Generating CDS template

HTAN.model.csv

@@ -7,6 +7,13 @@ 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",,"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
+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
@@ -1032,7 +1039,7 @@ 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,,,