From 50351da46b9c1874095598cebcceef093e5236fb Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Thu, 7 Sep 2023 21:25:44 -0400 Subject: [PATCH 01/16] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index a6d53a7b..626dba0a 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -55,13 +55,13 @@ Tumor Type,"The types of tumors that are banked, if applicable.","cutaneous neur Disease Type,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,Biobank,,,list Specimen Preparation Method,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,Biobank,,,list Specimen Format,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,Biobank,,,list -Observation,"A remark, statement, or comment based on the resource.",,"Component, Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Reference, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link",FALSE,,Observation,"Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Reference, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link","Resource, Investigator, Publication", +Observation,"A remark, statement, or comment based on the resource.",,"Component, Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link",FALSE,,Observation,"Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link","Resource, Investigator, Publication", Observation_id,A unique identifier for the observation.,,,TRUE,,Observation,,, Observation Submitter Name,The name of the person submitting the observation. ,,,TRUE,,Observation,,, Synapse ID,The synapse identifier for the person submitting the observation. ,,,FALSE,,Observation,,, Observation Text,Free text observation about the resource.,,,TRUE,,Observation,,, Observation Type,Type of observation,"pathologic, behavioral-non pathologic, issue, neurochemical, Depositor Comment, Usage Instructions, general comment/review, other",,TRUE,,Observation,,, -Observation Reference,What t=0 for the observationTime is,"tumor implantation, gestational day zero, birth, immortalization",,FALSE,,Observation,,, +Observation Phase,What t=0 for the observationTime is,"tumor implantation, gestational day zero, birth, immortalization",,FALSE,,Observation,,, Observation Time,When the observation was.,,,FALSE,,Observation,,, Observation Time Units,The unit of time pertaining to the observation,"hour, day, week, month, year",,FALSE,,Observation,,, Reliability Rating,A 1-5 rating of the reliability of the resource; does the resource produce consistent and reliable results? Does the resource reasonably recapitulate the human disease it is intended to model? ,"1,2,3,4,5",,FALSE,,Observation,,, From b2b6922213bc19ca29a65338ee128ef090bfdaf7 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 8 Sep 2023 01:27:20 +0000 Subject: [PATCH 02/16] Add changes --- nf-research-tools.jsonld | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 948d81fd..81033bd3 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -3806,7 +3806,7 @@ "@id": "bts:observationType" }, { - "@id": "bts:observationReference" + "@id": "bts:observationPhase" }, { "@id": "bts:observationTime" @@ -3938,10 +3938,10 @@ "sms:validationRules": [] }, { - "@id": "bts:observationReference", + "@id": "bts:observationPhase", "@type": "rdf:Property", "rdfs:comment": "What t=0 for the observationTime is", - "rdfs:label": "observationReference", + "rdfs:label": "observationPhase", "schema:domainIncludes": [ { "@id": "bts:Observation" @@ -3964,7 +3964,7 @@ "@id": "bts:Immortalization" } ], - "sms:displayName": "Observation Reference", + "sms:displayName": "Observation Phase", "sms:required": "sms:false", "sms:validationRules": [] }, From f8b2aa600aab35a291cc74d920f3cb1c3c0a8d0e Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 11:02:33 -0400 Subject: [PATCH 03/16] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 626dba0a..cf7db748 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -11,7 +11,7 @@ Usage Requirements,Any known restrictions on use of the resource. ,"non-commerci How to Acquire,How to acquire a particular resource. ,,,TRUE,,Resource,,, Date Added,The date that the resource was originally added.,,,TRUE,,Resource,,, Date Modified,The last update of the resource metadata (not including observations).,,,TRUE,,Resource,,, -Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, +Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert , nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, Genetic Reagent_id,A unique identifier for the reagent.,,,TRUE,,Genetic Reagent,,, Insert Name,Name of the main gene insert in the plasmid.,,,TRUE,,Genetic Reagent,,, Insert Entrez ID,The entrez gene id for the gene insert,,,TRUE,,Genetic Reagent,,, @@ -55,7 +55,7 @@ Tumor Type,"The types of tumors that are banked, if applicable.","cutaneous neur Disease Type,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,Biobank,,,list Specimen Preparation Method,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,Biobank,,,list Specimen Format,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,Biobank,,,list -Observation,"A remark, statement, or comment based on the resource.",,"Component, Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link",FALSE,,Observation,"Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link","Resource, Investigator, Publication", +Observation,"A remark, statement, or comment based on the resource.",,"Component, Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Species, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link",FALSE,,Observation,"Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Species, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link","Resource, Investigator, Publication", Observation_id,A unique identifier for the observation.,,,TRUE,,Observation,,, Observation Submitter Name,The name of the person submitting the observation. ,,,TRUE,,Observation,,, Synapse ID,The synapse identifier for the person submitting the observation. ,,,FALSE,,Observation,,, From 6337f451a36c3a913dea02b66960478594708fbe Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 8 Sep 2023 15:04:07 +0000 Subject: [PATCH 04/16] Add changes --- nf-research-tools.jsonld | 52 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 51 insertions(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 81033bd3..184e213e 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -2434,7 +2434,7 @@ "@id": "bts:insertSize" }, { - "@id": "bts:insertSpecies" + "@id": "bts:Insert" }, { "@id": "bts:nTerminalTag" @@ -3799,6 +3799,9 @@ { "@id": "bts:synapseId" }, + { + "@id": "bts:species" + }, { "@id": "bts:observationText" }, @@ -4682,6 +4685,9 @@ "rdfs:comment": "The species of the individual the resource was derived from.", "rdfs:label": "species", "schema:domainIncludes": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -7027,6 +7033,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Insert", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Insert", + "rdfs:subClassOf": [ + { + "@id": "bts:GeneticReagent" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Insert", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Homosapiens", "@type": "rdfs:Class", @@ -10178,6 +10201,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Musmusculus(humanized)", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10195,6 +10221,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Drosophilamelanogaster", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10212,6 +10241,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Rhesusmacaque", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10229,6 +10261,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Pantroglodytes", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10246,6 +10281,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Gallusgallus", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10263,6 +10301,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Susscrofa", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10280,6 +10321,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Oryctolaguscuniculus", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10297,6 +10341,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Daniorerio", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } @@ -10314,6 +10361,9 @@ "rdfs:comment": "TBD", "rdfs:label": "Escherichiacoli", "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + }, { "@id": "bts:Donor" } From 9c8b199ef16f74d9e343ea7416c79d397d8e826a Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 11:29:55 -0400 Subject: [PATCH 05/16] edited observation phase and time --- nf_research_tools.rdb.model.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index cf7db748..275509ad 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -60,10 +60,10 @@ Observation_id,A unique identifier for the observation.,,,TRUE,,Observation,,, Observation Submitter Name,The name of the person submitting the observation. ,,,TRUE,,Observation,,, Synapse ID,The synapse identifier for the person submitting the observation. ,,,FALSE,,Observation,,, Observation Text,Free text observation about the resource.,,,TRUE,,Observation,,, -Observation Type,Type of observation,"pathologic, behavioral-non pathologic, issue, neurochemical, Depositor Comment, Usage Instructions, general comment/review, other",,TRUE,,Observation,,, -Observation Phase,What t=0 for the observationTime is,"tumor implantation, gestational day zero, birth, immortalization",,FALSE,,Observation,,, +Observation Type,Type of observation,"Body Length, Body weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Other",,TRUE,,Observation,,, +Observation Phase,What t=0 for the observationTime is,"Adolescent, Adult, Death Phase, Embryo, Juvenile, Larval, Log Phase, Neonatal, Postnatal, Prenatal, Pupal, Stationary Phase, Weanling",,FALSE,,Observation,,, Observation Time,When the observation was.,,,FALSE,,Observation,,, -Observation Time Units,The unit of time pertaining to the observation,"hour, day, week, month, year",,FALSE,,Observation,,, +Observation Time Units,The unit of time pertaining to the observation,"E, hour, day, week, month, year",,FALSE,,Observation,,, Reliability Rating,A 1-5 rating of the reliability of the resource; does the resource produce consistent and reliable results? Does the resource reasonably recapitulate the human disease it is intended to model? ,"1,2,3,4,5",,FALSE,,Observation,,, Ease of Use Rating,"A 1-5 rating of the ease of use of the resource; how easy is it to obtain the resource, comply with any agreements like material transfer agreements, etc? ","1,2,3,4,5",,FALSE,,Observation,,, Observation Link,"A link/reference related to the observation being recorded. If the reference has a DOI or PubMed ID, use ""publication_id"" instead. ",,,FALSE,,Observation,,, From cb4bc283224f1f3e5ff2d9c1cc13bbc9f1bd8890 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 8 Sep 2023 15:31:21 +0000 Subject: [PATCH 06/16] Add changes --- nf-research-tools.jsonld | 411 ++++++++++++++++++++++++++++++++++----- 1 file changed, 367 insertions(+), 44 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 184e213e..5c5752bc 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -3912,25 +3912,46 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pathologic" + "@id": "bts:BodyLength" }, { - "@id": "bts:Behavioral-nonpathologic" + "@id": "bts:Bodyweight" }, { - "@id": "bts:Issue" + "@id": "bts:CoatColor" }, { - "@id": "bts:Neurochemical" + "@id": "bts:DiseaseSusceptibility" }, { - "@id": "bts:DepositorComment" + "@id": "bts:FeedIntake" }, { - "@id": "bts:UsageInstructions" + "@id": "bts:FeedingBehavior" }, { - "@id": "bts:Generalcomment/review" + "@id": "bts:Growthrate" + }, + { + "@id": "bts:MotorActivity" + }, + { + "@id": "bts:OrganDevelopment" + }, + { + "@id": "bts:ReflexDevelopment" + }, + { + "@id": "bts:ReproductiveBehavior" + }, + { + "@id": "bts:SocialBehavior" + }, + { + "@id": "bts:SwimmingBehavior" + }, + { + "@id": "bts:TumorGrowth" }, { "@id": "bts:Other" @@ -3955,16 +3976,43 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Tumorimplantation" + "@id": "bts:Adolescent" + }, + { + "@id": "bts:Adult" }, { - "@id": "bts:Gestationaldayzero" + "@id": "bts:DeathPhase" }, { - "@id": "bts:Birth" + "@id": "bts:Embryo" }, { - "@id": "bts:Immortalization" + "@id": "bts:Juvenile" + }, + { + "@id": "bts:Larval" + }, + { + "@id": "bts:LogPhase" + }, + { + "@id": "bts:Neonatal" + }, + { + "@id": "bts:Postnatal" + }, + { + "@id": "bts:Prenatal" + }, + { + "@id": "bts:Pupal" + }, + { + "@id": "bts:StationaryPhase" + }, + { + "@id": "bts:Weanling" } ], "sms:displayName": "Observation Phase", @@ -4002,6 +4050,9 @@ "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ + { + "@id": "bts:E" + }, { "@id": "bts:Hour" }, @@ -8938,10 +8989,282 @@ "sms:validationRules": [] }, { - "@id": "bts:Pathologic", + "@id": "bts:BodyLength", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BodyLength", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Body Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Bodyweight", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Bodyweight", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Body weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CoatColor", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "CoatColor", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Coat Color", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DiseaseSusceptibility", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "DiseaseSusceptibility", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Disease Susceptibility", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FeedIntake", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FeedIntake", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Feed Intake", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FeedingBehavior", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FeedingBehavior", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Feeding Behavior", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Growthrate", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Growthrate", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Growth rate", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MotorActivity", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MotorActivity", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Motor Activity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OrganDevelopment", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "OrganDevelopment", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Organ Development", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ReflexDevelopment", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ReflexDevelopment", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Reflex Development", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ReproductiveBehavior", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ReproductiveBehavior", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Reproductive Behavior", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SocialBehavior", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SocialBehavior", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Social Behavior", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SwimmingBehavior", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SwimmingBehavior", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Swimming Behavior", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorGrowth", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "TumorGrowth", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tumor Growth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Adolescent", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Adolescent", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adolescent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Adult", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Adult", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adult", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DeathPhase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pathologic", + "rdfs:label": "DeathPhase", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -8950,15 +9273,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "pathologic", + "sms:displayName": "Death Phase", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Behavioral-nonpathologic", + "@id": "bts:Embryo", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Behavioral-nonpathologic", + "rdfs:label": "Embryo", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -8967,15 +9290,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "behavioral-non pathologic", + "sms:displayName": "Embryo", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Issue", + "@id": "bts:Juvenile", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Issue", + "rdfs:label": "Juvenile", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -8984,15 +9307,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "issue", + "sms:displayName": "Juvenile", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Neurochemical", + "@id": "bts:Larval", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Neurochemical", + "rdfs:label": "Larval", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9001,15 +9324,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "neurochemical", + "sms:displayName": "Larval", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DepositorComment", + "@id": "bts:LogPhase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "DepositorComment", + "rdfs:label": "LogPhase", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9018,15 +9341,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Depositor Comment", + "sms:displayName": "Log Phase", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UsageInstructions", + "@id": "bts:Neonatal", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "UsageInstructions", + "rdfs:label": "Neonatal", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9035,15 +9358,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Usage Instructions", + "sms:displayName": "Neonatal", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Generalcomment/review", + "@id": "bts:Postnatal", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Generalcomment/review", + "rdfs:label": "Postnatal", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9052,15 +9375,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "general comment/review", + "sms:displayName": "Postnatal", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tumorimplantation", + "@id": "bts:Prenatal", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tumorimplantation", + "rdfs:label": "Prenatal", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9069,15 +9392,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tumor implantation", + "sms:displayName": "Prenatal", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Gestationaldayzero", + "@id": "bts:Pupal", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Gestationaldayzero", + "rdfs:label": "Pupal", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9086,15 +9409,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "gestational day zero", + "sms:displayName": "Pupal", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Birth", + "@id": "bts:StationaryPhase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Birth", + "rdfs:label": "StationaryPhase", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9103,15 +9426,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "birth", + "sms:displayName": "Stationary Phase", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Immortalization", + "@id": "bts:Weanling", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Immortalization", + "rdfs:label": "Weanling", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9120,7 +9443,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "immortalization", + "sms:displayName": "Weanling", "sms:required": "sms:false", "sms:validationRules": [] }, From ba515ad54570ac75d7052e0c5569121ea6003d09 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 12:24:19 -0400 Subject: [PATCH 07/16] Update nf_research_tools.rdb.model.csv Co-authored-by: Robert Allaway --- nf_research_tools.rdb.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 275509ad..3e24afb1 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -60,7 +60,8 @@ Observation_id,A unique identifier for the observation.,,,TRUE,,Observation,,, Observation Submitter Name,The name of the person submitting the observation. ,,,TRUE,,Observation,,, Synapse ID,The synapse identifier for the person submitting the observation. ,,,FALSE,,Observation,,, Observation Text,Free text observation about the resource.,,,TRUE,,Observation,,, -Observation Type,Type of observation,"Body Length, Body weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Other",,TRUE,,Observation,,, +Observation Type,Type of observation,"Body Length, Body weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,Observation,,, + Observation Phase,What t=0 for the observationTime is,"Adolescent, Adult, Death Phase, Embryo, Juvenile, Larval, Log Phase, Neonatal, Postnatal, Prenatal, Pupal, Stationary Phase, Weanling",,FALSE,,Observation,,, Observation Time,When the observation was.,,,FALSE,,Observation,,, Observation Time Units,The unit of time pertaining to the observation,"E, hour, day, week, month, year",,FALSE,,Observation,,, From 346d253f680f61d179c027c0cfd5e8034dabf410 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 12:24:31 -0400 Subject: [PATCH 08/16] Update nf_research_tools.rdb.model.csv Co-authored-by: Robert Allaway --- nf_research_tools.rdb.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 3e24afb1..3391d4cf 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -11,7 +11,8 @@ Usage Requirements,Any known restrictions on use of the resource. ,"non-commerci How to Acquire,How to acquire a particular resource. ,,,TRUE,,Resource,,, Date Added,The date that the resource was originally added.,,,TRUE,,Resource,,, Date Modified,The last update of the resource metadata (not including observations).,,,TRUE,,Resource,,, -Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert , nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, +Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Cloning Site, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, + Genetic Reagent_id,A unique identifier for the reagent.,,,TRUE,,Genetic Reagent,,, Insert Name,Name of the main gene insert in the plasmid.,,,TRUE,,Genetic Reagent,,, Insert Entrez ID,The entrez gene id for the gene insert,,,TRUE,,Genetic Reagent,,, From af2264f7efed1fa58075af92fba6e24e3a724967 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 12:25:15 -0400 Subject: [PATCH 09/16] Update nf_research_tools.rdb.model.csv Co-authored-by: Robert Allaway --- nf_research_tools.rdb.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 3391d4cf..8701b88d 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -56,7 +56,8 @@ Tumor Type,"The types of tumors that are banked, if applicable.","cutaneous neur Disease Type,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,Biobank,,,list Specimen Preparation Method,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,Biobank,,,list Specimen Format,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,Biobank,,,list -Observation,"A remark, statement, or comment based on the resource.",,"Component, Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Species, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link",FALSE,,Observation,"Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Species, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link","Resource, Investigator, Publication", +Observation,"A remark, statement, or comment based on the resource.",,"Component, Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link",FALSE,,Observation,"Observation_id, Resource_id, Publication_id, Observation Submitter Name, Synapse_id, Observation Text, Observation Type, Observation Phase, Observation Time, Observation Time Units, Reliability Rating, Ease of Use Rating, Observation Link","Resource, Investigator, Publication", + Observation_id,A unique identifier for the observation.,,,TRUE,,Observation,,, Observation Submitter Name,The name of the person submitting the observation. ,,,TRUE,,Observation,,, Synapse ID,The synapse identifier for the person submitting the observation. ,,,FALSE,,Observation,,, From fc7e7a49519e65b1d00b64e4bb605cbdf1437bc3 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 8 Sep 2023 16:26:37 +0000 Subject: [PATCH 10/16] Add changes --- nf-research-tools.jsonld | 176 ++++++++++++++++++--------------------- 1 file changed, 82 insertions(+), 94 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 5c5752bc..89cfc196 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -2744,10 +2744,10 @@ }, { "@id": "bts:3primeCloningSite", - "@type": "rdfs:Class", + "@type": "rdf:Property", "rdfs:comment": "If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert", "rdfs:label": "3primeCloningSite", - "rdfs:subClassOf": [ + "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" } @@ -3799,9 +3799,6 @@ { "@id": "bts:synapseId" }, - { - "@id": "bts:species" - }, { "@id": "bts:observationText" }, @@ -3953,6 +3950,18 @@ { "@id": "bts:TumorGrowth" }, + { + "@id": "bts:Issue" + }, + { + "@id": "bts:DepositorComment" + }, + { + "@id": "bts:UsageInstructions" + }, + { + "@id": "bts:GeneralCommentorReview" + }, { "@id": "bts:Other" } @@ -4736,9 +4745,6 @@ "rdfs:comment": "The species of the individual the resource was derived from.", "rdfs:label": "species", "schema:domainIncludes": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -6612,65 +6618,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:3primeCloningSite", - "@type": "rdf:Property", - "rdfs:comment": "TBD", - "rdfs:label": "3primeCloningSite", - "schema:domainIncludes": [ - { - "@id": "bts:G" - }, - { - "@id": "bts:E" - }, - { - "@id": "bts:N" - }, - { - "@id": "bts:E" - }, - { - "@id": "bts:T" - }, - { - "@id": "bts:I" - }, - { - "@id": "bts:C" - }, - { - "@id": "bts:" - }, - { - "@id": "bts:R" - }, - { - "@id": "bts:E" - }, - { - "@id": "bts:A" - }, - { - "@id": "bts:G" - }, - { - "@id": "bts:E" - }, - { - "@id": "bts:N" - }, - { - "@id": "bts:T" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "3prime Clonin gSite", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:vendorUrl", "@type": "rdf:Property", @@ -9226,6 +9173,74 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Issue", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Issue", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Issue", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DepositorComment", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "DepositorComment", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Depositor Comment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:UsageInstructions", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "UsageInstructions", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Usage Instructions", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GeneralCommentorReview", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "GeneralCommentorReview", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "General Comment or Review", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Adolescent", "@type": "rdfs:Class", @@ -10524,9 +10539,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Musmusculus(humanized)", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10544,9 +10556,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Drosophilamelanogaster", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10564,9 +10573,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Rhesusmacaque", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10584,9 +10590,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Pantroglodytes", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10604,9 +10607,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Gallusgallus", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10624,9 +10624,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Susscrofa", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10644,9 +10641,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Oryctolaguscuniculus", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10664,9 +10658,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Daniorerio", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } @@ -10684,9 +10675,6 @@ "rdfs:comment": "TBD", "rdfs:label": "Escherichiacoli", "rdfs:subClassOf": [ - { - "@id": "bts:Observation" - }, { "@id": "bts:Donor" } From 648d461fb985f38b01069eaf366c9a9086b18a33 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 12:37:16 -0400 Subject: [PATCH 11/16] Update nf_research_tools.rdb.model.csv Co-authored-by: Robert Allaway --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 8701b88d..2ec43338 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -66,7 +66,7 @@ Observation Type,Type of observation,"Body Length, Body weight, Coat Color, Dise Observation Phase,What t=0 for the observationTime is,"Adolescent, Adult, Death Phase, Embryo, Juvenile, Larval, Log Phase, Neonatal, Postnatal, Prenatal, Pupal, Stationary Phase, Weanling",,FALSE,,Observation,,, Observation Time,When the observation was.,,,FALSE,,Observation,,, -Observation Time Units,The unit of time pertaining to the observation,"E, hour, day, week, month, year",,FALSE,,Observation,,, +Observation Time Units,The unit of time pertaining to the observation,"days, weeks, months, years, hours, minutes, seconds, milliseconds",,FALSE,,Observation,,, Reliability Rating,A 1-5 rating of the reliability of the resource; does the resource produce consistent and reliable results? Does the resource reasonably recapitulate the human disease it is intended to model? ,"1,2,3,4,5",,FALSE,,Observation,,, Ease of Use Rating,"A 1-5 rating of the ease of use of the resource; how easy is it to obtain the resource, comply with any agreements like material transfer agreements, etc? ","1,2,3,4,5",,FALSE,,Observation,,, Observation Link,"A link/reference related to the observation being recorded. If the reference has a DOI or PubMed ID, use ""publication_id"" instead. ",,,FALSE,,Observation,,, From b437f0d1e60d99b82051245f6f6b20a74723de6f Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 8 Sep 2023 16:38:43 +0000 Subject: [PATCH 12/16] Add changes --- nf-research-tools.jsonld | 99 +++++++++++++++++++++++++++++++--------- 1 file changed, 78 insertions(+), 21 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 89cfc196..0648b27f 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -4060,22 +4060,28 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:E" + "@id": "bts:Days" + }, + { + "@id": "bts:Weeks" }, { - "@id": "bts:Hour" + "@id": "bts:Months" }, { - "@id": "bts:Day" + "@id": "bts:Years" }, { - "@id": "bts:Week" + "@id": "bts:Hours" }, { - "@id": "bts:Month" + "@id": "bts:Minutes" }, { - "@id": "bts:Year" + "@id": "bts:Seconds" + }, + { + "@id": "bts:Milliseconds" } ], "sms:displayName": "Observation Time Units", @@ -9463,10 +9469,61 @@ "sms:validationRules": [] }, { - "@id": "bts:Hour", + "@id": "bts:Days", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Days", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "days", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Weeks", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Weeks", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "weeks", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Months", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Months", + "rdfs:subClassOf": [ + { + "@id": "bts:Observation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "months", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Years", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Hour", + "rdfs:label": "Years", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9475,15 +9532,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "hour", + "sms:displayName": "years", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Day", + "@id": "bts:Hours", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Day", + "rdfs:label": "Hours", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9492,15 +9549,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "day", + "sms:displayName": "hours", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Week", + "@id": "bts:Minutes", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Week", + "rdfs:label": "Minutes", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9509,15 +9566,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "week", + "sms:displayName": "minutes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Month", + "@id": "bts:Seconds", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Month", + "rdfs:label": "Seconds", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9526,15 +9583,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "month", + "sms:displayName": "seconds", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Year", + "@id": "bts:Milliseconds", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Year", + "rdfs:label": "Milliseconds", "rdfs:subClassOf": [ { "@id": "bts:Observation" @@ -9543,7 +9600,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "year", + "sms:displayName": "milliseconds", "sms:required": "sms:false", "sms:validationRules": [] }, From 928ab3c2ca3c926d32f37743ba75c38770734a7c Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Fri, 8 Sep 2023 11:42:11 -0500 Subject: [PATCH 13/16] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 1 - 1 file changed, 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 2ec43338..6e5a202f 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -63,7 +63,6 @@ Observation Submitter Name,The name of the person submitting the observation. ,, Synapse ID,The synapse identifier for the person submitting the observation. ,,,FALSE,,Observation,,, Observation Text,Free text observation about the resource.,,,TRUE,,Observation,,, Observation Type,Type of observation,"Body Length, Body weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,Observation,,, - Observation Phase,What t=0 for the observationTime is,"Adolescent, Adult, Death Phase, Embryo, Juvenile, Larval, Log Phase, Neonatal, Postnatal, Prenatal, Pupal, Stationary Phase, Weanling",,FALSE,,Observation,,, Observation Time,When the observation was.,,,FALSE,,Observation,,, Observation Time Units,The unit of time pertaining to the observation,"days, weeks, months, years, hours, minutes, seconds, milliseconds",,FALSE,,Observation,,, From f04ef0fadf0ad16bd4d8b44e5d69843379bbceb6 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Fri, 8 Sep 2023 12:43:46 -0400 Subject: [PATCH 14/16] Update nf_research_tools.rdb.model.csv Co-authored-by: Robert Allaway --- nf_research_tools.rdb.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 6e5a202f..9cbd7ae9 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -11,7 +11,8 @@ Usage Requirements,Any known restrictions on use of the resource. ,"non-commerci How to Acquire,How to acquire a particular resource. ,,,TRUE,,Resource,,, Date Added,The date that the resource was originally added.,,,TRUE,,Resource,,, Date Modified,The last update of the resource metadata (not including observations).,,,TRUE,,Resource,,, -Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Cloning Site, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, +Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Cloning Site, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, + Genetic Reagent_id,A unique identifier for the reagent.,,,TRUE,,Genetic Reagent,,, Insert Name,Name of the main gene insert in the plasmid.,,,TRUE,,Genetic Reagent,,, From e6f10969ee0a9626480cc414a0a9cbc90f1a6cd5 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Fri, 8 Sep 2023 11:44:56 -0500 Subject: [PATCH 15/16] Apply suggestions from code review --- nf_research_tools.rdb.model.csv | 2 -- 1 file changed, 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 9cbd7ae9..58fc5745 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -12,8 +12,6 @@ How to Acquire,How to acquire a particular resource. ,,,TRUE,,Resource,,, Date Added,The date that the resource was originally added.,,,TRUE,,Resource,,, Date Modified,The last update of the resource metadata (not including observations).,,,TRUE,,Resource,,, Genetic Reagent,Genetic reagents.,,"Component, Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Clonin gSite, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",FALSE,,Genetic Reagent,"Genetic Reagent_id, Insert Name, Insert Entrez_id, gRNA shRNA sequence, Insert Size, Insert Species, nTerminal Tag, cTerminal Tag, Cloning Method, 5prime Cloning Site, 5prime Site Destroyed, 3prime Cloning Site, 3prime Site Destroyed, Promoter, 5primer, 3primer, Vector Backbone, Vector Type, Backbone Size, Total Size, Bacterial Resistance, Selectable Marker, Copy Number, Growth Temp, Growth Strain, Hazardous",, - - Genetic Reagent_id,A unique identifier for the reagent.,,,TRUE,,Genetic Reagent,,, Insert Name,Name of the main gene insert in the plasmid.,,,TRUE,,Genetic Reagent,,, Insert Entrez ID,The entrez gene id for the gene insert,,,TRUE,,Genetic Reagent,,, From 7265633c61acb76252e48a6bba6c4985947d4fe5 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 8 Sep 2023 16:46:24 +0000 Subject: [PATCH 16/16] Add changes --- nf-research-tools.jsonld | 19 +------------------ 1 file changed, 1 insertion(+), 18 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 0648b27f..98cf5315 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -2434,7 +2434,7 @@ "@id": "bts:insertSize" }, { - "@id": "bts:Insert" + "@id": "bts:insertSpecies" }, { "@id": "bts:nTerminalTag" @@ -7037,23 +7037,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Insert", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Insert", - "rdfs:subClassOf": [ - { - "@id": "bts:GeneticReagent" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Insert", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:Homosapiens", "@type": "rdfs:Class",