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Merge pull request #142 from adknowledgeportal/clear-ad-updates-v2
updates for CLEAR-AD needed for individual and biospecimen templates
2 parents 9dfeb84 + 4fe0461 commit f5608da

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8 files changed

+322
-16
lines changed

‎AD.model.csv‎

Lines changed: 7 additions & 5 deletions
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‎AD.model.jsonld‎

Lines changed: 306 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -2759,6 +2759,18 @@
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},
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{
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"@id": "bts:ZenoElectronicWalkway"
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},
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{
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"@id": "bts:TotalRNAseq"
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},
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{
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"@id": "bts:MRNAseq"
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},
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{
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"@id": "bts:RRBS"
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},
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{
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"@id": "bts:IlluminaEPICArray"
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}
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],
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"sms:displayName": "assay",
@@ -8175,7 +8187,7 @@
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"@id": "bts:Schwann"
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},
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{
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"@id": "bts:Schwanncellprecusor"
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"@id": "bts:Schwanncellprecursor"
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},
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{
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"@id": "bts:Schwannoma"
@@ -9455,10 +9467,10 @@
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"sms:validationRules": []
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},
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{
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"@id": "bts:Schwanncellprecusor",
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"@id": "bts:Schwanncellprecursor",
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"@type": "rdfs:Class",
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"rdfs:comment": "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19.",
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"rdfs:label": "Schwanncellprecusor",
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"rdfs:label": "Schwanncellprecursor",
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"rdfs:subClassOf": [
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{
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"@id": "bts:CellType"
@@ -9467,7 +9479,7 @@
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Schwann cell precusor",
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"sms:displayName": "Schwann cell precursor",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
@@ -10179,6 +10191,24 @@
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},
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{
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"@id": "bts:WHICAP"
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},
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{
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"@id": "bts:MayoClinicStudyofAging(MCSA)"
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},
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{
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"@id": "bts:MayoClinicBrainBank(MCBB)"
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},
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{
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"@id": "bts:MichiganADRC(MADC)"
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},
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{
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"@id": "bts:KnightADRC"
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},
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{
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"@id": "bts:1FloridaADRC(1FLADRC)"
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},
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{
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"@id": "bts:IndianaADRC(IADRC)"
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}
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],
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"sms:displayName": "cohort",
@@ -10785,10 +10815,10 @@
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"rdfs:label": "KnightADRC",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Cohort"
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"@id": "bts:DataContributionGroup"
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},
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{
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"@id": "bts:DataContributionGroup"
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"@id": "bts:Cohort"
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}
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],
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"schema:isPartOf": {
@@ -11908,6 +11938,18 @@
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},
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{
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"@id": "bts:Wholebrain"
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},
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{
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"@id": "bts:CerebellarHemisphere"
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},
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{
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"@id": "bts:InferiorParietalGyrus"
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},
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{
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"@id": "bts:Occipitalpole"
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},
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{
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"@id": "bts:TransentorhinalCortex"
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}
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],
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"sms:displayName": "tissue",
@@ -14654,6 +14696,9 @@
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{
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"@id": "bts:MayoDx"
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},
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{
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"@id": "bts:CollectionMethod"
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},
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{
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"@id": "bts:Diabetes"
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},
@@ -18795,6 +18840,74 @@
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:TotalRNAseq",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "TotalRNAseq",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Assay"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "TotalRNAseq",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:MRNAseq",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "MRNAseq",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Assay"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "mRNAseq",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:RRBS",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "RRBS",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Assay"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "RRBS",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:IlluminaEPICArray",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "IlluminaEPICArray",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Assay"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Illumina EPIC Array",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:Batch",
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"@type": "rdfs:Class",
@@ -19050,6 +19163,108 @@
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"sms:required": "sms:true",
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"sms:validationRules": []
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},
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{
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"@id": "bts:CollectionMethod",
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"@type": "rdfs:Class",
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"rdfs:comment": "For CLEAR-AD.Blood samples that are collected in heparin tubes will be sent directly to NCRAD for them to extract and store PBMCs for eventual generation of iPSCs.",
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"rdfs:label": "CollectionMethod",
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"rdfs:subClassOf": [
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{
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"@id": "bts:ManifestColumn"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"schema:rangeIncludes": [
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{
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"@id": "bts:PAXgeneBloodTube"
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},
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{
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"@id": "bts:EDTAPurpleTopTube"
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},
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{
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"@id": "bts:Heparin(NaHep)GreenTopTubes"
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},
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{
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"@id": "bts:Other"
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},
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{
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"@id": "bts:Notcollected"
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}
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],
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"sms:displayName": "collectionMethod",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:PAXgeneBloodTube",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "PAXgeneBloodTube",
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"rdfs:subClassOf": [
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{
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"@id": "bts:CollectionMethod"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "PAXgene Blood Tube",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:EDTAPurpleTopTube",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "EDTAPurpleTopTube",
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"rdfs:subClassOf": [
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{
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"@id": "bts:CollectionMethod"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "EDTA Purple Top Tube",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:Heparin(NaHep)GreenTopTubes",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "Heparin(NaHep)GreenTopTubes",
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"rdfs:subClassOf": [
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{
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"@id": "bts:CollectionMethod"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Heparin (NaHep) Green Top Tubes",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:Notcollected",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "Notcollected",
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"rdfs:subClassOf": [
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{
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"@id": "bts:CollectionMethod"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "not collected",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:ContrastAgent",
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"@type": "rdfs:Class",
@@ -19659,6 +19874,23 @@
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:FreezeThawCycles",
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"@type": "rdfs:Class",
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"rdfs:comment": "The number of freeze thaw cycles of fluid samples as multiple freeze thaw cycles may compromise sample integrity",
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"rdfs:label": "FreezeThawCycles",
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"rdfs:subClassOf": [
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{
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"@id": "bts:ManifestColumn"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "freezeThawCycles",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:GDNAconc",
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"@type": "rdfs:Class",
@@ -31088,6 +31320,74 @@
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:CerebellarHemisphere",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CerebellarHemisphere",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Tissue"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Cerebellar Hemisphere",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:InferiorParietalGyrus",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "InferiorParietalGyrus",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Tissue"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "inferior Parietal Gyrus",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:Occipitalpole",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "Occipitalpole",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Tissue"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "occipital pole",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:TransentorhinalCortex",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "TransentorhinalCortex",
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"rdfs:subClassOf": [
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{
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"@id": "bts:Tissue"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Transentorhinal Cortex",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:TissueWeight",
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"@type": "rdfs:Class",

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