "bts:RX" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Residual Disease", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SynchronousMalignancy", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Synchronous Malignancy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorConfinedtoOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Confined to Organ of Origin", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorFocality", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", - "rdfs:label": "TumorFocality", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Multifocal" - }, - { - "@id": "bts:Unifocal" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Focality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GrossTumorWeight", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", - "rdfs:label": "GrossTumorWeight", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gross Tumor Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreslowThickness", - "@type": "rdfs:Class", - "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", - "rdfs:label": "BreslowThickness", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breslow Thickness", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VascularInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", - "rdfs:label": "VascularInvasionPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-VascularInvasionPresent" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Vascular Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VascularInvasionType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Extramural" - }, - { - "@id": "bts:Intramural" - }, - { - "@id": "bts:Macro" - }, - { - "@id": "bts:Micro" - }, - { - "@id": "bts:NoVascularInvasion" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vascular Invasion Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnaplasiaPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", - "rdfs:label": "AnaplasiaPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-AnaplasiaPresent" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Anaplasia Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnaplasiaPresentType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", - "rdfs:label": "AnaplasiaPresentType", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Diffuse" - }, - { - "@id": "bts:Equivocal" - }, - { - "@id": "bts:Focal" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Sclerosis" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Anaplasia Present Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Laterality", - "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", - "rdfs:label": "Laterality", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bilateral" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Midline" - }, - { - "@id": "bts:Right" - }, - { - "@id": "bts:Unilateral" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Laterality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerineuralInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Perineural Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphaticInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", - "rdfs:label": "LymphaticInvasionPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lymphatic Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphNodesPositive", - "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", - "rdfs:label": "LymphNodesPositive", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lymph Nodes Positive", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphNodesTested", - "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", - "rdfs:label": "LymphNodesTested", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lymph Nodes Tested", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PeritonealFluidCytologicalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Atypical" - }, - { - "@id": "bts:Malignant" - }, - { - "@id": "bts:Non-Malignant" - }, - { - "@id": "bts:Unsatisfactory" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Peritoneal Fluid Cytological Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ClassificationofTumor", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", - "rdfs:label": "ClassificationofTumor", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Primary" - }, - { - "@id": "bts:Metastasis" - }, - { - "@id": "bts:Recurrence" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Classification of Tumor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BestOverallResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", - "rdfs:label": "BestOverallResponse", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AJ-AdjuvantTherapy" - }, - { - "@id": "bts:CPD-ClinicalProgression" - }, - { - "@id": "bts:CR-CompleteResponse" - }, - { - "@id": "bts:CRU-CompleteResponseUnconfirmed" - }, - { - "@id": "bts:DU-DiseaseUnchanged" - }, - { - "@id": "bts:IMR-Immunoresponse" - }, - { - "@id": "bts:IPD-Immunoprogression" - }, - { - "@id": "bts:MR-Minimal/MarginalResponse" - }, - { - "@id": "bts:MX-MixedResponse" - }, - { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" - }, - { - "@id": "bts:NPB-NoPalliativeBenefit" - }, - { - "@id": "bts:NR-NoResponse" - }, - { - "@id": "bts:PA-PalliativeTherapy" - }, - { - "@id": "bts:PB-PalliativeBenefit" - }, - { - "@id": "bts:PD-ProgressiveDisease" - }, - { - "@id": "bts:PPD-Pseudoprogression" - }, - { - "@id": "bts:PR-PartialResponse" - }, - { - "@id": "bts:PSR-Pseudoresponse" - }, - { - "@id": "bts:RD-ResponsiveDisease" - }, - { - "@id": "bts:RP-Response" - }, - { - "@id": "bts:RPD-RadiographicProgressiveDisease" - }, - { - "@id": "bts:SCR-StringentCompleteResponse" - }, - { - "@id": "bts:SD-StableDisease" - }, - { - "@id": "bts:SPD-SurgicalProgression" - }, - { - "@id": "bts:TE-TooEarly" - }, - { - "@id": "bts:VGPR-VeryGoodPartialResponse" - } - ], - "sms:displayName": "Best Overall Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MitoticCount", - "@type": "rdfs:Class", - "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mitotic Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalM", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalM", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:M0" - }, - { - "@id": "bts:M1" - }, - { - "@id": "bts:M1a" - }, - { - "@id": "bts:M1b" - }, - { - "@id": "bts:M1c" - }, - { - "@id": "bts:MX" - }, - { - "@id": "bts:CM0(i+)" - }, - { - 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Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "PrimaryGleasonGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pattern1" - }, - { - "@id": "bts:Pattern2" - }, - { - "@id": "bts:Pattern3" - }, - { - "@id": "bts:Pattern4" - }, - { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Primary Gleason Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondaryGleasonGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "SecondaryGleasonGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pattern1" - }, - { - "@id": "bts:Pattern2" - }, - { - "@id": "bts:Pattern3" - }, - { - "@id": "bts:Pattern4" - }, - { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Secondary Gleason Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SupratentorialLocalization", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", - "rdfs:label": "SupratentorialLocalization", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CerebralCortex" - }, - { - "@id": "bts:DeepGray" - }, - { - "@id": "bts:SpinalCord" - }, - { - "@id": "bts:WhiteMatter" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Supratentorial Localization", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorDepth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", - "rdfs:label": "TumorDepth", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Depth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WHOCNSGrade", - "@type": "rdfs:Class", - "rdfs:comment": "WHO CNS Grade", - "rdfs:label": "WHOCNSGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:GradeI" - }, - { - "@id": "bts:GradeII" - }, - { - "@id": "bts:GradeIII" - }, - { - "@id": "bts:GradeIV" - }, - { - "@id": "bts:GradeNotAssigned" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "WHO CNS Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WHONTEGrade", - "@type": "rdfs:Class", - "rdfs:comment": "WHO NTE Grade", - "rdfs:label": "WHONTEGrade", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:G1" - }, - { - "@id": "bts:G2" - }, - { - "@id": "bts:G3" - }, - { - "@id": "bts:GX" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "WHO NTE Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AAChange", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. 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Do not include data related to research assay outputs here.", - "rdfs:label": "Antigen", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BCL6" - }, - { - "@id": "bts:CA-125" - }, - { - "@id": "bts:CA19-9" - }, - { - "@id": "bts:CCND1" - }, - { - "@id": "bts:CD10" - }, - { - "@id": "bts:CD117" - }, - { - "@id": "bts:CD138" - }, - { - "@id": "bts:CD14" - }, - { - "@id": "bts:CD15" - }, - { - "@id": "bts:CD19" - }, - { - "@id": "bts:CD20" - }, - { - "@id": "bts:CD22" - }, - { - "@id": "bts:CD23" - }, - { - "@id": "bts:CD25" - }, - { - "@id": "bts:CD3" - }, - { - "@id": "bts:CD30" - }, - { - "@id": "bts:CD33" - }, - { - "@id": "bts:CD34" - }, - { - "@id": "bts:CD45" - }, - { - "@id": "bts:CD5" - }, - { - "@id": "bts:CD56" - }, - { - "@id": "bts:CD7" - }, - { - "@id": "bts:CD79A" - }, - { - "@id": "bts:CEA" - }, - { - "@id": "bts:HLA-DR" - }, - { - "@id": "bts:Mesothelin" - }, - { - "@id": "bts:NSE" - }, - { - "@id": "bts:SquamousCellCarcinomaAntigen" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Antigen", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ClinicalBiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "ClinicalBiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Blood" - }, - { - "@id": "bts:BoneMarrow" - }, - { - "@id": "bts:BuccalMucosa" - }, - { - "@id": "bts:BuffyCoat" - }, - { - "@id": "bts:CerebrospinalFluid" - }, - { - "@id": "bts:ConnectiveTissue" - }, - { - "@id": "bts:EmbryonicFluid" - }, - { - "@id": "bts:EmbryonicTissue" - }, - { - "@id": "bts:Feces" - }, - { - "@id": "bts:Granulocyte" - }, - { - "@id": "bts:MuscleTissue" - }, - { - "@id": "bts:NerveTissue" - }, - { - "@id": "bts:PeritonealFluid" - }, - { - "@id": "bts:Plasma" - }, - { - "@id": "bts:PleuralFluid" - }, - { - "@id": "bts:Saliva" - }, - { - "@id": "bts:Serum" - }, - { - "@id": "bts:Skin" - }, - { - "@id": "bts:SoftTissue" - }, - { - "@id": "bts:TissueNOS" - }, - { - "@id": "bts:UninvolvedTissueNOS" - }, - { - "@id": "bts:Urine" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Clinical Biospecimen Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BloodTestNormalRangeUpper", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeUpper", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blood Test Normal Range Upper", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BloodTestNormalRangeLower", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeLower", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blood Test Normal Range Lower", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CellCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CellCount", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chromosome", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Chromosome", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Chr1" - }, - { - "@id": "bts:Chr2" - }, - { - "@id": "bts:Chr3" - }, - { - "@id": "bts:Chr4" - }, - { - "@id": "bts:Chr5" - }, - { - "@id": "bts:Chr6" - }, - { - "@id": "bts:Chr7" - }, - { - "@id": "bts:Chr8" - }, - { - "@id": "bts:Chr9" - }, - { - "@id": "bts:Chr10" - }, - { - "@id": "bts:Chr11" - }, - { - "@id": "bts:Chr12" - }, - { - "@id": "bts:Chr13" - }, - { - "@id": "bts:Chr14" - }, - { - "@id": "bts:Chr15" - }, - { - "@id": "bts:Chr16" - }, - { - "@id": "bts:Chr17" - }, - { - "@id": "bts:Chr18" - }, - { - "@id": "bts:Chr19" - }, - { - "@id": "bts:Chr20" - }, - { - "@id": "bts:Chr21" - }, - { - "@id": "bts:Chr22" - }, - { - "@id": "bts:Chr23" - }, - { - "@id": "bts:ChrM" - }, - { - "@id": "bts:ChrX" - }, - { - "@id": "bts:ChrY" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Chromosome", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Clonality", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Clonality", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Clonal" - }, - { - "@id": "bts:Non-clonal" - } - ], - "sms:displayName": "Clonality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CopyNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CopyNumber", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Copy Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Cytoband", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Cytoband", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cytoband", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Exon", - "@type": "rdfs:Class", - "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Exon", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Exon", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoneFamily", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", - "rdfs:label": "HistoneFamily", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:H1" - }, - { - "@id": "bts:H2A" - }, - { - "@id": "bts:H2B" - }, - { - "@id": "bts:H3" - }, - { - "@id": "bts:H4" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Histone Family", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoneVariant", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "HistoneVariant", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CENP-A" - }, - { - "@id": "bts:H2A-Bbd" - }, - { - "@id": "bts:H2A.X" - }, - { - "@id": "bts:H2A.Z" - }, - { - "@id": "bts:H2A.Z.1" - }, - { - "@id": "bts:H2A.Z.2" - }, - { - "@id": "bts:H2A.Z.2.2" - }, - { - "@id": "bts:H3.1" - }, - { - "@id": "bts:H3.2" - }, - { - "@id": "bts:H3.3" - }, - { - "@id": "bts:H3.5" - }, - { - "@id": "bts:H3.X" - }, - { - "@id": "bts:H3.Y" - }, - { - "@id": "bts:H3t(H3.4)" - }, - { - "@id": "bts:MH2A" - }, - { - "@id": "bts:MH2A.1" - }, - { - "@id": "bts:MH2A.2" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Histone Variant", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Intron", - "@type": "rdfs:Class", - "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", - "rdfs:label": "Intron", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Intron", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LaboratoryTest", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", - "rdfs:label": "LaboratoryTest", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbsoluteNeutrophil" - }, - { - "@id": "bts:Albumin" - }, - { - "@id": "bts:AlphaFetoprotein" - }, - { - "@id": "bts:B-cellgenotyping" - }, - { - "@id": "bts:Basophil" - }, - { - "@id": "bts:Beta2Microglobulin" - }, - { - "@id": "bts:BloodUreaNitrogen" - }, - { - "@id": "bts:C-ReactiveProtein" - }, - { - "@id": "bts:Calcium" - }, - { - "@id": "bts:Cellularity" - }, - { - "@id": "bts:CirculatingTumorCells" - }, - { - "@id": "bts:Creatinine" - }, - { - "@id": "bts:Eosinophil" - }, - { - "@id": "bts:Epstein-BarrVirus" - }, - { - "@id": "bts:Glucose" - }, - { - "@id": "bts:Hematocrit" - }, - { - "@id": "bts:Hemoglobin" - }, - { - "@id": "bts:HPV-E6/E7" - }, - { - "@id": "bts:HumanChorionicGonadotropin" - }, - { - "@id": "bts:HumanPapillomavirus" - }, - { - "@id": "bts:ImmunoglobulinA" - }, - { - "@id": "bts:ImmunoglobulinG" - }, - { - "@id": "bts:ImmunoglobulinM" - }, - { - "@id": "bts:LactateDehydrogenase" - }, - { - "@id": "bts:Leukocytes" - }, - { - "@id": "bts:LuteinizingHormone" - }, - { - "@id": "bts:Lymphoblasts" - }, - { - "@id": "bts:Lymphocytes" - }, - { - "@id": "bts:MProtein" - }, - { - "@id": "bts:Metamyelocytes" - }, - { - "@id": "bts:Myeloblasts" - }, - { - "@id": "bts:Myelocytes" - }, - { - "@id": "bts:NeutrophilBands" - }, - { - "@id": "bts:Platelets" - }, - { - "@id": "bts:Prolymphocytes" - }, - { - "@id": "bts:Promonocytes" - }, - { - "@id": "bts:Promyelocytes" - }, - { - "@id": "bts:SegmentedNeutrophil" - }, - { - "@id": "bts:SerumFreeImmunoglobulinLightChain" - }, - { - "@id": "bts:Kappa" - }, - { - "@id": "bts:Lambda" - }, - { - "@id": "bts:NOS" - }, - { - "@id": "bts:Testosterone" - }, - { - "@id": "bts:TotalBilirubin" - }, - { - "@id": "bts:TotalProtein" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Laboratory Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LociAbnormalCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", - "rdfs:label": "LociAbnormalCount", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loci Abnormal Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LociCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci tested.", - "rdfs:label": "LociCount", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loci Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Locus", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", - "rdfs:label": "Locus", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Locus", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MismatchRepairMutation", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MismatchRepairMutation", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mismatch Repair Mutation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MolecularConsequence", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularConsequence", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:3PrimeUTRVariant" - }, - { - "@id": "bts:5PrimeUTRVariant" - }, - { - "@id": "bts:CodingSequenceVariant" - }, - { - "@id": "bts:DownstreamGeneVariant" - }, - { - "@id": "bts:FeatureElongation" - }, - { - "@id": "bts:FeatureTruncation" - }, - { - "@id": "bts:FrameshiftVariant" - }, - { - "@id": "bts:IncompleteTerminalCodonVariant" - }, - { - "@id": "bts:InframeDeletion" - }, - { - "@id": "bts:InframeInsertion" - }, - { - "@id": "bts:IntergenicVariant" - }, - { - "@id": "bts:IntronVariant" - }, - { - "@id": "bts:MaturemiRNAVariant" - }, - { - "@id": "bts:MissenseVariant" - }, - { - "@id": "bts:NMDTranscriptVariant" - }, - { - "@id": "bts:Non-codingTranscriptExonVariant" - }, - { - "@id": "bts:Non-codingTranscriptVariant" - }, - { - "@id": "bts:ProteinAlteringVariant" - }, - { - "@id": "bts:RegulatoryRegionAblation" - }, - { - "@id": "bts:RegulatoryRegionAmplification" - }, - { - "@id": "bts:RegulatoryRegionVariant" - }, - { - "@id": "bts:SpliceAcceptorVariant" - }, - { - "@id": "bts:SpliceDonorVariant" - }, - { - "@id": "bts:SpliceRegionVariant" - }, - { - "@id": "bts:StartLost" - }, - { - "@id": "bts:StopGain" - }, - { - "@id": "bts:StopLost" - }, - { - "@id": "bts:StopRetainedVariant" - }, - { - "@id": "bts:SynonymousVariant" - }, - { - "@id": "bts:TFBindingSiteVariant" - }, - { - "@id": "bts:TFBSAblation" - }, - { - "@id": "bts:TFBSAmplification" - }, - { - "@id": "bts:TranscriptAblation" - }, - { - "@id": "bts:TranscriptAmplification" - }, - { - "@id": "bts:UpstreamGeneVariant" - } - ], - "sms:displayName": "Molecular Consequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pathogenicity", - "@type": "rdfs:Class", - "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", - "rdfs:label": "Pathogenicity", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Benign" - }, - { - "@id": "bts:LikelyBenign" - }, - { - "@id": "bts:LikelyPathogenic" - }, - { - "@id": "bts:Pathogenic" - }, - { - "@id": "bts:UncertainSignificance" - } - ], - "sms:displayName": "Pathogenicity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ploidy", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", - "rdfs:label": "Ploidy", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Aneuploid" - }, - { - "@id": "bts:Diploid" - }, - { - "@id": "bts:Hyperdiploid" - }, - { - "@id": "bts:Hypodiploid" - }, - { - "@id": "bts:NearDiploid" - }, - { - "@id": "bts:Tetraploid" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Ploidy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondExon", - "@type": "rdfs:Class", - "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", - "rdfs:label": "SecondExon", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second Exon", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondGeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SecondGeneSymbol", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Second Gene Symbol", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SpecializedMolecularTest", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SpecializedMolecularTest", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Specialized Molecular Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestAnalyteType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestAnalyteType", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:DNA" - }, - { - "@id": "bts:MRNA" - }, - { - "@id": "bts:MiRNA" - }, - { - "@id": "bts:ProteinAnalyte" - }, - { - "@id": "bts:TotalRNA" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Test Analyte Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestUnits", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestUnits", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Test Units", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TestValue", - "@type": "rdfs:Class", - "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", - "rdfs:label": "TestValue", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Test Value", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Transcript", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Transcript", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VariantOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "VariantOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Germline" - }, - { - "@id": "bts:Somatic" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Variant Origin", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VariantType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of genetic variation.", - "rdfs:label": "VariantType", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alleles" - }, - { - "@id": "bts:Amplification" - }, - { - "@id": "bts:Chrimerism" - }, - { - "@id": "bts:Conversion" - }, - { - "@id": "bts:Deletion" - }, - { - "@id": "bts:Deletion-Insertion" - }, - { - "@id": "bts:Duplication" - }, - { - "@id": "bts:Extension" - }, - { - "@id": "bts:Gain" - }, - { - "@id": "bts:Hypermethylation" - }, - { - "@id": "bts:Insertion" - }, - { - "@id": "bts:Inversion" - }, - { - "@id": "bts:Loss" - }, - { - "@id": "bts:Methylation" - }, - { - "@id": "bts:Mosaicism" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:PartialMethylation" - }, - { - "@id": "bts:Rearrangement" - }, - { - "@id": "bts:RepeatedSequences" - }, - { - "@id": "bts:Splice" - }, - { - "@id": "bts:Substitution" - }, - { - "@id": "bts:Translocation" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Variant Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Zygosity", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", - "rdfs:label": "Zygosity", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Heterozygous" - }, - { - "@id": "bts:Hemizygous" - }, - { - "@id": "bts:Homozygous" - }, - { - "@id": "bts:Nullizygous" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Zygosity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SourceHTANBiospecimenID", - "@type": "rdfs:Class", - "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", - "rdfs:label": "SourceHTANBiospecimenID", - "rdfs:subClassOf": [ - { - "@id": "bts:Biosample" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Source HTAN Biospecimen ID", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", - "rdfs:label": "CollectionDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:AdjacentBiospecimenIDs", - "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenIDs", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adjacent Biospecimen IDs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Biospecimen Type", - "rdfs:label": "BiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:TissueBiospecimenType" - }, - { - "@id": "bts:BloodBiospecimenType" - }, - { - "@id": "bts:AnalyteBiospecimenType" - }, - { - "@id": "bts:MouthRinseBiospecimenType" - }, - { - "@id": "bts:StoolBiospecimenType" - }, - { - "@id": "bts:UrineBiospecimenType" - }, - { - "@id": "bts:AscitesBiospecimenType" - }, - { - "@id": "bts:SputumBiospecimenType" - }, - { - "@id": "bts:FluidsBiospecimenType" - }, - { - "@id": "bts:BoneMarrowBiospecimenType" - }, - { - "@id": "bts:CellsBiospecimenType" - } - ], - "sms:displayName": "Biospecimen Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" - }, - { - "@id": "bts:FineNeedleAspirate" - }, - { - "@id": "bts:SurgicalResection" - }, - { - "@id": "bts:PunchBiopsy" - }, - { - "@id": "bts:ShaveBiopsy" - }, - { - "@id": "bts:Excision" - }, - { - "@id": "bts:Re-excision" - }, - { - "@id": "bts:SentinelNodeBiopsy" - }, - { - "@id": "bts:Lymphadenectomy-RegionalNodes" - }, - { - "@id": "bts:OtherAcquisitionMethod" - }, - { - "@id": "bts:Noninducedsputum" - }, - { - "@id": "bts:Inducedsputum" - }, - { - "@id": "bts:BAL(bronchialalveolarlavage)" - }, - { - "@id": "bts:Cytobrush" - }, - { - "@id": "bts:Blooddraw" - }, - { - "@id": "bts:Fluidcollection" - }, - { - "@id": "bts:Forcepsbiopsy" - }, - { - "@id": "bts:Coreneedlebiopsy" - }, - { - "@id": "bts:Endoscopicbiopsy" - }, - { - "@id": "bts:Notspecified" - } - ], - "sms:displayName": "Acquisition Method Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:FixativeType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Acetone" - }, - { - "@id": "bts:Alcohol" - }, - { - "@id": "bts:Formalin" - }, - { - "@id": "bts:Glutaraldehyde" - }, - { - "@id": "bts:OCTmedia" - }, - { - "@id": "bts:RNAlater" - }, - { - "@id": "bts:Saline" - }, - { - "@id": "bts:95%Ethanol" - }, - { - "@id": "bts:Dimidoester" - }, - { - "@id": "bts:Carbodiimide" - }, - { - "@id": "bts:Dimethylacetamide" - }, - { - "@id": "bts:Para-benzoquinone" - }, - { - "@id": "bts:PAXgenetissue" - }, - { - "@id": "bts:TCLlysisbuffer" - }, - { - "@id": "bts:NP40lysisbuffer" - }, - { - "@id": "bts:Methacarn" - }, - { - "@id": "bts:Cryo-store" - }, - { - "@id": "bts:Carnoy'sFixative" - }, - { - "@id": "bts:Polaxamer" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Unfixed" - } - ], - "sms:displayName": "Fixative Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StorageMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Ambienttemperature" - }, - { - "@id": "bts:Cutslide" - }, - { - "@id": "bts:Fresh" - }, - { - "@id": "bts:Frozenat-20C" - }, - { - "@id": "bts:Frozenat-70C" - }, - { - "@id": "bts:Frozenat-80C" - }, - { - "@id": "bts:Frozenat-150C" - }, - { - "@id": "bts:Frozeninliquidnitrogen" - }, - { - "@id": "bts:Frozeninvaporphase" - }, - { - "@id": "bts:Paraffinblock" - }, - { - "@id": "bts:RNAlaterat4C" - }, - { - "@id": "bts:RNAlaterat25C" - }, - { - "@id": "bts:RNAlaterat-20C" - }, - { - "@id": "bts:Refrigeratedat4degrees" - }, - { - "@id": "bts:Refrigeratedvacuumchamber" - }, - { - "@id": "bts:4Cinvacuumchamber" - }, - { - "@id": "bts:Desiccantat4C" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", - "rdfs:label": "ProcessingDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:ProtocolLink", - "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label": "ProtocolLink", - "rdfs:subClassOf": [ - { - "@id": "bts:InformationContentEntity" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Protocol Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteDataSource", - "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Site Data Source", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionMedia", - "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:DMEM" - }, - { - "@id": "bts:DMEM+Serum" - }, - { - "@id": "bts:RPMI" - }, - { - "@id": "bts:RPMI+Serum" - }, - { - "@id": "bts:PBS" - }, - { - "@id": "bts:PBS+Serum" - }, - { - "@id": "bts:None" - } - ], - "sms:displayName": "Collection Media", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MountingMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Aqueouswaterbased" - }, - { - "@id": "bts:Non-AqueousSolventbased" - }, - { - "@id": "bts:Xylene" - }, - { - "@id": "bts:Toluene" - }, - { - "@id": "bts:AntifadewithDAPI" - }, - { - "@id": "bts:AntifadewithoutDAPI" - }, - { - "@id": "bts:PBS" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mounting Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingLocation", - "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentBy", - "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pathologist" - }, - { - "@id": "bts:ResearchScientist" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment By", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Digital" - }, - { - "@id": "bts:Microscopy" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PreinvasiveMorphology", - "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", - "rdfs:label": "PreinvasiveMorphology", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Melanocytichyperplasia" - }, - { - "@id": "bts:Atypicalmelanocyticproliferation" - }, - { - "@id": "bts:Melanomainsitu-superficialspreading" - }, - { - "@id": "bts:Melanomainsitu-lentigomalignatype" - }, - { - "@id": "bts:Melanomainsitu-acral-lentiginous" - }, - { - "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" - }, - { - "@id": "bts:Persistentmelanomainsitu" - }, - { - "@id": "bts:Melanomainsitu-nototherwiseclassified" - }, - { - "@id": "bts:Scar-noresidualmelanoma" - }, - { - "@id": "bts:Invasivemelanoma-superficialspreading" - }, - { - "@id": "bts:Invasivemelanoma-nodulartype" - }, - { - "@id": "bts:Invasivemelanoma-lentigomaligna" - }, - { - "@id": "bts:Invasivemelanoma-acrallentiginous" - }, - { - "@id": "bts:Invasivemelanoma-desmoplastic" - }, - { - "@id": "bts:Invasivemelanoma-nevoid" - }, - { - "@id": "bts:Invasivemelanoma-other" - }, - { - "@id": "bts:NormalWDA" - }, - { - "@id": "bts:Reservecellhyperplasia" - }, - { - "@id": "bts:Squamousmetaplasia-mature" - }, - { - "@id": "bts:Squamousmetaplasia-immature" - }, - { - "@id": "bts:Milddysplasia" - }, - { - "@id": "bts:Moderatedysplasia" - }, - { - "@id": "bts:Severedysplasia" - }, - { - "@id": "bts:SquamousCarcinomainsitu" - }, - { - "@id": "bts:Atypicaladenomatoushyperplasia" - }, - { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" - }, - { - "@id": "bts:Adenocarcinomainsitu-mucinous" - }, - { - "@id": "bts:BenigntumorNOS" - }, - { - "@id": "bts:Hamartoma" - }, - { - "@id": "bts:CarcinomaNOS" - }, - { - "@id": "bts:Nodiagnosispossible" - } - ], - "sms:displayName": "Preinvasive Morphology", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorInfiltratingLymphocytes", - "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DegreeofDysplasia", - "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" - }, - { - "@id": "bts:Milddysplasia" - }, - { - "@id": "bts:Moderatedysplasia" - }, - { - "@id": "bts:Severedysplasia" - }, - { - "@id": "bts:CarcinomainSitu" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Degree of Dysplasia", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DysplasiaFraction", - "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. 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}, - { - "@id": "bts:DMRCallingWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMRCallingWorkflowURL", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DMR Calling Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] - }, - { - "@id": "bts:PUC19methylationratio", - "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", - "rdfs:label": "PUC19methylationratio", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "pUC19 methylation ratio", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Lambdamethylationratio", - "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", - "rdfs:label": "Lambdamethylationratio", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lambda methylation ratio", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DMCdatafileformat", - "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files", - "rdfs:label": "DMCdatafileformat", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, - { - "@id": "bts:BedGraph" - } - ], - "sms:displayName": "DMC data file format", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DMRdatafileFormat", - "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files.", - "rdfs:label": "DMRdatafileFormat", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, - { - "@id": "bts:BedGraph" - } - ], - "sms:displayName": "DMR data file Format", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Raw imaging data", - "rdfs:label": "ImagingLevel1", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:CommitSHA" - }, - { - "@id": "bts:Pre-processingCompleted" - }, - { - "@id": "bts:Pre-processingRequired" - }, - { - "@id": "bts:Comment" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingAssayType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of imaging assay", - "rdfs:label": "ImagingAssayType", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:H&E" - }, - { - "@id": "bts:CyCIF" - }, - { - "@id": "bts:T-CyCIF" - }, - { - "@id": "bts:IHC" - }, - { - "@id": "bts:MIHC" - }, - { - "@id": "bts:MxIF" - }, - { - "@id": "bts:SABER" - }, - { - "@id": "bts:IMC" - }, - { - "@id": "bts:CODEX" - }, - { - "@id": "bts:GeoMX-DSP" - }, - { - "@id": "bts:MIBI" - }, - { - "@id": "bts:MERFISH" - }, - { - "@id": "bts:ExSeq" - }, - { - "@id": "bts:RareCyteOrion" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Imaging Assay Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SoftwareandVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Name of software used to generate expression values. String", - "rdfs:label": "SoftwareandVersion", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Software and Version", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CommitSHA", - "@type": "rdfs:Class", - "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", - "rdfs:label": "CommitSHA", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Commit SHA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pre-processingCompleted", - "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingCompleted", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Pre-processing Completed", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Pre-processingRequired", - "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingRequired", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Pre-processing Required", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Comment", - "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Comment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingLevel2", - "@type": "rdfs:Class", - "rdfs:comment": "Raw and pre-processed image data", - "rdfs:label": "ImagingLevel2", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ImagingLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:Microscope" - }, - { - "@id": "bts:Objective" - }, - { - "@id": "bts:NominalMagnification" - }, - { - "@id": "bts:LensNA" - }, - { - "@id": "bts:WorkingDistance" - }, - { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:Immersion" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:Comment" - }, - { - "@id": "bts:FOVnumber" - }, - { - "@id": "bts:FOVX" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVY" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:FrameAveraging" - }, - { - "@id": "bts:ImageID" - }, - { - "@id": "bts:DimensionOrder" - }, - { - "@id": "bts:PhysicalSizeX" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeY" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZ" - }, - { - "@id": "bts:PhysicalSizeZUnit" - }, - { - "@id": "bts:PixelsBigEndian" - }, - { - "@id": "bts:PlaneCount" - }, - { - "@id": "bts:SizeC" - }, - { - "@id": "bts:SizeT" - }, - { - "@id": "bts:SizeX" - }, - { - "@id": "bts:SizeY" - }, - { - "@id": "bts:SizeZ" - }, - { - "@id": "bts:PixelType" - }, - { - "@id": "bts:MERFISHPositionsFile" - }, - { - "@id": "bts:MERFISHCodebookFile" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ChannelMetadataFilename", - "@type": "rdfs:Class", - "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label": "ChannelMetadataFilename", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Channel Metadata Filename", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Microscope", - "@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Objective", - "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Objective", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NominalMagnification", - "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:LensNA", - "@type": "rdfs:Class", - "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", - "rdfs:label": "LensNA", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "LensNA", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:WorkingDistance", - "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "WorkingDistance", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:WorkingDistanceUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:WorkingDistanceUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Immersion", - "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Air" - }, - { - "@id": "bts:Oil" - }, - { - "@id": "bts:Water" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pyramid", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Zstack", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Zstack", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Tseries", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Tseries", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PassedQC", - "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVnumber", - "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOV number", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:FOVX", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVX", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:FOVXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVY", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVY", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVYUnit" - } - ], - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:FOVYUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVYUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FrameAveraging", - "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). 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This level depends on GeoMx Level 1 and Imaging Level 2.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" - }, - { - "@id": "bts:ImagingLevel2" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:GeoMxDSPAssayType" - }, - { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" - }, - { - "@id": "bts:GeoMxDSPUniqueProbeCount" - }, - { - "@id": "bts:GeoMxDSPUniqueTargetCount" - }, - { - "@id": "bts:GeoMxDSPGenomicReference" - }, - { - "@id": "bts:MatrixType" - }, - { - "@id": "bts:GeoMxDSPWorkflowType" - }, - { - "@id": "bts:GeoMxDSPWorkflowParameterDescription" - }, - { - "@id": "bts:GeoMxDSPWorkflowLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", - "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", - "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", - "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] - }, - { - "@id": "bts:GeoMxDSPUniqueProbeCount", - "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique probes reported.", - "rdfs:label": "GeoMxDSPUniqueProbeCount", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Unique Probe Count", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:GeoMxDSPUniqueTargetCount", - "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique genes reported.", - "rdfs:label": "GeoMxDSPUniqueTargetCount", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Unique Target Count", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:GeoMxDSPGenomicReference", - "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", - "rdfs:label": "GeoMxDSPGenomicReference", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Genomic Reference", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:GeoMxDSPWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", - "rdfs:label": "GeoMxDSPWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GeoMxDSPWorkflowParameterDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", - "rdfs:label": "GeoMxDSPWorkflowParameterDescription", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Workflow Parameter Description", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GeoMxDSPWorkflowLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "GeoMxDSPWorkflowLink", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Workflow Link", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Scanname", - "@type": "rdfs:Class", - "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", - "rdfs:label": "Scanname", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIname", - "@type": "rdfs:Class", - "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", - "rdfs:label": "ROIname", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Segmentname", - "@type": "rdfs:Class", - "rdfs:comment": "Name given to segment at time of generation", - "rdfs:label": "Segmentname", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Segment name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIXCoordinate", - "@type": "rdfs:Class", - "rdfs:comment": "X location within the image", - "rdfs:label": "ROIXCoordinate", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI X Coordinate", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIYCoordinate", - "@type": "rdfs:Class", - "rdfs:comment": "Y location within the image", - "rdfs:label": "ROIYCoordinate", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI Y Coordinate", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Tags", - "@type": "rdfs:Class", - "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", - "rdfs:label": "Tags", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tags", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:QCstatus", - "@type": "rdfs:Class", - "rdfs:comment": "ROI quality control flag as reported by the application", - "rdfs:label": "QCstatus", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanHeight", - "@type": "rdfs:Class", - "rdfs:comment": "Height of the scan for GeoMx Analysis", - "rdfs:label": "ScanHeight", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Height", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanWidth", - "@type": "rdfs:Class", - "rdfs:comment": "Width of the scan for GeoMx Analysis", - "rdfs:label": "ScanWidth", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Width", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanOffsetX", - "@type": "rdfs:Class", - "rdfs:comment": "Offset X of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetX", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Offset X", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanOffsetY", - "@type": "rdfs:Class", - "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetY", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Offset Y", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:BindingDensity", - "@type": "rdfs:Class", - "rdfs:comment": "The binding density as reported by the application", - "rdfs:label": "BindingDensity", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Binding Density", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Positivenormfactor", - "@type": "rdfs:Class", - "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", - "rdfs:label": "Positivenormfactor", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Positive norm factor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Surfacearea", - "@type": "rdfs:Class", - "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", - "rdfs:label": "Surfacearea", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Surface area", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Nucleicount", - "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", - "rdfs:label": "Nucleicount", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei count", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TissueStain", - "@type": "rdfs:Class", - "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", - "rdfs:label": "TissueStain", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tissue Stain", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Slidename", - "@type": "rdfs:Class", - "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", - "rdfs:label": "Slidename", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Rawreads", - "@type": "rdfs:Class", - "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", - "rdfs:label": "Rawreads", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Raw reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Stitchedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", - "rdfs:label": "Stitchedreads", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Stitched reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Alignedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", - "rdfs:label": "Alignedreads", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Aligned reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Deduplicatedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", - "rdfs:label": "Deduplicatedreads", - "rdfs:subClassOf": [ - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Deduplicated reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InSituNegativemedian", - "@type": "rdfs:Class", - "rdfs:comment": "Is the median of all negative control probes for a given segment. 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"rdfs:label": "MedicallyUnderservedArea-No", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - }, - { - "@id": "bts:MedicallyUnderservedArea" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Medically Underserved Area - No", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedArea-Unknown", - "@type": "rdfs:Class", - "rdfs:comment": "Insufficient data to look up the Medically Underserved Area value", - "rdfs:label": "MedicallyUnderservedArea-Unknown", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - }, - { - "@id": "bts:MedicallyUnderservedArea" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Medically Underserved Area - Unknown", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedScore", - "@type": "rdfs:Class", - "rdfs:comment": "Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.", - "rdfs:label": "MedicallyUnderservedScore", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Medically Underserved Score", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:UrbanPopulation(population>50000)", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "UrbanPopulation(population>50000)", - "rdfs:subClassOf": [ - { - "@id": "bts:RuralvsUrban" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Urban Population (population >50000)", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:UrbanCluster(population2500-50000)", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "UrbanCluster(population2500-50000)", - "rdfs:subClassOf": [ - { - "@id": "bts:RuralvsUrban" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Urban Cluster (population 2500 - 50000)", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RuralPopulation(population<2500)", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RuralPopulation(population<2500)", - "rdfs:subClassOf": [ - { - "@id": "bts:RuralvsUrban" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Rural Population (population <2500)", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RelationshipGender", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the gender of the patient's relative with a history of cancer.", - "rdfs:label": "RelationshipGender", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Female" - }, - { - "@id": "bts:Male" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Unspecified" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relationship Gender", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RelationshipAgeatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The age (in years) when the patient's relative was first diagnosed.", - "rdfs:label": "RelationshipAgeatDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Relationship Age at Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RelationshipPrimaryDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", - "rdfs:label": "RelationshipPrimaryDiagnosis", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AdrenalGlandCancer" - }, - { - "@id": "bts:BasalCellCancer" - }, - { - "@id": "bts:BileDuctCancer" - }, - { - "@id": "bts:BladderCancer" - }, - { - "@id": "bts:BloodCancer" - }, - { - "@id": "bts:BoneCancer" - }, - { - "@id": "bts:BrainCancer" - }, - { - "@id": "bts:BreastCancer" - }, - { - "@id": "bts:Cancer" - }, - { - "@id": "bts:CervicalCancer" - }, - { - "@id": "bts:Chondrosarcoma" - }, - { - "@id": "bts:CNSCancer" - }, - { - "@id": "bts:ColorectalCancer" - }, - { - "@id": "bts:EsophagealCancer" - }, - { - "@id": "bts:EwingSarcoma" - }, - { - "@id": "bts:GallbladderCancer" - }, - { - "@id": "bts:GastricCancer" - }, - { - "@id": "bts:Glioblastoma" - }, - { - "@id": "bts:GynecologicCancer" - }, - { - "@id": "bts:HeadandNeckCancer" - }, - { - "@id": "bts:HematologicCancer" - }, - { - "@id": "bts:KaposiSarcoma" - }, - { - "@id": "bts:KidneyCancer" - }, - { - "@id": "bts:LaryngealCancer" - }, - { - "@id": "bts:Leukemia" - }, - { - "@id": "bts:LiverCancer" - }, - { - "@id": "bts:LungCancer" - }, - { - "@id": "bts:LymphNodeCancer" - }, - { - "@id": "bts:Lymphoma" - }, - { - "@id": "bts:Melanoma" - }, - { - "@id": "bts:Mesothelioma" - }, - { - "@id": "bts:MultipleMyeloma" - }, - { - "@id": "bts:Neuroblastoma" - }, - { - "@id": "bts:Osteosarcoma" - }, - { - "@id": "bts:OvarianCancer" - }, - { - "@id": "bts:PancreasCancer" - }, - { - "@id": "bts:ProstateCancer" - }, - { - "@id": "bts:RectalCancer" - }, - { - "@id": "bts:Rhabdomyosarcoma" - }, - { - "@id": "bts:Sarcoma" - }, - { - "@id": "bts:SkinCancer" - }, - { - "@id": "bts:SpleenCancer" - }, - { - "@id": "bts:TesticularCancer" - }, - { - "@id": "bts:ThroatCancer" - }, - { - "@id": "bts:ThyroidCancer" - }, - { - "@id": "bts:TongueCancer" - }, - { - "@id": "bts:TonsillarCancer" - }, - { - "@id": "bts:UterineCancer" - }, - { - "@id": "bts:WilmsTumor" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relationship Primary Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdrenalGlandCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "AdrenalGlandCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adrenal Gland Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BasalCellCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BasalCellCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Basal Cell Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BileDuctCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BileDuctCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bile Duct Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BladderCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BladderCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bladder Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BloodCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BloodCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blood Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BoneCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BoneCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bone Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BrainCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BrainCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Brain Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BreastCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Cancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cancer", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastBiopsyProcedureFindingType" - }, - { - "@id": "bts:ColorectalPolypType" - }, - { - "@id": "bts:RelationshipPrimaryDiagnosis" - }, - { - "@id": "bts:Comorbidity" - }, - { - "@id": "bts:RiskFactor" - }, - { - "@id": "bts:PrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CervicalCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "CervicalCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cervical Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chondrosarcoma", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Chondrosarcoma", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Chondrosarcoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CNSCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "CNSCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "CNS Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ColorectalCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EsophagealCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "EsophagealCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Esophageal Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EwingSarcoma", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "EwingSarcoma", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ewing Sarcoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GallbladderCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "GallbladderCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gallbladder Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GastricCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "GastricCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gastric Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Glioblastoma", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Glioblastoma", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - }, - { - "@id": "bts:PrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Glioblastoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GynecologicCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "GynecologicCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gynecologic Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HeadandNeckCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HeadandNeckCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Head and Neck Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HematologicCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HematologicCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Hematologic Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KaposiSarcoma", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "KaposiSarcoma", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Kaposi Sarcoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KidneyCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "KidneyCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Kidney Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LaryngealCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "LaryngealCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Laryngeal Cancer", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Leukemia", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Leukemia", - "rdfs:subClassOf": [ - { - "@id": "bts:NCIAtlasCancerSite" - }, - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Leukemia", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LiverCancer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "LiverCancer", - "rdfs:subClassOf": [ - { - "@id": "bts:RelationshipPrimaryDiagnosis" - } - ], - "schema:isPartOf": { - "@id": 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"bts:TypeofTobaccoUsed" - }, - { - "@id": "bts:SecondhandSmokeasChild" - }, - { - "@id": "bts:SmokeExposureDuration" - }, - { - "@id": "bts:TobaccoUseperDay" - }, - { - "@id": "bts:SmokelessTobaccoQuitAge" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:No-SmokingExposure", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "No-SmokingExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:SmokingExposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "No - Smoking Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CigarettesperDay", - "@type": "rdfs:Class", - "rdfs:comment": "The average number of cigarettes smoked per day.", - "rdfs:label": "CigarettesperDay", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cigarettes per Day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokingFrequency", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to generally decribe how often the patient smokes.", - "rdfs:label": "SmokingFrequency", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Everyday" - }, - { - "@id": "bts:Somedays" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Smoking Frequency", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TypeofSmokeExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the patient's specific type of smoke exposure.", - "rdfs:label": "TypeofSmokeExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Accidentalbuildingfiresmoke" - }, - { - "@id": "bts:Accidentalgrassfiresmoke" - }, - { - "@id": "bts:AccidentalfiresmokeNOS" - }, - { - "@id": "bts:Accidentalforestfiresmoke" - }, - { - "@id": "bts:Accidentalvehiclefiresmoke" - }, - { - "@id": "bts:Aircraftsmoke" - }, - { - "@id": "bts:Burningtreesmoke" - }, - { - "@id": "bts:CoalsmokeNOS" - }, - { - "@id": "bts:CookingrelatedsmokeNOS" - }, - { - "@id": "bts:ElectroniccigarettesmokeNOS" - }, - { - "@id": "bts:Electricalfiresmoke" - }, - { - "@id": "bts:Environmentaltobaccosmoke" - }, - { - "@id": "bts:Factorysmokestacksmoke" - }, - { - "@id": "bts:Fieldburningsmoke" - }, - { - "@id": "bts:FiresmokeNOS" - }, - { - "@id": "bts:Furnaceorboilersmoke" - }, - { - "@id": "bts:Gasburningsmokepropane" - }, - { - "@id": "bts:Greasefiresmoke" - }, - { - "@id": "bts:Grillingsmoke" - }, - { - "@id": "bts:Hashishsmoke" - }, - { - "@id": "bts:Indoorcoalburningstoveorfireplacesmoke" - }, - { - "@id": "bts:IndoorstoveorfireplacesmokeNOS" - }, - { - "@id": "bts:Indoorwoodburningstoveorfireplacesmoke" - }, - { - "@id": "bts:Machinesmoke" - }, - { - "@id": "bts:Marijuanasmoke" - }, - { - "@id": "bts:NoSmokeExposure" - }, - { - "@id": "bts:OilburningsmokeKerosene" - }, - { - "@id": "bts:OilburningsmokeNOS" - }, - { - "@id": "bts:Recreationalfiresmoke" - }, - { - "@id": "bts:SmokeexposureNOS" - }, - { - "@id": "bts:Smokehousesmoke" - }, - { - "@id": "bts:Tobaccosmokecigar" - }, - { - "@id": "bts:Tobaccosmokecigarettes" - }, - { - "@id": "bts:Tobaccosmokepipe" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Volcanicsmoke" - }, - { - "@id": "bts:Wasteburningsmoke" - }, - { - "@id": "bts:Woodburningsmokefactory" - }, - { - "@id": "bts:WoodburningsmokeNOS" - }, - { - "@id": "bts:Workrelatedsmokeartificialsmokemachines" - }, - { - "@id": "bts:Workrelatedsmokefirefighting" - }, - { - "@id": "bts:Workrelatedsmokefoundry" - }, - { - "@id": "bts:Workrelatedsmokegenerators" - }, - { - "@id": "bts:Workrelatedsmokemilitary" - }, - { - "@id": "bts:WorkrelatedsmokeNOS" - }, - { - "@id": "bts:Workrelatedsmokepaintbaking" - }, - { - "@id": "bts:Workrelatedsmokeplasticsfactory" - }, - { - "@id": "bts:Workrelatedsmokeplumbing" - }, - { - "@id": "bts:Workrelatedsmokesoldering/welding" - } - ], - "sms:displayName": "Type of Smoke Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TimebetweenWakingandFirstSmoke", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.", - "rdfs:label": "TimebetweenWakingandFirstSmoke", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Within5Minutes" - }, - { - "@id": "bts:6-30Minutes" - }, - { - "@id": "bts:31-60Minutes" - }, - { - "@id": "bts:After60Minutes" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Time between Waking and First Smoke", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TobaccoSmokingOnsetYear", - "@type": "rdfs:Class", - "rdfs:comment": "The year in which the participant began smoking.", - "rdfs:label": "TobaccoSmokingOnsetYear", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tobacco Smoking Onset Year", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TobaccoSmokingQuitYear", - "@type": "rdfs:Class", - "rdfs:comment": "The year in which the participant quit smoking.", - "rdfs:label": "TobaccoSmokingQuitYear", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tobacco Smoking Quit Year", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TobaccoSmokingStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Category describing current smoking status and smoking history as self-reported by a patient", - "rdfs:label": "TobaccoSmokingStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LifelongNon-Smoker" - }, - { - "@id": "bts:CurrentSmoker" - }, - { - "@id": "bts:CurrentReformedSmokerfor>15yrs" - }, - { - "@id": "bts:CurrentReformedSmokerfor15yrs", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "CurrentReformedSmokerfor>15yrs", - "rdfs:subClassOf": [ - { - "@id": "bts:TobaccoSmokingStatus" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Current Reformed Smoker for > 15 yrs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CurrentReformedSmokerfor Date: Mon, 3 Jun 2024 19:07:04 +0000 Subject: [PATCH 12/14] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 151886 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 151886 insertions(+) create mode 100644 HTAN.model.jsonld diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld new file mode 100644 index 00000000..78f348d2 --- /dev/null +++ b/HTAN.model.jsonld @@ -0,0 +1,151886 @@ +{ + "@context": { + "bts": "http://schema.biothings.io/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "schema": "http://schema.org/", + "xsd": "http://www.w3.org/2001/XMLSchema#" + }, + "@graph": [ + { + "@id": "bts:Assay", + "@type": "rdfs:Class", + "rdfs:comment": "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]", + "rdfs:label": "Assay", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Device", + "@type": "rdfs:Class", + "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", + "rdfs:label": "Device", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Device", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Sequencing", + "@type": "rdfs:Class", + "rdfs:comment": "Module for next generation sequencing assays", + "rdfs:label": "Sequencing", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sequencing", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Component", + "@type": "rdfs:Class", + "rdfs:comment": "Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.", + "rdfs:label": "Component", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Component", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Patient", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN patient", + "rdfs:label": "Patient", + "rdfs:subClassOf": [ + { + "@id": "bts:IndividualOrganism" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Patient", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Demographics" + }, + { + "@id": "bts:FamilyHistory" + }, + { + "@id": "bts:Exposure" + }, + { + "@id": "bts:FollowUp" + }, + { + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:Therapy" + }, + { + "@id": "bts:MolecularTest" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParticipantID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )", + "rdfs:label": "HTANParticipantID", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Participant ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))$ warning" + ] + }, + { + "@id": "bts:Demographics", + "@type": "rdfs:Class", + "rdfs:comment": "Demographic attributes", + "rdfs:label": "Demographics", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Demographics", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:Ethnicity" + }, + { + "@id": "bts:Gender" + }, + { + "@id": "bts:Race" + }, + { + "@id": "bts:VitalStatus" + }, + { + "@id": "bts:DaystoBirth" + }, + { + "@id": "bts:CountryofResidence" + }, + { + "@id": "bts:AgeIsObfuscated" + }, + { + "@id": "bts:YearOfBirth" + }, + { + "@id": "bts:OccupationDurationYears" + }, + { + "@id": "bts:PrematureAtBirth" + }, + { + "@id": "bts:WeeksGestationatBirth" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyHistory", + "@type": "rdfs:Class", + "rdfs:comment": "Family cancer history", + "rdfs:label": "FamilyHistory", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Family History", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:RelativewithCancerHistory" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Exposure", + "@type": "rdfs:Class", + "rdfs:comment": "Exposure to carcinogens", + "rdfs:label": "Exposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exposure", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:SmokingExposure" + }, + { + "@id": "bts:AlcoholExposure" + }, + { + "@id": "bts:AsbestosExposure" + }, + { + "@id": "bts:CoalDustExposure" + }, + { + "@id": "bts:EnvironmentalTobaccoSmokeExposure" + }, + { + "@id": "bts:RadonExposure" + }, + { + "@id": "bts:RespirableCrystallineSilicaExposure" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:FollowUp", + "@type": "rdfs:Class", + "rdfs:comment": "Follow up clinical visits", + "rdfs:label": "FollowUp", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Follow Up", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:DaystoFollowUp" + }, + { + "@id": "bts:AdverseEvent" + }, + { + "@id": "bts:ProgressionorRecurrence" + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent" + }, + { + "@id": "bts:BMI" + }, + { + "@id": "bts:CauseofResponse" + }, + { + "@id": "bts:Comorbidity" + }, + { + "@id": "bts:ComorbidityMethodofDiagnosis" + }, + { + "@id": "bts:DaystoAdverseEvent" + }, + { + "@id": "bts:DaystoComorbidity" + }, + { + "@id": "bts:DiabetesTreatmentType" + }, + { + "@id": "bts:DiseaseResponse" + }, + { + "@id": "bts:DLCORefPredictivePercent" + }, + { + "@id": "bts:ECOGPerformanceStatus" + }, + { + "@id": "bts:FEV1FVCPostBronchPercent" + }, + { + "@id": "bts:FEV1FVCPreBronchPercent" + }, + { + "@id": "bts:FEV1RefPostBronchPercent" + }, + { + "@id": "bts:FEV1RefPreBronchPercent" + }, + { + "@id": "bts:Height" + }, + { + "@id": "bts:HepatitisSustainedVirologicalResponse" + }, + { + "@id": "bts:HPVPositiveType" + }, + { + "@id": "bts:KarnofskyPerformanceStatus" + }, + { + "@id": "bts:MenopauseStatus" + }, + { + "@id": "bts:PancreatitisOnsetYear" + }, + { + "@id": "bts:RefluxTreatmentType" + }, + { + "@id": "bts:RiskFactor" + }, + { + "@id": "bts:RiskFactorTreatment" + }, + { + "@id": "bts:ViralHepatitisSerologies" + }, + { + "@id": "bts:Weight" + }, + { + "@id": "bts:AdverseEventGrade" + }, + { + "@id": "bts:AIDSRiskFactors" + }, + { + "@id": "bts:BodySurfaceArea" + }, + { + "@id": "bts:CD4Count" + }, + { + "@id": "bts:CDCHIVRiskFactors" + }, + { + "@id": "bts:DaystoImaging" + }, + { + "@id": "bts:EvidenceofRecurrenceType" + }, + { + "@id": "bts:HAARTTreatmentIndicator" + }, + { + "@id": "bts:HIVViralLoad" + }, + { + "@id": "bts:HormonalContraceptiveUse" + }, + { + "@id": "bts:HysterectomyMarginsInvolved" + }, + { + "@id": "bts:HysterectomyType" + }, + { + "@id": "bts:ImagingResult" + }, + { + "@id": "bts:ImagingType" + }, + { + "@id": "bts:ImmunosuppressiveTreatmentType" + }, + { + "@id": "bts:NadirCD4Count" + }, + { + "@id": "bts:PregnancyOutcome" + }, + { + "@id": "bts:RecistTargetedRegionsNumber" + }, + { + "@id": "bts:RecistTargetedRegionsSum" + }, + { + "@id": "bts:ScanTracerUsed" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Diagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Disease diagnosis", + "rdfs:label": "Diagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Diagnosis", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:AgeatDiagnosis" + }, + { + "@id": "bts:YearofDiagnosis" + }, + { + "@id": "bts:PrimaryDiagnosis" + }, + { + "@id": "bts:PrecancerousConditionType" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:TissueorOrganofOrigin" + }, + { + "@id": "bts:Morphology" + }, + { + "@id": "bts:TumorGrade" + }, + { + "@id": "bts:ProgressionorRecurrence" + }, + { + "@id": "bts:LastKnownDiseaseStatus" + }, + { + "@id": "bts:DaystoLastFollowup" + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus" + }, + { + "@id": "bts:MethodofDiagnosis" + }, + { + "@id": "bts:PriorMalignancy" + }, + { + "@id": "bts:PriorTreatment" + }, + { + "@id": "bts:MetastasisatDiagnosis" + }, + { + "@id": "bts:MetastasisatDiagnosisSite" + }, + { + "@id": "bts:FirstSymptomPriortoDiagnosis" + }, + { + "@id": "bts:DaystoDiagnosis" + }, + { + "@id": "bts:PercentTumorInvasion" + }, + { + "@id": "bts:ResidualDisease" + }, + { + "@id": "bts:SynchronousMalignancy" + }, + { + "@id": "bts:TumorConfinedtoOrganofOrigin" + }, + { + "@id": "bts:TumorFocality" + }, + { + "@id": "bts:TumorLargestDimensionDiameter" + }, + { + "@id": "bts:GrossTumorWeight" + }, + { + "@id": "bts:BreslowThickness" + }, + { + "@id": "bts:VascularInvasionPresent" + }, + { + "@id": "bts:VascularInvasionType" + }, + { + "@id": "bts:AnaplasiaPresent" + }, + { + "@id": "bts:AnaplasiaPresentType" + }, + { + "@id": "bts:Laterality" + }, + { + "@id": "bts:PerineuralInvasionPresent" + }, + { + "@id": "bts:LymphaticInvasionPresent" + }, + { + "@id": "bts:LymphNodesPositive" + }, + { + "@id": "bts:LymphNodesTested" + }, + { + "@id": "bts:PeritonealFluidCytologicalStatus" + }, + { + "@id": "bts:ClassificationofTumor" + }, + { + "@id": "bts:BestOverallResponse" + }, + { + "@id": "bts:MitoticCount" + }, + { + "@id": "bts:AJCCClinicalM" + }, + { + "@id": "bts:AJCCClinicalN" + }, + { + "@id": "bts:AJCCClinicalStage" + }, + { + "@id": "bts:AJCCClinicalT" + }, + { + "@id": "bts:AJCCPathologicM" + }, + { + "@id": "bts:AJCCPathologicN" + }, + { + "@id": "bts:AJCCPathologicStage" + }, + { + "@id": "bts:AJCCPathologicT" + }, + { + "@id": 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "StartDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:StopDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stop Days from Index", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SentinelLymphNodeCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric count of sentinel lymph nodes.", + "rdfs:label": "SentinelLymphNodeCount", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Lymph Node Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount", + "@type": "rdfs:Class", + "rdfs:comment": "The number or amount of metastatic 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"@id": "bts:Axilla" + }, + { + "@id": "bts:Back" + }, + { + "@id": "bts:BileDuct" + }, + { + "@id": "bts:Bladder" + }, + { + "@id": "bts:Blood" + }, + { + "@id": "bts:BloodVessel" + }, + { + "@id": "bts:Bodytotal" + }, + { + "@id": "bts:Bone" + }, + { + "@id": "bts:BoneMarrow" + }, + { + "@id": "bts:Bonenon-spine" + }, + { + "@id": "bts:Bowel" + }, + { + "@id": "bts:Brain" + }, + { + "@id": "bts:BrainStem" + }, + { + "@id": "bts:Breast" + }, + { + "@id": "bts:BroadLigament" + }, + { + "@id": "bts:Bronchiole" + }, + { + "@id": "bts:Bronchus" + }, + { + "@id": "bts:Brow" + }, + { + "@id": "bts:BuccalCavity" + }, + { + "@id": "bts:BuccalMucosa" + }, + { + "@id": "bts:Buttock" + }, + { + "@id": "bts:Calf" + }, + { + "@id": "bts:Capillary" + }, + { + "@id": "bts:Cardia" + }, + { + "@id": "bts:Carina" + }, + { + "@id": "bts:CarotidArtery" + }, + { + "@id": "bts:CarotidBody" + }, + { + "@id": "bts:Cartilage" + }, + { + "@id": "bts:Cecum" + }, + { + "@id": "bts:Cell-Line" + }, + { + "@id": 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"bts:Pleura" + }, + { + "@id": "bts:PoplitealFossa" + }, + { + "@id": "bts:Pouch" + }, + { + "@id": "bts:PrimaryTumorField" + }, + { + "@id": "bts:Primarytumorsite" + }, + { + "@id": "bts:Prostate" + }, + { + "@id": "bts:ProstateBed" + }, + { + "@id": "bts:ProstateSeminalVesiclesandLymphNodes" + }, + { + "@id": "bts:Pylorus" + }, + { + "@id": "bts:RectosigmoidJunction" + }, + { + "@id": "bts:Rectum" + }, + { + "@id": "bts:RegionalSite" + }, + { + "@id": "bts:Retina" + }, + { + "@id": "bts:Retro-OrbitalRegion" + }, + { + "@id": "bts:Retroperitoneum" + }, + { + "@id": "bts:Rib" + }, + { + "@id": "bts:RingFinger" + }, + { + "@id": "bts:RoundLigament" + }, + { + "@id": "bts:Sacrum" + }, + { + "@id": "bts:SalivaryGland" + }, + { + "@id": "bts:Scalp" + }, + { + "@id": "bts:Scapula" + }, + { + "@id": "bts:SciaticNerve" + }, + { + "@id": "bts:Scrotum" + }, + { + "@id": "bts:SeminalVesicle" + }, + { + "@id": "bts:Shoulder" + }, + { + "@id": "bts:SigmoidColon" + }, + { + "@id": "bts:Sinus" + }, + { + "@id": "bts:Sinus(es)Maxillary" + }, + { + "@id": "bts:SkeletalMuscle" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:Skinlowerextremitylocal" + }, + { + "@id": "bts:Skintotal" + }, + { + "@id": "bts:Skintrunklocal" + }, + { + "@id": "bts:Skinupperextremitylocal" + }, + { + "@id": "bts:Skull" + }, + { + "@id": "bts:SmallBowel" + }, + { + "@id": "bts:SmallBowelMucosaOnly" + }, + { + "@id": "bts:SmallFinger" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:SpinalColumn" + }, + { + "@id": "bts:SpinalCord" + }, + { + "@id": "bts:Spine" + }, + { + "@id": "bts:Spleen" + }, + { + "@id": "bts:SplenicFlexure" + }, + { + "@id": "bts:Sternum" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:StomachMucosaOnly" + }, + { + "@id": "bts:SubcutaneousTissue" + }, + { + "@id": "bts:Synovium" + }, + { + "@id": "bts:TemporalCortex" + }, + { + "@id": "bts:Tendon" + }, + { + "@id": "bts:Testis" + }, + { + "@id": "bts:Thigh" + }, + { + "@id": "bts:ThoracicSpine" + }, + { + "@id": 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(Extension to GDC attributes in Family History Tier 1)", + "rdfs:label": "FamilyMemberVitalStatusIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:VitalStatusAlive" + }, + { + "@id": "bts:VitalStatusDead" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Family Member Vital Status Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19OccurrenceIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", + "rdfs:label": "COVID19OccurrenceIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": 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"sms:displayName": "COVID19 Current Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19PositiveLabTestIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", + "rdfs:label": "COVID19PositiveLabTestIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Positive Lab Test Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19AntibodyTesting", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", + "rdfs:label": "COVID19AntibodyTesting", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:SARS-CoV-2IgMantibodypositive" + }, + { + "@id": "bts:SARS-CoV-2IgGantibodypositive" + }, + { + "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" + }, + { + "@id": "bts:SARS-CoV-2IgMantibodynegative" + }, + { + "@id": "bts:SARS-CoV-2IgGantibodynegative" + }, + { + "@id": "bts:SARS-CoV-2IgG/IgMantibodynegative" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Antibody Testing", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19ComplicationsSeverity", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.", + "rdfs:label": "COVID19ComplicationsSeverity", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cardiaccomplications" + }, + { + "@id": "bts:Pulmonarycomplications" + }, + { + "@id": "bts:Systemiccomplications" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "COVID19 Complications Severity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CancerTreatmentFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder", + "rdfs:label": "COVID19CancerTreatmentFollowup", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "COVID19 Cancer Treatment Followup", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ecigvapeuse", + "@type": "rdfs:Class", + "rdfs:comment": "Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)", + "rdfs:label": "Ecigvapeuse", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Current" + }, + { + "@id": "bts:Former" + }, + { + "@id": "bts:Never" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Ecig vape use", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ecigvape30dayusenum", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days e-cigarettes or vaping device was used in the last 30 days", + "rdfs:label": "Ecigvape30dayusenum", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ecig vape 30 day use num", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ecigvapetimesperday", + "@type": "rdfs:Class", + "rdfs:comment": "e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)", + "rdfs:label": "Ecigvapetimesperday", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ecig vape times per day", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Typeofsmokeexposurecumulativeyears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", + "rdfs:label": "Typeofsmokeexposurecumulativeyears", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Type of smoke exposure cumulative years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Chewingtobaccodailyusecount", + "@type": "rdfs:Class", + "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", + "rdfs:label": "Chewingtobaccodailyusecount", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Chewing tobacco daily use count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Secondhandsmokeexposureyears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of cumulative years of the patient's exposure to second-hand cigarette smoke", + "rdfs:label": "Secondhandsmokeexposureyears", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second hand smoke exposure years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KnownGeneticPredispositionMutation", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", + "rdfs:label": "KnownGeneticPredispositionMutation", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Known Genetic Predisposition Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome", + "@type": "rdfs:Class", + "rdfs:comment": "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", + "rdfs:label": "HereditaryCancerPredispositionSyndrome", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Alpha-1antitrypsin" + }, + { + "@id": "bts:Attenuatedfamilialadenomatouspolyposis" + }, + { + "@id": "bts:BAP1mutantdisease" + }, + { + "@id": "bts:Beckwith-Wiedemann" + }, + { + "@id": "bts:Biliarydisorder" + }, + { + "@id": "bts:Birt-Hogg-Dubesyndrome" + }, + { + "@id": "bts:Carneycomplex" + }, + { + "@id": "bts:Cirrhosisunknownetiology" + }, + { + "@id": "bts:Constitutionalmismatchrepairdeficiency" + }, + { + "@id": "bts:Familialadenomatouspolyposis" + }, + { + "@id": "bts:Familialgastrointestinalstromaltumor" + }, + { + "@id": "bts:Familialpancreaticcancer" + }, + { + "@id": "bts:Familialprostatecancer" + }, + { + "@id": 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"bts:MultipleendocrineneoplasiatypeII" + }, + { + "@id": "bts:MUTYH-associatedpolyposis" + }, + { + "@id": "bts:Nevoidbasalcellcarcinomasyndrome" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Peutz–Jegherssyndrome" + }, + { + "@id": "bts:Cowdensyndrome" + }, + { + "@id": "bts:RhabdoidtumorpredispositionsyndrometypeI" + }, + { + "@id": "bts:RhabdoidtumorpredispositionsyndrometypeII" + }, + { + "@id": "bts:Rubinstein-Taybisyndrome" + }, + { + "@id": "bts:SDHassociatedrenalcancer" + }, + { + "@id": "bts:Serratedpolyposissyndrome" + }, + { + "@id": "bts:Tuberoussclerosiscomplex" + }, + { + "@id": "bts:Turcotsyndrome" + }, + { + "@id": "bts:Tyrosinemia" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:VonHippel-LindauSyndrome" + } + ], + "sms:displayName": "Hereditary Cancer Predisposition Syndrome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerAssociatedGeneMutations", + "@type": "rdfs:Class", + "rdfs:comment": "Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history", + "rdfs:label": "CancerAssociatedGeneMutations", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:APCmutation" + }, + { + "@id": "bts:ALKmutation" + }, + { + "@id": "bts:ARFmutation" + }, + { + "@id": "bts:ATMmutation" + }, + { + "@id": "bts:ATRXmutation" + }, + { + "@id": "bts:ACVR1mutation" + }, + { + "@id": "bts:BAP1mutation" + }, + { + "@id": "bts:BMPR1Amutation" + }, + { + "@id": "bts:BLMmutation" + }, + { + "@id": "bts:BRCA1mutation" + }, + { + "@id": "bts:BRCA1and2mutation" + }, + { + "@id": "bts:BRCA2mutation" + }, + { + "@id": "bts:BRAFmutation" + }, + { + "@id": "bts:CDH1mutation" + }, + { + "@id": "bts:CDKN2Amutation" + }, + { + "@id": "bts:CDKN2Aandp14ARFmutation" + }, + { + "@id": 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Associated Gene Mutations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MutationalSignatures", + "@type": "rdfs:Class", + "rdfs:comment": "Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done.", + "rdfs:label": "MutationalSignatures", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:UVlightinducedmutations" + }, + { + "@id": "bts:AlkylatingAgents(Temozolomide)inducedmutations" + }, + { + "@id": "bts:Tobaccouseassociatedmutations" + }, + { + "@id": "bts:Ageofcancerdiagnosis" + }, + { + "@id": "bts:Transcriptionalstrandbias" + }, + { + "@id": "bts:Microsatelliteinstability(additionsanddeletions)" + }, + { + "@id": "bts:MethylatedCpGsequencesmutagenesis(deaminationof5-methyl-cytosine)" + }, + { + "@id": "bts:ActivationInducedDeaminases(AID)associatedmutations" + }, + { + "@id": "bts:APOBECenzymesassociatedmutations" + }, + { + "@id": 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"bts:Bachelor'sdegree" + }, + { + "@id": "bts:Doctoraldegreeorprofessionaldegree" + }, + { + "@id": "bts:Gradeschool" + }, + { + "@id": "bts:Graduateorprofessionaldegree" + }, + { + "@id": "bts:Highschoolgraduate(includingequivalency)" + }, + { + "@id": "bts:Master'sdegree" + }, + { + "@id": "bts:Noformaleducation" + }, + { + "@id": "bts:Nothighschoolgraduate" + }, + { + "@id": "bts:Somecollegeorassociatedegree" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Education Level", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CountryofBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Country where the patient was born.", + "rdfs:label": "CountryofBirth", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Afghanistan" + }, + { + "@id": "bts:Albania" + }, + { + "@id": "bts:Algeria" + }, + { + "@id": "bts:Andorra" + }, + { + "@id": "bts:Angola" + }, + { + "@id": "bts:Anguilla" + }, + { + "@id": "bts:AntiguaandBarbuda" + }, + { + "@id": "bts:Argentina" + }, + { + "@id": "bts:Armenia" + }, + { + "@id": "bts:Aruba" + }, + { + "@id": "bts:Australia" + }, + { + "@id": "bts:Austria" + }, + { + "@id": "bts:Azerbaijan" + }, + { + "@id": "bts:Bahamas" + }, + { + "@id": "bts:Bahrain" + }, + { + "@id": "bts:Bangladesh" + }, + { + "@id": "bts:Barbados" + }, + { + "@id": "bts:Belarus" + }, + { + "@id": "bts:Belgium" + }, + { + "@id": "bts:Belize" + }, + { + "@id": "bts:Benin" + }, + { + "@id": "bts:Bermuda" + }, + { + "@id": "bts:Bhutan" + }, + { + "@id": "bts:Bolivia" + }, + { + "@id": "bts:BosniaandHerzegovina" + }, + { + "@id": "bts:Botswana" + }, + { + "@id": "bts:Brazil" + }, + { + "@id": "bts:Brunei" + }, + { + "@id": "bts:Bulgaria" + }, + { + "@id": "bts:BurkinaFaso" + }, + { + "@id": "bts:Burundi" + }, + { + "@id": "bts:Cambodia" + }, + { + "@id": "bts:Cameroon" + }, + { + "@id": "bts:Canada" + }, + { + "@id": "bts:CapeVerde" + }, + { + "@id": "bts:CaymanIslands" + }, + { + "@id": "bts:CentralAfricanRepublic" + }, + { + "@id": "bts:Chad" + }, + { + "@id": "bts:Chile" + }, + { + "@id": "bts:China" + }, + { + "@id": "bts:Colombia" + }, + { + "@id": "bts:Comoros" + }, + { + "@id": "bts:Congo" + }, + { + "@id": "bts:CookIslands" + }, + { + "@id": "bts:CostaRica" + }, + { + "@id": "bts:Coted'Ivoire" + }, + { + "@id": "bts:Croatia" + }, + { + "@id": "bts:Cuba" + }, + { + "@id": "bts:Curacao" + }, + { + "@id": "bts:Cyprus" + }, + { + "@id": "bts:CzechRepublic(Czechia)" + }, + { + "@id": "bts:DemocraticRepublicoftheCongo" + }, + { + "@id": "bts:Denmark" + }, + { + "@id": "bts:Djibouti" + }, + { + "@id": "bts:Dominica" + }, + { + "@id": "bts:DominicanRepublic" + }, + { + "@id": "bts:Ecuador" + }, + { + "@id": "bts:Egypt" + }, + { + "@id": "bts:ElSalvador" + }, + { + "@id": "bts:EquatorialGuinea" + }, + { + "@id": "bts:Eritrea" + }, + { + "@id": "bts:Estonia" + }, + { + "@id": "bts:Eswatini" + }, + { + "@id": "bts:Ethiopia" + }, + { + "@id": "bts:FalklandIslands(Malvinas)" + }, + { + "@id": "bts:FaroeIslands" + }, + { + "@id": "bts:FederatedStatesofMicronesia" + }, + { + "@id": "bts:Fiji" + }, + { + "@id": "bts:Finland" + }, + { + "@id": "bts:France" + }, + { + "@id": "bts:FrenchGuiana" + }, + { + "@id": "bts:FrenchPolynesia" + }, + { + "@id": "bts:Gabon" + }, + { + "@id": "bts:Gambia" + }, + { + "@id": "bts:Georgia" + }, + { + "@id": "bts:Germany" + }, + { + "@id": "bts:Ghana" + }, + { + "@id": "bts:Gibraltar" + }, + { + "@id": "bts:Greece" + }, + { + "@id": "bts:Greenland" + }, + { + "@id": "bts:Grenada" + }, + { + "@id": "bts:Guadeloupe" + }, + { + "@id": "bts:Guam" + }, + { + "@id": "bts:Guatemala" + }, + { + "@id": "bts:Guernsey" + }, + { + "@id": "bts:Guinea" + }, + { + "@id": "bts:Guinea-Bissau" + }, + { + "@id": "bts:Guyana" + }, + { + "@id": "bts:Haiti" + }, + { + "@id": "bts:HolySee" + }, + { + "@id": "bts:Honduras" + }, + { + "@id": "bts:HongKong" + }, + { + "@id": "bts:Hungary" + }, + { + "@id": "bts:Iceland" + }, + { + "@id": "bts:India" + }, + { + "@id": "bts:Indonesia" + }, + { + "@id": "bts:Iran" + }, + { + "@id": "bts:Iraq" + }, + { + "@id": "bts:Ireland" + }, + { + "@id": "bts:IsleofMan" + }, + { + "@id": "bts:Israel" + }, + { + "@id": "bts:Italy" + }, + { + "@id": "bts:Jamaica" + }, + { + "@id": "bts:Japan" + }, + { + "@id": "bts:Jersey" + }, + { + "@id": "bts:Jordan" + }, + { + "@id": "bts:Kazakhstan" + }, + { + "@id": "bts:Kenya" + }, + { + "@id": "bts:Kiribati" + }, + { + "@id": "bts:Kosovo" + }, + { + "@id": "bts:Kuwait" + }, + { + "@id": "bts:Kyrgyzstan" + }, + { + "@id": "bts:Laos" + }, + { + "@id": "bts:Latvia" + }, + { + "@id": "bts:Lebanon" + }, + { + "@id": "bts:Lesotho" + }, + { + "@id": "bts:Liberia" + }, + { + "@id": "bts:Libya" + }, + { + "@id": "bts:Liechtenstein" + }, + { + "@id": "bts:Lithuania" + }, + { + "@id": "bts:Luxembourg" + }, + { + "@id": "bts:Macau" + }, + { + "@id": "bts:Madagascar" + }, + { + "@id": "bts:Malawi" + }, + { + "@id": "bts:Malaysia" + }, + { + "@id": "bts:Maldives" + }, + { + "@id": "bts:Mali" + }, + { + "@id": "bts:Malta" + }, + { + "@id": "bts:MarshallIslands" + }, + { + "@id": "bts:Martinique" + }, + { + "@id": "bts:Mauritania" + }, + { + "@id": "bts:Mauritius" + }, + { + "@id": "bts:Mayotte" + }, + { + "@id": "bts:Mexico" + }, + { + "@id": "bts:Moldova" + }, + { + "@id": "bts:Monaco" + }, + { + "@id": "bts:Mongolia" + }, + { + "@id": "bts:Montenegro" + }, + { + "@id": "bts:Montserrat" + }, + { + "@id": "bts:Morocco" + }, + { + "@id": "bts:Mozambique" + }, + { + "@id": "bts:Myanmar" + }, + { + "@id": "bts:Namibia" + }, + { + "@id": "bts:Nauru" + }, + { + "@id": "bts:Nepal" + }, + { + "@id": "bts:Netherlands" + }, + { + "@id": "bts:NewCaledonia" + }, + { + "@id": "bts:NewZealand" + }, + { + "@id": "bts:Nicaragua" + }, + { + "@id": "bts:Niger" + }, + { + "@id": "bts:Nigeria" + }, + { + "@id": "bts:Niue" + }, + { + "@id": "bts:NorthKorea" + }, + { + "@id": "bts:NorthMacedonia" + }, + { + "@id": "bts:NorthernMarianaIslands" + }, + { + "@id": "bts:Norway" + }, + { + "@id": "bts:Oman" + }, + { + "@id": "bts:Pakistan" + }, + { + "@id": "bts:Palau" + }, + { + "@id": "bts:Panama" + }, + { + "@id": "bts:PapuaNewGuinea" + }, + { + "@id": "bts:Paraguay" + }, + { + "@id": "bts:Peru" + }, + { + "@id": "bts:Philippines" + }, + { + "@id": "bts:Poland" + }, + { + "@id": "bts:Portugal" + }, + { + "@id": "bts:PuertoRico" + }, + { + "@id": "bts:Qatar" + }, + { + "@id": "bts:Reunion" + }, + { + "@id": "bts:Romania" + }, + { + "@id": "bts:Russia" + }, + { + "@id": "bts:Rwanda" + }, + { + "@id": "bts:SaintHelenaAscensionandTristandaCunha" + }, + { + "@id": "bts:SaintKittsandNevis" + }, + { + "@id": "bts:SaintLucia" + }, + { + "@id": "bts:SaintPierreandMiquelon" + }, + { + "@id": "bts:SaintVincentandtheGrenadines" + }, + { + "@id": "bts:Samoa" + }, + { + "@id": "bts:SanMarino" + }, + { + "@id": "bts:SaoTomeandPrincipe" + }, + { + "@id": "bts:SaudiArabia" + }, + { + "@id": "bts:Senegal" + }, + { + "@id": "bts:Serbia" + }, + { + "@id": "bts:Seychelles" + }, + { + "@id": "bts:SierraLeone" + }, + { + "@id": "bts:Singapore" + }, + { + "@id": "bts:Slovakia" + }, + { + "@id": "bts:Slovenia" + }, + { + "@id": "bts:SolomonIslands" + }, + { + "@id": "bts:Somalia" + }, + { + "@id": "bts:SouthAfrica" + }, + { + "@id": "bts:SouthKorea" + }, + { + "@id": "bts:SouthSudan" + }, + { + "@id": "bts:Spain" + }, + { + "@id": "bts:SriLanka" + }, + { + "@id": "bts:StateofPalestine" + }, + { + "@id": "bts:Sudan" + }, + { + "@id": "bts:Suriname" + }, + { + "@id": "bts:Svalbard&JanMayenIslands" + }, + { + "@id": "bts:Sweden" + }, + { + "@id": "bts:Switzerland" + }, + { + "@id": "bts:Syria" + }, + { + "@id": "bts:Taiwan" + }, + { + "@id": "bts:Tajikistan" + }, + { + "@id": "bts:Tanzania" + }, + { + "@id": "bts:Thailand" + }, + { + "@id": "bts:Timor-Leste" + }, + { + "@id": "bts:Togo" + }, + { + "@id": "bts:Tokelau" + }, + { + "@id": "bts:Tonga" + }, + { + "@id": "bts:TrinidadandTobago" + }, + { + "@id": "bts:Tunisia" + }, + { + "@id": "bts:Turkey" + }, + { + "@id": "bts:Turkmenistan" + }, + { + "@id": "bts:Tuvalu" + }, + { + "@id": "bts:Uganda" + }, + { + "@id": "bts:Ukraine" + }, + { + "@id": "bts:UnitedArabEmirates" + }, + { + "@id": "bts:UnitedKingdom" + }, + { + "@id": "bts:UnitedStates" + }, + { + "@id": "bts:Uruguay" + }, + { + "@id": "bts:Uzbekistan" + }, + { + "@id": "bts:Vanuatu" + }, + { + "@id": "bts:Venezuela" + }, + { + "@id": "bts:Vietnam" + }, + { + "@id": "bts:VirginIslandsBritish" + }, + { + "@id": "bts:VirginIslandsU.S." + }, + { + "@id": "bts:WallisandFutuna" + }, + { + "@id": "bts:WesternSahara" + }, + { + "@id": "bts:Yemen" + }, + { + "@id": "bts:Zambia" + }, + { + "@id": "bts:Zimbabwe" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Country of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea", + "@type": "rdfs:Class", + "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", + "rdfs:label": "MedicallyUnderservedArea", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:MedicallyUnderservedArea-Yes" + }, + { + "@id": "bts:MedicallyUnderservedArea-No" + }, + { + "@id": "bts:MedicallyUnderservedArea-Unknown" + } + ], + "sms:displayName": "Medically Underserved Area", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RuralvsUrban", + "@type": "rdfs:Class", + "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", + "rdfs:label": "RuralvsUrban", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:UrbanPopulation(population>50000)" + }, + { + "@id": "bts:UrbanCluster(population2500-50000)" + }, + { + "@id": "bts:RuralPopulation(population<2500)" + } + ], + "sms:displayName": "Rural vs Urban", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidence", + "@type": "rdfs:Class", + "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", + "rdfs:label": "CancerIncidence", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CancerIncidenceLocation", + "@type": "rdfs:Class", + "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", + "rdfs:label": "CancerIncidenceLocation", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer Incidence Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Cancer related clinical data specific to SRRS", + "rdfs:label": "SRRSClinicalDataTier2", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:EducationLevel" + }, + { + "@id": "bts:CountryofBirth" + }, + { + "@id": "bts:MedicallyUnderservedArea" + }, + { + "@id": "bts:RuralvsUrban" + }, + { + "@id": "bts:CancerIncidence" + }, + { + "@id": "bts:CancerIncidenceLocation" + }, + { + "@id": "bts:Ethnicity" + }, + { + "@id": "bts:Gender" + }, + { + "@id": "bts:Race" + }, + { + "@id": "bts:VitalStatus" + }, + { + "@id": "bts:AgeatDiagnosis" + }, + { + "@id": "bts:DaystoLastFollowup" + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus" + }, + { + "@id": "bts:DaystoRecurrence" + }, + { + "@id": "bts:LastKnownDiseaseStatus" + }, + { + "@id": "bts:Morphology" + }, + { + "@id": "bts:PrimaryDiagnosis" + }, + { + "@id": "bts:ProgressionorRecurrence" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:TissueorOrganofOrigin" + }, + { + "@id": "bts:NCIAtlasCancerSite" + }, + { + "@id": "bts:TumorGrade" + }, + { + "@id": "bts:PackYearsSmoked" + }, + { + "@id": "bts:YearsSmoked" + }, + { + "@id": "bts:DaystoFollowUp" + }, + { + "@id": "bts:GeneSymbol" + }, + { + "@id": "bts:MolecularAnalysisMethod" + }, + { + "@id": "bts:TestResult" + }, + { + "@id": "bts:TreatmentType" + }, + { + "@id": "bts:TumorLargestDimensionDiameter" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Ethnicity", + "@type": "rdfs:Class", + "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "rdfs:label": "Ethnicity", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Hispanicorlatino" + }, + { + "@id": "bts:Nothispanicorlatino" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Ethnicity", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Gender", + "@type": "rdfs:Class", + "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "rdfs:label": "Gender", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Female" + }, + { + "@id": "bts:Male" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unspecified" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Gender", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Race", + "@type": "rdfs:Class", + "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "rdfs:label": "Race", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:White" + }, + { + "@id": "bts:Americanindianoralaskanative" + }, + { + "@id": "bts:Blackorafricanamerican" + }, + { + "@id": "bts:Asian" + }, + { + "@id": "bts:Nativehawaiianorotherpacificislander" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" + } + ], + "sms:displayName": "Race", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:VitalStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Alive" + }, + { + "@id": "bts:Dead" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Vital Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label": "AgeatDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Age at Diagnosis", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoLastFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastFollowup", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Follow up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastKnownDiseaseStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoRecurrence", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoRecurrence", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:LastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", + "rdfs:label": "LastKnownDiseaseStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Distantmetrecurrence/progression" + }, + { + "@id": "bts:Loco-regionalrecurrence/progression" + }, + { + "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" + }, + { + "@id": "bts:Tumorfree" + }, + { + "@id": "bts:Unknowntumorstatus" + }, + { + "@id": "bts:Withtumor" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Morphology", + "@type": "rdfs:Class", + "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", + "rdfs:label": "Morphology", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Morphology", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "PrimaryDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Acinarcellcarcinoma" + }, + { + "@id": "bts:Acutebasophilicleukaemia" + }, + { + "@id": "bts:AcuteleukemiaBurkitttype" + }, + { + "@id": "bts:AcuteleukemiaNOS" + }, + { + "@id": "bts:Acutelymphaticleukemia" + }, + { + "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" + }, + { + "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" + }, + { + "@id": "bts:AcutelymphoblasticleukemiaNOS" + }, + { + "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" + }, + { + "@id": "bts:Acutelymphocyticleukemia" + }, + { + "@id": "bts:Acutelymphoidleukemia" + }, + { + "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" + }, + { + "@id": "bts:AcutemyeloidleukemiaMLL" + }, + { + "@id": "bts:AcutemyeloidleukemiaNOS" + }, + { + "@id": "bts:Acutemyelomonocyticleukemia" + }, + { + "@id": "bts:AcutepromyelocyticleukemiaNOS" + }, + { + "@id": "bts:Adenocarcinoidtumor" + }, + { + "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" + }, + { + "@id": "bts:AdenocarcinomainapolypNOS" + }, + { + "@id": "bts:Adenocarcinomainadenomatouspolyp" + }, + { + "@id": "bts:Adenocarcinomainpolypoidadenoma" + }, + { + "@id": "bts:AdenocarcinomainsituinapolypNOS" + }, + { + "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" + }, + { + "@id": "bts:Adenocarcinomainsituintubularadenoma" + }, + { + "@id": "bts:Adenocarcinomainsitumucinous" + }, + { + "@id": "bts:Adenocarcinomainsitunon-mucinous" + }, + { + "@id": "bts:AdenocarcinomainsituNOS" + }, + { + "@id": "bts:Adenocarcinomaintubularadenoma" + }, + { + "@id": "bts:Adenocarcinomainvillousadenoma" + }, + { + "@id": "bts:Adenocarcinomaofanalducts" + }, + { + "@id": "bts:Adenocarcinomaofanalglands" + }, + { + "@id": "bts:Adenocarcinomadiffusetype" + }, + { + "@id": "bts:Adenocarcinomaendocervicaltype" + }, + { + "@id": "bts:Adenocarcinomaintestinaltype" + }, + { + "@id": "bts:AdenocarcinomametastaticNOS" + }, + { + "@id": "bts:AdenocarcinomaNOS" + }, + { + "@id": "bts:Adenocarcinomapancreatobiliarytype" + }, + { + "@id": "bts:Adultrhabdomyoma" + }, + { + "@id": "bts:AdultT-celllymphoma" + }, + { + "@id": "bts:AdultT-celllymphoma/leukemia" + }, + { + "@id": "bts:Astrocytomaanaplastic" + }, + { + "@id": "bts:Astrocytomalowgrade" + }, + { + "@id": "bts:AstrocytomaNOS" + }, + { + "@id": "bts:BcelllymphomaNOS" + }, + { + "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + }, + { + "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + }, + { + "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" + }, + { + "@id": "bts:B-ALL" + }, + { + "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" + }, + { + "@id": "bts:Basalcelladenocarcinoma" + }, + { + "@id": "bts:Basalcelladenoma" + }, + { + "@id": "bts:BasalcellcarcinomaNOS" + }, + { + "@id": "bts:Basalcellepithelioma" + }, + { + "@id": "bts:Basalcelltumor" + }, + { + "@id": "bts:Basophiladenocarcinoma" + }, + { + "@id": "bts:Basophiladenoma" + }, + { + "@id": "bts:Basophilcarcinoma" + }, + { + "@id": "bts:Bileductadenocarcinoma" + }, + { + "@id": "bts:Bileductadenoma" + }, + { + "@id": "bts:Bileductcarcinoma" + }, + { + "@id": "bts:Bileductcystadenocarcinoma" + }, + { + "@id": "bts:Bileductcystadenoma" + }, + { + "@id": "bts:Bronchialadenomacarcinoid" + }, + { + "@id": "bts:Bronchialadenomacylindroid" + }, + { + "@id": "bts:BronchialadenomaNOS" + }, + { + "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" + }, + { + "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + }, + { + "@id": "bts:Bronchio-alveolarcarcinomamucinous" + }, + { + "@id": "bts:Bronchiolaradenocarcinoma" + }, + { + "@id": "bts:Bronchiolarcarcinoma" + }, + { + "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" + }, + { + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" + }, + { + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + }, + { + "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" + }, + { + "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + }, + { + "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + }, + { + "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" + }, + { + "@id": "bts:Burkittcellleukemia" + }, + { + "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" + }, + { + "@id": "bts:Burkitttumor" + }, + { + "@id": "bts:Burkitt-likelymphoma" + }, + { + "@id": "bts:C-ALL" + }, + { + "@id": "bts:Cancer" + }, + { + "@id": "bts:Capillaryhemangioma" + }, + { + "@id": "bts:Capillarylymphangioma" + }, + { + "@id": "bts:CarcinomainapolypNOS" + }, + { + "@id": "bts:Carcinomainadenomatouspolyp" + }, + { + "@id": "bts:Carcinomainpleomorphicadenoma" + }, + { + "@id": "bts:CarcinomainsituinapolypNOS" + }, + { + "@id": "bts:Carcinomainsituinadenomatouspolyp" + }, + { + "@id": "bts:CarcinomainsituNOS" + }, + { + "@id": "bts:CarcinomaanaplasticNOS" + }, + { + "@id": "bts:Carcinomadiffusetype" + }, + { + "@id": "bts:Carcinomaintestinaltype" + }, + { + "@id": "bts:CarcinomametastaticNOS" + }, + { + "@id": "bts:CarcinomaNOS" + }, + { + "@id": "bts:CarcinosarcomaNOS" + }, + { + "@id": "bts:CarcinomaundifferentiatedNOS" + }, + { + "@id": "bts:CementomaNOS" + }, + { + "@id": "bts:Centralneuroblastoma" + }, + { + "@id": "bts:Centralneurocytoma" + }, + { + "@id": "bts:Cerebellarliponeurocytoma" + }, + { + "@id": "bts:CerebellarsarcomaNOS" + }, + { + "@id": "bts:CervicalintraepithelialneoplasiagradeIII" + }, + { + "@id": "bts:Cervicalintraepithelialneoplasialowgrade" + }, + { + "@id": "bts:ChondromaNOS" + }, + { + "@id": "bts:Chondrosarcomagrade2/3" + }, + { + "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" + }, + { + "@id": "bts:ChronicgranulocyticleukemiaNOS" + }, + { + "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + }, + { + "@id": "bts:ChronicleukemiaNOS" + }, + { + "@id": "bts:Chroniclymphaticleukemia" + }, + { + "@id": "bts:Chroniclymphocyticleukemia" + }, + { + "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" + }, + { + "@id": "bts:Chroniclymphoidleukemia" + }, + { + "@id": "bts:Chronicmonocyticleukemia" + }, + { + "@id": "bts:ChronicmyelocyticleukemiaNOS" + }, + { + "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" + }, + { + "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + }, + { + "@id": "bts:ChronicmyeloidleukemiaNOS" + }, + { + "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" + }, + { + "@id": "bts:ChronicmyelomonocyticleukemiaNOS" + }, + { + "@id": "bts:ChronicmyelomonocyticleukemiaType1" + }, + { + "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" + }, + { + "@id": "bts:ChronicmyeloproliferativediseaseNOS" + }, + { + "@id": "bts:Chronicmyeloproliferativedisorder" + }, + { + "@id": "bts:Chronicneutrophilicleukemia" + }, + { + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" + }, + { + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" + }, + { + "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + }, + { + "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" + }, + { + "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" + }, + { + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" + }, + { + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + }, + { + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + }, + { + "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + }, + { + "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" + }, + { + "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" + }, + { + "@id": "bts:Combinedsmallcellcarcinoma" + }, + { + "@id": "bts:Combinedsmallcell-adenocarcinoma" + }, + { + "@id": "bts:Combinedsmallcell-largecarcinoma" + }, + { + "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" + }, + { + "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" + }, + { + "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" + }, + { + "@id": "bts:Dermalnevus" + }, + { + "@id": "bts:DermatofibromaNOS" + }, + { + "@id": "bts:DiffuseastrocytomaIDH-mutant" + }, + { + "@id": "bts:DiffuseastrocytomaIDH-wildtype" + }, + { + "@id": "bts:Diffuseastrocytomalowgrade" + }, + { + "@id": "bts:DiffuselargeB-celllymphomaNOS" + }, + { + "@id": "bts:Diffusemelanocytosis" + }, + { + "@id": "bts:DuctadenocarcinomaNOS" + }, + { + "@id": "bts:DuctadenomaNOS" + }, + { + "@id": "bts:Ductcarcinomadesmoplastictype" + }, + { + "@id": "bts:DuctcarcinomaNOS" + }, + { + "@id": "bts:Ductcellcarcinoma" + }, + { + "@id": "bts:DuctalcarcinomainsituNOS" + }, + { + "@id": "bts:DuctalcarcinomaNOS" + }, + { + "@id": "bts:Dysplasticnevus" + }, + { + "@id": "bts:EndometrialsarcomaNOS" + }, + { + "@id": "bts:EndometrioidadenocarcinomaNOS" + }, + { + "@id": "bts:EndometrioidadenofibromaNOS" + }, + { + "@id": "bts:EndometrioidadenomaNOS" + }, + { + "@id": "bts:EndometrioidcarcinomaNOS" + }, + { + "@id": "bts:Eosinophiladenocarcinoma" + }, + { + "@id": "bts:Eosinophiladenoma" + }, + { + "@id": "bts:Eosinophilcarcinoma" + }, + { + "@id": "bts:Eosinophilicgranuloma" + }, + { + "@id": "bts:Eosinophilicleukemia" + }, + { + "@id": "bts:EpendymomaNOS" + }, + { + "@id": "bts:EpidermoidcarcinomainsituNOS" + }, + { + "@id": "bts:EpidermoidcarcinomaNOS" + }, + { + "@id": "bts:Epithelialtumorbenign" + }, + { + "@id": "bts:Epithelialtumormalignant" + }, + { + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" + }, + { + "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" + }, + { + "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" + }, + { + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" + }, + { + "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" + }, + { + "@id": "bts:Ewingsarcoma" + }, + { + "@id": "bts:GangliogliomaNOS" + }, + { + "@id": "bts:Familialadenomatouspolyposis" + }, + { + "@id": "bts:Gastrincelltumor" + }, + { + "@id": "bts:Gastrincelltumormalignant" + }, + { + "@id": "bts:Gastrinomamalignant" + }, + { + "@id": "bts:GastrinomaNOS" + }, + { + "@id": "bts:Gastrointestinalstromaltumormalignant" + }, + { + "@id": "bts:Glioblastoma" + }, + { + "@id": "bts:Gliomamalignant" + }, + { + "@id": "bts:GliomaNOS" + }, + { + "@id": "bts:Haemangioblastoma" + }, + { + "@id": "bts:Haemangiosarcoma" + }, + { + "@id": "bts:Hepatocarcinoma" + }, + { + "@id": "bts:Hepatocellularadenoma" + }, + { + "@id": "bts:HepatocellularcarcinomaNOS" + }, + { + "@id": "bts:Hepatocholangiocarcinoma" + }, + { + "@id": "bts:Hepatoidadenocarcinoma" + }, + { + "@id": "bts:Hepatoidcarcinoma" + }, + { + "@id": "bts:HodgkindiseaseNOS" + }, + { + "@id": "bts:Hodgkingranuloma" + }, + { + "@id": "bts:HodgkinlymphomamixedcellularityNOS" + }, + { + "@id": "bts:HodgkinlymphomanodularsclerosisNOS" + }, + { + "@id": "bts:HodgkinlymphomaNOS" + }, + { + "@id": "bts:HodgkinparagranulomaNOS" + }, + { + "@id": "bts:Hodgkinsarcoma" + }, + { + "@id": "bts:InfiltratingbasalcellcarcinomaNOS" + }, + { + "@id": "bts:InfiltratingductcarcinomaNOS" + }, + { + "@id": "bts:Infiltratingductandcolloidcarcinoma" + }, + { + "@id": "bts:Infiltratingductandcribriformcarcinoma" + }, + { + "@id": "bts:Inflammatoryadenocarcinoma" + }, + { + "@id": "bts:Inflammatorycarcinoma" + }, + { + "@id": "bts:Interstitialcelltumorbenign" + }, + { + "@id": "bts:Interstitialcelltumormalignant" + }, + { + "@id": "bts:InterstitialcelltumorNOS" + }, + { + "@id": "bts:Intracysticpapilloma" + }, + { + "@id": "bts:Intradermalnevus" + }, + { + "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" + }, + { + "@id": "bts:Intraductalandlobularcarcinoma" + }, + { + "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" + }, + { + "@id": "bts:Intraductalcarcinomaclinging" + }, + { + "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" + }, + { + "@id": "bts:IntraductalcarcinomaNOS" + }, + { + "@id": "bts:Intraductalcarcinomasolidtype" + }, + { + "@id": "bts:Intraductalmicropapillarycarcinoma" + }, + { + "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" + }, + { + "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" + }, + { + "@id": "bts:Intraductalpapillarycarcinoma" + }, + { + "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" + }, + { + "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" + }, + { + "@id": "bts:Intraductaltubulopapillaryneoplasm" + }, + { + "@id": "bts:IntraepidermalcarcinomaNOS" + }, + { + "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" + }, + { + "@id": "bts:IntravascularB-celllymphoma" + }, + { + "@id": "bts:Juvenilemyelomonocyticleukemia" + }, + { + "@id": "bts:Kaposisarcoma" + }, + { + "@id": "bts:LargecellcarcinomaNOS" + }, + { + "@id": "bts:Liposarcomadifferentiated" + }, + { + "@id": "bts:LiposarcomaNOS" + }, + { + "@id": "bts:Liposarcomawelldifferentiated" + }, + { + "@id": "bts:Livercelladenoma" + }, + { + "@id": "bts:Livercellcarcinoma" + }, + { + "@id": "bts:Lobularadenocarcinoma" + }, + { + "@id": "bts:Lobularandductalcarcinoma" + }, + { + "@id": "bts:LobularcarcinomainsituNOS" + }, + { + "@id": "bts:Lobularcarcinomanoninfiltrating" + }, + { + "@id": "bts:LobularcarcinomaNOS" + }, + { + "@id": "bts:LymphaticleukemicNOS" + }, + { + "@id": "bts:LymphoblasticleukemiaNOS" + }, + { + "@id": "bts:Lymphoblastoma" + }, + { + "@id": "bts:LymphocyticleukemiaNOS" + }, + { + "@id": "bts:LymphomaNOS" + }, + { + "@id": "bts:Malignancy" + }, + { + "@id": "bts:MalignantlymphomadiffuseNOS" + }, + { + "@id": "bts:MalignantlymphomaHodgkin" + }, + { + "@id": "bts:MalignantlymphomaimmunoblasticNOS" + }, + { + "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" + }, + { + "@id": "bts:MalignantlymphomalargeB-cellNOS" + }, + { + "@id": "bts:MalignantlymphomalargecellNOS" + }, + { + "@id": "bts:MalignantlymphomalymphoblasticNOS" + }, + { + "@id": "bts:MalignantlymphomalymphocyticdiffuseNOS" + }, + { + "@id": "bts:MalignantlymphomalymphocyticnodularNOS" + }, + { + "@id": "bts:MalignantlymphomalymphocyticNOS" + }, + { + "@id": "bts:Malignantlymphomamixedcelltypediffuse" + }, + { + "@id": "bts:Malignantlymphomamixedcelltypefollicular" + }, + { + "@id": "bts:Malignantlymphomamixedcelltypenodular" + }, + { + "@id": "bts:MalignantlymphomanodularNOS" + }, + { + "@id": "bts:Malignantlymphomanon-HodgkinNOS" + }, + { + "@id": "bts:MalignantlymphomaNOS" + }, + { + "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" + }, + { + "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" + }, + { + "@id": "bts:Malignantmelanomaingiantpigmentednevus" + }, + { + "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" + }, + { + "@id": "bts:Malignantmelanomainjunctionalnevus" + }, + { + "@id": "bts:Malignantmelanomainprecancerousmelanosis" + }, + { + "@id": "bts:MalignantmelanomaNOS" + }, + { + "@id": "bts:Malignantmelanomaregressing" + }, + { + "@id": "bts:Mammarycarcinomainsitu" + }, + { + "@id": "bts:Medullaryadenocarcinoma" + }, + { + "@id": "bts:MedullarycarcinomaNOS" + }, + { + "@id": "bts:Medullaryosteosarcoma" + }, + { + "@id": "bts:MedulloblastomaNOS" + }, + { + "@id": "bts:Melanoameloblastoma" + }, + { + "@id": "bts:Melanocyticnevus" + }, + { + "@id": "bts:Melanocytomaeyeball" + }, + { + "@id": "bts:MelanocytomaNOS" + }, + { + "@id": "bts:Melanomainsitu" + }, + { + "@id": "bts:Melanomamalignantofsoftparts" + }, + { + "@id": "bts:MelanomaNOS" + }, + { + "@id": "bts:Melanoticmedulloblastoma" + }, + { + "@id": "bts:MelanoticMPNST" + }, + { + "@id": "bts:Melanoticneuroectodermaltumor" + }, + { + "@id": "bts:Melanoticneurofibroma" + }, + { + "@id": "bts:Melanoticprogonoma" + }, + { + "@id": "bts:MelanoticpsammomatousMPNST" + }, + { + "@id": "bts:Melanoticschwannoma" + }, + { + "@id": "bts:Meningealmelanocytoma" + }, + { + "@id": "bts:Meningealmelanoma" + }, + { + "@id": "bts:Meningiomaanaplastic" + }, + { + "@id": "bts:Meningiomamalignant" + }, + { + "@id": "bts:MeningiomaNOS" + }, + { + "@id": "bts:MicropapillarycarcinomaNOS" + }, + { + "@id": "bts:Mixedadenocarcinomaandepidermoidcarcinoma" + }, + { + "@id": "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" + }, + { + "@id": "bts:Mixedmedullary-follicularcarcinoma" + }, + { + "@id": "bts:Mixedmedullary-papillarycarcinoma" + }, + { + "@id": 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Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "SiteofResectionorBiopsy", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdomenNOS" + }, + { + "@id": "bts:Abdominalesophagus" + }, + { + "@id": "bts:AccessorysinusNOS" + }, + { + "@id": "bts:Acousticnerve" + }, + { + "@id": "bts:AdrenalglandNOS" + }, + { + "@id": "bts:AmpullaofVater" + }, + { + "@id": "bts:Analcanal" + }, + { + "@id": "bts:Anterior2/3oftongueNOS" + }, + { + "@id": "bts:Anteriorfloorofmouth" + }, + { + "@id": "bts:Anteriormediastinum" + }, + { + "@id": "bts:Anteriorsurfaceofepiglottis" + }, + { + "@id": "bts:Anteriorwallofbladder" + }, + { + "@id": "bts:Anteriorwallofnasopharynx" + }, + { + "@id": "bts:AnusNOS" + }, + { + "@id": "bts:Aorticbodyandotherparaganglia" + }, + { + "@id": "bts:Appendix" + }, + { + "@id": "bts:Ascendingcolon" + }, + { + "@id": 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+ "@id": "bts:Frontallobe" + }, + { + "@id": "bts:Frontalsinus" + }, + { + "@id": "bts:Fundusofstomach" + }, + { + "@id": "bts:Fundusuteri" + }, + { + "@id": "bts:Gallbladder" + }, + { + "@id": "bts:Gastricantrum" + }, + { + "@id": "bts:GastrointestinaltractNOS" + }, + { + "@id": "bts:Glanspenis" + }, + { + "@id": "bts:Glottis" + }, + { + "@id": "bts:GreatercurvatureofstomachNOS" + }, + { + "@id": "bts:GumNOS" + }, + { + "@id": "bts:Hardpalate" + }, + { + "@id": "bts:Headofpancreas" + }, + { + "@id": "bts:HeadfaceorneckNOS" + }, + { + "@id": "bts:Heart" + }, + { + "@id": "bts:HematopoieticsystemNOS" + }, + { + "@id": "bts:Hepaticflexureofcolon" + }, + { + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + }, + { + "@id": "bts:HypopharynxNOS" + }, + { + "@id": "bts:Ileum" + }, + { + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + }, + { + "@id": "bts:IntestinaltractNOS" + }, + { + "@id": "bts:Intra-abdominallymphnodes" + }, + { + "@id": "bts:Intrahepaticbileduct" + }, + { + "@id": "bts:Intrathoraciclymphnodes" + }, + { + "@id": "bts:IsletsofLangerhans" + }, + { + "@id": "bts:Isthmusuteri" + }, + { + "@id": "bts:Jejunum" + }, + { + "@id": "bts:KidneyNOS" + }, + { + "@id": "bts:Labiummajus" + }, + { + "@id": "bts:Labiumminus" + }, + { + "@id": "bts:Lacrimalgland" + }, + { + "@id": "bts:Laryngealcartilage" + }, + { + "@id": "bts:LarynxNOS" + }, + { + "@id": "bts:Lateralfloorofmouth" + }, + { + "@id": "bts:Lateralwallofbladder" + }, + { + "@id": "bts:Lateralwallofnasopharynx" + }, + { + "@id": "bts:Lateralwalloforopharynx" + }, + { + "@id": "bts:LessercurvatureofstomachNOS" + }, + { + "@id": "bts:Lingualtonsil" + }, + { + "@id": "bts:LipNOS" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + }, + { + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + }, + { + "@id": "bts:Lowergum" + }, + { + "@id": "bts:LowerlimbNOS" + }, + { + "@id": "bts:Lowerlobelung" + }, + { + "@id": "bts:Lowerthirdofesophagus" + }, + { + "@id": "bts:Lower-innerquadrantofbreast" + }, + { + "@id": "bts:Lower-outerquadrantofbreast" + }, + { + "@id": "bts:LungNOS" + }, + { + "@id": "bts:LymphnodeNOS" + }, + { + "@id": "bts:Lymphnodesofaxillaorarm" + }, + { + "@id": "bts:Lymphnodesofheadfaceandneck" + }, + { + "@id": "bts:Lymphnodesofinguinalregionorleg" + }, + { + "@id": "bts:Lymphnodesofmultipleregions" + }, + { + "@id": "bts:Mainbronchus" + }, + { + "@id": "bts:MajorsalivaryglandNOS" + }, + { + "@id": "bts:MalegenitalorgansNOS" + }, + { + "@id": "bts:Mandible" + }, + { + "@id": "bts:Maxillarysinus" + }, + { + "@id": "bts:Meckeldiverticulum" + }, + { + "@id": "bts:MediastinumNOS" + }, + { + "@id": "bts:Medullaofadrenalgland" + }, + { + "@id": "bts:MeningesNOS" + }, + { + "@id": "bts:Middleear" + }, + { + "@id": "bts:Middlelobelung" + }, + { + "@id": "bts:Middlethirdofesophagus" + }, + { + "@id": "bts:MouthNOS" + }, + { + "@id": "bts:MucosaoflipNOS" + }, + { + "@id": "bts:Mucosaoflowerlip" + }, + { + "@id": "bts:Mucosaofupperlip" + }, + { + "@id": "bts:Myometrium" + }, + { + "@id": "bts:Nasalcavity" + }, + { + "@id": "bts:NasopharynxNOS" + }, + { + "@id": "bts:NervoussystemNOS" + }, + { + "@id": "bts:Nipple" + }, + { + "@id": "bts:Occipitallobe" + }, + { + "@id": "bts:Olfactorynerve" + }, + { + "@id": "bts:Opticnerve" + }, + { + "@id": "bts:OrbitNOS" + }, + { + "@id": "bts:OropharynxNOS" + }, + { + "@id": "bts:Otherill-definedsites" + }, + { + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + }, + { + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + }, + { + "@id": "bts:Otherspecifiedpartsofpancreas" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Overlappinglesionofaccessorysinuses" + }, + { + "@id": "bts:Overlappinglesionofbladder" + }, + { + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + }, + { + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + }, + { + "@id": "bts:Overlappinglesionofbrain" + }, + { + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + }, + { + "@id": "bts:Overlappinglesionofbreast" + }, + { + "@id": "bts:Overlappinglesionofcervixuteri" + }, + { + "@id": "bts:Overlappinglesionofcolon" + }, + { + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + }, + { + "@id": "bts:Overlappinglesionofcorpusuteri" + }, + { + "@id": "bts:Overlappinglesionofdigestivesystem" + }, + { + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + }, + { + "@id": "bts:Overlappinglesionofesophagus" + }, + { + "@id": "bts:Overlappinglesionofeyeandadnexa" + }, + { + "@id": "bts:Overlappinglesionoffemalegenitalorgans" + }, + { + "@id": "bts:Overlappinglesionoffloorofmouth" + }, + { + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + }, + { + "@id": "bts:Overlappinglesionofhypopharynx" + }, + { + "@id": "bts:Overlappinglesionofill-definedsites" + }, + { + "@id": "bts:Overlappinglesionoflarynx" + }, + { + "@id": "bts:Overlappinglesionoflip" + }, + { + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + }, + { + "@id": "bts:Overlappinglesionoflung" + }, + { + "@id": "bts:Overlappinglesionofmajorsalivaryglands" + }, + { + "@id": "bts:Overlappinglesionofmalegenitalorgans" + }, + { + "@id": "bts:Overlappinglesionofnasopharynx" + }, + { + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + }, + { + "@id": "bts:Overlappinglesionofpalate" + }, + { + "@id": "bts:Overlappinglesionofpancreas" + }, + { + "@id": "bts:Overlappinglesionofpenis" + }, + { + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + }, + { + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + }, + { + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + }, + { + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + }, + { + "@id": "bts:Overlappinglesionofskin" + }, + { + "@id": "bts:Overlappinglesionofsmallintestine" + }, + { + "@id": "bts:Overlappinglesionofstomach" + }, + { + "@id": "bts:Overlappinglesionoftongue" + }, + { + "@id": "bts:Overlappinglesionoftonsil" + }, + { + "@id": "bts:Overlappinglesionofurinaryorgans" + }, + { + "@id": "bts:Overlappinglesionofvulva" + }, + { + "@id": "bts:Overlappinglesionsoforopharynx" + }, + { + "@id": "bts:PalateNOS" + }, + { + "@id": "bts:PancreasNOS" + }, + { + "@id": "bts:Pancreaticduct" + }, + { + "@id": "bts:Parametrium" + }, + { + "@id": "bts:Paraspinal" + }, + { + "@id": "bts:Parathyroidgland" + }, + { + "@id": "bts:Paraurethralgland" + }, + { + "@id": "bts:Parietallobe" + }, + { + "@id": "bts:Parotidgland" + }, + { + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + }, + { + "@id": "bts:Pelviclymphnodes" + }, + { + "@id": "bts:PelvisNOS" + }, + { + "@id": "bts:PenisNOS" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + }, + { + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + }, + { + "@id": "bts:PeritoneumNOS" + }, + { + "@id": "bts:PharynxNOS" + }, + { + "@id": "bts:Pinealgland" + }, + { + "@id": "bts:Pituitarygland" + }, + { + "@id": "bts:Placenta" + }, + { + "@id": "bts:PleuraNOS" + }, + { + "@id": "bts:Postcricoidregion" + }, + { + "@id": "bts:Posteriormediastinum" + }, + { + "@id": "bts:Posteriorwallofbladder" + }, + { + "@id": "bts:Posteriorwallofhypopharynx" + }, + { + "@id": "bts:Posteriorwallofnasopharynx" + }, + { + "@id": "bts:Posteriorwalloforopharynx" + }, + { + "@id": "bts:Prepuce" + }, + { + "@id": "bts:Prostategland" + }, + { + "@id": "bts:Pylorus" + }, + { + "@id": "bts:Pyriformsinus" + }, + { + "@id": "bts:Rectosigmoidjunction" + }, + { + "@id": "bts:RectumNOS" + }, + { + "@id": "bts:Renalpelvis" + }, + { + "@id": "bts:ReticuloendothelialsystemNOS" + }, + { + "@id": "bts:Retina" + }, + { + "@id": "bts:Retromolararea" + }, + { + "@id": "bts:Retroperitoneum" + }, + { + "@id": "bts:Ribsternumclavicleandassociatedjoints" + }, + { + "@id": "bts:Roundligament" + }, + { + "@id": "bts:ScrotumNOS" + }, + { + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + }, + { + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + }, + { + "@id": "bts:Sigmoidcolon" + }, + { + "@id": "bts:SkinoflipNOS" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofotherandunspecifiedpartsofface" + }, + { + "@id": "bts:Skinofscalpandneck" + }, + { + "@id": "bts:Skinoftrunk" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:SmallintestineNOS" + }, + { + "@id": "bts:SoftpalateNOS" + }, + { + "@id": "bts:Specifiedpartsofperitoneum" + }, + { + "@id": "bts:Spermaticcord" + }, + { + "@id": "bts:Sphenoidsinus" + }, + { + "@id": "bts:Spinalcord" + }, + { + "@id": "bts:Spinalmeninges" + }, + { + "@id": "bts:Spleen" + }, + { + "@id": "bts:Splenicflexureofcolon" + }, + { + "@id": "bts:StomachNOS" + }, + { + "@id": "bts:Subglottis" + }, + { + "@id": "bts:Sublingualgland" + }, + { + "@id": "bts:Submandibulargland" + }, + { + "@id": "bts:Superiorwallofnasopharynx" + }, + { + "@id": "bts:Supraglottis" + }, + { + "@id": "bts:Tailofpancreas" + }, + { + "@id": "bts:Temporallobe" + }, + { + "@id": "bts:TestisNOS" + }, + { + "@id": "bts:Thoracicesophagus" + }, + { + "@id": "bts:ThoraxNOS" + }, + { + "@id": "bts:Thymus" + }, + { + "@id": "bts:Thyroidgland" + }, + { + "@id": "bts:TongueNOS" + }, + { + "@id": "bts:TonsilNOS" + }, + { + "@id": "bts:Tonsillarfossa" + }, + { + "@id": "bts:Tonsillarpillar" + }, + { + "@id": "bts:Trachea" + }, + { + "@id": "bts:Transversecolon" + }, + { + "@id": "bts:Trigoneofbladder" + }, + { + "@id": "bts:Undescendedtestis" + }, + { + "@id": "bts:Unknownprimarysite" + }, + { + "@id": "bts:Uppergum" + }, + { + "@id": "bts:UpperlimbNOS" + }, + { + "@id": "bts:Upperlobelung" + }, + { + "@id": "bts:UpperrespiratorytractNOS" + }, + { + "@id": "bts:Upperthirdofesophagus" + }, + { + "@id": "bts:Upper-innerquadrantofbreast" + }, + { + "@id": "bts:Upper-outerquadrantofbreast" + }, + { + "@id": "bts:Urachus" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": "bts:Uretericorifice" + }, + { + "@id": "bts:Urethra" + }, + { + "@id": "bts:UrinarysystemNOS" + }, + { + "@id": "bts:Uterineadnexa" + }, + { + "@id": "bts:UterusNOS" + }, + { + "@id": "bts:Uvula" + }, + { + "@id": "bts:VaginaNOS" + }, + { + "@id": "bts:Vallecula" + }, + { + "@id": "bts:VentralsurfaceoftongueNOS" + }, + { + "@id": "bts:VentricleNOS" + }, + { + "@id": "bts:Vertebralcolumn" + }, + { + "@id": "bts:Vestibuleofmouth" + }, + { + "@id": "bts:VulvaNOS" + }, + { + "@id": "bts:Waldeyerring" + }, + { + "@id": "bts:BiliarytractNOS" + }, + { + "@id": "bts:Cheekmucosa" + }, + { + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Site of Resection or Biopsy", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TissueorOrganofOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "TissueorOrganofOrigin", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdomenNOS" + }, + { + "@id": "bts:Abdominalesophagus" + }, + { + "@id": "bts:AccessorysinusNOS" + }, + { + "@id": "bts:Acousticnerve" + }, + { + "@id": "bts:AdrenalglandNOS" + }, + { + "@id": "bts:AmpullaofVater" + }, + { + "@id": "bts:Analcanal" + }, + { + "@id": "bts:Anterior2/3oftongueNOS" + }, + { + "@id": "bts:Anteriorfloorofmouth" + }, + { + "@id": "bts:Anteriormediastinum" + }, + { + "@id": "bts:Anteriorsurfaceofepiglottis" + }, + { + "@id": "bts:Anteriorwallofbladder" + }, + { + "@id": "bts:Anteriorwallofnasopharynx" + }, + { + "@id": "bts:AnusNOS" + }, + { + "@id": "bts:Aorticbodyandotherparaganglia" + }, + { + "@id": "bts:Appendix" + }, + { + "@id": "bts:Ascendingcolon" + }, + { + "@id": "bts:AutonomicnervoussystemNOS" + }, + { + "@id": "bts:Axillarytailofbreast" + }, + { + "@id": "bts:BaseoftongueNOS" + }, + { + "@id": "bts:Bladderneck" + }, + { + "@id": "bts:BladderNOS" + }, + { + "@id": "bts:Blood" + }, + { + "@id": "bts:Bodyofpancreas" + }, + { + "@id": "bts:Bodyofpenis" + }, + { + "@id": "bts:Bodyofstomach" + }, + { + "@id": "bts:Bonemarrow" + }, + { + "@id": "bts:BoneoflimbNOS" + }, + { + "@id": "bts:BoneNOS" + }, + { + "@id": "bts:Bonesofskullandfaceandassociatedjoints" + }, + { + "@id": "bts:Borderoftongue" + }, + { + "@id": "bts:Brainstem" + }, + { + "@id": "bts:BrainNOS" + }, + { + "@id": "bts:Branchialcleft" + }, + { + "@id": "bts:BreastNOS" + }, + { + "@id": "bts:Broadligament" + }, + { + "@id": "bts:CardiaNOS" + }, + { + "@id": "bts:Carotidbody" + }, + { + "@id": "bts:Caudaequina" + }, + { + "@id": "bts:Cecum" + }, + { + "@id": "bts:Centralportionofbreast" + }, + { + "@id": "bts:CerebellumNOS" + }, + { + "@id": "bts:Cerebralmeninges" + }, + { + "@id": "bts:Cerebrum" + }, + { + "@id": "bts:Cervicalesophagus" + }, + { + "@id": "bts:Cervixuteri" + }, + { + "@id": "bts:Choroid" + }, + { + "@id": "bts:Ciliarybody" + }, + { + "@id": "bts:Cloacogeniczone" + }, + { + "@id": "bts:ColonNOS" + }, + { + "@id": "bts:Commissureoflip" + }, + { + "@id": "bts:Conjunctiva" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + }, + { + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + }, + { + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + }, + { + "@id": "bts:CorneaNOS" + }, + { + "@id": "bts:Corpusuteri" + }, + { + "@id": "bts:Cortexofadrenalgland" + }, + { + "@id": "bts:CranialnerveNOS" + }, + { + "@id": "bts:Craniopharyngealduct" + }, + { + "@id": "bts:Descendedtestis" + }, + { + "@id": "bts:Descendingcolon" + }, + { + "@id": "bts:Domeofbladder" + }, + { + "@id": "bts:DorsalsurfaceoftongueNOS" + }, + { + "@id": "bts:Duodenum" + }, + { + "@id": "bts:Endocervix" + }, + { + "@id": "bts:EndocrineglandNOS" + }, + { + "@id": "bts:Endometrium" + }, + { + "@id": "bts:Epididymis" + }, + { + "@id": "bts:EsophagusNOS" + }, + { + "@id": "bts:Ethmoidsinus" + }, + { + "@id": "bts:Exocervix" + }, + { + "@id": "bts:Externalear" + }, + { + "@id": "bts:ExternallipNOS" + }, + { + "@id": "bts:Externallowerlip" + }, + { + "@id": "bts:Externalupperlip" + }, + { + "@id": "bts:Extrahepaticbileduct" + }, + { + "@id": "bts:EyeNOS" + }, + { + "@id": "bts:Eyelid" + }, + { + "@id": "bts:Fallopiantube" + }, + { + "@id": "bts:FemalegenitaltractNOS" + }, + { + "@id": "bts:FloorofmouthNOS" + }, + { + "@id": "bts:Frontallobe" + }, + { + "@id": "bts:Frontalsinus" + }, + { + "@id": "bts:Fundusofstomach" + }, + { + "@id": "bts:Fundusuteri" + }, + { + "@id": "bts:Gallbladder" + }, + { + "@id": "bts:Gastricantrum" + }, + { + "@id": "bts:GastrointestinaltractNOS" + }, + { + "@id": "bts:Glanspenis" + }, + { + "@id": "bts:Glottis" + }, + { + "@id": "bts:GreatercurvatureofstomachNOS" + }, + { + "@id": "bts:GumNOS" + }, + { + "@id": "bts:Hardpalate" + }, + { + "@id": "bts:Headofpancreas" + }, + { + "@id": "bts:HeadfaceorneckNOS" + }, + { + "@id": "bts:Heart" + }, + { + "@id": "bts:HematopoieticsystemNOS" + }, + { + "@id": "bts:Hepaticflexureofcolon" + }, + { + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + }, + { + "@id": "bts:HypopharynxNOS" + }, + { + "@id": "bts:Ileum" + }, + { + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + }, + { + "@id": "bts:IntestinaltractNOS" + }, + { + "@id": "bts:Intra-abdominallymphnodes" + }, + { + "@id": "bts:Intrahepaticbileduct" + }, + { + "@id": "bts:Intrathoraciclymphnodes" + }, + { + "@id": "bts:IsletsofLangerhans" + }, + { + "@id": "bts:Isthmusuteri" + }, + { + "@id": "bts:Jejunum" + }, + { + "@id": "bts:KidneyNOS" + }, + { + "@id": "bts:Labiummajus" + }, + { + "@id": "bts:Labiumminus" + }, + { + "@id": "bts:Lacrimalgland" + }, + { + "@id": "bts:Laryngealcartilage" + }, + { + "@id": "bts:LarynxNOS" + }, + { + "@id": "bts:Lateralfloorofmouth" + }, + { + "@id": "bts:Lateralwallofbladder" + }, + { + "@id": "bts:Lateralwallofnasopharynx" + }, + { + "@id": "bts:Lateralwalloforopharynx" + }, + { + "@id": "bts:LessercurvatureofstomachNOS" + }, + { + "@id": "bts:Lingualtonsil" + }, + { + "@id": "bts:LipNOS" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + }, + { + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + }, + { + "@id": "bts:Lowergum" + }, + { + "@id": "bts:LowerlimbNOS" + }, + { + "@id": "bts:Lowerlobelung" + }, + { + "@id": "bts:Lowerthirdofesophagus" + }, + { + "@id": "bts:Lower-innerquadrantofbreast" + }, + { + "@id": "bts:Lower-outerquadrantofbreast" + }, + { + "@id": "bts:LungNOS" + }, + { + "@id": "bts:LymphnodeNOS" + }, + { + "@id": "bts:Lymphnodesofaxillaorarm" + }, + { + "@id": "bts:Lymphnodesofheadfaceandneck" + }, + { + "@id": "bts:Lymphnodesofinguinalregionorleg" + }, + { + "@id": "bts:Lymphnodesofmultipleregions" + }, + { + "@id": "bts:Mainbronchus" + }, + { + "@id": "bts:MajorsalivaryglandNOS" + }, + { + "@id": "bts:MalegenitalorgansNOS" + }, + { + "@id": "bts:Mandible" + }, + { + "@id": "bts:Maxillarysinus" + }, + { + "@id": "bts:Meckeldiverticulum" + }, + { + "@id": "bts:MediastinumNOS" + }, + { + "@id": "bts:Medullaofadrenalgland" + }, + { + "@id": "bts:MeningesNOS" + }, + { + "@id": "bts:Middleear" + }, + { + "@id": "bts:Middlelobelung" + }, + { + "@id": "bts:Middlethirdofesophagus" + }, + { + "@id": "bts:MouthNOS" + }, + { + "@id": "bts:MucosaoflipNOS" + }, + { + "@id": "bts:Mucosaoflowerlip" + }, + { + "@id": "bts:Mucosaofupperlip" + }, + { + "@id": "bts:Myometrium" + }, + { + "@id": "bts:Nasalcavity" + }, + { + "@id": "bts:NasopharynxNOS" + }, + { + "@id": "bts:NervoussystemNOS" + }, + { + "@id": "bts:Nipple" + }, + { + "@id": "bts:Occipitallobe" + }, + { + "@id": "bts:Olfactorynerve" + }, + { + "@id": "bts:Opticnerve" + }, + { + "@id": "bts:OrbitNOS" + }, + { + "@id": "bts:OropharynxNOS" + }, + { + "@id": "bts:Otherill-definedsites" + }, + { + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + }, + { + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + }, + { + "@id": "bts:Otherspecifiedpartsofpancreas" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Overlappinglesionofaccessorysinuses" + }, + { + "@id": "bts:Overlappinglesionofbladder" + }, + { + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + }, + { + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + }, + { + "@id": "bts:Overlappinglesionofbrain" + }, + { + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + }, + { + "@id": "bts:Overlappinglesionofbreast" + }, + { + "@id": "bts:Overlappinglesionofcervixuteri" + }, + { + "@id": "bts:Overlappinglesionofcolon" + }, + { + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + }, + { + "@id": "bts:Overlappinglesionofcorpusuteri" + }, + { + "@id": "bts:Overlappinglesionofdigestivesystem" + }, + { + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + }, + { + "@id": "bts:Overlappinglesionofesophagus" + }, + { + "@id": "bts:Overlappinglesionofeyeandadnexa" + }, + { + "@id": "bts:Overlappinglesionoffemalegenitalorgans" + }, + { + "@id": "bts:Overlappinglesionoffloorofmouth" + }, + { + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + }, + { + "@id": "bts:Overlappinglesionofhypopharynx" + }, + { + "@id": "bts:Overlappinglesionofill-definedsites" + }, + { + "@id": "bts:Overlappinglesionoflarynx" + }, + { + "@id": "bts:Overlappinglesionoflip" + }, + { + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + }, + { + "@id": "bts:Overlappinglesionoflung" + }, + { + "@id": "bts:Overlappinglesionofmajorsalivaryglands" + }, + { + "@id": "bts:Overlappinglesionofmalegenitalorgans" + }, + { + "@id": "bts:Overlappinglesionofnasopharynx" + }, + { + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + }, + { + "@id": "bts:Overlappinglesionofpalate" + }, + { + "@id": "bts:Overlappinglesionofpancreas" + }, + { + "@id": "bts:Overlappinglesionofpenis" + }, + { + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + }, + { + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + }, + { + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + }, + { + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + }, + { + "@id": "bts:Overlappinglesionofskin" + }, + { + "@id": "bts:Overlappinglesionofsmallintestine" + }, + { + "@id": "bts:Overlappinglesionofstomach" + }, + { + "@id": "bts:Overlappinglesionoftongue" + }, + { + "@id": "bts:Overlappinglesionoftonsil" + }, + { + "@id": "bts:Overlappinglesionofurinaryorgans" + }, + { + "@id": "bts:Overlappinglesionofvulva" + }, + { + "@id": "bts:Overlappinglesionsoforopharynx" + }, + { + "@id": "bts:PalateNOS" + }, + { + "@id": "bts:PancreasNOS" + }, + { + "@id": "bts:Pancreaticduct" + }, + { + "@id": "bts:Parametrium" + }, + { + "@id": "bts:Paraspinal" + }, + { + "@id": "bts:Parathyroidgland" + }, + { + "@id": "bts:Paraurethralgland" + }, + { + "@id": "bts:Parietallobe" + }, + { + "@id": "bts:Parotidgland" + }, + { + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + }, + { + "@id": "bts:Pelviclymphnodes" + }, + { + "@id": "bts:PelvisNOS" + }, + { + "@id": "bts:PenisNOS" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + }, + { + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + }, + { + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + }, + { + "@id": "bts:PeritoneumNOS" + }, + { + "@id": "bts:PharynxNOS" + }, + { + "@id": "bts:Pinealgland" + }, + { + "@id": "bts:Pituitarygland" + }, + { + "@id": "bts:Placenta" + }, + { + "@id": "bts:PleuraNOS" + }, + { + "@id": "bts:Postcricoidregion" + }, + { + "@id": "bts:Posteriormediastinum" + }, + { + "@id": "bts:Posteriorwallofbladder" + }, + { + "@id": "bts:Posteriorwallofhypopharynx" + }, + { + "@id": "bts:Posteriorwallofnasopharynx" + }, + { + "@id": "bts:Posteriorwalloforopharynx" + }, + { + "@id": "bts:Prepuce" + }, + { + "@id": "bts:Prostategland" + }, + { + "@id": "bts:Pylorus" + }, + { + "@id": "bts:Pyriformsinus" + }, + { + "@id": "bts:Rectosigmoidjunction" + }, + { + "@id": "bts:RectumNOS" + }, + { + "@id": "bts:Renalpelvis" + }, + { + "@id": "bts:ReticuloendothelialsystemNOS" + }, + { + "@id": "bts:Retina" + }, + { + "@id": "bts:Retromolararea" + }, + { + "@id": "bts:Retroperitoneum" + }, + { + "@id": "bts:Ribsternumclavicleandassociatedjoints" + }, + { + "@id": "bts:Roundligament" + }, + { + "@id": "bts:ScrotumNOS" + }, + { + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + }, + { + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + }, + { + "@id": "bts:Sigmoidcolon" + }, + { + "@id": "bts:SkinoflipNOS" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofotherandunspecifiedpartsofface" + }, + { + "@id": "bts:Skinofscalpandneck" + }, + { + "@id": "bts:Skinoftrunk" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:SmallintestineNOS" + }, + { + "@id": "bts:SoftpalateNOS" + }, + { + "@id": "bts:Specifiedpartsofperitoneum" + }, + { + "@id": "bts:Spermaticcord" + }, + { + "@id": "bts:Sphenoidsinus" + }, + { + "@id": "bts:Spinalcord" + }, + { + "@id": "bts:Spinalmeninges" + }, + { + "@id": "bts:Spleen" + }, + { + "@id": "bts:Splenicflexureofcolon" + }, + { + "@id": "bts:StomachNOS" + }, + { + "@id": "bts:Subglottis" + }, + { + "@id": "bts:Sublingualgland" + }, + { + "@id": "bts:Submandibulargland" + }, + { + "@id": "bts:Superiorwallofnasopharynx" + }, + { + "@id": "bts:Supraglottis" + }, + { + "@id": "bts:Tailofpancreas" + }, + { + "@id": "bts:Temporallobe" + }, + { + "@id": "bts:TestisNOS" + }, + { + "@id": "bts:Thoracicesophagus" + }, + { + "@id": "bts:ThoraxNOS" + }, + { + "@id": "bts:Thymus" + }, + { + "@id": "bts:Thyroidgland" + }, + { + "@id": "bts:TongueNOS" + }, + { + "@id": "bts:TonsilNOS" + }, + { + "@id": "bts:Tonsillarfossa" + }, + { + "@id": "bts:Tonsillarpillar" + }, + { + "@id": "bts:Trachea" + }, + { + "@id": "bts:Transversecolon" + }, + { + "@id": "bts:Trigoneofbladder" + }, + { + "@id": "bts:Undescendedtestis" + }, + { + "@id": "bts:Unknownprimarysite" + }, + { + "@id": "bts:Uppergum" + }, + { + "@id": "bts:UpperlimbNOS" + }, + { + "@id": "bts:Upperlobelung" + }, + { + "@id": "bts:UpperrespiratorytractNOS" + }, + { + "@id": "bts:Upperthirdofesophagus" + }, + { + "@id": "bts:Upper-innerquadrantofbreast" + }, + { + "@id": "bts:Upper-outerquadrantofbreast" + }, + { + "@id": "bts:Urachus" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": "bts:Uretericorifice" + }, + { + "@id": "bts:Urethra" + }, + { + "@id": "bts:UrinarysystemNOS" + }, + { + "@id": "bts:Uterineadnexa" + }, + { + "@id": "bts:UterusNOS" + }, + { + "@id": "bts:Uvula" + }, + { + "@id": "bts:VaginaNOS" + }, + { + "@id": "bts:Vallecula" + }, + { + "@id": "bts:VentralsurfaceoftongueNOS" + }, + { + "@id": "bts:VentricleNOS" + }, + { + "@id": "bts:Vertebralcolumn" + }, + { + "@id": "bts:Vestibuleofmouth" + }, + { + "@id": "bts:VulvaNOS" + }, + { + "@id": "bts:Waldeyerring" + }, + { + "@id": "bts:BiliarytractNOS" + }, + { + "@id": "bts:Cheekmucosa" + }, + { + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tissue or Organ of Origin", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NCIAtlasCancerSite", + "@type": "rdfs:Class", + "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", + "rdfs:label": "NCIAtlasCancerSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Bladder" + }, + { + "@id": "bts:BrainAndOtherNervousSystem" + }, + { + "@id": "bts:FemaleBreast" + }, + { + "@id": "bts:InsituFemaleBreast" + }, + { + "@id": "bts:CervixUteri" + }, + { + "@id": "bts:LessThanAge" + }, + { + "@id": "bts:MalignantChildhoodNeoplasm" + }, + { + "@id": "bts:ColonAndRectum" + }, + { + "@id": "bts:Esophagus" + }, + { + "@id": "bts:KidneyAndRenalPelvis" + }, + { + "@id": "bts:Leukemia" + }, + { + "@id": "bts:LiverAndBileDuct" + }, + { + "@id": "bts:LungAndBronchus" + }, + { + "@id": "bts:CutaneousMelanoma" + }, + { + "@id": "bts:Non-Hodgkin'sLymphoma" + }, + { + "@id": "bts:OralCavityAndPharynx" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Pancreas" + }, + { + "@id": "bts:ProstateGland" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:ThyroidGland" + }, + { + "@id": "bts:Uterus" + } + ], + "sms:displayName": "NCI Atlas Cancer Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorGrade", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", + "rdfs:label": "TumorGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:G1" + }, + { + "@id": "bts:G2" + }, + { + "@id": "bts:G3" + }, + { + "@id": "bts:G4" + }, + { + "@id": "bts:GX" + }, + { + "@id": "bts:GB" + }, + { + "@id": "bts:HighGrade" + }, + { + "@id": "bts:IntermediateGrade" + }, + { + "@id": "bts:LowGrade" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Tumor Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PackYearsSmoked", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", + "rdfs:label": "PackYearsSmoked", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pack Years Smoked", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:YearsSmoked", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", + "rdfs:label": "YearsSmoked", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Years Smoked", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoFollowUp", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoFollowUp", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Follow Up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:GeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "GeneSymbol", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gene Symbol", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularAnalysisMethod", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularAnalysisMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ComparativeGenomicHybridization" + }, + { + "@id": "bts:CytogeneticsNOS" + }, + { + "@id": "bts:FISH" + }, + { + "@id": "bts:FlowCytometry" + }, + { + "@id": "bts:IHC" + }, + { + "@id": "bts:ISH" + }, + { + "@id": "bts:Karyotype" + }, + { + "@id": "bts:Microarray" + }, + { + "@id": "bts:MicrosatelliteAnalysis" + }, + { + "@id": "bts:NuclearStaining" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:RNASequencing" + }, + { + "@id": "bts:RT-PCR" + }, + { + "@id": "bts:SequencingNOS" + }, + { + "@id": "bts:SouthernBlotting" + }, + { + "@id": "bts:TargetedSequencing" + }, + { + "@id": "bts:WGS" + }, + { + "@id": "bts:WXS" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Molecular Analysis Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TestResult", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestResult", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbnormalNOS" + }, + { + "@id": "bts:CopyNumberReported" + }, + { + "@id": "bts:Equivocal" + }, + { + "@id": "bts:High" + }, + { + "@id": "bts:Intermediate" + }, + { + "@id": "bts:LossofExpression" + }, + { + "@id": "bts:Low" + }, + { + "@id": "bts:Negative" + }, + { + "@id": "bts:Normal" + }, + { + "@id": "bts:Overexpressed" + }, + { + "@id": "bts:Positive" + }, + { + "@id": "bts:TestValueReported" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Test Result", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of treatment administered.", + "rdfs:label": "TreatmentType", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AblationCryo" + }, + { + "@id": "bts:AblationEthanolInjection" + }, + { + "@id": "bts:AblationMicrowave" + }, + { + "@id": "bts:AblationNOS" + }, + { + "@id": "bts:AblationRadiofrequency" + }, + { + "@id": "bts:AblationRadiosurgical" + }, + { + "@id": "bts:AncillaryTreatment" + }, + { + "@id": "bts:AntiseizureTreatment" + }, + { + "@id": "bts:BisphosphonateTherapy" + }, + { + "@id": "bts:BlindedStudyTreatmentunknown" + }, + { + "@id": "bts:BrachytherapyHighDose" + }, + { + "@id": "bts:BrachytherapyLowDose" + }, + { + "@id": "bts:BrachytherapyNOS" + }, + { + "@id": "bts:Chemoembolization" + }, + { + "@id": "bts:Chemoprotectant" + }, + { + "@id": "bts:Chemotherapy" + }, + { + "@id": "bts:ConcurrentChemoradiation" + }, + { + "@id": "bts:Cryoablation" + }, + { + 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systematic course of actions performed in order to discover or identify breast cancer.", + "rdfs:label": "BreastCarcinomaDetectionMethodType", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ClinicalExam" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:NippleDischarge" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:ScreeningMammography" + }, + { + "@id": "bts:ScreeningMRI" + }, + { + "@id": "bts:Selfexam" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Detection Method Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHistologyCategory", + "@type": "rdfs:Class", + "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", + "rdfs:label": "BreastCarcinomaHistologyCategory", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Infiltratingductalcarcinoma" + }, + { + "@id": "bts:Infiltratinglobularcarcinoma" + }, + { + "@id": "bts:InvasivemammarycarcinomaNOS" + }, + { + "@id": "bts:Invasivemixedductalandlobularcarcinoma" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Carcinoma Histology Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", + "@type": "rdfs:Class", + "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", + "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Alveolartype" + }, + { + "@id": "bts:Classicaltype" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Pleomorphictype" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", + "@type": "rdfs:Class", + "rdfs:comment": "The histologic subtype for the most common type of invasive breast carcinoma.", + "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Classicaltype" + }, + { + "@id": "bts:Invasivecarcinoma-typecannotbedetermined" + }, + { + "@id": "bts:Invasivecribriformcarcinoma" + }, + { + "@id": "bts:Invasivemicropapillarycarcinoma" + }, + { + "@id": "bts:Invasivepapillarycarcinoma" + }, + { + "@id": 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}, + { + "@id": "bts:Nocancer" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Biopsy Procedure Finding Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastQuadrantSite", + "@type": "rdfs:Class", + "rdfs:comment": "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", + "rdfs:label": "BreastQuadrantSite", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Upperouterquadrant" + }, + { + "@id": "bts:Lowerouterquadrant" + }, + { + "@id": "bts:Upperinnerquadrant" + }, + { + "@id": "bts:Lowerinnerquadrant" + }, + { + "@id": "bts:Central" + }, + { + "@id": "bts:Nipple" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Quadrant Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAssessmentTests", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", + "rdfs:label": "BreastCancerAssessmentTests", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:EstrogenreceptorIHC" + }, + { + "@id": "bts:ProgesteronereceptorIHC" + }, + { + "@id": "bts:HER2IHC" + }, + { + "@id": "bts:HER2FISH-CISH" + }, + { + "@id": "bts:HER2FISH" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Cancer Assessment Tests", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerGenomicTestPerformed", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", + "rdfs:label": "BreastCancerGenomicTestPerformed", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Oncotype" + }, + { + "@id": "bts:MammaPrint" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Notperformed" + } + ], + "sms:displayName": "Breast Cancer Genomic Test Performed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MammaprintRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "rdfs:label": "MammaprintRiskGroup", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Highrisk" + }, 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"bts:BreastCarcinomaEstrogenReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaEstrogenReceptorStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Borderline" + }, + { + "@id": "bts:Equivocal" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Negative" + }, + { + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:PerformedbutNotAvailable" + }, + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Estrogen Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Borderline" + }, + { + "@id": "bts:Equivocal" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Negative" + }, + { + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:PerformedbutNotAvailable" + }, + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancerAllredEstrogenReceptorScore", + "@type": "rdfs:Class", + "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "rdfs:label": "BreastCancerAllredEstrogenReceptorScore", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:0" + }, + { + "@id": "bts:1" + }, + { + "@id": "bts:2" + }, + { + "@id": "bts:3" + }, + { + "@id": "bts:4" + }, + { + "@id": "bts:5" + }, + { + "@id": "bts:6" + }, + { + "@id": "bts:7" + }, + { + "@id": "bts:8" + }, + { + "@id": "bts:10" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Cancer Allred Estrogen Receptor Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorInvasiveBreastDisease", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate prior invasive breast condition in the participant", + "rdfs:label": "PriorInvasiveBreastDisease", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + 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"bts:BreastCarcinomaPRStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStatusPercentageValue", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label": "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Breast 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"schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", + "@type": "rdfs:Class", + "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaSurgicalProcedureName", + "@type": "rdfs:Class", + "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "rdfs:label": "BreastCarcinomaSurgicalProcedureName", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCancerTier3" + } 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"bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Outdooroccupational" + }, + { + "@id": "bts:Outdoorrecreational" + }, + { + "@id": "bts:Therapeutic" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Chronic UV Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofBlisteringSunburn", + "@type": "rdfs:Class", + "rdfs:comment": "Patient has history of blistering sunburn", + "rdfs:label": "HistoryofBlisteringSunburn", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Blistering Sunburn", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofTanningBedUse", + "@type": "rdfs:Class", + "rdfs:comment": "History of tanning bed use of the patient", + "rdfs:label": "HistoryofTanningBedUse", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Never" + }, + { + "@id": "bts:Lessthan10times" + }, + { + "@id": "bts:10-50times" + }, + { + "@id": "bts:50-100times" + }, + { + "@id": "bts:Morethan100times" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Tanning Bed Use", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmediateFamilyHistoryMelanoma", + "@type": "rdfs:Class", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryMelanoma", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Beforeage50" + }, + { + "@id": "bts:Notbeforeage50" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Immediate Family History Melanoma", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaBiopsyResectionSites", + "@type": "rdfs:Class", + "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", + "rdfs:label": "MelanomaBiopsyResectionSites", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Skinofscalp" + }, + { + "@id": "bts:Skinofeyelid" + }, + { + "@id": "bts:Skinofnose" + }, + { + "@id": "bts:Skinoflip" + }, + { + "@id": "bts:Skinofear" + }, + { + "@id": "bts:Skinofneck" + }, + { + "@id": "bts:Skinofotherpartsofface" + }, + { + "@id": "bts:Skinofchest" + }, + { + "@id": "bts:Skinofback" + }, + { + "@id": "bts:Skinofabdomen" + }, + { + "@id": "bts:Skinoftrunk-other" + }, + { + "@id": "bts:Skinofbreast" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:Skinofpalm" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:Skinother" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Melanoma Biopsy Resection Sites", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaUlceration", + "@type": "rdfs:Class", + "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaUlceration", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cutaneous Melanoma Ulceration", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaAdditionalFindings", + "@type": "rdfs:Class", + "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaAdditionalFindings", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ActinicKeratosis" + }, + { + "@id": "bts:NevusRemnant" + }, + { + "@id": "bts:SolarElastosis" + }, + { + "@id": "bts:FibrosingRegression" + }, + { + "@id": "bts:NestingMelanoma" + }, + { + "@id": "bts:PagetoidSpread" + }, + { + "@id": "bts:VascularProliferation" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Cutaneous Melanoma Additional Findings", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoBirth", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Birth", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:CountryofResidence", + "@type": "rdfs:Class", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Afghanistan" + }, + { + "@id": "bts:Albania" + }, + { + "@id": "bts:Algeria" + }, + { + "@id": "bts:Andorra" + }, + { + "@id": "bts:Angola" + }, + { + "@id": "bts:Anguilla" + }, + { + "@id": "bts:AntiguaandBarbuda" + }, + { + "@id": "bts:Argentina" + }, + { + "@id": "bts:Armenia" + }, + { + "@id": "bts:Aruba" + }, + { + "@id": "bts:Australia" + }, + { + "@id": "bts:Austria" + }, + { + "@id": "bts:Azerbaijan" + }, + { + "@id": "bts:Bahamas" + }, + { + "@id": "bts:Bahrain" + }, + { + "@id": "bts:Bangladesh" + }, + { + "@id": "bts:Barbados" + }, + { + "@id": "bts:Belarus" + }, + { + "@id": "bts:Belgium" + }, + { + "@id": "bts:Belize" + }, + { + "@id": "bts:Benin" + }, + { + "@id": "bts:Bermuda" + }, + { + "@id": "bts:Bhutan" + }, + { + "@id": "bts:Bolivia" + }, + { + "@id": "bts:BosniaandHerzegovina" + }, + { + "@id": "bts:Botswana" + }, + { + "@id": "bts:Brazil" + }, + { + "@id": "bts:Brunei" + }, + { + "@id": "bts:Bulgaria" + }, + { + "@id": "bts:BurkinaFaso" + }, + { + "@id": "bts:Burundi" + }, + { + "@id": "bts:Cambodia" + }, + { + "@id": "bts:Cameroon" + }, + { + "@id": "bts:Canada" + }, + { + "@id": "bts:CapeVerde" + }, + { + "@id": "bts:CaymanIslands" + }, + { + "@id": "bts:CentralAfricanRepublic" + }, + { + "@id": "bts:Chad" + }, + { + "@id": "bts:Chile" + }, + { + "@id": "bts:China" + }, + { + "@id": "bts:Colombia" + }, + { + "@id": "bts:Comoros" + }, + { + "@id": "bts:Congo" + }, + { + "@id": "bts:CookIslands" + }, + { + "@id": "bts:CostaRica" + }, + { + "@id": "bts:Coted'Ivoire" + }, + { + "@id": "bts:Croatia" + }, + { + "@id": "bts:Cuba" + }, + { + "@id": "bts:Curacao" + }, + { + "@id": "bts:Cyprus" + }, + { + "@id": "bts:CzechRepublic(Czechia)" + }, + { + "@id": "bts:DemocraticRepublicoftheCongo" + }, + { + "@id": "bts:Denmark" + }, + { + "@id": "bts:Djibouti" + }, + { + "@id": "bts:Dominica" + }, + { + "@id": "bts:DominicanRepublic" + }, + { + "@id": "bts:Ecuador" + }, + { + "@id": "bts:Egypt" + }, + { + "@id": "bts:ElSalvador" + }, + { + "@id": "bts:EquatorialGuinea" + }, + { + "@id": "bts:Eritrea" + }, + { + "@id": "bts:Estonia" + }, + { + "@id": "bts:Eswatini" + }, + { + "@id": "bts:Ethiopia" + }, + { + "@id": "bts:FalklandIslands(Malvinas)" + }, + { + "@id": "bts:FaroeIslands" + }, + { + "@id": "bts:FederatedStatesofMicronesia" + }, + { + "@id": "bts:Fiji" + }, + { + "@id": "bts:Finland" + }, + { + "@id": "bts:France" + }, + { + "@id": "bts:FrenchGuiana" + }, + { + "@id": "bts:FrenchPolynesia" + }, + { + "@id": "bts:Gabon" + }, + { + "@id": "bts:Gambia" + }, + { + "@id": "bts:Georgia" + }, + { + "@id": "bts:Germany" + }, + { + "@id": "bts:Ghana" + }, + { + "@id": "bts:Gibraltar" + }, + { + "@id": "bts:Greece" + }, + { + "@id": "bts:Greenland" + }, + { + "@id": "bts:Grenada" + }, + { + "@id": "bts:Guadeloupe" + }, + { + "@id": "bts:Guam" + }, + { + "@id": "bts:Guatemala" + }, + { + "@id": "bts:Guernsey" + }, + { + "@id": "bts:Guinea" + }, + { + "@id": "bts:Guinea-Bissau" + }, + { + "@id": "bts:Guyana" + }, + { + "@id": "bts:Haiti" + }, + { + "@id": "bts:HolySee" + }, + { + "@id": "bts:Honduras" + }, + { + "@id": "bts:HongKong" + }, + { + "@id": "bts:Hungary" + }, + { + "@id": "bts:Iceland" + }, + { + "@id": "bts:India" + }, + { + "@id": "bts:Indonesia" + }, + { + "@id": "bts:Iran" + }, + { + "@id": "bts:Iraq" + }, + { + "@id": "bts:Ireland" + }, + { + "@id": "bts:IsleofMan" + }, + { + "@id": "bts:Israel" + }, + { + "@id": "bts:Italy" + }, + { + "@id": "bts:Jamaica" + }, + { + "@id": "bts:Japan" + }, + { + "@id": "bts:Jersey" + }, + { + "@id": "bts:Jordan" + }, + { + "@id": "bts:Kazakhstan" + }, + { + "@id": "bts:Kenya" + }, + { + "@id": "bts:Kiribati" + }, + { + "@id": "bts:Kosovo" + }, + { + "@id": "bts:Kuwait" + }, + { + "@id": "bts:Kyrgyzstan" + }, + { + "@id": "bts:Laos" + }, + { + "@id": "bts:Latvia" + }, + { + "@id": "bts:Lebanon" + }, + { + "@id": "bts:Lesotho" + }, + { + "@id": "bts:Liberia" + }, + { + "@id": "bts:Libya" + }, + { + "@id": "bts:Liechtenstein" + }, + { + "@id": "bts:Lithuania" + }, + { + "@id": "bts:Luxembourg" + }, + { + "@id": "bts:Macau" + }, + { + "@id": "bts:Madagascar" + }, + { + "@id": "bts:Malawi" + }, + { + "@id": "bts:Malaysia" + }, + { + "@id": "bts:Maldives" + }, + { + "@id": "bts:Mali" + }, + { + "@id": "bts:Malta" + }, + { + "@id": "bts:MarshallIslands" + }, + { + "@id": "bts:Martinique" + }, + { + "@id": "bts:Mauritania" + }, + { + "@id": "bts:Mauritius" + }, + { + "@id": "bts:Mayotte" + }, + { + "@id": "bts:Mexico" + }, + { + "@id": "bts:Moldova" + }, + { + "@id": "bts:Monaco" + }, + { + "@id": "bts:Mongolia" + }, + { + "@id": "bts:Montenegro" + }, + { + "@id": "bts:Montserrat" + }, + { + "@id": "bts:Morocco" + }, + { + "@id": "bts:Mozambique" + }, + { + "@id": "bts:Myanmar" + }, + { + "@id": "bts:Namibia" + }, + { + "@id": "bts:Nauru" + }, + { + "@id": "bts:Nepal" + }, + { + "@id": "bts:Netherlands" + }, + { + "@id": "bts:NewCaledonia" + }, + { + "@id": "bts:NewZealand" + }, + { + "@id": "bts:Nicaragua" + }, + { + "@id": "bts:Niger" + }, + { + "@id": "bts:Nigeria" + }, + { + "@id": "bts:Niue" + }, + { + "@id": "bts:NorthKorea" + }, + { + "@id": "bts:NorthMacedonia" + }, + { + "@id": "bts:NorthernMarianaIslands" + }, + { + "@id": "bts:Norway" + }, + { + "@id": "bts:Oman" + }, + { + "@id": "bts:Pakistan" + }, + { + "@id": "bts:Palau" + }, + { + "@id": "bts:Panama" + }, + { + "@id": "bts:PapuaNewGuinea" + }, + { + "@id": "bts:Paraguay" + }, + { + "@id": "bts:Peru" + }, + { + "@id": "bts:Philippines" + }, + { + "@id": "bts:Poland" + }, + { + "@id": "bts:Portugal" + }, + { + "@id": "bts:PuertoRico" + }, + { + "@id": "bts:Qatar" + }, + { + "@id": "bts:Reunion" + }, + { + "@id": "bts:Romania" + }, + { + "@id": "bts:Russia" + }, + { + "@id": "bts:Rwanda" + }, + { + "@id": "bts:SaintHelenaAscensionandTristandaCunha" + }, + { + "@id": "bts:SaintKittsandNevis" + }, + { + "@id": "bts:SaintLucia" + }, + { + "@id": "bts:SaintPierreandMiquelon" + }, + { + "@id": "bts:SaintVincentandtheGrenadines" + }, + { + "@id": "bts:Samoa" + }, + { + "@id": "bts:SanMarino" + }, + { + "@id": "bts:SaoTomeandPrincipe" + }, + { + "@id": "bts:SaudiArabia" + }, + { + "@id": "bts:Senegal" + }, + { + "@id": "bts:Serbia" + }, + { + "@id": "bts:Seychelles" + }, + { + "@id": "bts:SierraLeone" + }, + { + "@id": "bts:Singapore" + }, + { + "@id": "bts:Slovakia" + }, + { + "@id": "bts:Slovenia" + }, + { + "@id": "bts:SolomonIslands" + }, + { + "@id": "bts:Somalia" + }, + { + "@id": "bts:SouthAfrica" + }, + { + "@id": "bts:SouthKorea" + }, + { + "@id": "bts:SouthSudan" + }, + { + "@id": "bts:Spain" + }, + { + "@id": "bts:SriLanka" + }, + { + "@id": "bts:StateofPalestine" + }, + { + "@id": "bts:Sudan" + }, + { + "@id": "bts:Suriname" + }, + { + "@id": "bts:Svalbard&JanMayenIslands" + }, + { + "@id": "bts:Sweden" + }, + { + "@id": "bts:Switzerland" + }, + { + "@id": "bts:Syria" + }, + { + "@id": "bts:Taiwan" + }, + { + "@id": "bts:Tajikistan" + }, + { + "@id": "bts:Tanzania" + }, + { + "@id": "bts:Thailand" + }, + { + "@id": "bts:Timor-Leste" + }, + { + "@id": "bts:Togo" + }, + { + "@id": "bts:Tokelau" + }, + { + "@id": "bts:Tonga" + }, + { + "@id": "bts:TrinidadandTobago" + }, + { + "@id": "bts:Tunisia" + }, + { + "@id": "bts:Turkey" + }, + { + "@id": "bts:Turkmenistan" + }, + { + "@id": "bts:Tuvalu" + }, + { + "@id": "bts:Uganda" + }, + { + "@id": "bts:Ukraine" + }, + { + "@id": "bts:UnitedArabEmirates" + }, + { + "@id": "bts:UnitedKingdom" + }, + { + "@id": "bts:UnitedStates" + }, + { + "@id": "bts:Uruguay" + }, + { + "@id": "bts:Uzbekistan" + }, + { + "@id": "bts:Vanuatu" + }, + { + "@id": "bts:Venezuela" + }, + { + "@id": "bts:Vietnam" + }, + { + "@id": "bts:VirginIslandsBritish" + }, + { + "@id": "bts:VirginIslandsU.S." + }, + { + "@id": "bts:WallisandFutuna" + }, + { + "@id": "bts:WesternSahara" + }, + { + "@id": "bts:Yemen" + }, + { + "@id": "bts:Zambia" + }, + { + "@id": "bts:Zimbabwe" + } + ], + "sms:displayName": "Country of Residence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AgeIsObfuscated", + "@type": "rdfs:Class", + "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "rdfs:label": "AgeIsObfuscated", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:True" + }, + { + "@id": "bts:False" + } + ], + "sms:displayName": "Age Is Obfuscated", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:YearOfBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label": "YearOfBirth", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Year Of Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OccupationDurationYears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of years a patient worked in a specific occupation.", + "rdfs:label": "OccupationDurationYears", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Occupation Duration Years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrematureAtBirth", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", + "rdfs:label": "PrematureAtBirth", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Premature At Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WeeksGestationatBirth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", + "rdfs:label": "WeeksGestationatBirth", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Weeks Gestation at Birth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RelativewithCancerHistory", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "rdfs:label": "RelativewithCancerHistory", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-CancerHistoryRelative" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Relative with Cancer History", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SmokingExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if individual has smoking exposure", + "rdfs:label": "SmokingExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-SmokingExposure" + }, + { + "@id": "bts:No-SmokingExposure" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Smoking Exposure", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AlcoholExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if individual has alcohol exposure", + "rdfs:label": "AlcoholExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AlcoholExposure" + }, + { + "@id": "bts:No-AlcoholExposure" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Alcohol Exposure", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AsbestosExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", + "rdfs:label": "AsbestosExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Asbestos Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CoalDustExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", + "rdfs:label": "CoalDustExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Coal Dust Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", + "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Environmental Tobacco Smoke Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RadonExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", + "rdfs:label": "RadonExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Radon Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RespirableCrystallineSilicaExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", + "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdverseEvent", + "@type": "rdfs:Class", + "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", + "rdfs:label": "AdverseEvent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdominalDistension" + }, + { + "@id": "bts:AbdominalInfection" + }, + { + "@id": "bts:AbdominalPain" + }, + { + "@id": "bts:AbdominalSoftTissueNecrosis" + }, + { + "@id": "bts:AbducensNerveDisorder" + }, + { + "@id": "bts:AccessoryNerveDisorder" + }, + { + "@id": "bts:Acidosis" + }, + { + "@id": "bts:AcousticNerveDisorderNOS" + }, + { + "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" + }, + { + "@id": "bts:AcuteCoronarySyndrome" + }, + { + "@id": "bts:AcuteKidneyInjury" + }, + { + "@id": "bts:AdrenalInsufficiency" + }, + { + "@id": "bts:AdultRespiratoryDistressSyndrome" + }, + { + "@id": "bts:Agitation" + }, + { + "@id": "bts:Akathisia" + }, + { + "@id": "bts:AlanineAminotransferaseIncreased" + }, + { + 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{ + "@id": "bts:Arachnoiditis" + }, + { + "@id": "bts:ArterialInjury" + }, + { + "@id": "bts:ArteritisInfective" + }, + { + "@id": "bts:Arthralgia" + }, + { + "@id": "bts:Arthritis" + }, + { + "@id": "bts:Ascites" + }, + { + "@id": "bts:AspartateAminotransferaseIncreased" + }, + { + "@id": "bts:Aspiration" + }, + { + "@id": "bts:Asystole" + }, + { + "@id": "bts:Ataxia" + }, + { + "@id": "bts:Atelectasis" + }, + { + "@id": "bts:AtrialFibrillation" + }, + { + "@id": "bts:AtrialFlutter" + }, + { + "@id": "bts:AtrioventricularBlockComplete" + }, + { + "@id": "bts:AtrioventricularBlockFirstDegree" + }, + { + "@id": "bts:AutoimmuneDisorder" + }, + { + "@id": "bts:AvascularNecrosis" + }, + { + "@id": "bts:Azoospermia" + }, + { + "@id": "bts:BackPain" + }, + { + "@id": "bts:BileDuctStenosis" + }, + { + "@id": "bts:BiliaryAnastomoticLeak" + }, + { + "@id": "bts:BiliaryFistula" + }, + { + "@id": "bts:BiliaryTractInfection" + }, + { + "@id": "bts:BladderAnastomoticLeak" + }, + { + "@id": "bts:BladderInfection" + }, + { + "@id": "bts:BladderPerforation" + }, + { + "@id": "bts:BladderSpasm" + }, + { + "@id": "bts:Bloating" + }, + { + "@id": "bts:BloodandLymphaticSystemDisordersOther" + }, + { + "@id": "bts:BloodAntidiureticHormoneAbnormal" + }, + { + "@id": "bts:BloodBilirubinIncreased" + }, + { + "@id": "bts:BloodCorticotrophinDecreased" + }, + { + "@id": "bts:BloodGonadotrophinAbnormal" + }, + { + "@id": "bts:BloodProlactinAbnormal" + }, + { + "@id": "bts:BlurredVision" + }, + { + "@id": "bts:BodyOdor" + }, + { + "@id": "bts:BoneInfection" + }, + { + "@id": "bts:BoneMarrowHypocellular" + }, + { + "@id": "bts:BonePain" + }, + { + "@id": "bts:BrachialPlexopathy" + }, + { + "@id": "bts:BreastAtrophy" + }, + { + "@id": "bts:BreastInfection" + }, + { + "@id": "bts:BreastPain" + }, + { + "@id": "bts:BronchialFistula" + }, + { + "@id": "bts:BronchialInfection" + }, + { + "@id": "bts:BronchialObstruction" + }, + { + "@id": "bts:BronchialStricture" + }, + { + "@id": "bts:BronchopleuralFistula" + }, + { + "@id": "bts:BronchopulmonaryHemorrhage" + }, + { + "@id": "bts:Bronchospasm" + }, + { + "@id": "bts:Bruising" + }, + { + "@id": "bts:BullousDermatitis" + }, + { + "@id": "bts:Burn" + }, + { + "@id": "bts:ButtockPain" + }, + { + "@id": "bts:CapillaryLeakSyndrome" + }, + { + "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" + }, + { + "@id": "bts:CardiacArrest" + }, + { + "@id": "bts:CardiacDisordersOther" + }, + { + "@id": "bts:CardiacTroponinIIncreased" + }, + { + "@id": "bts:CardiacTroponinTIncreased" + }, + { + "@id": "bts:Cataract" + }, + { + "@id": "bts:CatheterRelatedInfection" + }, + { + "@id": "bts:CD4LymphocytesDecreased" + }, + { + "@id": "bts:CecalHemorrhage" + }, + { + "@id": "bts:CecalInfection" + }, + { + "@id": "bts:CentralNervousSystemNecrosis" + }, + { + "@id": "bts:CerebrospinalFluidLeakage" + }, + { + "@id": "bts:CervicitisInfection" + }, + { + "@id": "bts:Cheilitis" + }, + { + "@id": "bts:ChestPainCardiac" + }, + { + "@id": "bts:ChestWallPain" + }, + { + "@id": "bts:Chills" + }, + { + "@id": "bts:Cholecystitis" + }, + { + "@id": "bts:CholesterolHigh" + }, + { + "@id": "bts:ChronicKidneyDisease" + }, + { + "@id": "bts:Chylothorax" + }, + { + "@id": "bts:CognitiveDisturbance" + }, + { + "@id": "bts:Colitis" + }, + { + "@id": "bts:ColonicFistula" + }, + { + "@id": "bts:ColonicHemorrhage" + }, + { + "@id": "bts:ColonicObstruction" + }, + { + "@id": "bts:ColonicPerforation" + }, + { + "@id": "bts:ColonicStenosis" + }, + { + "@id": "bts:ColonicUlcer" + }, + { + "@id": "bts:ConcentrationImpairment" + }, + { + "@id": "bts:ConductionDisorder" + }, + { + "@id": "bts:Confusion" + }, + { + "@id": "bts:Congenital" + }, + { + "@id": "bts:FamilialandGeneticDisordersOther" + }, + { + "@id": "bts:Conjunctivitis" + }, + { + "@id": "bts:ConjunctivitisInfective" + }, + { + "@id": "bts:Constipation" + }, + { + "@id": "bts:ConstrictivePericarditis" + }, + { + "@id": "bts:CornealInfection" + }, + { + "@id": "bts:CornealUlcer" + }, + { + "@id": "bts:Cough" + }, + { + "@id": "bts:CPKIncreased" + }, + { + "@id": "bts:CranialNerveInfection" + }, + { + "@id": "bts:CreatinineIncreased" + }, + { + "@id": "bts:Cushingoid" + }, + { + "@id": "bts:CystitisNoninfective" + }, + { + "@id": "bts:CytokineReleaseSyndrome" + }, + { + "@id": "bts:DeathNeonatal" + }, + { + "@id": "bts:DeathNOS" + }, + { + "@id": "bts:Dehydration" + }, + { + "@id": "bts:DelayedOrgasm" + }, + { + "@id": "bts:DelayedPuberty" + }, + { + "@id": "bts:Delirium" + }, + { + "@id": "bts:Delusions" + }, + { + "@id": "bts:DentalCaries" + }, + { + "@id": "bts:DepressedLevelofConsciousness" + }, + { + "@id": "bts:Depression" + }, + { + "@id": "bts:DermatitisRadiation" + }, + { + "@id": "bts:DeviceRelatedInfection" + }, + { + "@id": "bts:Diarrhea" + }, + { + "@id": "bts:DisseminatedIntravascularCoagulation" + }, + { + "@id": "bts:Dizziness" + }, + { + "@id": "bts:DryEye" + }, + { + "@id": "bts:DryMouth" + }, + { + "@id": "bts:DrySkin" + }, + { + "@id": 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"bts:GastricHemorrhage" + }, + { + "@id": "bts:GastricNecrosis" + }, + { + "@id": "bts:GastricPerforation" + }, + { + "@id": "bts:GastricStenosis" + }, + { + "@id": "bts:GastricUlcer" + }, + { + "@id": "bts:Gastritis" + }, + { + "@id": "bts:GastroesophagealRefluxDisease" + }, + { + "@id": "bts:GastrointestinalAnastomoticLeak" + }, + { + "@id": "bts:GastrointestinalDisordersOther" + }, + { + "@id": "bts:GastrointestinalFistula" + }, + { + "@id": "bts:GastrointestinalPain" + }, + { + "@id": "bts:GastrointestinalStomaNecrosis" + }, + { + "@id": "bts:Gastroparesis" + }, + { + "@id": "bts:GeneralDisordersandAdministrationSiteConditionsOther" + }, + { + "@id": "bts:GeneralizedMuscleWeakness" + }, + { + "@id": "bts:GenitalEdema" + }, + { + "@id": "bts:GGTIncreased" + }, + { + "@id": "bts:GingivalPain" + }, + { + "@id": "bts:Glaucoma" + }, + { + "@id": "bts:GlossopharyngealNerveDisorder" + }, + { + "@id": "bts:GlucoseIntolerance" + }, + { + "@id": "bts:GrowthAccelerated" + }, + { + "@id": "bts:GrowthHormoneAbnormal" + }, + { + "@id": "bts:GrowthSuppression" + }, + { + "@id": "bts:GumInfection" + }, + { + "@id": "bts:Gynecomastia" + }, + { + "@id": "bts:Hallucinations" + }, + { + "@id": "bts:HaptoglobinDecreased" + }, + { + "@id": "bts:HeadSoftTissueNecrosis" + }, + { + "@id": "bts:Headache" + }, + { + "@id": "bts:HearingImpaired" + }, + { + "@id": "bts:HeartFailure" + }, + { + "@id": "bts:Hematoma" + }, + { + "@id": "bts:Hematosalpinx" + }, + { + "@id": "bts:Hematuria" + }, + { + "@id": "bts:HemoglobinIncreased" + }, + { + "@id": "bts:Hemoglobinuria" + }, + { + "@id": "bts:Hemolysis" + }, + { + "@id": "bts:HemolyticUremicSyndrome" + }, + { + "@id": "bts:HemorrhoidalHemorrhage" + }, + { + "@id": "bts:Hemorrhoids" + }, + { + "@id": "bts:HepaticFailure" + }, + { + "@id": "bts:HepaticHemorrhage" + }, + { + "@id": "bts:HepaticInfection" + }, + { + "@id": "bts:HepaticNecrosis" + }, + { + "@id": "bts:HepaticPain" + }, + { + "@id": "bts:HepatitisViral" + }, + { + "@id": "bts:HepatobiliaryDisordersOther" + }, + { + "@id": "bts:Hiccups" + }, + { + "@id": "bts:HipFracture" + }, + { + "@id": "bts:Hirsutism" + }, + { + "@id": "bts:Hoarseness" + }, + { + "@id": "bts:HotFlashes" + }, + { + "@id": "bts:Hydrocephalus" + }, + { + "@id": "bts:Hypercalcemia" + }, + { + "@id": "bts:Hyperglycemia" + }, + { + "@id": "bts:Hyperhidrosis" + }, + { + "@id": "bts:Hyperkalemia" + }, + { + "@id": "bts:Hypermagnesemia" + }, + { + "@id": "bts:Hypernatremia" + }, + { + "@id": "bts:Hyperparathyroidism" + }, + { + "@id": "bts:Hypersomnia" + }, + { + "@id": "bts:Hypertension" + }, + { + "@id": "bts:Hyperthyroidism" + }, + { + "@id": "bts:Hypertrichosis" + }, + { + "@id": "bts:Hypertriglyceridemia" + }, + { + "@id": "bts:Hyperuricemia" + }, + { + "@id": "bts:Hypoalbuminemia" + }, + { + "@id": "bts:Hypocalcemia" + }, + { + "@id": "bts:HypoglossalNerveDisorder" + }, + { + "@id": "bts:Hypoglycemia" + }, + { + "@id": "bts:Hypohidrosis" + }, + { + "@id": "bts:Hypokalemia" + }, + { + "@id": "bts:Hypomagnesemia" + }, + { + "@id": "bts:Hyponatremia" + }, + { + "@id": "bts:Hypoparathyroidism" + }, + { + "@id": "bts:Hypophosphatemia" + }, + { + "@id": "bts:Hypotension" + }, + { + "@id": "bts:Hypothermia" + }, + { + "@id": "bts:Hypothyroidism" + }, + { + "@id": "bts:Hypoxia" + }, + { + "@id": "bts:IlealFistula" + }, + { + "@id": "bts:IlealHemorrhage" + }, + { + "@id": "bts:IlealObstruction" + }, + { + "@id": "bts:IlealPerforation" + }, + { + "@id": "bts:IlealStenosis" + }, + { + "@id": "bts:IlealUlcer" + }, + { + "@id": "bts:Ileus" + }, + { + "@id": "bts:ImmuneSystemDisordersOther" + }, + { + "@id": "bts:InfectionsandInfestationsOther" + }, + { + "@id": "bts:InfectiveMyositis" + }, + { + "@id": "bts:InfusionRelatedReaction" + }, + { + "@id": "bts:InfusionSiteExtravasation" + }, + { + "@id": "bts:InjectionSiteReaction" + }, + { + "@id": "bts:InjurytoCarotidArtery" + }, + { + "@id": "bts:InjurytoInferiorVenaCava" + }, + { + "@id": "bts:InjurytoJugularVein" + }, + { + "@id": "bts:InjurytoSuperiorVenaCava" + }, + { + "@id": "bts:Injury" + }, + { + "@id": "bts:PoisoningandProceduralComplicationsOther" + }, + { + "@id": "bts:INRIncreased" + }, + { + "@id": "bts:Insomnia" + }, + { + "@id": "bts:IntestinalStomaLeak" + }, + { + "@id": "bts:IntestinalStomaObstruction" + }, + { + "@id": "bts:IntestinalStomaSiteBleeding" + }, + { + "@id": "bts:Intra-AbdominalHemorrhage" + }, + { + "@id": "bts:IntracranialHemorrhage" + }, + { + "@id": "bts:IntraoperativeArterialInjury" + }, + { + "@id": "bts:IntraoperativeBreastInjury" + }, + { + "@id": "bts:IntraoperativeCardiacInjury" + }, + { + "@id": "bts:IntraoperativeEarInjury" + }, + { + "@id": "bts:IntraoperativeEndocrineInjury" + }, + { + "@id": "bts:IntraoperativeGastrointestinalInjury" + }, + { + "@id": "bts:IntraoperativeHeadandNeckInjury" + }, + { + "@id": "bts:IntraoperativeHemorrhage" + }, + { + "@id": "bts:IntraoperativeHepatobiliaryInjury" + }, + { + "@id": "bts:IntraoperativeMusculoskeletalInjury" + }, + { + "@id": "bts:IntraoperativeNeurologicalInjury" + }, + { + "@id": "bts:IntraoperativeOcularInjury" + }, + { + "@id": "bts:IntraoperativeRenalInjury" + }, + { + "@id": "bts:IntraoperativeReproductiveTractInjury" + }, + { + "@id": "bts:IntraoperativeRespiratoryInjury" + }, + { + "@id": "bts:IntraoperativeSkinInjury" + }, + { + "@id": "bts:IntraoperativeSplenicInjury" + }, + { + "@id": "bts:IntraoperativeUrinaryInjury" + }, + { + "@id": "bts:IntraoperativeVenousInjury" + }, + { + "@id": "bts:InvestigationsOther" + }, + { + "@id": "bts:IronOverload" + }, + { + "@id": "bts:IrregularMenstruation" + }, + { + "@id": "bts:Irritability" + }, + { + "@id": "bts:IschemiaCerebrovascular" + }, + { + "@id": "bts:IVthNerveDisorder" + }, + { + "@id": "bts:JejunalFistula" + }, + { + "@id": "bts:JejunalHemorrhage" + }, + { + "@id": "bts:JejunalObstruction" + }, + { + "@id": "bts:JejunalPerforation" + }, + { + "@id": "bts:JejunalStenosis" + }, + { + "@id": "bts:JejunalUlcer" + }, + { + "@id": "bts:JointEffusion" + }, + { + "@id": "bts:JointInfection" + }, + { + "@id": "bts:JointRangeofMotionDecreased" + }, + { + "@id": "bts:JointRangeofMotionDecreasedCervicalSpine" + }, + { + "@id": "bts:JointRangeofMotionDecreasedLumbarSpine" + }, + { + "@id": "bts:Keratitis" + }, + { + "@id": "bts:KidneyAnastomoticLeak" + }, + { + "@id": "bts:KidneyInfection" + }, + { + "@id": "bts:Kyphosis" + }, + { + "@id": "bts:LactationDisorder" + }, + { + "@id": "bts:LargeIntestinalAnastomoticLeak" + }, + { + "@id": "bts:LaryngealEdema" + }, + { + "@id": "bts:LaryngealFistula" + }, + { + "@id": "bts:LaryngealHemorrhage" + }, + { + "@id": "bts:LaryngealInflammation" + }, + { + "@id": "bts:LaryngealMucositis" + }, + { + "@id": "bts:LaryngealObstruction" + }, + { + "@id": "bts:LaryngealStenosis" + }, + { + "@id": "bts:Laryngitis" + }, + { + "@id": "bts:LaryngopharyngealDysesthesia" + }, + { + "@id": "bts:Laryngospasm" + }, + { + "@id": "bts:LeftVentricularSystolicDysfunction" + }, + { + "@id": "bts:Lethargy" + }, + { + "@id": "bts:LeukemiaSecondarytoOncologyChemotherapy" + }, + { + "@id": "bts:Leukocytosis" + }, + { + "@id": "bts:Leukoencephalopathy" + }, + { + "@id": "bts:LibidoDecreased" + }, + { + "@id": "bts:LibidoIncreased" + }, + { + "@id": "bts:LipInfection" + }, + { + "@id": "bts:LipPain" + }, + { + "@id": "bts:LipaseIncreased" + }, + { + "@id": "bts:Lipohypertrophy" + }, + { + "@id": "bts:LocalizedEdema" + }, + { + "@id": "bts:Lordosis" + }, + { + "@id": "bts:LowerGastrointestinalHemorrhage" + }, + { + "@id": "bts:LungInfection" + }, + { + "@id": "bts:LymphGlandInfection" + }, + { + "@id": "bts:LymphLeakage" + }, + { + "@id": "bts:LymphNodePain" + }, + { + "@id": "bts:Lymphedema" + }, + { + "@id": "bts:Lymphocele" + }, + { + "@id": "bts:LymphocyteCountDecreased" + }, + { + "@id": "bts:LymphocyteCountIncreased" + }, + { + "@id": "bts:Malabsorption" + }, + { + "@id": "bts:Malaise" + }, + { + "@id": "bts:Mania" + }, + { + "@id": "bts:MediastinalHemorrhage" + }, + { + "@id": "bts:MediastinalInfection" + }, + { + "@id": "bts:MemoryImpairment" + }, + { + "@id": "bts:Meningismus" + }, + { + "@id": "bts:Meningitis" + }, + { + "@id": "bts:Menopause" + }, + { + "@id": "bts:Menorrhagia" + }, + { + "@id": "bts:MetabolismandNutritionDisordersOther" + }, + { + "@id": "bts:MiddleEarInflammation" + }, + { + "@id": "bts:MitralValveDisease" + }, + { + "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" + }, + { + "@id": "bts:MobitzTypeI" + }, + { + "@id": "bts:MovementsInvoluntary" + }, + { + "@id": "bts:MucosalInfection" + }, + { + "@id": "bts:MucositisOral" + }, + { + "@id": "bts:Multi-OrganFailure" + }, + { + "@id": "bts:MuscleWeaknessLeft-Sided" + }, + { + "@id": "bts:MuscleWeaknessLowerLimb" + }, + { + "@id": "bts:MuscleWeaknessRight-Sided" + }, + { + "@id": "bts:MuscleWeaknessTrunk" + }, + { + "@id": "bts:MuscleWeaknessUpperLimb" + }, + { + "@id": "bts:MusculoskeletalandConnectiveTissueDisordersOther" + }, + { + "@id": "bts:MusculoskeletalDeformity" + }, + { + "@id": "bts:Myalgia" + }, + { + "@id": "bts:Myelitis" + }, + { + "@id": "bts:MyelodysplasticSyndrome" + }, + { + "@id": "bts:MyocardialInfarction" + }, + { + "@id": "bts:Myocarditis" + }, + { + "@id": "bts:Myositis" + }, + { + "@id": "bts:NailDiscoloration" + }, + { + "@id": "bts:NailInfection" + }, + { + "@id": "bts:NailLoss" + }, + { + "@id": "bts:NailRidging" + }, + { + "@id": "bts:NasalCongestion" + }, + { + "@id": "bts:Nausea" + }, + { + "@id": "bts:NeckEdema" + }, + { + "@id": "bts:NeckPain" + }, + { + "@id": "bts:NeckSoftTissueNecrosis" + }, + { + "@id": "bts:NeoplasmsBenign" + }, + { + "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" + }, + { + "@id": "bts:NervousSystemDisordersOther" + }, + { + "@id": "bts:Neuralgia" + }, + { + "@id": "bts:NeutrophilCountDecreased" + }, + { + "@id": "bts:NightBlindness" + }, + { + "@id": "bts:NippleDeformity" + }, + { + "@id": "bts:Non-CardiacChestPain" + }, + { + "@id": "bts:Nystagmus" + }, + { + "@id": "bts:Obesity" + }, + { + "@id": "bts:ObstructionGastric" + }, + { + "@id": "bts:OculomotorNerveDisorder" + }, + { + "@id": "bts:OlfactoryNerveDisorder" + }, + { + "@id": "bts:Oligospermia" + }, + { + "@id": "bts:OpticNerveDisorder" + }, + { + "@id": "bts:OralCavityFistula" + }, + { + "@id": "bts:OralDysesthesia" + }, + { + "@id": "bts:OralHemorrhage" + }, + { + "@id": "bts:OralPain" + }, + { + "@id": "bts:OsteonecrosisofJaw" + }, + { + "@id": "bts:Osteoporosis" + }, + { + "@id": "bts:OtitisExterna" + }, + { + "@id": "bts:OtitisMedia" + }, + { + "@id": "bts:OvarianHemorrhage" + }, + { + "@id": "bts:OvarianInfection" + }, + { + "@id": "bts:OvarianRupture" + }, + { + "@id": "bts:OvulationPain" + }, + { + "@id": "bts:Pain" + }, + { + "@id": "bts:PaininExtremity" + }, + { + "@id": "bts:PainofSkin" + }, + { + "@id": "bts:Palmar-PlantarErythrodysesthesiaSyndrome" + }, + { + "@id": "bts:Palpitations" + }, + { + "@id": "bts:PancreasInfection" + }, + { + "@id": "bts:PancreaticAnastomoticLeak" + }, + { + "@id": "bts:PancreaticDuctStenosis" + }, + { + "@id": "bts:PancreaticEnzymesDecreased" + }, + { + "@id": "bts:PancreaticFistula" + }, + { + "@id": "bts:PancreaticHemorrhage" + }, + { + "@id": "bts:PancreaticNecrosis" + }, + { + "@id": "bts:Pancreatitis" + }, + { + "@id": "bts:Papilledema" + }, + { + "@id": "bts:PapulopustularRash" + }, + { + "@id": "bts:Paresthesia" + }, + { + "@id": "bts:Paronychia" + }, + { + "@id": "bts:ParoxysmalAtrialTachycardia" + }, + { + "@id": "bts:PelvicFloorMuscleWeakness" + }, + { + "@id": "bts:PelvicInfection" + }, + { + "@id": "bts:PelvicPain" + }, + { + "@id": "bts:PelvicSoftTissueNecrosis" + }, + { + "@id": "bts:PenileInfection" + }, + { + "@id": "bts:PenilePain" + }, + { + "@id": "bts:PerforationBileDuct" + }, + { + "@id": "bts:PericardialEffusion" + }, + { + "@id": "bts:PericardialTamponade" + }, + { + "@id": "bts:Pericarditis" + }, + { + "@id": "bts:PerinealPain" + }, + { + "@id": "bts:PeriodontalDisease" + }, + { + "@id": "bts:PeriorbitalEdema" + }, + { + "@id": "bts:PeriorbitalInfection" + }, + { + "@id": "bts:PeripheralIschemia" + }, + { + "@id": "bts:PeripheralMotorNeuropathy" + }, + { + "@id": "bts:PeripheralNerveInfection" + }, + { + "@id": "bts:PeripheralSensoryNeuropathy" + }, + { + "@id": "bts:PeritonealInfection" + }, + { + "@id": "bts:PeritonealNecrosis" + }, + { + "@id": "bts:PersonalityChange" + }, + { + "@id": "bts:PhantomPain" + }, + { + "@id": "bts:PharyngealAnastomoticLeak" + }, + { + "@id": "bts:PharyngealFistula" + }, + { + "@id": "bts:PharyngealHemorrhage" + }, + { + "@id": "bts:PharyngealMucositis" + }, + { + "@id": "bts:PharyngealNecrosis" + }, + { + "@id": "bts:PharyngealStenosis" + }, + { + "@id": "bts:Pharyngitis" + }, + { + "@id": "bts:PharyngolaryngealPain" + }, + { + "@id": "bts:Phlebitis" + }, + { + "@id": "bts:PhlebitisInfective" + }, + { + "@id": "bts:Photophobia" + }, + { + "@id": "bts:Photosensitivity" + }, + { + "@id": "bts:PlateletCountDecreased" + }, + { + "@id": "bts:PleuralEffusion" + }, + { + "@id": "bts:PleuralHemorrhage" + }, + { + "@id": "bts:PleuralInfection" + }, + { + "@id": "bts:PleuriticPain" + }, + { + "@id": "bts:Pneumonitis" + }, + { + "@id": "bts:Pneumothorax" + }, + { + "@id": "bts:PortalHypertension" + }, + { + "@id": "bts:PortalVeinThrombosis" + }, + { + "@id": "bts:PostnasalDrip" + }, + { + "@id": "bts:PostoperativeHemorrhage" + }, + { + "@id": "bts:PostoperativeThoracicProcedureComplication" + }, + { + "@id": "bts:PrecociousPuberty" + }, + { + "@id": "bts:Pregnancy" + }, + { + "@id": "bts:PuerperiumandPerinatalConditionsOther" + }, + { + "@id": "bts:PrematureDelivery" + }, + { + "@id": "bts:PrematureMenopause" + }, + { + "@id": "bts:Presyncope" + }, + { + "@id": "bts:Proctitis" + }, + { + "@id": "bts:ProductiveCough" + }, + { + "@id": "bts:ProlapseofIntestinalStoma" + }, + { + "@id": "bts:ProlapseofUrostomy" + }, + { + "@id": "bts:ProstateInfection" + }, + { + "@id": "bts:ProstaticHemorrhage" + }, + { + "@id": "bts:ProstaticObstruction" + }, + { + "@id": "bts:ProstaticPain" + }, + { + "@id": "bts:Proteinuria" + }, + { + "@id": "bts:Pruritus" + }, + { + "@id": "bts:PsychiatricDisordersOther" + }, + { + "@id": "bts:Psychosis" + }, + { + "@id": "bts:PulmonaryEdema" + }, + { + "@id": "bts:PulmonaryFibrosis" + }, + { + "@id": "bts:PulmonaryFistula" + }, + { + "@id": "bts:PulmonaryHypertension" + }, + { + "@id": "bts:PulmonaryValveDisease" + }, + { + "@id": "bts:Purpura" + }, + { + "@id": "bts:PyramidalTractSyndrome" + }, + { + "@id": "bts:RadiationRecallReaction(Dermatologic)" + }, + { + "@id": "bts:Radiculitis" + }, + { + "@id": "bts:RashAcneiform" + }, + { + "@id": "bts:RashMaculo-Papular" + }, + { + "@id": "bts:RashPustular" + }, + { + "@id": "bts:RectalAnastomoticLeak" + }, + { + "@id": "bts:RectalFistula" + }, + { + "@id": "bts:RectalHemorrhage" + }, + { + "@id": "bts:RectalMucositis" + }, + { + "@id": "bts:RectalNecrosis" + }, + { + "@id": "bts:RectalObstruction" + }, + { + "@id": "bts:RectalPain" + }, + { + "@id": "bts:RectalPerforation" + }, + { + "@id": "bts:RectalStenosis" + }, + { + "@id": "bts:RectalUlcer" + }, + { + "@id": "bts:RecurrentLaryngealNervePalsy" + }, + { + "@id": "bts:RenalandUrinaryDisordersOther" + }, + { + "@id": "bts:RenalCalculi" + }, + { + "@id": "bts:RenalColic" + }, + { + "@id": "bts:RenalHemorrhage" + }, + { + "@id": "bts:ReproductiveSystemandBreastDisordersOther" + }, + { + "@id": "bts:RespiratoryFailure" + }, + { + "@id": "bts:Respiratory" + }, + { + "@id": "bts:ThoracicandMediastinalDisordersOther" + }, + { + "@id": "bts:Restlessness" + }, + { + "@id": "bts:RestrictiveCardiomyopathy" + }, + { + "@id": "bts:RetinalDetachment" + }, + { + "@id": "bts:RetinalTear" + }, + { + "@id": "bts:RetinalVascularDisorder" + }, + { + "@id": "bts:RetinoicAcidSyndrome" + }, + { + "@id": "bts:Retinopathy" + }, + { + "@id": "bts:RetroperitonealHemorrhage" + }, + { + "@id": "bts:ReversiblePosteriorLeukoencephalopathySyndrome" + }, + { + "@id": "bts:RhinitisInfective" + }, + { + "@id": "bts:RightVentricularDysfunction" + }, + { + "@id": "bts:SalivaryDuctInflammation" + }, + { + "@id": "bts:SalivaryGlandFistula" + }, + { + "@id": "bts:SalivaryGlandInfection" + }, + { + "@id": "bts:ScalpPain" + }, + { + "@id": "bts:ScleralDisorder" + }, + { + "@id": "bts:Scoliosis" + }, + { + "@id": "bts:ScrotalInfection" + }, + { + "@id": "bts:ScrotalPain" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:Sepsis" + }, + { + "@id": "bts:Seroma" + }, + { + "@id": "bts:SerumAmylaseIncreased" + }, + { + "@id": "bts:SerumSickness" + }, + { + "@id": "bts:SickSinusSyndrome" + }, + { + "@id": "bts:SinusBradycardia" + }, + { + "@id": "bts:SinusDisorder" + }, + { + "@id": "bts:SinusPain" + }, + { + "@id": "bts:SinusTachycardia" + }, + { + "@id": "bts:Sinusitis" + }, + { + "@id": "bts:SkinandSubcutaneousTissueDisordersOther" + }, + { + "@id": "bts:SkinAtrophy" + }, + { + "@id": "bts:SkinHyperpigmentation" + }, + { + "@id": "bts:SkinHypopigmentation" + }, + { + "@id": "bts:SkinInduration" + }, + { + "@id": "bts:SkinInfection" + }, + { + "@id": "bts:SkinUlceration" + }, + { + "@id": "bts:SleepApnea" + }, + { + "@id": "bts:SmallIntestinalAnastomoticLeak" + }, + { + "@id": "bts:SmallIntestinalMucositis" + }, + { + "@id": "bts:SmallIntestinalObstruction" + }, + { + "@id": "bts:SmallIntestinalPerforation" + }, + { + "@id": "bts:SmallIntestinalStenosis" + }, + { + "@id": "bts:SmallIntestineInfection" + }, + { + "@id": "bts:SmallIntestineUlcer" + }, + { + "@id": "bts:Sneezing" + }, + { + "@id": "bts:SocialCircumstancesOther" + }, + { + "@id": "bts:SoftTissueInfection" + }, + { + "@id": "bts:SoftTissueNecrosisLowerLimb" + }, + { + "@id": "bts:SoftTissueNecrosisUpperLimb" + }, + { + "@id": "bts:Somnolence" + }, + { + "@id": "bts:SoreThroat" + }, + { + "@id": "bts:Spasticity" + }, + { + "@id": "bts:SpermaticCordAnastomoticLeak" + }, + { + "@id": "bts:SpermaticCordHemorrhage" + }, + { + "@id": "bts:SpermaticCordObstruction" + }, + { + "@id": "bts:SpinalFracture" + }, + { + "@id": "bts:SpleenDisorder" + }, + { + "@id": "bts:SplenicInfection" + }, + { + "@id": "bts:StenosisofGastrointestinalStoma" + }, + { + "@id": "bts:Stevens-JohnsonSyndrome" + }, + { + "@id": "bts:StomaSiteInfection" + }, + { + "@id": "bts:StomachPain" + }, + { + "@id": "bts:StomalUlcer" + }, + { + "@id": "bts:Stridor" + }, + { + "@id": "bts:Stroke" + }, + { + "@id": "bts:SuddenDeathNOS" + }, + { + "@id": "bts:SuicidalIdeation" + }, + { + "@id": "bts:SuicideAttempt" + }, + { + "@id": "bts:SuperficialSoftTissueFibrosis" + }, + { + "@id": "bts:SuperficialThrombophlebitis" + }, + { + "@id": "bts:SuperiorVenaCavaSyndrome" + }, + { + "@id": "bts:SupraventricularTachycardia" + }, + { + "@id": "bts:SurgicalandMedicalProceduresOther" + }, + { + "@id": "bts:Syncope" + }, + { + "@id": "bts:Telangiectasia" + }, + { + "@id": "bts:TesticularDisorder" + }, + { + "@id": "bts:TesticularHemorrhage" + }, + { + "@id": "bts:TesticularPain" + }, + { + "@id": "bts:ThromboembolicEvent" + }, + { + "@id": "bts:ThromboticThrombocytopenicPurpura" + }, + { + "@id": "bts:Tinnitus" + }, + { + "@id": "bts:ToothDevelopmentDisorder" + }, + { + "@id": "bts:ToothDiscoloration" + }, + { + "@id": "bts:ToothInfection" + }, + { + "@id": "bts:Toothache" + }, + { + "@id": "bts:ToxicEpidermalNecrolysis" + }, + { + "@id": "bts:TrachealFistula" + }, + { + "@id": "bts:TrachealHemorrhage" + }, + { + "@id": "bts:TrachealMucositis" + }, + { + "@id": "bts:TrachealObstruction" + }, + { + "@id": "bts:TrachealStenosis" + }, + { + "@id": "bts:Tracheitis" + }, + { + "@id": "bts:TracheostomySiteBleeding" + }, + { + "@id": "bts:TransientIschemicAttacks" + }, + { + "@id": "bts:TreatmentRelatedSecondaryMalignancy" + }, + { + "@id": "bts:Tremor" + }, + { + "@id": "bts:TricuspidValveDisease" + }, + { + "@id": "bts:TrigeminalNerveDisorder" + }, + { + "@id": "bts:Trismus" + }, + { + "@id": "bts:TumorLysisSyndrome" + }, + { + "@id": "bts:TumorPain" + }, + { + "@id": "bts:Typhlitis" + }, + { + "@id": "bts:UnequalLimbLength" + }, + { + "@id": "bts:UnintendedPregnancy" + }, + { + "@id": "bts:UpperGastrointestinalHemorrhage" + }, + { + "@id": "bts:UpperRespiratoryInfection" + }, + { + "@id": "bts:UretericAnastomoticLeak" + }, + { + "@id": "bts:UrethralAnastomoticLeak" + }, + { + "@id": "bts:UrethralInfection" + }, + { + "@id": "bts:UrinaryFistula" + }, + { + "@id": "bts:UrinaryFrequency" + }, + { + "@id": "bts:UrinaryIncontinence" + }, + { + "@id": "bts:UrinaryRetention" + }, + { + "@id": "bts:UrinaryTractInfection" + }, + { + "@id": "bts:UrinaryTractObstruction" + }, + { + "@id": "bts:UrinaryTractPain" + }, + { + "@id": "bts:UrinaryUrgency" + }, + { + "@id": "bts:UrineDiscoloration" + }, + { + "@id": "bts:UrineOutputDecreased" + }, + { + "@id": "bts:UrostomyLeak" + }, + { + "@id": "bts:UrostomyObstruction" + }, + { + "@id": "bts:UrostomySiteBleeding" + }, + { + "@id": "bts:UrostomyStenosis" + }, + { + "@id": "bts:Urticaria" + }, + { + "@id": "bts:UterineAnastomoticLeak" + }, + { + "@id": "bts:UterineFistula" + }, + { + "@id": "bts:UterineHemorrhage" + }, + { + "@id": "bts:UterineInfection" + }, + { + "@id": "bts:UterineObstruction" + }, + { + "@id": "bts:UterinePain" + }, + { + "@id": "bts:UterinePerforation" + }, + { + "@id": "bts:Uveitis" + }, + { + "@id": "bts:VaginalAnastomoticLeak" + }, + { + "@id": "bts:VaginalDischarge" + }, + { + "@id": "bts:VaginalDryness" + }, + { + "@id": "bts:VaginalFistula" + }, + { + "@id": "bts:VaginalHemorrhage" + }, + { + "@id": "bts:VaginalInfection" + }, + { + "@id": "bts:VaginalInflammation" + }, + { + "@id": "bts:VaginalObstruction" + }, + { + "@id": "bts:VaginalPain" + }, + { + "@id": "bts:VaginalPerforation" + }, + { + "@id": "bts:VaginalStricture" + }, + { + "@id": "bts:Vaginismus" + }, + { + "@id": "bts:VagusNerveDisorder" + }, + { + "@id": "bts:VasDeferensAnastomoticLeak" + }, + { + "@id": "bts:VascularAccessComplication" + }, + { + "@id": "bts:VascularDisordersOther" + }, + { + "@id": "bts:Vasculitis" + }, + { + "@id": "bts:VasovagalReaction" + }, + { + "@id": "bts:VenousInjury" + }, + { + "@id": "bts:VentricularArrhythmia" + }, + { + "@id": "bts:VentricularFibrillation" + }, + { + "@id": "bts:VentricularTachycardia" + }, + { + "@id": "bts:Vertigo" + }, + { + "@id": "bts:VestibularDisorder" + }, + { + "@id": "bts:Virilization" + }, + { + "@id": "bts:VisceralArterialIschemia" + }, + { + "@id": "bts:VitalCapacityAbnormal" + }, + { + "@id": "bts:VitreousHemorrhage" + }, + { + "@id": "bts:VoiceAlteration" + }, + { + "@id": "bts:Vomiting" + }, + { + "@id": "bts:VulvalInfection" + }, + { + "@id": "bts:WateringEyes" + }, + { + "@id": "bts:WeightGain" + }, + { + "@id": "bts:WeightLoss" + }, + { + "@id": "bts:Wheezing" + }, + { + "@id": "bts:WhiteBloodCellDecreased" + }, + { + "@id": "bts:Wolff-Parkinson-WhiteSyndrome" + }, + { + "@id": "bts:WoundComplication" + }, + { + "@id": "bts:WoundDehiscence" + }, + { + "@id": "bts:WoundInfection" + }, + { + "@id": "bts:WristFracture" + } + ], + "sms:displayName": "Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", + "rdfs:label": "BarrettsEsophagusGobletCellsPresent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Barretts Esophagus Goblet Cells Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BMI", + "@type": "rdfs:Class", + "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", + "rdfs:label": "BMI", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "BMI", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CauseofResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", + "rdfs:label": "CauseofResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cause of Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Comorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", + "rdfs:label": "Comorbidity", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AcuteRenalFailure" + }, + { + "@id": "bts:Adenocarcinoma" + }, + { + "@id": "bts:AdrenocorticalInsufficiency" + }, + { + "@id": "bts:AdenomatousPolyposisColi" + }, + { + "@id": "bts:Allergies" + }, + { + "@id": "bts:Alpha-1Antitrypsin" + }, + { + "@id": "bts:Anemia" + }, + { + "@id": "bts:Anxiety" + }, + { + "@id": "bts:Arrhythmia" + }, + { + "@id": "bts:Arthritis" + }, + { + "@id": "bts:Asthma" + }, + { + "@id": "bts:AtrialFibrillation" + }, + { + "@id": "bts:AvascularNecrosis" + }, + { + "@id": "bts:Barrett'sEsophagus" + }, + { + "@id": "bts:BasalCellCarcinoma" + }, + { + "@id": "bts:Beckwith-Wiedemann" + }, + { + "@id": "bts:Behcet'sDisease" + }, + { + "@id": "bts:BiliaryDisorder" + }, + { + "@id": "bts:BloodClots" + }, + { + "@id": "bts:BoneFracture(s)" + }, + { + "@id": "bts:Bronchitis" + }, + { + "@id": "bts:CalciumChannelBlockers" + }, + { + "@id": "bts:Cancer" + }, + { + "@id": "bts:Cataracts" + }, + { + "@id": "bts:CeliacDisease" + }, + { + "@id": "bts:Cirrhosis" + }, + { + "@id": "bts:UnknownEtiology" + }, + { + "@id": "bts:CerebrovascularDisease" + }, + { + "@id": "bts:Cholelithiasis" + }, + { + "@id": "bts:ChronicRenalFailure" + }, + { + "@id": "bts:ColonPolyps" + }, + { + "@id": "bts:CommonVariableImmunodeficiency" + }, + { + "@id": "bts:CongestiveHeartFailure(CHF)" + }, + { + "@id": "bts:ConnectiveTissueDisorder" + }, + { + "@id": "bts:COPD" + }, + { + "@id": "bts:CoronaryArteryDisease" + }, + { + "@id": "bts:Crohn'sDisease" + }, + { + "@id": "bts:CryptogenicOrganizingPneumonia" + }, + { + "@id": "bts:DeepVeinThrombosis/Thromboembolism" + }, + { + "@id": "bts:Denys-DrashSyndrome" + }, + { + "@id": "bts:Depression" + }, + { + "@id": "bts:Diabetes" + }, + { + "@id": "bts:TypeII" + }, + { + "@id": "bts:DiabeticNeuropathy" + }, + { + "@id": "bts:DietControlledDiabetes" + }, + { + "@id": "bts:Diverticulitis" + }, + { + "@id": "bts:DVT/PE" + }, + { + "@id": "bts:Dyslipidemia" + }, + { + "@id": "bts:Epilepsy" + }, + { + "@id": "bts:Eczema" + }, + { + "@id": "bts:Epstein-BarrVirus" + }, + { + "@id": "bts:FamilialAdenomatousPolyposis" + }, + { + "@id": "bts:FanconiAnemia" + }, + { + "@id": "bts:Fibrosis" + }, + { + "@id": "bts:GastroesophagealRefluxDisease" + }, + { + "@id": "bts:GERD" + }, + { + "@id": "bts:Glaucoma" + }, + { + "@id": "bts:GlycogenStorageDisease" + }, + { + "@id": "bts:Gout" + }, + { + "@id": "bts:GonadalDysfunction" + }, + { + "@id": "bts:GorlinSyndrome" + }, + { + "@id": "bts:H.pyloriInfection" + }, + { + "@id": "bts:Hashimoto'sThyroiditis" + }, + { + "@id": "bts:Headache" + }, + { + "@id": "bts:HeartDisease" + }, + { + "@id": "bts:Hemihypertrophy" + }, + { + "@id": "bts:HemorrhagicCystitis" + }, + { + "@id": "bts:Hepatitis" + }, + { + "@id": "bts:HepatitisAInfection" + }, + { + "@id": "bts:HepatitisBInfection" + }, + { + "@id": "bts:HepatitisCInfection" + }, + { + "@id": "bts:ChronicHepatitis" + }, + { + "@id": "bts:HereditaryNon-polyposisColonCancer" + }, + { + "@id": "bts:Herpes" + }, + { + "@id": "bts:HighGradeLiverDysplasticNodule" + }, + { + "@id": "bts:HIV/AIDS" + }, + { + "@id": "bts:HumanPapillomavirusInfection" + }, + { + "@id": "bts:HUS/TTP" + }, + { + "@id": "bts:Hypercholesterolemia" + }, + { + "@id": "bts:Hypercalcemia" + }, + { + "@id": "bts:Hyperglycemia" + }, + { + "@id": "bts:Hyperlipidemia" + }, + { + "@id": "bts:Hypertension" + }, + { + "@id": "bts:Hypospadias" + }, + { + "@id": "bts:Hypothyroidism" + }, + { + "@id": "bts:InflammatoryBowelDisease" + }, + { + "@id": "bts:InsulinControlledDiabetes" + }, + { + "@id": "bts:InterstitialPneumontisorARDS" + }, + { + "@id": "bts:IntraductalPapillaryMucinousNeoplasm" + }, + { + "@id": "bts:IronOverload" + }, + { + "@id": "bts:IschemicHeartDisease" + }, + { + "@id": "bts:ITP" + }, + { + "@id": "bts:JointReplacement" + }, + { + "@id": "bts:KidneyDisease" + }, + { + "@id": "bts:LiverCirrhosis(LiverDisease)" + }, + { + "@id": "bts:LiverToxicity(Non-Infectious)" + }, + { + "@id": "bts:Li-FraumeniSyndrome" + }, + { + "@id": "bts:LowGradeLiverDysplasticNodule" + }, + { + "@id": "bts:Lupus" + }, + { + "@id": "bts:LynchSyndrome" + }, + { + "@id": "bts:MAI" + }, + { + "@id": "bts:MyastheniaGravis" + }, + { + "@id": "bts:MyocardialInfarction" + }, + { + "@id": "bts:NeuroendocrineTumor" + }, + { + "@id": "bts:NonalcoholicSteatohepatitis" + }, + { + "@id": "bts:Obesity" + }, + { + "@id": "bts:Organtransplant(site)" + }, + { + "@id": "bts:Osteoarthritis" + }, + { + "@id": "bts:OsteoporosisorOsteopenia" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:OtherCancerWithin5Years" + }, + { + "@id": "bts:OtherNonmalignantSystemicDisease" + }, + { + "@id": "bts:OtherPulmonaryComplications" + }, + { + "@id": "bts:Pancreatitis" + }, + { + "@id": "bts:Pain(Various)" + }, + { + "@id": "bts:PepticUlcer(Ulcer)" + }, + { + "@id": "bts:PeripheralNeuropathy" + }, + { + "@id": "bts:PeripheralVascularDisease" + }, + { + "@id": "bts:Peutz-JeghersDisease" + }, + { + "@id": "bts:PregnancyinPatientorPartner" + }, + { + "@id": "bts:PrimarySclerosingCholangitis" + }, + { + "@id": "bts:Psoriasis" + }, + { + "@id": "bts:PulmonaryFibrosis" + }, + { + "@id": "bts:PulmonaryHemorrhage" + }, + { + "@id": "bts:RenalFailure(RequiringDialysis)" + }, + { + "@id": "bts:RenalDialysis" + }, + { + "@id": "bts:RenalInsufficiency" + }, + { + "@id": "bts:RheumatologicDisease" + }, + { + "@id": "bts:RheumatoidArthritis" + }, + { + "@id": "bts:Rubinstein-TaybiSyndrome" + }, + { + "@id": "bts:Sarcoidosis" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:Sleepapnea" + }, + { + "@id": "bts:Smoking" + }, + { + "@id": "bts:Steatosis" + }, + { + "@id": "bts:Stroke" + }, + { + "@id": "bts:TransientIschemicAttack" + }, + { + "@id": "bts:Tuberculosis" + }, + { + "@id": "bts:TurcotSyndrome" + }, + { + "@id": "bts:Tyrosinemia" + }, + { + "@id": "bts:UlcerativeColitis" + }, + { + "@id": "bts:WagrSyndrome" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Comorbidity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ComorbidityMethodofDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", + "rdfs:label": "ComorbidityMethodofDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Histology" + }, + { + "@id": "bts:Pathology" + }, + { + "@id": "bts:Radiology" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Comorbidity Method of Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoAdverseEvent", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoAdverseEvent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoComorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoComorbidity", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Comorbidity", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DiabetesTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", + "rdfs:label": "DiabetesTreatmentType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Alpha-GlucosidaseInhibitor" + }, + { + "@id": "bts:Biguanide" + }, + { + "@id": "bts:Diet" + }, + { + "@id": "bts:InjectedInsulin" + }, + { + "@id": "bts:Insulin" + }, + { + "@id": "bts:OralHypoglycemic" + }, + { + "@id": "bts:Sulfonylurea" + }, + { + "@id": "bts:Thiazolidinedione" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Diabetes Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DiseaseResponse", + "@type": "rdfs:Class", + "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", + "rdfs:label": "DiseaseResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AJ-AdjuvantTherapy" + }, + { + "@id": "bts:BED-BiochemicalEvidenceofDisease" + }, + { + "@id": "bts:CPD-ClinicalProgression" + }, + { + "@id": "bts:CR-CompleteResponse" + }, + { + "@id": "bts:CRU-CompleteResponseUnconfirmed" + }, + { + "@id": "bts:DU-DiseaseUnchanged" + }, + { + "@id": "bts:IMR-Immunoresponse" + }, + { + "@id": "bts:IPD-Immunoprogression" + }, + { + "@id": "bts:MR-Minimal/Marginalresponse" + }, + { + "@id": "bts:MX-MixedResponse" + }, + { + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + }, + { + "@id": "bts:NPB-NoPalliativeBenefit" + }, + { + "@id": "bts:NR-NoResponse" + }, + { + "@id": "bts:PA-PalliativeTherapy" + }, + { + "@id": "bts:PB-PalliativeBenefit" + }, + { + "@id": "bts:PD-ProgressiveDisease" + }, + { + "@id": "bts:PDM-PersistentDistantMetastasis" + }, + { + "@id": "bts:PLD-PersistentLocoregionalDisease" + }, + { + "@id": "bts:PPD-Pseudoprogression" + }, + { + "@id": "bts:PR-PartialResponse" + }, + { + "@id": "bts:PSR-Pseudoresponse" + }, + { + "@id": "bts:RD-ResponsiveDisease" + }, + { + "@id": "bts:RP-Response" + }, + { + "@id": "bts:RPD-RadiographicProgressiveDisease" + }, + { + "@id": "bts:SCR-StringentCompleteResponse" + }, + { + "@id": "bts:SD-StableDisease" + }, + { + "@id": "bts:SPD-SurgicalProgression" + }, + { + "@id": "bts:TE-TooEarly" + }, + { + "@id": "bts:TF-TumorFree" + }, + { + "@id": "bts:VGPR-VeryGoodPartialResponse" + }, + { + "@id": "bts:WT-WithTumor" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Disease Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DLCORefPredictivePercent", + "@type": "rdfs:Class", + "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", + "rdfs:label": "DLCORefPredictivePercent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DLCO Ref Predictive Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ECOGPerformanceStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The ECOG functional performance status of the patient/participant.", + "rdfs:label": "ECOGPerformanceStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:\"0\"" + }, + { + "@id": "bts:\"1\"" + }, + { + "@id": "bts:\"2\"" + }, + { + "@id": "bts:\"3\"" + }, + { + "@id": "bts:\"4\"" + }, + { + "@id": "bts:\"5\"" + }, + { + "@id": "bts:\"0.0\"" + }, + { + "@id": "bts:\"1.0\"" + }, + { + "@id": "bts:\"2.0\"" + }, + { + "@id": "bts:\"3.0\"" + }, + { + "@id": "bts:\"4.0\"" + }, + { + "@id": "bts:\"5.0\"" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "ECOG Performance Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1FVCPostBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", + "rdfs:label": "FEV1FVCPostBronchPercent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 FVC Post Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1FVCPreBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", + "rdfs:label": "FEV1FVCPreBronchPercent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV 1 FVC Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1RefPostBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", + "rdfs:label": "FEV1RefPostBronchPercent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 Ref Post Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1RefPreBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", + "rdfs:label": "FEV1RefPreBronchPercent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 Ref Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Height", + "@type": "rdfs:Class", + "rdfs:comment": "The height of the patient in centimeters.", + "rdfs:label": "Height", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Height", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HepatitisSustainedVirologicalResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "HepatitisSustainedVirologicalResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Hepatitis Sustained Virological Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HPVPositiveType", + "@type": "rdfs:Class", + "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", + "rdfs:label": "HPVPositiveType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:\"16\"" + }, + { + "@id": "bts:\"18\"" + }, + { + "@id": "bts:\"26\"" + }, + { + "@id": "bts:\"31\"" + }, + { + "@id": "bts:\"33\"" + }, + { + "@id": "bts:\"35\"" + }, + { + "@id": "bts:\"39\"" + }, + { + "@id": "bts:\"45\"" + }, + { + "@id": "bts:\"51\"" + }, + { + "@id": "bts:\"52\"" + }, + { + "@id": "bts:\"53\"" + }, + { + "@id": "bts:\"56\"" + }, + { + "@id": "bts:\"58\"" + }, + { + "@id": "bts:\"59\"" + }, + { + "@id": "bts:\"63\"" + }, + { + "@id": "bts:\"66\"" + }, + { + "@id": "bts:\"68\"" + }, + { + "@id": "bts:\"70\"" + }, + { + "@id": "bts:\"73\"" + }, + { + "@id": "bts:\"82\"" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HPV Positive Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KarnofskyPerformanceStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", + "rdfs:label": "KarnofskyPerformanceStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:\"0\"" + }, + { + "@id": "bts:\"10\"" + }, + { + "@id": "bts:\"20\"" + }, + { + "@id": "bts:\"30\"" + }, + { + "@id": "bts:\"40\"" + }, + { + "@id": "bts:\"50\"" + }, + { + "@id": "bts:\"60\"" + }, + { + "@id": "bts:\"70\"" + }, + { + "@id": "bts:\"80\"" + }, + { + "@id": "bts:\"90\"" + }, + { + "@id": "bts:\"100\"" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Karnofsky Performance Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MenopauseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's menopause status.", + "rdfs:label": "MenopauseStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Premenopausal" + }, + { + "@id": "bts:Perimenopausal" + }, + { + "@id": "bts:Postmenopausal" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Menopause Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreatitisOnsetYear", + "@type": "rdfs:Class", + "rdfs:comment": "Date of onset of pancreatitis.", + "rdfs:label": "PancreatitisOnsetYear", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatitis Onset Year", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:RefluxTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", + "rdfs:label": "RefluxTreatmentType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Antacids" + }, + { + "@id": "bts:H2Blockers" + }, + { + "@id": "bts:MedicallyTreated" + }, + { + "@id": "bts:NoTreatment" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:ProtonPumpInhibitors" + }, + { + "@id": "bts:SurgicallyTreated" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Reflux Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RiskFactor", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactor", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AlcoholConsumption" + }, + { + "@id": "bts:AlcoholicLiverDisease" + }, + { + "@id": "bts:AllergyAnimalNOS" + }, + { + "@id": "bts:AllergyAnt" + }, + { + "@id": "bts:AllergyBee" + }, + { + "@id": "bts:AllergyCat" + }, + { + "@id": "bts:AllergyDairyorLactose" + }, + { + "@id": "bts:AllergyDog" + }, + { + "@id": "bts:AllergyEggs" + }, + { + "@id": "bts:AllergyFoodNOS" + }, + { + "@id": "bts:AllergyFruit" + }, + { + "@id": "bts:AllergyMeat" + }, + { + "@id": "bts:AllergyMoldorDust" + }, + { + "@id": "bts:AllergyNuts" + }, + { + "@id": "bts:AllergyProcessedFoods" + }, + { + "@id": "bts:AllergySeafood" + }, + { + "@id": "bts:AllergyWasp" + }, + { + "@id": "bts:Alpha-1AntitrypsinDeficiency" + }, + { + "@id": "bts:AutoimmuneAtrophicChronicGastritis" + }, + { + "@id": "bts:Barrett'sEsophagus" + }, + { + "@id": "bts:Beckwith-Wiedemann" + }, + { + "@id": "bts:Behcet'sDisease" + }, + { + "@id": "bts:Cancer" + }, + { + "@id": "bts:Cholelithiasis" + }, + { + "@id": "bts:ChronicHepatitis" + }, + { + "@id": "bts:Cirrhosis" + }, + { + "@id": "bts:ColonPolyps" + }, + { + "@id": "bts:Commonvariableimmunedeficiency(CVID)" + }, + { + "@id": "bts:Denys-DrashSyndrome" + }, + { + "@id": "bts:DiabetesNOS" + }, + { + "@id": "bts:DiabetesTypeI" + }, + { + "@id": "bts:DiabetesTypeII" + }, + { + "@id": "bts:Diet" + }, + { + "@id": "bts:Diverticulitis" + }, + { + "@id": "bts:Endometriosis" + }, + { + "@id": "bts:Endosalpingiosis" + }, + { + "@id": "bts:Eczema" + }, + { + "@id": "bts:Epstein-BarrVirus" + }, + { + "@id": "bts:FamilialAdenomatousPolyposis" + }, + { + "@id": "bts:FanconiAnemia" + }, + { + "@id": "bts:Fibrosis" + }, + { + "@id": "bts:GastricPolyp(s)" + }, + { + "@id": "bts:Gilbert'sSyndrome" + }, + { + "@id": "bts:GorlinSyndrome" + }, + { + "@id": "bts:Hashimoto'sThyroiditis" + }, + { + "@id": "bts:HayFever" + }, + { + "@id": "bts:Headache" + }, + { + "@id": "bts:HelicobacterPylori-AssociatedGastritis" + }, + { + "@id": "bts:HematologicDisorderNOS" + }, + { + "@id": "bts:Hemihypertrophy" + }, + { + "@id": "bts:Hemochromatosis" + }, + { + "@id": "bts:HepaticEncephalopathy" + }, + { + "@id": "bts:HepatitisBInfection" + }, + { + "@id": "bts:HepatitisCInfection" + }, + { + "@id": "bts:HepatitisNOS" + }, + { + "@id": "bts:HighGradeDysplasia" + }, + { + "@id": "bts:HIV" + }, + { + "@id": "bts:HumanPapillomavirusInfection" + }, + { + "@id": "bts:Hypospadias" + }, + { + "@id": "bts:IntestinalMetaplasia" + }, + { + "@id": "bts:IronOverload" + }, + { + "@id": "bts:Li-FraumeniSyndrome" + }, + { + "@id": "bts:LowGradeDysplasia" + }, + { + "@id": "bts:LymphocyticThyroiditis" + }, + { + "@id": "bts:LynchSyndrome" + }, + { + "@id": "bts:MyastheniaGravis" + }, + { + "@id": "bts:NonalcoholicFattyLiverDisease" + }, + { + "@id": "bts:NonalcoholicSteatohepatitis" + }, + { + "@id": "bts:Obesity" + }, + { + "@id": "bts:OralContraceptives" + }, + { + "@id": "bts:Pancreatitis" + }, + { + "@id": "bts:ParasiticDiseaseofBiliaryTract" + }, + { + "@id": "bts:PrimarySclerosingCholangitis" + }, + { + "@id": "bts:RecurrentPyogenicCholangitis" + }, + { + "@id": "bts:RefluxDisease" + }, + { + "@id": "bts:RheumatoidArthritis" + }, + { + "@id": "bts:Rubinstein-TaybiSyndrome" + }, + { + "@id": "bts:Sarcoidosis" + }, + { + "@id": "bts:Seizure" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + }, + { + "@id": "bts:Steatosis" + }, + { + "@id": "bts:Tattoo" + }, + { + "@id": "bts:ThyroidNodularHyperplasia" + }, + { + "@id": "bts:TobaccoNOS" + }, + { + "@id": "bts:TobaccoSmokeless" + }, + { + "@id": "bts:TobaccoSmoking" + }, + { + "@id": "bts:TurcotSyndrome" + }, + { + "@id": "bts:UndescendedTestis" + }, + { + "@id": "bts:VisionChanges" + }, + { + "@id": "bts:WagrSyndrome" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Risk Factor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RiskFactorTreatment", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactorTreatment", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Risk Factor Treatment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ViralHepatitisSerologies", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", + "rdfs:label": "ViralHepatitisSerologies", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:HBVCoreAntibody" + }, + { + "@id": "bts:HBVDNA" + }, + { + "@id": "bts:HBVGenotype" + }, + { + "@id": "bts:HBVSurfaceAntibody" + }, + { + "@id": "bts:HCVGenotype" + }, + { + "@id": "bts:HepatitisBSurfaceAntigen" + }, + { + "@id": "bts:HepatitisCAntibody" + }, + { + "@id": "bts:HepatitisCVirusRNA" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Viral Hepatitis Serologies", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Weight", + "@type": "rdfs:Class", + "rdfs:comment": "The weight of the patient measured in kilograms.", + 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text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", + "rdfs:label": "AIDSRiskFactors", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Candidiasis" + }, + { + "@id": "bts:Coccidioidomycosis" + }, + { + "@id": "bts:Cryptococcosis" + }, + { + "@id": "bts:Cytomegalovirus" + }, + { + "@id": "bts:Encephalopathy" + }, + { + "@id": "bts:HerpesSimplexVirus" + }, + { + "@id": "bts:Histoplasmosis" + }, + { + "@id": "bts:Isosporiasis" + }, + { + "@id": "bts:MycobacteriumaviumComplex" + }, + { + "@id": "bts:Mycobacteriumtuberculosis" + }, + { + "@id": "bts:Mycobacterium" + }, + { + "@id": "bts:NOS" + }, + { + "@id": "bts:Nocardiosis" + }, + { + "@id": "bts:PneumocystisPneumonia" + }, + { + "@id": "bts:Pneumonia" + }, + { + "@id": 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"@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CD4 Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CDCHIVRiskFactors", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", + "rdfs:label": "CDCHIVRiskFactors", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Hemophiliac" + }, + { + "@id": "bts:HeterosexualContact" + }, + { + "@id": "bts:HomosexualContact" + }, + { + "@id": "bts:IntravenousDrugUser" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:TransfusionRecipient" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "CDC HIV Risk Factors", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoImaging", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoImaging", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Imaging", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:EvidenceofRecurrenceType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", + "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:BiopsywithHistologicConfirmation" + }, + { + "@id": "bts:ConvincingImageSource" + }, + { + "@id": "bts:PositiveBiomarkers" + } + ], + "sms:displayName": "Evidence of Recurrence Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HAARTTreatmentIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", + "rdfs:label": "HAARTTreatmentIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HAART Treatment Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HIVViralLoad", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", + "rdfs:label": "HIVViralLoad", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HIV Viral Load", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HormonalContraceptiveUse", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", + "rdfs:label": "HormonalContraceptiveUse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CurrentUser" + }, + { + "@id": "bts:FormerUser" + }, + { + "@id": "bts:NeverUsed" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Hormonal Contraceptive Use", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HysterectomyMarginsInvolved", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", + "rdfs:label": "HysterectomyMarginsInvolved", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Bladder" + }, + { + "@id": "bts:MacroscopicParametrium" + }, + { + "@id": "bts:MicroscopicParametrium" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Vagina" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Hysterectomy Margins Involved", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HysterectomyType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", + "rdfs:label": "HysterectomyType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:HysterectomyNOS" + }, + { + "@id": "bts:Notperformed" + }, + { + "@id": "bts:RadicalHysterectomy" + }, + { + "@id": "bts:SimpleHysterectomy" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Hysterectomy Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingResult", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", + "rdfs:label": "ImagingResult", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Negative" + }, + { + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Imaging Result", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", + "rdfs:label": "ImagingType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:99mTcBoneScintigraphy" + }, + { + "@id": "bts:CTScan" + }, + { + "@id": "bts:MRI" + }, + { + "@id": "bts:PET" + } + ], + "sms:displayName": "Imaging Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmunosuppressiveTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of immunosuppresive treatment the patient received.", + "rdfs:label": "ImmunosuppressiveTreatmentType", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Anti-TNFTherapy" + }, + { + "@id": "bts:Azathioprine" + }, + { + "@id": "bts:Cyclophosphamide" + }, + { + "@id": "bts:Methotrexate" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Immunosuppressive Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NadirCD4Count", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).", + "rdfs:label": "NadirCD4Count", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nadir CD4 Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnancyOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of pregnancy the patient had", + "rdfs:label": "PregnancyOutcome", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:EctopicPregnancy" + }, + { + "@id": "bts:InducedAbortion" + }, + { + "@id": "bts:LiveBirth" + }, + { + "@id": "bts:Miscarriage" + }, + { + "@id": "bts:Stillbirth" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pregnancy Outcome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RecistTargetedRegionsNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria", + "rdfs:label": "RecistTargetedRegionsNumber", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Recist Targeted Regions Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RecistTargetedRegionsSum", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.", + "rdfs:label": "RecistTargetedRegionsSum", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Recist Targeted Regions Sum", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScanTracerUsed", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of tracer used during the imaging or scan of the patient.", + "rdfs:label": "ScanTracerUsed", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Acetate" + }, + { + "@id": "bts:Axumin" + }, + { + "@id": "bts:Choline" + }, + { + "@id": "bts:PSMA" + }, + { + "@id": "bts:SodiumFluoride" + } + ], + "sms:displayName": "Scan Tracer Used", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentorTherapy", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.", + "rdfs:label": "TreatmentorTherapy", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment or Therapy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentEffect", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the pathologic effect a treatment(s) had on the tumor.", + "rdfs:label": "TreatmentEffect", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CompleteNecrosis(NoViableTumor)" + }, + { + "@id": "bts:IncompleteNecrosis(ViableTumorPresent)" + }, + { + "@id": "bts:NoNecrosis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Effect", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the patient's final outcome after the treatment was administered.", + "rdfs:label": "TreatmentOutcome", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CompleteResponse" + }, + { + "@id": "bts:MixedResponse" + }, + { + "@id": "bts:NoMeasurableDisease" + }, + { + "@id": "bts:NoResponse" + }, + { + "@id": "bts:PartialResponse" + }, + { + "@id": "bts:PersistentDisease" + }, + { + "@id": "bts:ProgressiveDisease" + }, + { + "@id": "bts:StableDisease" + }, + { + "@id": "bts:TreatmentOngoing" + }, + { + "@id": "bts:TreatmentStoppedDuetoToxicity" + }, + { + "@id": "bts:VeryGoodPartialResponse" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Treatment Outcome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoTreatmentEnd", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentEnd", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Treatment End", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:TreatmentAnatomicSite", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment", + "rdfs:label": "TreatmentAnatomicSite", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbdomenNOS" + }, + { + "@id": "bts:Abdominalesophagus" + }, + { + "@id": "bts:AccessorysinusNOS" + }, + { + "@id": "bts:Acousticnerve" + }, + { + "@id": "bts:AdrenalglandNOS" + }, + { + "@id": "bts:AmpullaofVater" + }, + { + "@id": "bts:Analcanal" + }, + { + "@id": "bts:Anterior2/3oftongueNOS" + }, + { + "@id": "bts:Anteriorfloorofmouth" + }, + { + "@id": "bts:Anteriormediastinum" + }, + { + "@id": "bts:Anteriorsurfaceofepiglottis" + }, + { + "@id": "bts:Anteriorwallofbladder" + }, + { + "@id": "bts:Anteriorwallofnasopharynx" + }, + { + "@id": "bts:AnusNOS" + }, + { + "@id": "bts:Aorticbodyandotherparaganglia" + }, + { + "@id": "bts:Appendix" + }, + { + "@id": "bts:Ascendingcolon" + }, + { + "@id": "bts:AutonomicnervoussystemNOS" + }, + { + "@id": "bts:Axillarytailofbreast" + }, + { + "@id": "bts:BaseoftongueNOS" + }, + { + "@id": "bts:Bladderneck" + }, + { + "@id": "bts:BladderNOS" + }, + { + "@id": "bts:Blood" + }, + { + "@id": "bts:Bodyofpancreas" + }, + { + "@id": "bts:Bodyofpenis" + }, + { + "@id": "bts:Bodyofstomach" + }, + { + "@id": "bts:Bonemarrow" + }, + { + "@id": "bts:BoneoflimbNOS" + }, + { + "@id": "bts:BoneNOS" + }, + { + "@id": "bts:Bonesofskullandfaceandassociatedjoints" + }, + { + "@id": "bts:Borderoftongue" + }, + { + "@id": "bts:Brainstem" + }, + { + "@id": "bts:BrainNOS" + }, + { + "@id": "bts:Branchialcleft" + }, + { + "@id": "bts:BreastNOS" + }, + { + "@id": "bts:Broadligament" + }, + { + "@id": "bts:CardiaNOS" + }, + { + "@id": "bts:Carotidbody" + }, + { + "@id": "bts:Caudaequina" + }, + { + "@id": "bts:Cecum" + }, + { + "@id": "bts:Centralportionofbreast" + }, + { + "@id": "bts:CerebellumNOS" + }, + { + "@id": "bts:Cerebralmeninges" + }, + { + "@id": "bts:Cerebrum" + }, + { + "@id": "bts:Cervicalesophagus" + }, + { + "@id": "bts:Cervixuteri" + }, + { + "@id": "bts:Choroid" + }, + { + "@id": "bts:Ciliarybody" + }, + { + "@id": "bts:Cloacogeniczone" + }, + { + "@id": "bts:ColonNOS" + }, + { + "@id": "bts:Commissureoflip" + }, + { + "@id": "bts:Conjunctiva" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + }, + { + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + }, + { + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + }, + { + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + }, + { + "@id": "bts:CorneaNOS" + }, + { + "@id": "bts:Corpusuteri" + }, + { + "@id": "bts:Cortexofadrenalgland" + }, + { + "@id": "bts:CranialnerveNOS" + }, + { + "@id": "bts:Craniopharyngealduct" + }, + { + "@id": "bts:Descendedtestis" + }, + { + "@id": "bts:Descendingcolon" + }, + { + "@id": "bts:Domeofbladder" + }, + { + "@id": "bts:DorsalsurfaceoftongueNOS" + }, + { + "@id": "bts:Duodenum" + }, + { + "@id": "bts:Endocervix" + }, + { + "@id": "bts:EndocrineglandNOS" + }, + { + "@id": "bts:Endometrium" + }, + { + "@id": "bts:Epididymis" + }, + { + "@id": "bts:EsophagusNOS" + }, + { + "@id": "bts:Ethmoidsinus" + }, + { + "@id": "bts:Exocervix" + }, + { + "@id": "bts:Externalear" + }, + { + "@id": "bts:ExternallipNOS" + }, + { + "@id": "bts:Externallowerlip" + }, + { + "@id": "bts:Externalupperlip" + }, + { + "@id": "bts:Extrahepaticbileduct" + }, + { + "@id": "bts:EyeNOS" + }, + { + "@id": "bts:Eyelid" + }, + { + "@id": "bts:Fallopiantube" + }, + { + "@id": "bts:FemalegenitaltractNOS" + }, + { + "@id": "bts:FloorofmouthNOS" + }, + { + "@id": "bts:Frontallobe" + }, + { + "@id": "bts:Frontalsinus" + }, + { + "@id": "bts:Fundusofstomach" + }, + { + "@id": "bts:Fundusuteri" + }, + { + "@id": "bts:Gallbladder" + }, + { + "@id": "bts:Gastricantrum" + }, + { + "@id": "bts:GastrointestinaltractNOS" + }, + { + "@id": "bts:Glanspenis" + }, + { + "@id": "bts:Glottis" + }, + { + "@id": "bts:GreatercurvatureofstomachNOS" + }, + { + "@id": "bts:GumNOS" + }, + { + "@id": "bts:Hardpalate" + }, + { + "@id": "bts:Headofpancreas" + }, + { + "@id": "bts:HeadfaceorneckNOS" + }, + { + "@id": "bts:Heart" + }, + { + "@id": "bts:HematopoieticsystemNOS" + }, + { + "@id": "bts:Hepaticflexureofcolon" + }, + { + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + }, + { + "@id": "bts:HypopharynxNOS" + }, + { + "@id": "bts:Ileum" + }, + { + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + }, + { + "@id": "bts:IntestinaltractNOS" + }, + { + "@id": "bts:Intra-abdominallymphnodes" + }, + { + "@id": "bts:Intrahepaticbileduct" + }, + { + "@id": "bts:Intrathoraciclymphnodes" + }, + { + "@id": "bts:IsletsofLangerhans" + }, + { + "@id": "bts:Isthmusuteri" + }, + { + "@id": "bts:Jejunum" + }, + { + "@id": "bts:KidneyNOS" + }, + { + "@id": "bts:Labiummajus" + }, + { + "@id": "bts:Labiumminus" + }, + { + "@id": "bts:Lacrimalgland" + }, + { + "@id": "bts:Laryngealcartilage" + }, + { + "@id": "bts:LarynxNOS" + }, + { + "@id": "bts:Lateralfloorofmouth" + }, + { + "@id": "bts:Lateralwallofbladder" + }, + { + "@id": "bts:Lateralwallofnasopharynx" + }, + { + "@id": "bts:Lateralwalloforopharynx" + }, + { + "@id": "bts:LessercurvatureofstomachNOS" + }, + { + "@id": "bts:Lingualtonsil" + }, + { + "@id": "bts:LipNOS" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + }, + { + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + }, + { + "@id": "bts:Lowergum" + }, + { + "@id": "bts:LowerlimbNOS" + }, + { + "@id": "bts:Lowerlobelung" + }, + { + "@id": "bts:Lowerthirdofesophagus" + }, + { + "@id": "bts:Lower-innerquadrantofbreast" + }, + { + "@id": "bts:Lower-outerquadrantofbreast" + }, + { + "@id": "bts:LungNOS" + }, + { + "@id": "bts:LymphnodeNOS" + }, + { + "@id": "bts:Lymphnodesofaxillaorarm" + }, + { + "@id": "bts:Lymphnodesofheadfaceandneck" + }, + { + "@id": "bts:Lymphnodesofinguinalregionorleg" + }, + { + "@id": "bts:Lymphnodesofmultipleregions" + }, + { + "@id": "bts:Mainbronchus" + }, + { + "@id": "bts:MajorsalivaryglandNOS" + }, + { + "@id": "bts:MalegenitalorgansNOS" + }, + { + "@id": "bts:Mandible" + }, + { + "@id": "bts:Maxillarysinus" + }, + { + "@id": "bts:Meckeldiverticulum" + }, + { + "@id": "bts:MediastinumNOS" + }, + { + "@id": "bts:Medullaofadrenalgland" + }, + { + "@id": "bts:MeningesNOS" + }, + { + "@id": "bts:Middleear" + }, + { + "@id": "bts:Middlelobelung" + }, + { + "@id": "bts:Middlethirdofesophagus" + }, + { + "@id": "bts:MouthNOS" + }, + { + "@id": "bts:MucosaoflipNOS" + }, + { + "@id": "bts:Mucosaoflowerlip" + }, + { + "@id": "bts:Mucosaofupperlip" + }, + { + "@id": "bts:Myometrium" + }, + { + "@id": "bts:Nasalcavity" + }, + { + "@id": "bts:NasopharynxNOS" + }, + { + "@id": "bts:NervoussystemNOS" + }, + { + "@id": "bts:Nipple" + }, + { + "@id": "bts:Occipitallobe" + }, + { + "@id": "bts:Olfactorynerve" + }, + { + "@id": "bts:Opticnerve" + }, + { + "@id": "bts:OrbitNOS" + }, + { + "@id": "bts:OropharynxNOS" + }, + { + "@id": "bts:Otherill-definedsites" + }, + { + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + }, + { + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" + }, + { + "@id": "bts:Otherspecifiedpartsofpancreas" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Overlappinglesionofaccessorysinuses" + }, + { + "@id": "bts:Overlappinglesionofbladder" + }, + { + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + }, + { + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + }, + { + "@id": "bts:Overlappinglesionofbrain" + }, + { + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" + }, + { + "@id": "bts:Overlappinglesionofbreast" + }, + { + "@id": "bts:Overlappinglesionofcervixuteri" + }, + { + "@id": "bts:Overlappinglesionofcolon" + }, + { + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + }, + { + "@id": "bts:Overlappinglesionofcorpusuteri" + }, + { + "@id": "bts:Overlappinglesionofdigestivesystem" + }, + { + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + }, + { + "@id": "bts:Overlappinglesionofesophagus" + }, + { + "@id": "bts:Overlappinglesionofeyeandadnexa" + }, + { + "@id": "bts:Overlappinglesionoffemalegenitalorgans" + }, + { + "@id": "bts:Overlappinglesionoffloorofmouth" + }, + { + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + }, + { + "@id": "bts:Overlappinglesionofhypopharynx" + }, + { + "@id": "bts:Overlappinglesionofill-definedsites" + }, + { + "@id": "bts:Overlappinglesionoflarynx" + }, + { + "@id": "bts:Overlappinglesionoflip" + }, + { + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + }, + { + "@id": "bts:Overlappinglesionoflung" + }, + { + "@id": "bts:Overlappinglesionofmajorsalivaryglands" + }, + { + "@id": "bts:Overlappinglesionofmalegenitalorgans" + }, + { + "@id": "bts:Overlappinglesionofnasopharynx" + }, + { + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + }, + { + "@id": "bts:Overlappinglesionofpalate" 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}, + { + "@id": "bts:Tailofpancreas" + }, + { + "@id": "bts:Temporallobe" + }, + { + "@id": "bts:TestisNOS" + }, + { + "@id": "bts:Thoracicesophagus" + }, + { + "@id": "bts:ThoraxNOS" + }, + { + "@id": "bts:Thymus" + }, + { + "@id": "bts:Thyroidgland" + }, + { + "@id": "bts:TongueNOS" + }, + { + "@id": "bts:TonsilNOS" + }, + { + "@id": "bts:Tonsillarfossa" + }, + { + "@id": "bts:Tonsillarpillar" + }, + { + "@id": "bts:Trachea" + }, + { + "@id": "bts:Transversecolon" + }, + { + "@id": "bts:Trigoneofbladder" + }, + { + "@id": "bts:Undescendedtestis" + }, + { + "@id": "bts:Unknownprimarysite" + }, + { + "@id": "bts:Uppergum" + }, + { + "@id": "bts:UpperlimbNOS" + }, + { + "@id": "bts:Upperlobelung" + }, + { + "@id": "bts:UpperrespiratorytractNOS" + }, + { + "@id": "bts:Upperthirdofesophagus" + }, + { + "@id": "bts:Upper-innerquadrantofbreast" + }, + { + "@id": "bts:Upper-outerquadrantofbreast" + }, + { + "@id": "bts:Urachus" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentStart", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Treatment Start", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:InitialDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", + "rdfs:label": "InitialDiseaseStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:InitialDiagnosis" + }, + { + "@id": "bts:ProgressiveDisease" + }, + { + "@id": "bts:RecurrentDisease" + }, + { + "@id": "bts:ResidualDisease" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Initial Disease Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RegimenorLineofTherapy", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the regimen or line of therapy.", + "rdfs:label": "RegimenorLineofTherapy", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Regimen or Line of Therapy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TherapeuticAgents", + "@type": "rdfs:Class", + "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", + "rdfs:label": "TherapeuticAgents", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Therapeutic Agents", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentIntentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. 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cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", + "rdfs:label": "PrecancerousConditionType", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DuctalCarcinomaInSitu" + }, + { + "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" + }, + { + "@id": "bts:AtypicalAdenomatousLungHyperplasia" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:PancreaticIntraepithelialNeoplasia" + }, + { + "@id": "bts:ProstaticIntraepithelialNeoplasia" + }, + { + "@id": "bts:Melanocytichyperplasia" + }, + { + "@id": "bts:Atypicalmelanocyticproliferation" + }, + { + "@id": "bts:Melanomainsitu" + }, + { + "@id": "bts:Superficialspreading" + }, + { + "@id": "bts:Lentigomalignatype" + }, + { + "@id": "bts:Acral-lentiginous" + }, + { + "@id": 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"bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Treatment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MetastasisatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", + "rdfs:label": "MetastasisatDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DistantMetastasis" + }, + { + "@id": "bts:MetastasisNOS" + }, + { + "@id": "bts:NoMetastasis" + }, + { + "@id": "bts:RegionalMetastasis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Metastasis at Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MetastasisatDiagnosisSite", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", + "rdfs:label": "MetastasisatDiagnosisSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Abdomen" + }, + { + "@id": "bts:AdrenalGland" + }, + { + "@id": "bts:Ascites" + }, + { + "@id": "bts:Bone" + }, + { + "@id": "bts:BoneMarrow" + }, + { + "@id": "bts:Brain" + }, + { + "@id": "bts:CerebrospinalFluid" + }, + { + "@id": "bts:CentralNervousSystem" + }, + { + "@id": "bts:Colon" + }, + { + "@id": "bts:DistantNodes" + }, + { + "@id": "bts:DistantOrgan" + }, + { + "@id": "bts:Groin" + }, + { + "@id": "bts:Kidney" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:Lung" + }, + { + "@id": "bts:LymphNode" + }, + { + "@id": "bts:Axillary" + }, + { + "@id": "bts:Inguinal" + }, + { + "@id": "bts:LymphNodeNOS" + }, + { + "@id": "bts:Mediastinum" + }, + { + "@id": "bts:Omentum" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": 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"bts:MotororMovementChanges" + }, + { + "@id": "bts:Seizures" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:VisualChanges" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "First Symptom Prior to Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DaystoDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:PercentTumorInvasion", + "@type": "rdfs:Class", + "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", + "rdfs:label": "PercentTumorInvasion", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Percent Tumor Invasion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ResidualDisease", + "@type": "rdfs:Class", + "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", + "rdfs:label": "ResidualDisease", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:InitialDiseaseStatus" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:R0" + }, + { + "@id": "bts:R1" + }, + { + "@id": "bts:R2" + }, + { + "@id": "bts:RX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Residual Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SynchronousMalignancy", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", + "rdfs:label": "SynchronousMalignancy", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Synchronous Malignancy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorConfinedtoOrganofOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", + "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Confined to Organ of Origin", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorFocality", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", + "rdfs:label": "TumorFocality", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Multifocal" + }, + { + "@id": "bts:Unifocal" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Focality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GrossTumorWeight", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", + "rdfs:label": "GrossTumorWeight", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gross Tumor Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreslowThickness", + "@type": "rdfs:Class", + "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", + "rdfs:label": "BreslowThickness", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breslow Thickness", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", + "rdfs:label": "VascularInvasionPresent", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-VascularInvasionPresent" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Vascular Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", + "rdfs:label": "VascularInvasionType", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Extramural" + }, + { + "@id": "bts:Intramural" + }, + { + "@id": "bts:Macro" + }, + { + "@id": "bts:Micro" + }, + { + "@id": "bts:NoVascularInvasion" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Vascular Invasion Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AnaplasiaPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", + "rdfs:label": "AnaplasiaPresent", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AnaplasiaPresent" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AnaplasiaPresentType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", + "rdfs:label": "AnaplasiaPresentType", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Diffuse" + }, + { + "@id": "bts:Equivocal" + }, + { + "@id": "bts:Focal" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Sclerosis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Laterality", + "@type": "rdfs:Class", + "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", + "rdfs:label": "Laterality", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Bilateral" + }, + { + "@id": "bts:Left" + }, + { + "@id": "bts:Midline" + }, + { + "@id": "bts:Right" + }, + { + "@id": "bts:Unilateral" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laterality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerineuralInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", + "rdfs:label": "PerineuralInvasionPresent", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Perineural Invasion Present", + 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+ "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lymph Nodes Positive", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LymphNodesTested", + "@type": "rdfs:Class", + "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", + "rdfs:label": "LymphNodesTested", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lymph Nodes Tested", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PeritonealFluidCytologicalStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", + "rdfs:label": "PeritonealFluidCytologicalStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": 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Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "GleasonGradeGroup", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Group1" + }, + { + "@id": "bts:Group2" + }, + { + "@id": "bts:Group3" + }, + { + "@id": "bts:Group4" + }, + { + "@id": "bts:Group5" + } + ], + "sms:displayName": "Gleason Grade Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GleasonGradeTertiary", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", + "rdfs:label": "GleasonGradeTertiary", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Gleason Grade Tertiary", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GleasonPatternsPercent", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", + "rdfs:label": "GleasonPatternsPercent", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gleason Patterns Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GreatestTumorDimension", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", + "rdfs:label": "GreatestTumorDimension", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Greatest Tumor Dimension", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:IGCCCGStage", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", + "rdfs:label": "IGCCCGStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GoodPrognosis" + }, + { + "@id": "bts:IntermediatePrognosis" + }, + { + "@id": "bts:PoorPrognosis" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "IGCCCG Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INPCGrade", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", + "rdfs:label": "INPCGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Differentiating" + }, + { + "@id": "bts:PoorlyDifferentiated" + }, + { + "@id": "bts:Undifferentiated" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INPCHistologicGroup", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", + "rdfs:label": "INPCHistologicGroup", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Favorable" + }, + { + "@id": "bts:Unfavorable" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Histologic Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INRGStage", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", + "rdfs:label": "INRGStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:L1" + }, + { + "@id": "bts:L2" + }, + { + "@id": "bts:M" + }, + { + "@id": "bts:Ms" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INRG Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INSSStage", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", + "rdfs:label": "INSSStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Stage1" + }, + { + "@id": "bts:Stage2A" + }, + { + "@id": "bts:Stage2B" + }, + { + "@id": "bts:Stage3" + }, + { + "@id": "bts:Stage4" + }, + { + "@id": "bts:Stage4S" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + 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Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSGroup", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GroupI" + }, + { + "@id": "bts:GroupIa" + }, + { + "@id": "bts:GroupIb" + }, + { + "@id": "bts:GroupII" + }, + { + "@id": "bts:GroupIIa" + }, + { + "@id": "bts:GroupIIc" + }, + { + "@id": "bts:GroupIII" + }, + { + "@id": "bts:GroupIIIa" + }, + { + "@id": "bts:GroupIIIb" + }, + { + "@id": "bts:GroupIV" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "IRS Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:IRSStage", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:1" + }, + { + "@id": "bts:2" + }, + { + "@id": "bts:3" + }, + { + "@id": "bts:4" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "IRS Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ISSStage", + "@type": "rdfs:Class", + "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", + "rdfs:label": "ISSStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:I" + }, + { + "@id": "bts:II" + }, + { + "@id": "bts:III" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "ISS Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LymphNodeInvolvedSite", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", + "rdfs:label": "LymphNodeInvolvedSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Axillary" + }, + { + "@id": "bts:Cervical" + }, + { + "@id": "bts:Epitrochlear" + }, + { + "@id": "bts:Femoral" + }, + { + "@id": "bts:Hilar" + }, + { + "@id": "bts:Iliac-common" + }, + { + "@id": "bts:Iliac-external" + }, + { + "@id": "bts:Iliac" + }, + { + "@id": "bts:NOS" + }, + { + "@id": "bts:Inguinal" + }, + { + "@id": "bts:Mediastinal" + }, + { + "@id": "bts:Mesenteric" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Occipital" + }, + { + "@id": "bts:Paraaortic" + }, + { + "@id": "bts:Parotid" + }, + { + "@id": "bts:Popliteal" + }, + { + "@id": "bts:Retroperitoneal" + }, + { + "@id": "bts:Splenic" + }, + { + "@id": "bts:Submandibular" + }, + { + "@id": "bts:Supraclavicular" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lymph Node Involved Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MarginDistance", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", + "rdfs:label": "MarginDistance", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Margin Distance", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MarginsInvolvedSite", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", + "rdfs:label": "MarginsInvolvedSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GerotaFascia" + }, + { + "@id": "bts:Parenchyma" + }, + { + "@id": "bts:PerinephricFat" + }, + { + "@id": "bts:Renal" + }, + { + "@id": "bts:RenalCapsule" + }, + { + "@id": "bts:RenalSinus" + }, + { + "@id": "bts:RenalVein" + }, + { + "@id": "bts:Ureter" + } + ], + "sms:displayName": "Margins Involved Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedulloblastomaMolecularClassification", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", + "rdfs:label": "MedulloblastomaMolecularClassification", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:NotDetermined" + }, + { + "@id": "bts:Non-WNT/non-SHHActivated" + }, + { + "@id": "bts:SHH-Activated" + }, + { + "@id": "bts:WNT-Activated" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Medulloblastoma Molecular Classification", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MicropapillaryFeatures", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", + "rdfs:label": "MicropapillaryFeatures", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Micropapillary Features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MitosisKaryorrhexisIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", + "rdfs:label": "MitosisKaryorrhexisIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:High" + }, + { + "@id": "bts:Intermediate" + }, + { + "@id": "bts:Low" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mitosis Karyorrhexis Index", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NonNodalRegionalDisease", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", + "rdfs:label": "NonNodalRegionalDisease", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Regional Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NonNodalTumorDeposits", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", + "rdfs:label": "NonNodalTumorDeposits", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Tumor Deposits", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianSpecimenStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", + "rdfs:label": "OvarianSpecimenStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:OvarianCapsuleIntact" + }, + { + "@id": "bts:OvarianCapsuleRuptured" + }, + { + "@id": "bts:OvarianCapsuleFragmented" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ovarian Specimen Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianSurfaceInvolvement", + "@type": "rdfs:Class", + "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", + "rdfs:label": "OvarianSurfaceInvolvement", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ovarian Surface Involvement", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PregnantatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", + "rdfs:label": "PregnantatDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pregnant at Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryGleasonGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "PrimaryGleasonGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Pattern1" + }, + { + "@id": "bts:Pattern2" + }, + { + "@id": "bts:Pattern3" + }, + { + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Primary Gleason Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondaryGleasonGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "SecondaryGleasonGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Pattern1" + }, + { + "@id": "bts:Pattern2" + }, + { + "@id": "bts:Pattern3" + }, + { + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Secondary Gleason Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SupratentorialLocalization", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", + "rdfs:label": "SupratentorialLocalization", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CerebralCortex" + }, + { + "@id": "bts:DeepGray" + }, + { + "@id": "bts:SpinalCord" + }, + { + "@id": "bts:WhiteMatter" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Supratentorial Localization", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorDepth", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", + "rdfs:label": "TumorDepth", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tumor Depth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHOCNSGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO CNS Grade", + "rdfs:label": "WHOCNSGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GradeI" + }, + { + "@id": "bts:GradeII" + }, + { + "@id": "bts:GradeIII" + }, + { + "@id": "bts:GradeIV" + }, + { + "@id": "bts:GradeNotAssigned" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO CNS Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:WHONTEGrade", + "@type": "rdfs:Class", + "rdfs:comment": "WHO NTE Grade", + "rdfs:label": "WHONTEGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:G1" + }, + { + "@id": "bts:G2" + }, + { + "@id": "bts:G3" + }, + { + "@id": "bts:GX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO NTE Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AAChange", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "AAChange", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "AA Change", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Antigen", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Antigen", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:BCL6" + }, + { + "@id": "bts:CA-125" + }, + { + "@id": "bts:CA19-9" + }, + { + "@id": "bts:CCND1" + }, + { + "@id": "bts:CD10" + }, + { + "@id": "bts:CD117" + }, + { + "@id": "bts:CD138" + }, + { + "@id": "bts:CD14" + }, + { + "@id": "bts:CD15" + }, + { + "@id": "bts:CD19" + }, + { + "@id": "bts:CD20" + }, + { + "@id": "bts:CD22" + }, + { + "@id": "bts:CD23" + }, + { + "@id": "bts:CD25" + }, + { + "@id": "bts:CD3" + }, + { + "@id": "bts:CD30" + }, + { + "@id": "bts:CD33" + }, + { + "@id": "bts:CD34" + }, + { + "@id": "bts:CD45" + }, + { + "@id": "bts:CD5" + }, + { + "@id": "bts:CD56" + }, + { + "@id": "bts:CD7" + }, + { + "@id": "bts:CD79A" + }, + { + "@id": "bts:CEA" + }, + { + "@id": "bts:HLA-DR" + }, + { + "@id": "bts:Mesothelin" + }, + { + "@id": "bts:NSE" + }, + { + "@id": "bts:SquamousCellCarcinomaAntigen" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Antigen", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalBiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "ClinicalBiospecimenType", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Blood" + }, + { + "@id": "bts:BoneMarrow" + }, + { + "@id": "bts:BuccalMucosa" + }, + { + "@id": "bts:BuffyCoat" + }, + { + "@id": "bts:CerebrospinalFluid" + }, + { + "@id": "bts:ConnectiveTissue" + }, + { + "@id": "bts:EmbryonicFluid" + }, + { + "@id": "bts:EmbryonicTissue" + }, + { + "@id": "bts:Feces" + }, + { + "@id": "bts:Granulocyte" + }, + { + "@id": "bts:MuscleTissue" + }, + { + "@id": "bts:NerveTissue" + }, + { + "@id": "bts:PeritonealFluid" + }, + { + "@id": "bts:Plasma" + }, + { + "@id": "bts:PleuralFluid" + }, + { + "@id": "bts:Saliva" + }, + { + "@id": "bts:Serum" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:TissueNOS" + }, + { + "@id": "bts:UninvolvedTissueNOS" + }, + { + "@id": "bts:Urine" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Clinical Biospecimen Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeUpper", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeUpper", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Upper", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeLower", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Lower", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CellCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CellCount", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Chromosome", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Chromosome", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Chr1" + }, + { + "@id": "bts:Chr2" + }, + { + "@id": "bts:Chr3" + }, + { + "@id": "bts:Chr4" + }, + { + "@id": "bts:Chr5" + }, + { + "@id": "bts:Chr6" + }, + { + "@id": "bts:Chr7" + }, + { + "@id": "bts:Chr8" + }, + { + "@id": "bts:Chr9" + }, + { + "@id": "bts:Chr10" + }, + { + "@id": "bts:Chr11" + }, + { + "@id": "bts:Chr12" + }, + { + "@id": "bts:Chr13" + }, + { + "@id": "bts:Chr14" + }, + { + "@id": "bts:Chr15" + }, + { + "@id": "bts:Chr16" + }, + { + "@id": "bts:Chr17" + }, + { + "@id": "bts:Chr18" + }, + { + "@id": "bts:Chr19" + }, + { + "@id": "bts:Chr20" + }, + { + "@id": "bts:Chr21" + }, + { + "@id": "bts:Chr22" + }, + { + "@id": "bts:Chr23" + }, + { + "@id": "bts:ChrM" + }, + { + "@id": "bts:ChrX" + }, + { + "@id": "bts:ChrY" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Chromosome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Clonality", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Clonality", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Clonal" + }, + { + "@id": "bts:Non-clonal" + } + ], + "sms:displayName": "Clonality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CopyNumber", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Copy Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cytoband", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Cytoband", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cytoband", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Exon", + "@type": "rdfs:Class", + "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Exon", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneFamily", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "rdfs:label": "HistoneFamily", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:H1" + }, + { + "@id": "bts:H2A" + }, + { + "@id": "bts:H2B" + }, + { + "@id": "bts:H3" + }, + { + "@id": "bts:H4" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Family", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneVariant", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "HistoneVariant", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CENP-A" + }, + { + "@id": "bts:H2A-Bbd" + }, + { + "@id": "bts:H2A.X" + }, + { + "@id": "bts:H2A.Z" + }, + { + "@id": "bts:H2A.Z.1" + }, + { + "@id": "bts:H2A.Z.2" + }, + { + "@id": "bts:H2A.Z.2.2" + }, + { + "@id": "bts:H3.1" + }, + { + "@id": "bts:H3.2" + }, + { + "@id": "bts:H3.3" + }, + { + "@id": "bts:H3.5" + }, + { + "@id": "bts:H3.X" + }, + { + "@id": "bts:H3.Y" + }, + { + "@id": "bts:H3t(H3.4)" + }, + { + "@id": "bts:MH2A" + }, + { + "@id": "bts:MH2A.1" + }, + { + "@id": "bts:MH2A.2" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Variant", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Intron", + "@type": "rdfs:Class", + "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", + "rdfs:label": "Intron", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Intron", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LaboratoryTest", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", + "rdfs:label": "LaboratoryTest", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AbsoluteNeutrophil" + }, + { + "@id": "bts:Albumin" + }, + { + "@id": "bts:AlphaFetoprotein" + }, + { + "@id": "bts:B-cellgenotyping" + }, + { + "@id": "bts:Basophil" + }, + { + "@id": "bts:Beta2Microglobulin" + }, + { + "@id": "bts:BloodUreaNitrogen" + }, + { + "@id": "bts:C-ReactiveProtein" + }, + { + "@id": "bts:Calcium" + }, + { + "@id": "bts:Cellularity" + }, + { + "@id": "bts:CirculatingTumorCells" + }, + { + "@id": "bts:Creatinine" + }, + { + "@id": "bts:Eosinophil" + }, + { + "@id": "bts:Epstein-BarrVirus" + }, + { + "@id": "bts:Glucose" + }, + { + "@id": "bts:Hematocrit" + }, + { + "@id": "bts:Hemoglobin" + }, + { + "@id": "bts:HPV-E6/E7" + }, + { + "@id": "bts:HumanChorionicGonadotropin" + }, + { + "@id": "bts:HumanPapillomavirus" + }, + { + "@id": "bts:ImmunoglobulinA" + }, + { + "@id": "bts:ImmunoglobulinG" + }, + { + "@id": "bts:ImmunoglobulinM" + }, + { + "@id": "bts:LactateDehydrogenase" + }, + { + "@id": "bts:Leukocytes" + }, + { + "@id": "bts:LuteinizingHormone" + }, + { + "@id": "bts:Lymphoblasts" + }, + { + "@id": "bts:Lymphocytes" + }, + { + "@id": "bts:MProtein" + }, + { + "@id": "bts:Metamyelocytes" + }, + { + "@id": "bts:Myeloblasts" + }, + { + "@id": "bts:Myelocytes" + }, + { + "@id": "bts:NeutrophilBands" + }, + { + "@id": "bts:Platelets" + }, + { + "@id": "bts:Prolymphocytes" + }, + { + "@id": "bts:Promonocytes" + }, + { + "@id": "bts:Promyelocytes" + }, + { + "@id": "bts:SegmentedNeutrophil" + }, + { + "@id": "bts:SerumFreeImmunoglobulinLightChain" + }, + { + "@id": "bts:Kappa" + }, + { + "@id": "bts:Lambda" + }, + { + "@id": "bts:NOS" + }, + { + "@id": "bts:Testosterone" + }, + { + "@id": "bts:TotalBilirubin" + }, + { + "@id": "bts:TotalProtein" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laboratory Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociAbnormalCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", + "rdfs:label": "LociAbnormalCount", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Abnormal Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci tested.", + "rdfs:label": "LociCount", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Locus", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label": "Locus", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Locus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MismatchRepairMutation", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MismatchRepairMutation", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mismatch Repair Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularConsequence", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularConsequence", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:3PrimeUTRVariant" + }, + { + "@id": "bts:5PrimeUTRVariant" + }, + { + "@id": "bts:CodingSequenceVariant" + }, + { + "@id": "bts:DownstreamGeneVariant" + }, + { + "@id": "bts:FeatureElongation" + }, + { + "@id": "bts:FeatureTruncation" + }, + { + "@id": "bts:FrameshiftVariant" + }, + { + "@id": "bts:IncompleteTerminalCodonVariant" + }, + { + "@id": "bts:InframeDeletion" + }, + { + "@id": "bts:InframeInsertion" + }, + { + "@id": "bts:IntergenicVariant" + }, + { + "@id": "bts:IntronVariant" + }, + { + "@id": "bts:MaturemiRNAVariant" + }, + { + "@id": "bts:MissenseVariant" + }, + { + "@id": "bts:NMDTranscriptVariant" + }, + { + "@id": "bts:Non-codingTranscriptExonVariant" + }, + { + "@id": "bts:Non-codingTranscriptVariant" + }, + { + "@id": "bts:ProteinAlteringVariant" + }, + { + "@id": "bts:RegulatoryRegionAblation" + }, + { + "@id": "bts:RegulatoryRegionAmplification" + }, + { + "@id": "bts:RegulatoryRegionVariant" + }, + { + "@id": "bts:SpliceAcceptorVariant" + }, + { + "@id": "bts:SpliceDonorVariant" + }, + { + "@id": "bts:SpliceRegionVariant" + }, + { + "@id": "bts:StartLost" + }, + { + "@id": "bts:StopGain" + }, + { + "@id": "bts:StopLost" + }, + { + "@id": "bts:StopRetainedVariant" + }, + { + "@id": "bts:SynonymousVariant" + }, + { + "@id": "bts:TFBindingSiteVariant" + }, + { + "@id": "bts:TFBSAblation" + }, + { + "@id": "bts:TFBSAmplification" + }, + { + "@id": "bts:TranscriptAblation" + }, + { + "@id": "bts:TranscriptAmplification" + }, + { + "@id": "bts:UpstreamGeneVariant" + } + ], + "sms:displayName": "Molecular Consequence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pathogenicity", + "@type": "rdfs:Class", + "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "rdfs:label": "Pathogenicity", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Benign" + }, + { + "@id": "bts:LikelyBenign" + }, + { + "@id": "bts:LikelyPathogenic" + }, + { + "@id": "bts:Pathogenic" + }, + { + "@id": "bts:UncertainSignificance" + } + ], + "sms:displayName": "Pathogenicity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ploidy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", + "rdfs:label": "Ploidy", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Aneuploid" + }, + { + "@id": "bts:Diploid" + }, + { + "@id": "bts:Hyperdiploid" + }, + { + "@id": "bts:Hypodiploid" + }, + { + "@id": "bts:NearDiploid" + }, + { + "@id": "bts:Tetraploid" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ploidy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondExon", + "@type": "rdfs:Class", + "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label": "SecondExon", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondGeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SecondGeneSymbol", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Gene Symbol", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpecializedMolecularTest", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SpecializedMolecularTest", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Specialized Molecular Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestAnalyteType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestAnalyteType", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DNA" + }, + { + "@id": "bts:MRNA" + }, + { + "@id": "bts:MiRNA" + }, + { + "@id": "bts:ProteinAnalyte" + }, + { + "@id": "bts:TotalRNA" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Test Analyte Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestUnits", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestUnits", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Units", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestValue", + "@type": "rdfs:Class", + "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", + "rdfs:label": "TestValue", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Transcript", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Transcript", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Transcript", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VariantOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "VariantOrigin", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Germline" + }, + { + "@id": "bts:Somatic" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Variant Origin", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VariantType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of genetic variation.", + "rdfs:label": "VariantType", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Alleles" + }, + { + "@id": "bts:Amplification" + }, + { + "@id": "bts:Chrimerism" + }, + { + "@id": "bts:Conversion" + }, + { + "@id": "bts:Deletion" + }, + { + "@id": "bts:Deletion-Insertion" + }, + { + "@id": "bts:Duplication" + }, + { + "@id": "bts:Extension" + }, + { + "@id": "bts:Gain" + }, + { + "@id": "bts:Hypermethylation" + }, + { + "@id": "bts:Insertion" + }, + { + "@id": "bts:Inversion" + }, + { + "@id": "bts:Loss" + }, + { + "@id": "bts:Methylation" + }, + { + "@id": "bts:Mosaicism" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:PartialMethylation" + }, + { + "@id": "bts:Rearrangement" + }, + { + "@id": "bts:RepeatedSequences" + }, + { + "@id": "bts:Splice" + }, + { + "@id": "bts:Substitution" + }, + { + "@id": "bts:Translocation" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Variant Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Zygosity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", + "rdfs:label": "Zygosity", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Heterozygous" + }, + { + "@id": "bts:Hemizygous" + }, + { + "@id": "bts:Homozygous" + }, + { + "@id": "bts:Nullizygous" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Zygosity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SourceHTANBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", + "rdfs:label": "SourceHTANBiospecimenID", + "rdfs:subClassOf": [ + { + "@id": "bts:Biosample" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Source HTAN Biospecimen ID", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CollectionDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", + "rdfs:label": "CollectionDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Collection Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:AdjacentBiospecimenIDs", + "@type": "rdfs:Class", + "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", + "rdfs:label": "AdjacentBiospecimenIDs", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adjacent Biospecimen IDs", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "Biospecimen Type", + "rdfs:label": "BiospecimenType", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:TissueBiospecimenType" + }, + { + "@id": "bts:BloodBiospecimenType" + }, + { + "@id": "bts:AnalyteBiospecimenType" + }, + { + "@id": "bts:MouthRinseBiospecimenType" + }, + { + "@id": "bts:StoolBiospecimenType" + }, + { + "@id": "bts:UrineBiospecimenType" + }, + { + "@id": "bts:AscitesBiospecimenType" + }, + { + "@id": "bts:SputumBiospecimenType" + }, + { + "@id": "bts:FluidsBiospecimenType" + }, + { + "@id": "bts:BoneMarrowBiospecimenType" + }, + { + "@id": "bts:CellsBiospecimenType" + } + ], + "sms:displayName": "Biospecimen Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AcquisitionMethodType", + "@type": "rdfs:Class", + "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", + "rdfs:label": "AcquisitionMethodType", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Autopsy" + }, + { + "@id": "bts:Biopsy" + }, + { + "@id": "bts:FineNeedleAspirate" + }, + { + "@id": "bts:SurgicalResection" + }, + { + "@id": "bts:PunchBiopsy" + }, + { + "@id": "bts:ShaveBiopsy" + }, + { + "@id": "bts:Excision" + }, + { + "@id": "bts:Re-excision" + }, + { + "@id": "bts:SentinelNodeBiopsy" + }, + { + "@id": "bts:Lymphadenectomy-RegionalNodes" + }, + { + "@id": "bts:OtherAcquisitionMethod" + }, + { + "@id": "bts:Noninducedsputum" + }, + { + "@id": "bts:Inducedsputum" + }, + { + "@id": "bts:BAL(bronchialalveolarlavage)" + }, + { + "@id": "bts:Cytobrush" + }, + { + "@id": "bts:Blooddraw" + }, + { + "@id": "bts:Fluidcollection" + }, + { + "@id": "bts:Forcepsbiopsy" + }, + { + "@id": "bts:Coreneedlebiopsy" + }, + { + "@id": "bts:Endoscopicbiopsy" + }, + { + "@id": "bts:Notspecified" + } + ], + "sms:displayName": "Acquisition Method Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:FixativeType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", + "rdfs:label": "FixativeType", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Acetone" + }, + { + "@id": "bts:Alcohol" + }, + { + "@id": "bts:Formalin" + }, + { + "@id": "bts:Glutaraldehyde" + }, + { + "@id": "bts:OCTmedia" + }, + { + "@id": "bts:RNAlater" + }, + { + "@id": "bts:Saline" + }, + { + "@id": "bts:95%Ethanol" + }, + { + "@id": "bts:Dimidoester" + }, + { + "@id": "bts:Carbodiimide" + }, + { + "@id": "bts:Dimethylacetamide" + }, + { + "@id": "bts:Para-benzoquinone" + }, + { + "@id": "bts:PAXgenetissue" + }, + { + "@id": "bts:TCLlysisbuffer" + }, + { + "@id": "bts:NP40lysisbuffer" + }, + { + "@id": "bts:Methacarn" + }, + { + "@id": "bts:Cryo-store" + }, + { + "@id": "bts:Carnoy'sFixative" + }, + { + "@id": "bts:Polaxamer" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unfixed" + } + ], + "sms:displayName": "Fixative Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:StorageMethod", + "@type": "rdfs:Class", + "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", + "rdfs:label": "StorageMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Ambienttemperature" + }, + { + "@id": "bts:Cutslide" + }, + { + "@id": "bts:Fresh" + }, + { + "@id": "bts:Frozenat-20C" + }, + { + "@id": "bts:Frozenat-70C" + }, + { + "@id": "bts:Frozenat-80C" + }, + { + "@id": "bts:Frozenat-150C" + }, + { + "@id": "bts:Frozeninliquidnitrogen" + }, + { + "@id": "bts:Frozeninvaporphase" + }, + { + "@id": "bts:Paraffinblock" + }, + { + "@id": "bts:RNAlaterat4C" + }, + { + "@id": "bts:RNAlaterat25C" + }, + { + "@id": "bts:RNAlaterat-20C" + }, + { + "@id": "bts:Refrigeratedat4degrees" + }, + { + "@id": "bts:Refrigeratedvacuumchamber" + }, + { + "@id": "bts:4Cinvacuumchamber" + }, + { + "@id": "bts:Desiccantat4C" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Storage Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProcessingDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", + "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:ProtocolLink", + "@type": "rdfs:Class", + "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label": "ProtocolLink", + "rdfs:subClassOf": [ + { + "@id": "bts:InformationContentEntity" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Protocol Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SiteDataSource", + "@type": "rdfs:Class", + "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", + "rdfs:label": "SiteDataSource", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Site Data Source", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CollectionMedia", + "@type": "rdfs:Class", + "rdfs:comment": "Material Specimen is collected into post procedure", + "rdfs:label": "CollectionMedia", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DMEM" + }, + { + "@id": "bts:DMEM+Serum" + }, + { + "@id": "bts:RPMI" + }, + { + "@id": "bts:RPMI+Serum" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:PBS+Serum" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Collection Media", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MountingMedium", + "@type": "rdfs:Class", + "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", + "rdfs:label": "MountingMedium", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Aqueouswaterbased" + }, + { + "@id": "bts:Non-AqueousSolventbased" + }, + { + "@id": "bts:Xylene" + }, + { + "@id": "bts:Toluene" + }, + { + "@id": "bts:AntifadewithDAPI" + }, + { + "@id": "bts:AntifadewithoutDAPI" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mounting Medium", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProcessingLocation", + "@type": "rdfs:Class", + "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. 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String", + "rdfs:label": "AlignmentWorkflowUrl", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Alignment Workflow Url", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AlignmentWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "AlignmentWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:BWA" + }, + { + "@id": "bts:BWAwithBQSR" + }, + { + "@id": "bts:BWA-aln" + }, + { + "@id": "bts:BWA-mem" + }, + { + "@id": "bts:BWAwithMarkDuplicatesandBQSR" + }, + { + "@id": "bts:STAR2-Pass" + }, + { + "@id": "bts:STAR2-PassChimeric" + }, + { + "@id": "bts:STAR2-PassGenome" + }, + { + "@id": "bts:STAR2-PassTranscriptome" + }, + { + "@id": "bts:Bowtie" + }, + { + "@id": "bts:Bismark" + }, + { + "@id": "bts:GSNAP" + }, + { + "@id": "bts:BSMAP" + }, + { + "@id": "bts:BSmooth" + }, + { + "@id": "bts:BS-Seeker2" + }, + { + "@id": "bts:BS-Seeker" + }, + { + "@id": "bts:RMAP" + }, + { + "@id": "bts:MethylCoder" + }, + { + "@id": "bts:BRAT-BW" + }, + { + "@id": "bts:Pash" + }, + { + "@id": "bts:Segemehl" + }, + { + "@id": "bts:Bisulfighter" + }, + { + "@id": "bts:BatMeth" + }, + { + "@id": "bts:LAST" + }, + { + "@id": "bts:ERNE-BS5" + }, + { + "@id": "bts:B-SOLANA" + }, + { + "@id": "bts:SOCS-B" + }, + { + "@id": "bts:BWA-meth" + }, + { + "@id": "bts:OtherAlignmentWorkflow" + }, + { + "@id": "bts:None" + } + ], + "sms:displayName": "Alignment Workflow Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:IndexFileName", + "@type": "rdfs:Class", + "rdfs:comment": "The name (or part of a name) of a file (of any type). 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See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "WorkingDistanceUnit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Immersion", + "@type": "rdfs:Class", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Air" + }, + { + "@id": "bts:Oil" + }, + { + "@id": "bts:Water" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Immersion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pyramid", + "@type": "rdfs:Class", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Pyramid", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Zstack", + "@type": "rdfs:Class", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Zstack", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Tseries", + "@type": "rdfs:Class", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Tseries", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PassedQC", + "@type": "rdfs:Class", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelsQC" + } + ], + "sms:displayName": "Passed QC", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:FOVnumber", + "@type": "rdfs:Class", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FOV number", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:FOVX", + "@type": "rdfs:Class", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FOVX", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:FOVXUnit" + } + ], + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:FOVXUnit", + "@type": "rdfs:Class", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVXUnit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FOVY", + "@type": "rdfs:Class", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FOVY", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:FOVYUnit" + } + ], + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:FOVYUnit", + "@type": "rdfs:Class", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVYUnit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FrameAveraging", + "@type": "rdfs:Class", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Frame Averaging", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImageID", + "@type": "rdfs:Class", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Image ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DimensionOrder", + "@type": "rdfs:Class", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:XYZCT" + }, + { + "@id": "bts:XYZTC" + }, + { + "@id": "bts:XYCTZ" + }, + { + "@id": "bts:XYCZT" + }, + { + "@id": "bts:XYTZC" + }, + { + "@id": "bts:ZYX" + } + ], + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeX", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeXUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeXUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeXUnit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeY", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeY", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeYUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeYUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeZ", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeZ", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeZ", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeZUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeZUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeZUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeZUnit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PixelsBigEndian", + "@type": "rdfs:Class", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:True" + }, + { + "@id": "bts:False" + } + ], + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PlaneCount", + "@type": "rdfs:Class", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PlaneCount", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SizeC", + "@type": "rdfs:Class", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeC", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeT", + "@type": "rdfs:Class", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeT", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeX", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeY", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeY", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeZ", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeZ", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:PixelType", + "@type": "rdfs:Class", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Int8" + }, + { + "@id": "bts:Int16" + }, + { + "@id": "bts:Int32" + }, + { + "@id": "bts:Uint8" + }, + { + "@id": "bts:Uint16" + }, + { + "@id": "bts:Uint32" + }, + { + "@id": "bts:Float" + }, + { + "@id": "bts:Double" + }, + { + "@id": "bts:Bit" + } + ], + "sms:displayName": "PixelType", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MERFISHPositionsFile", + "@type": "rdfs:Class", + "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", + "rdfs:label": "MERFISHPositionsFile", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MERFISH Positions File", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MERFISHCodebookFile", + "@type": "rdfs:Class", + "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", + "rdfs:label": "MERFISHCodebookFile", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MERFISH Codebook File", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingLevel3Segmentation", + "@type": "rdfs:Class", + "rdfs:comment": "Object segmentations", + "rdfs:label": "ImagingLevel3Segmentation", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Imaging Level 3 Segmentation", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ImagingLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingSegmentationDataType" + }, + { + "@id": "bts:Parameterfile" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:ImagingObjectClass" + }, + { + "@id": "bts:NumberofObjects" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingSegmentationDataType", + "@type": "rdfs:Class", + "rdfs:comment": "Specifies how the segmentation is stored", + "rdfs:label": "ImagingSegmentationDataType", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Mask" + }, + { + "@id": "bts:Outline" + }, + { + "@id": "bts:Polygon" + }, + { + "@id": "bts:ProbabilityMap" + }, + { + "@id": "bts:Point" + } + ], + "sms:displayName": "Imaging Segmentation Data Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Parameterfile", + "@type": "rdfs:Class", + "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", + "rdfs:label": "Parameterfile", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Parameter file", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingObjectClass", + "@type": "rdfs:Class", + "rdfs:comment": "Defines the structure that the mask delineates", + "rdfs:label": "ImagingObjectClass", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Nucleus" + }, + { + "@id": "bts:Cytoplasm" + }, + { + "@id": "bts:Plasmamembrane" + }, + { + "@id": 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This level depends on GeoMx Level 1 and Imaging Level 2.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" + }, + { + "@id": "bts:ImagingLevel2" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:GeoMxDSPAssayType" + }, + { + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" + }, + { + "@id": "bts:GeoMxDSPUniqueProbeCount" + }, + { + "@id": "bts:GeoMxDSPUniqueTargetCount" + }, + { + "@id": "bts:GeoMxDSPGenomicReference" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:GeoMxDSPWorkflowType" + }, + { + "@id": "bts:GeoMxDSPWorkflowParameterDescription" + }, + { + "@id": "bts:GeoMxDSPWorkflowLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "@type": "rdfs:Class", + "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", + "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", + "sms:required": "sms:true", + "sms:validationRules": [ + "list", + "regex match syn\\d+" + ] + }, + { + "@id": "bts:GeoMxDSPUniqueProbeCount", + "@type": "rdfs:Class", + "rdfs:comment": "Total number of unique probes reported.", + "rdfs:label": "GeoMxDSPUniqueProbeCount", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "GeoMx DSP Unique Probe Count", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:GeoMxDSPUniqueTargetCount", + "@type": "rdfs:Class", + "rdfs:comment": "Total number of unique genes reported.", + "rdfs:label": "GeoMxDSPUniqueTargetCount", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "GeoMx DSP Unique Target Count", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:GeoMxDSPGenomicReference", + "@type": "rdfs:Class", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). 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In Xenium, this is referred to as the Region Area", + "rdfs:label": "Surfacearea", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Surface area", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Nucleicount", + "@type": "rdfs:Class", + "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", + "rdfs:label": "Nucleicount", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei count", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TissueStain", + "@type": "rdfs:Class", + "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", + "rdfs:label": "TissueStain", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tissue Stain", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Slidename", + "@type": "rdfs:Class", + "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", + "rdfs:label": "Slidename", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Rawreads", + "@type": "rdfs:Class", + "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", + "rdfs:label": "Rawreads", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Raw reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Stitchedreads", + "@type": "rdfs:Class", + "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", + "rdfs:label": "Stitchedreads", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stitched reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Alignedreads", + "@type": "rdfs:Class", + "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", + "rdfs:label": "Alignedreads", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Aligned reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Deduplicatedreads", + "@type": "rdfs:Class", + "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", + "rdfs:label": "Deduplicatedreads", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Deduplicated reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InSituNegativemedian", + "@type": "rdfs:Class", + "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", + "rdfs:label": "InSituNegativemedian", + "rdfs:subClassOf": [ + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "In Situ Negative median", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Biologicalprobemedian", + "@type": "rdfs:Class", + "rdfs:comment": "Is the median count from all probes except the negative control probes. 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"http://schema.biothings.io" + }, + "sms:displayName": "Grade school", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Graduateorprofessionaldegree", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Graduateorprofessionaldegree", + "rdfs:subClassOf": [ + { + "@id": "bts:EducationLevel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Graduate or professional degree", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Highschoolgraduate(includingequivalency)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Highschoolgraduate(includingequivalency)", + "rdfs:subClassOf": [ + { + "@id": "bts:EducationLevel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "High school graduate (including equivalency)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Master'sdegree", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Master'sdegree", + "rdfs:subClassOf": [ + { + "@id": "bts:EducationLevel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Master's degree", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Noformaleducation", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Noformaleducation", + "rdfs:subClassOf": [ + { + "@id": "bts:EducationLevel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "No formal education", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Nothighschoolgraduate", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Nothighschoolgraduate", + "rdfs:subClassOf": [ + { + "@id": "bts:EducationLevel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Not high school graduate", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Somecollegeorassociatedegree", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Somecollegeorassociatedegree", + "rdfs:subClassOf": [ + { + "@id": "bts:EducationLevel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Some college or associate degree", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Datanotavailable", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Datanotavailable", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastCarcinomaDetectionMethodType" + }, + { + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + }, + { + "@id": "bts:BreastCancerGenomicTestPerformed" + }, + { + "@id": "bts:MammaprintRiskGroup" + }, + { + "@id": "bts:OncotypeRiskGroup" + }, + { + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + }, + { + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + }, + { + "@id": "bts:OvarianCancerPlatinumStatus" + }, + { + "@id": "bts:ModeofCancerDetection" + }, + { + "@id": "bts:LungCancerDetectionMethodType" + }, + { + "@id": "bts:PriorInvasiveBreastDisease" + }, + { + "@id": "bts:BIRADSMammographyBreastDensityCategory" + }, + { + "@id": "bts:OvarianCancerSurgicalOutcome" + }, + { + "@id": "bts:ColorectalCancerDetectionMethodType" + }, + { + "@id": "bts:BreastQuadrantSite" + }, + { + "@id": "bts:BreastCancerAssessmentTests" + }, + { + "@id": "bts:BreastImagingPerformedType" + }, + { + "@id": "bts:EducationLevel" + }, + { + "@id": "bts:OvarianCancerHistologicSubtype" + }, + { + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + }, + { + "@id": "bts:MutationalSignatures" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Data not available", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalTier2", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ClinicalTier2", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Clinical Tier 2", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea-Yes", + "@type": "rdfs:Class", + "rdfs:comment": "Patient's zip code is in a medically underserved area", + "rdfs:label": "MedicallyUnderservedArea-Yes", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + }, + { + "@id": "bts:MedicallyUnderservedArea" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Medically Underserved Area - Yes", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:MedicallyUnderservedScore" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea-No", + "@type": "rdfs:Class", + "rdfs:comment": "Patient's zip code is not in a medically underserved area", + "rdfs:label": "MedicallyUnderservedArea-No", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + }, + { + "@id": "bts:MedicallyUnderservedArea" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Medically Underserved Area - No", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedArea-Unknown", + "@type": "rdfs:Class", + "rdfs:comment": "Insufficient data to look up the Medically Underserved Area value", + "rdfs:label": "MedicallyUnderservedArea-Unknown", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + }, + { + "@id": "bts:MedicallyUnderservedArea" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Medically Underserved Area - Unknown", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MedicallyUnderservedScore", + "@type": "rdfs:Class", + "rdfs:comment": "Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.", + "rdfs:label": "MedicallyUnderservedScore", + "rdfs:subClassOf": [ + { + "@id": "bts:ClinicalTier2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Medically Underserved Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:UrbanPopulation(population>50000)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "UrbanPopulation(population>50000)", + "rdfs:subClassOf": [ + { + "@id": "bts:RuralvsUrban" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Urban Population (population >50000)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:UrbanCluster(population2500-50000)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "UrbanCluster(population2500-50000)", + "rdfs:subClassOf": [ + { + "@id": "bts:RuralvsUrban" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Urban Cluster (population 2500 - 50000)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RuralPopulation(population<2500)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RuralPopulation(population<2500)", + "rdfs:subClassOf": [ + { + "@id": "bts:RuralvsUrban" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Rural Population (population <2500)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RelationshipGender", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the gender of the patient's relative with a history of cancer.", + "rdfs:label": "RelationshipGender", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Female" + }, + { + "@id": "bts:Male" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unspecified" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Relationship Gender", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RelationshipAgeatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The age (in years) when the patient's relative was first diagnosed.", + "rdfs:label": "RelationshipAgeatDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Relationship Age at Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RelationshipPrimaryDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", + "rdfs:label": "RelationshipPrimaryDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AdrenalGlandCancer" + }, + { + "@id": "bts:BasalCellCancer" + }, + { + "@id": "bts:BileDuctCancer" + }, + { + "@id": "bts:BladderCancer" + }, + { + "@id": "bts:BloodCancer" + }, + { + "@id": "bts:BoneCancer" + }, + { + "@id": "bts:BrainCancer" + }, + { + "@id": "bts:BreastCancer" + }, + { + "@id": "bts:Cancer" + }, + { + "@id": "bts:CervicalCancer" + }, + { + "@id": "bts:Chondrosarcoma" + }, + { + "@id": "bts:CNSCancer" + }, + { + "@id": "bts:ColorectalCancer" + }, + { + "@id": "bts:EsophagealCancer" + }, + { + "@id": "bts:EwingSarcoma" + }, + { + "@id": "bts:GallbladderCancer" + }, + { + "@id": "bts:GastricCancer" + }, + { + "@id": "bts:Glioblastoma" + }, + { + "@id": "bts:GynecologicCancer" + }, + { + "@id": "bts:HeadandNeckCancer" + }, + { + "@id": "bts:HematologicCancer" + }, + { + "@id": "bts:KaposiSarcoma" + }, + { + "@id": "bts:KidneyCancer" + }, + { + "@id": "bts:LaryngealCancer" + }, + { + "@id": "bts:Leukemia" + }, + { + "@id": "bts:LiverCancer" + }, + { + "@id": "bts:LungCancer" + }, + { + "@id": "bts:LymphNodeCancer" + }, + { + "@id": "bts:Lymphoma" + }, + { + "@id": "bts:Melanoma" + }, + { + "@id": "bts:Mesothelioma" + }, + { + "@id": "bts:MultipleMyeloma" + }, + { + "@id": "bts:Neuroblastoma" + }, + { + "@id": "bts:Osteosarcoma" + }, + { + "@id": "bts:OvarianCancer" + }, + { + "@id": "bts:PancreasCancer" + }, + { + "@id": "bts:ProstateCancer" + }, + { + "@id": "bts:RectalCancer" + }, + { + "@id": "bts:Rhabdomyosarcoma" + }, + { + "@id": "bts:Sarcoma" + }, + { + "@id": "bts:SkinCancer" + }, + { + "@id": "bts:SpleenCancer" + }, + { + "@id": "bts:TesticularCancer" + }, + { + "@id": "bts:ThroatCancer" + }, + { + "@id": "bts:ThyroidCancer" + }, + { + "@id": "bts:TongueCancer" + }, + { + "@id": "bts:TonsillarCancer" + }, + { + "@id": "bts:UterineCancer" + }, + { + "@id": "bts:WilmsTumor" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Relationship Primary Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdrenalGlandCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AdrenalGlandCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adrenal Gland Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BasalCellCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BasalCellCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Basal Cell Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BileDuctCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BileDuctCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bile Duct Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BladderCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BladderCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bladder Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BloodCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BoneCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BoneCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bone Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BrainCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BrainCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Brain Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BreastCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cancer", + "rdfs:subClassOf": [ + { + "@id": "bts:BreastBiopsyProcedureFindingType" + }, + { + "@id": "bts:ColorectalPolypType" + }, + { + "@id": "bts:RelationshipPrimaryDiagnosis" + }, + { + "@id": "bts:Comorbidity" + }, + { + "@id": "bts:RiskFactor" + }, + { + "@id": "bts:PrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cancer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CervicalCancer", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "CervicalCancer", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipPrimaryDiagnosis" + } + ], + "schema:isPartOf": { + "@id": 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"@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stepfather", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Stepmother", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Stepmother", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stepmother", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Stepsister", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Stepsister", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stepsister", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Stepson", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Stepson", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stepson", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TwinSibling", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "TwinSibling", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Twin Sibling", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Uncle", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Uncle", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Uncle", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Unrelated", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Unrelated", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Unrelated", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ward", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ward", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ward", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Wife", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Wife", + "rdfs:subClassOf": [ + { + "@id": "bts:RelationshipType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Wife", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Yes-CancerHistoryRelative", + "@type": "rdfs:Class", + "rdfs:comment": "Individual has a relative with cancer history", + "rdfs:label": "Yes-CancerHistoryRelative", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + }, + { + "@id": "bts:RelativewithCancerHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Yes - Cancer History Relative", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:RelativeswithCancerHistoryCount" + }, + { + "@id": "bts:RelationshipType" + }, + { + "@id": "bts:RelationshipPrimaryDiagnosis" + }, + { + "@id": "bts:RelationshipGender" + }, + { + "@id": "bts:RelationshipAgeatDiagnosis" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:RelativeswithCancerHistoryCount", + "@type": "rdfs:Class", + "rdfs:comment": "The number of relatives the patient has with a known history of cancer.", + "rdfs:label": "RelativeswithCancerHistoryCount", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Relatives with Cancer History Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Yes-SmokingExposure", + "@type": "rdfs:Class", + "rdfs:comment": "Individual has been exposed to smoke; requires additional metadata", + "rdfs:label": "Yes-SmokingExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + }, + { + "@id": "bts:SmokingExposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Yes - Smoking Exposure", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:YearsSmoked" + }, + { + "@id": "bts:PackYearsSmoked" + }, + { + "@id": "bts:CigarettesperDay" + }, + { + "@id": "bts:SmokingFrequency" + }, + { + "@id": "bts:TypeofSmokeExposure" + }, + { + "@id": "bts:TimebetweenWakingandFirstSmoke" + }, + { + "@id": "bts:TobaccoSmokingOnsetYear" + }, + { + "@id": "bts:TobaccoSmokingQuitYear" + }, + { + "@id": "bts:TobaccoSmokingStatus" + }, + { + "@id": "bts:TypeofTobaccoUsed" + }, + { + "@id": "bts:SecondhandSmokeasChild" + }, + { + "@id": "bts:SmokeExposureDuration" + }, + { + "@id": "bts:TobaccoUseperDay" + }, + { + "@id": "bts:SmokelessTobaccoQuitAge" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:No-SmokingExposure", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "No-SmokingExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:SmokingExposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "No - Smoking Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CigarettesperDay", + "@type": "rdfs:Class", + "rdfs:comment": "The average number of cigarettes smoked per day.", + "rdfs:label": "CigarettesperDay", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cigarettes per Day", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SmokingFrequency", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to generally decribe how often the patient smokes.", + "rdfs:label": "SmokingFrequency", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Everyday" + }, + { + "@id": "bts:Somedays" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Smoking Frequency", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TypeofSmokeExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the patient's specific type of smoke exposure.", + "rdfs:label": "TypeofSmokeExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Accidentalbuildingfiresmoke" + }, + { + "@id": "bts:Accidentalgrassfiresmoke" + }, + { + "@id": "bts:AccidentalfiresmokeNOS" + }, + { + "@id": "bts:Accidentalforestfiresmoke" + }, + { + "@id": "bts:Accidentalvehiclefiresmoke" + }, + { + "@id": "bts:Aircraftsmoke" + }, + { + "@id": "bts:Burningtreesmoke" + }, + { + "@id": "bts:CoalsmokeNOS" + }, + { + "@id": "bts:CookingrelatedsmokeNOS" + }, + { + "@id": "bts:ElectroniccigarettesmokeNOS" + }, + { + "@id": "bts:Electricalfiresmoke" + }, + { + "@id": "bts:Environmentaltobaccosmoke" + }, + { + "@id": "bts:Factorysmokestacksmoke" + }, + { + "@id": "bts:Fieldburningsmoke" + }, + { + "@id": "bts:FiresmokeNOS" + }, + { + "@id": "bts:Furnaceorboilersmoke" + }, + { + "@id": "bts:Gasburningsmokepropane" + }, + { + "@id": "bts:Greasefiresmoke" + }, + { + "@id": "bts:Grillingsmoke" + }, + { + "@id": "bts:Hashishsmoke" + }, + { + "@id": "bts:Indoorcoalburningstoveorfireplacesmoke" + }, + { + "@id": "bts:IndoorstoveorfireplacesmokeNOS" + }, + { + "@id": "bts:Indoorwoodburningstoveorfireplacesmoke" + }, + { + "@id": "bts:Machinesmoke" + }, + { + "@id": "bts:Marijuanasmoke" + }, + { + "@id": "bts:NoSmokeExposure" + }, + { + "@id": "bts:OilburningsmokeKerosene" + }, + { + "@id": "bts:OilburningsmokeNOS" + }, + { + "@id": "bts:Recreationalfiresmoke" + }, + { + "@id": "bts:SmokeexposureNOS" + }, + { + "@id": "bts:Smokehousesmoke" + }, + { + "@id": "bts:Tobaccosmokecigar" + }, + { + "@id": "bts:Tobaccosmokecigarettes" + }, + { + "@id": "bts:Tobaccosmokepipe" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Volcanicsmoke" + }, + { + "@id": "bts:Wasteburningsmoke" + }, + { + "@id": "bts:Woodburningsmokefactory" + }, + { + "@id": "bts:WoodburningsmokeNOS" + }, + { + "@id": "bts:Workrelatedsmokeartificialsmokemachines" + }, + { + "@id": "bts:Workrelatedsmokefirefighting" + }, + { + "@id": "bts:Workrelatedsmokefoundry" + }, + { + "@id": "bts:Workrelatedsmokegenerators" + }, + { + "@id": "bts:Workrelatedsmokemilitary" + }, + { + "@id": "bts:WorkrelatedsmokeNOS" + }, + { + "@id": "bts:Workrelatedsmokepaintbaking" + }, + { + "@id": "bts:Workrelatedsmokeplasticsfactory" + }, + { + "@id": "bts:Workrelatedsmokeplumbing" + }, + { + "@id": "bts:Workrelatedsmokesoldering/welding" + } + ], + "sms:displayName": "Type of Smoke Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TimebetweenWakingandFirstSmoke", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.", + "rdfs:label": "TimebetweenWakingandFirstSmoke", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Within5Minutes" + }, + { + "@id": "bts:6-30Minutes" + }, + { + "@id": "bts:31-60Minutes" + }, + { + "@id": "bts:After60Minutes" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Time between Waking and First Smoke", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TobaccoSmokingOnsetYear", + "@type": "rdfs:Class", + "rdfs:comment": "The year in which the participant began smoking.", + "rdfs:label": "TobaccoSmokingOnsetYear", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tobacco Smoking Onset Year", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TobaccoSmokingQuitYear", + "@type": "rdfs:Class", + "rdfs:comment": "The year in which the participant quit smoking.", + "rdfs:label": "TobaccoSmokingQuitYear", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tobacco Smoking Quit Year", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TobaccoSmokingStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Category describing current smoking status and smoking history as self-reported by a patient", + "rdfs:label": "TobaccoSmokingStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:LifelongNon-Smoker" + }, + { + "@id": "bts:CurrentSmoker" + }, + { + "@id": "bts:CurrentReformedSmokerfor>15yrs" + }, + { + "@id": "bts:CurrentReformedSmokerfor15yrs", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "CurrentReformedSmokerfor>15yrs", + "rdfs:subClassOf": [ + { + "@id": "bts:TobaccoSmokingStatus" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Current Reformed Smoker for > 15 yrs", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CurrentReformedSmokerfor Date: Mon, 3 Jun 2024 20:48:34 +0100 Subject: [PATCH 13/14] Fix CDS other data type --- HTAN.model.csv | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index 1470ec53..cf42c7aa 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -13,6 +13,7 @@ CDS Library Layout,The read strategy or method that was used for sequencing and CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,https://dataservice.datacommons.cancer.gov/#/resources,list like CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://dataservice.datacommons.cancer.gov/#/resources, CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, +CDS Other Data Type Specified,Other types of data associated with the content.,,CDS Data Type,,FALSE,Sequencing,,, Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning @@ -923,7 +924,7 @@ Publication Abstract,The abstract or short description of the content presented/ License,The type of license applicable to the content.,"0BSD, AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement, Proprietary, Other, Not licensed, Freeware",,,FALSE,Publication,,,list like PMID,The PubMed identifier associated with the publication (applicable to published manuscripts). Provide as a URL of the form https://pubmed.ncbi.nlm.nih.gov/{pmid},,,,FALSE,Publication,,,url Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like -Other Data Type Specified,Other types of data associated with the content.,,CDS Data Type,,FALSE,Publication,,,list like +Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,,,list like Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url warning Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,, @@ -1050,4 +1051,4 @@ Days to Vital Status Reference,Number of days between the date used for index an Precancer Case,Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).,"Yes - Precancer Case, No, Not Reported, unknown",,,TRUE,Patient,,, Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,, Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int -WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ \ No newline at end of file +WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ From 489b6b3c2bd59908a6d4cec4c026f4d4d8188e43 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 19:55:16 +0000 Subject: [PATCH 14/14] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 78f348d2..0bdbb642 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -3716,11 +3716,6 @@ }, "sms:displayName": "Other Data Type Specified", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:CDSDataType" - } - ], "sms:validationRules": [ "list like" ] @@ -5970,6 +5965,28 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:CDSOtherDataTypeSpecified", + "@type": "rdfs:Class", + "rdfs:comment": "Other types of data associated with the content.", + "rdfs:label": "CDSOtherDataTypeSpecified", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDS Other Data Type Specified", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:CDSDataType" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:Checksum", "@type": "rdfs:Class",