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Merge pull request #407 from ncihtan/306-implement-precancerclinical-…
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…data-updates-and-testing

Implement Participant Vital Status Update and Precancer Diagnosis templates
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@aditigopalan
aditigopalan authored May 30, 2024
2 parents f8798bf + 021c933 commit 1f9a7cd
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8 changes: 8 additions & 0 deletions HTAN.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -1030,3 +1030,11 @@ Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophag
Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num
HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,,
Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,,
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]$
194 changes: 193 additions & 1 deletion HTAN.model.jsonld
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Expand Up @@ -42718,6 +42718,9 @@
{
"@id": "bts:BarrettsEsophagusGobletCellsPresent"
},
{
"@id": "bts:PrecancerCase"
},
{
"@id": "bts:TreatmentorTherapy"
},
Expand Down Expand Up @@ -51054,6 +51057,9 @@
{
"@id": "bts:HistoryofAtypicalNevi"
},
{
"@id": "bts:PrecancerCase"
},
{
"@id": "bts:CauseofDeathSource"
},
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{
"@id": "bts:TreatmentEffectIndicator"
},
{
"@id": "bts:PrecancerCase"
},
{
"@id": "bts:Ethnicity"
},
Expand Down Expand Up @@ -59276,9 +59285,12 @@
{
"@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 @@ -59288,6 +59300,11 @@
},
"sms:displayName": "Alive",
"sms:required": "sms:false",
"sms:requiresDependency": [
{
"@id": "bts:DaystoVitalStatusReference"
}
],
"sms:validationRules": []
},
{
Expand Down Expand Up @@ -150942,6 +150959,181 @@
"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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