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Merge branch 'main' into add-microarray-assay
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@Gibbsdavidl
Gibbsdavidl authored May 30, 2024
2 parents 412c637 + 1f9a7cd commit 7c4da67
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10 changes: 9 additions & 1 deletion HTAN.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -472,7 +472,7 @@ Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology
Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5227611&version=1.0,
Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3024951&version=1.0,
Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,
Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -20C, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,
Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Specimen at Room Temperature, Other Shipping Environment, Not Shipped",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5495533&version=1.0,
Site Data Source,"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.",,,,FALSE,Biospecimen,,,
Expand Down Expand Up @@ -1037,3 +1037,11 @@ Microarray Molecule,Microarray is measuring this kind of molecule,"DNA, RNA",,,T
Microarray Label,Microarray used this kind of label,,,,TRUE,Microarray Level 1,,,
Microarray Value Definition,What the provided value signifies,,,,TRUE,Microarray Level 1,,,
Microarray Protocol Auxiliary File,"Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).",,,,True,Microarray Level 1,,,regex match syn\d+
Participant Vital Status Update,Updates to a participants vital status,,"Component, HTAN Participant ID, Vital Status",,FALSE,Patient,,,
Precancer Diagnosis,Diagnosis of a precancerous condition,,"Component, HTAN Participant ID, Precancer Case",,FALSE,Patient,,,
Alive,This indicates the participant is alive and defines further required metadata,,Days to Vital Status Reference,,FALSE,Patient,,,
Days to Vital Status Reference,Number of days between the date used for index and the reference date for designation of vital status,,,,TRUE,Patient,,,int
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]$
220 changes: 216 additions & 4 deletions HTAN.model.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -27725,6 +27725,9 @@
{
"@id": "bts:Fresh"
},
{
"@id": "bts:Frozenat-20C"
},
{
"@id": "bts:Frozenat-70C"
},
Expand Down Expand Up @@ -42936,6 +42939,9 @@
{
"@id": "bts:BarrettsEsophagusGobletCellsPresent"
},
{
"@id": "bts:PrecancerCase"
},
{
"@id": "bts:TreatmentorTherapy"
},
Expand Down Expand Up @@ -51275,6 +51281,9 @@
{
"@id": "bts:HistoryofAtypicalNevi"
},
{
"@id": "bts:PrecancerCase"
},
{
"@id": "bts:CauseofDeathSource"
},
Expand Down Expand Up @@ -51563,15 +51572,15 @@
{
"@id": "bts:LungAdjacentHistologyType"
},
{
"@id": "bts:StorageMethod"
},
{
"@id": "bts:HistoneVariant"
},
{
"@id": "bts:PreservationMethod"
},
{
"@id": "bts:StorageMethod"
},
{
"@id": "bts:MolecularAnalysisMethod"
},
Expand Down Expand Up @@ -51727,6 +51736,9 @@
{
"@id": "bts:TreatmentEffectIndicator"
},
{
"@id": "bts:PrecancerCase"
},
{
"@id": "bts:Ethnicity"
},
Expand Down Expand Up @@ -58672,6 +58684,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Frozenat-20C",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "Frozenat-20C",
"rdfs:subClassOf": [
{
"@id": "bts:StorageMethod"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Frozen at -20C",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Frozenat-70C",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -59480,9 +59509,12 @@
{
"@id": "bts:Alive",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:comment": "This indicates the participant is alive and defines further required metadata",
"rdfs:label": "Alive",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
},
{
"@id": "bts:VitalStatus"
}
Expand All @@ -59492,6 +59524,11 @@
},
"sms:displayName": "Alive",
"sms:required": "sms:false",
"sms:requiresDependency": [
{
"@id": "bts:DaystoVitalStatusReference"
}
],
"sms:validationRules": []
},
{
Expand Down Expand Up @@ -151149,6 +151186,181 @@
"sms:displayName": "droplet",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:ParticipantVitalStatusUpdate",
"@type": "rdfs:Class",
"rdfs:comment": "Updates to a participants vital status",
"rdfs:label": "ParticipantVitalStatusUpdate",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Participant Vital Status Update",
"sms:required": "sms:false",
"sms:requiresDependency": [
{
"@id": "bts:Component"
},
{
"@id": "bts:HTANParticipantID"
},
{
"@id": "bts:VitalStatus"
}
],
"sms:validationRules": []
},
{
"@id": "bts:PrecancerDiagnosis",
"@type": "rdfs:Class",
"rdfs:comment": "Diagnosis of a precancerous condition",
"rdfs:label": "PrecancerDiagnosis",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Precancer Diagnosis",
"sms:required": "sms:false",
"sms:requiresDependency": [
{
"@id": "bts:Component"
},
{
"@id": "bts:HTANParticipantID"
},
{
"@id": "bts:PrecancerCase"
}
],
"sms:validationRules": []
},
{
"@id": "bts:PrecancerCase",
"@type": "rdfs:Class",
"rdfs:comment": "Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).",
"rdfs:label": "PrecancerCase",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Yes-PrecancerCase"
},
{
"@id": "bts:No"
},
{
"@id": "bts:NotReported"
},
{
"@id": "bts:Unknown"
}
],
"sms:displayName": "Precancer Case",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:DaystoVitalStatusReference",
"@type": "rdfs:Class",
"rdfs:comment": "Number of days between the date used for index and the reference date for designation of vital status",
"rdfs:label": "DaystoVitalStatusReference",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Days to Vital Status Reference",
"sms:required": "sms:true",
"sms:validationRules": [
"int"
]
},
{
"@id": "bts:Yes-PrecancerCase",
"@type": "rdfs:Class",
"rdfs:comment": "Indicates that the participant is a precancer case",
"rdfs:label": "Yes-PrecancerCase",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
},
{
"@id": "bts:PrecancerCase"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Yes - Precancer Case",
"sms:required": "sms:false",
"sms:requiresDependency": [
{
"@id": "bts:PrecancerousConditionType"
},
{
"@id": "bts:DaystoPrecancerCaseDesignation"
},
{
"@id": "bts:WHOPrecursorLesionCode"
}
],
"sms:validationRules": []
},
{
"@id": "bts:DaystoPrecancerCaseDesignation",
"@type": "rdfs:Class",
"rdfs:comment": "Number of days between the date used for index and the reference date for designation of precancer status.",
"rdfs:label": "DaystoPrecancerCaseDesignation",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Days to Precancer Case Designation",
"sms:required": "sms:false",
"sms:validationRules": [
"int"
]
},
{
"@id": "bts:WHOPrecursorLesionCode",
"@type": "rdfs:Class",
"rdfs:comment": "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",
"rdfs:label": "WHOPrecursorLesionCode",
"rdfs:subClassOf": [
{
"@id": "bts:Patient"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "WHO Precursor Lesion Code",
"sms:required": "sms:false",
"sms:validationRules": [
"regex match ^\\d{4}\\/[0-3]$"
]
}
],
"@id": "http://schema.biothings.io/#0.1"
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