Cavatica project to work from: https://cavatica.sbgenomics.com/u/mmattioni/include-htp-meta
Main idea is:
for all the files in project:
- extract
fhir_document_reference
This is how it looks like:
// 20220714112305
// https://include-api-fhir-service.includedcc.org/DocumentReference?identifier=HTP.0012022d-c855-4087-9dde-c522f0632024.kallisto.abundance.tsv.gz&_format=json
{
"resourceType": "Bundle",
"id": "17a64462-2c75-49ff-9045-018f5876fccd",
"meta": {
"lastUpdated": "2022-07-14T09:22:59.484+00:00"
},
"type": "searchset",
"total": 1,
"link": [
{
"relation": "self",
"url": "https://include-api-fhir-service.includedcc.org/DocumentReference?_format=json&identifier=HTP.0012022d-c855-4087-9dde-c522f0632024.kallisto.abundance.tsv.gz"
}
],
"entry": [
{
"fullUrl": "https://include-api-fhir-service.includedcc.org/DocumentReference/317218",
"resource": {
"resourceType": "DocumentReference",
"id": "317218",
"meta": {
"versionId": "2",
"lastUpdated": "2022-06-27T20:13:06.978+00:00",
"source": "#09XK9onJ1OBmDYxw",
"profile": [
"https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-document-reference"
],
"tag": [
{
"system": "https://include.org/htp/fhir/researchstudy",
"code": "HTP"
}
]
},
"identifier": [
{
"use": "official",
"system": "https://include.org/htp/fhir/documentreference",
"value": "HTP.0012022d-c855-4087-9dde-c522f0632024.kallisto.abundance.tsv.gz"
}
],
"status": "current",
"docStatus": "final",
"type": {
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_types",
"version": "v1",
"code": "Gene-Expression-Quantifications",
"display": "Gene Expression Quantifications"
}
],
"text": "Gene Expression"
},
"category": [
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/experimental_strategies",
"version": "v1",
"code": "RNA-Seq",
"display": "RNA-Seq"
}
],
"text": "RNA-Seq"
},
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_categories",
"version": "v1",
"code": "Transcriptomic",
"display": "Transcriptomic"
}
],
"text": "Transcriptomic"
}
],
"subject": {
"reference": "Patient/4941"
},
"securityLabel": [
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_access_types",
"version": "v1",
"code": "registered",
"display": "Registered"
}
]
},
{
"text": "*"
}
],
"content": [
{
"attachment": {
"extension": [
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/file-size",
"valueDecimal": 2743960
},
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/hashes",
"valueCodeableConcept": {
"coding": [
{
"display": "md5"
}
],
"text": "69b98f149df72d8de23a6a1333a43515"
}
}
],
"url": "drs://data.kidsfirstdrc.org/733f0956-dac4-4ad9-b787-4e186c6530b0",
"title": "0012022d-c855-4087-9dde-c522f0632024.kallisto.abundance.tsv.gz"
},
"format": {
"display": "tsv"
}
}
],
"context": {
"related": [
{
"reference": "Specimen/297344"
}
]
}
},
"search": {
"mode": "match"
}
}
]
}
entry --> subject gives me the patient
There could be an option to reverse chanin, but it does not work nicely, so the idea is:
Search for condition == MONDO:000860 and verification-status-confirmed and subject with the Patient Id
if nothing found, we get search list equal to zero
// 20220714114620
// https://include-api-fhir-service.includedcc.org/Condition?code=MONDO%3A0008608&subject=Patient%2F4927&verification-status=confirmed&_format=json
{
"resourceType": "Bundle",
"id": "2811c99d-d2f8-488c-9ac9-3d605180e0c9",
"meta": {
"lastUpdated": "2022-07-14T09:46:20.427+00:00"
},
"type": "searchset",
"total": 0,
"link": [
{
"relation": "self",
"url": "https://include-api-fhir-service.includedcc.org/Condition?_format=json&code=MONDO%3A0008608&subject=Patient%2F4927&verification-status=confirmed"
}
]
}
which means we can search the total and if 0 set the sample_type to DS21
if instead the Patient has Trisomy
instead if we have trosomy this is what we obtained:
// 20220714115105
// https://include-api-fhir-service.includedcc.org/Condition?code=MONDO%3A0008608&subject=Patient%2F4929&verification-status=confirmed&_format=json
{
"resourceType": "Bundle",
"id": "c5ad06d5-fc1e-4133-9270-38c1af212d28",
"meta": {
"lastUpdated": "2022-07-14T09:50:50.668+00:00"
},
"type": "searchset",
"total": 1,
"link": [
{
"relation": "self",
"url": "https://include-api-fhir-service.includedcc.org/Condition?_format=json&code=MONDO%3A0008608&subject=Patient%2F4929&verification-status=confirmed"
}
],
"entry": [
{
"fullUrl": "https://include-api-fhir-service.includedcc.org/Condition/9089",
"resource": {
"resourceType": "Condition",
"id": "9089",
"meta": {
"versionId": "1",
"lastUpdated": "2022-03-11T01:36:57.396+00:00",
"source": "#DFc1zpVt8Cb0oeZd",
"tag": [
{
"system": "https://include.org/htp/fhir/researchstudy",
"code": "HTP"
}
]
},
"identifier": [
{
"use": "official",
"system": "https://include.org/htp/fhir/condition",
"value": "HTP0005.MONDO:0008608"
}
],
"verificationStatus": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"version": "v1",
"code": "confirmed",
"display": "Confirmed"
}
]
},
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-category",
"code": "encounter-diagnosis",
"display": "Encounter Diagnosis"
}
]
}
],
"code": {
"coding": [
{
"system": "http://purl.obolibrary.org/obo/mondo.owl",
"version": "v1",
"code": "MONDO:0008608",
"display": "Down Syndrome"
},
{
"system": "https://nih-ncpi.github.io/ncpi-fhir-ig/data-dictionary/HTP/ds_condition",
"code": "OfficialDSDiagnosis",
"display": "Typically self/parent report."
}
],
"text": "Complete trisomy 21"
},
"subject": {
"reference": "Patient/4929"
}
},
"search": {
"mode": "match"
}
}
]
}
if total is instead 1, we can set it to T21