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Update disease ontology codes to always include "DOID:" prefix.
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@rhdolin
rhdolin committed Nov 15, 2024
1 parent 1150e14 commit 797ce2d
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Showing 11 changed files with 889 additions and 1,739 deletions.
3 changes: 2 additions & 1 deletion .gitignore
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.pytest_cache
__pycache__
.venv
utilities/FASTA
utilities/FASTA
utilities/mongo_utilities.py
20 changes: 11 additions & 9 deletions FHIRGenomicsOperations.postman_collection.json
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Expand Up @@ -1099,7 +1099,7 @@
"method": "GET",
"header": [],
"url": {
"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/phenotype-operations/$find-subject-tx-implications?subject=TCGA-DD-A1EH&variants=NC_000001.10:27106893::T&conditions=https://disease-ontology.org|684&ranges=NC_000001.10:27106890-27106900",
"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/phenotype-operations/$find-subject-tx-implications?subject=CA12345&conditions=https://disease-ontology.org|DOID:3908",
"protocol": "https",
"host": [
"fhir-gen-ops",
Expand All @@ -1114,19 +1114,21 @@
"query": [
{
"key": "subject",
"value": "TCGA-DD-A1EH"
"value": "CA12345"
},
{
"key": "variants",
"value": "NC_000001.10:27106893::T"
"value": "NC_000001.10:27106893::T",
"disabled": true
},
{
"key": "conditions",
"value": "https://disease-ontology.org|684"
"value": "https://disease-ontology.org|DOID:3908"
},
{
"key": "ranges",
"value": "NC_000001.10:27106890-27106900"
"value": "NC_000001.10:27106890-27106900",
"disabled": true
}
]
}
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"method": "GET",
"header": [],
"url": {
"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/phenotype-operations/$find-subject-tx-implications?subject=CA12345&variants=NM_002524.5:c.182A>C,NM_001354609.2:c.1799T>A&conditions=https://disease-ontology.org|3908",
"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/phenotype-operations/$find-subject-tx-implications?subject=CA12345&variants=NM_002524.5:c.182A>C,NM_001354609.2:c.1799T>A&conditions=https://disease-ontology.org|DOID:3908",
"protocol": "https",
"host": [
"fhir-gen-ops",
Expand Down Expand Up @@ -1445,7 +1447,7 @@
},
{
"key": "conditions",
"value": "https://disease-ontology.org|3908"
"value": "https://disease-ontology.org|DOID:3908"
}
]
}
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"method": "GET",
"header": [],
"url": {
"raw": "https://fhir-gen-ops.herokuapp.com/population-operations/phenotype-operations/$find-population-tx-implications?conditions=https://disease-ontology.org|3908&includePatientList=true",
"raw": "https://fhir-gen-ops.herokuapp.com/population-operations/phenotype-operations/$find-population-tx-implications?conditions=https://disease-ontology.org|DOID:3908&includePatientList=true",
"protocol": "https",
"host": [
"fhir-gen-ops",
Expand Down Expand Up @@ -2682,7 +2684,7 @@
},
{
"key": "conditions",
"value": "https://disease-ontology.org|3908"
"value": "https://disease-ontology.org|DOID:3908"
},
{
"key": "includePatientList",
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2 changes: 1 addition & 1 deletion app/api_spec.yml
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Expand Up @@ -561,7 +561,7 @@ paths:
items:
type: string
example:
- "https://disease-ontology.org|3908"
- "https://disease-ontology.org|DOID:3908"
style: "form"
explode: false
- name: testIdentifiers
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32 changes: 16 additions & 16 deletions tests/expected_outputs/find_subject_tx_implications/1.json
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Expand Up @@ -5,7 +5,7 @@
"name": "implication",
"resource": {
"resourceType": "Observation",
"id": "dv-63287c9ff7c8d34d272a3d7a",
"id": "dv-6737a82bd7c0d2714e4ae561",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
Expand Down Expand Up @@ -53,7 +53,7 @@
"coding": [
{
"system": "https://disease-ontology.org",
"code": "3908",
"code": "DOID:3908",
"display": "Lung Non-small Cell Carcinoma"
}
]
Expand All @@ -70,7 +70,7 @@
]
},
"valueCodeableConcept": {
"text": "B (Clinical evidence)"
"text": "C (Case study)"
}
},
{
Expand All @@ -87,8 +87,8 @@
"coding": [
{
"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
"code": "1147220",
"display": "Vemurafenib"
"code": "1424911",
"display": "Dabrafenib"
}
]
}
Expand All @@ -104,7 +104,7 @@
]
},
"valueCodeableConcept": {
"text": "Supports Sensitivity/Response"
"text": "Supports Resistance"
}
}
],
Expand All @@ -115,7 +115,7 @@
},
{
"system": "https://civicdb.org/evidence",
"value": "5958"
"value": "91"
}
]
}
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"name": "implication",
"resource": {
"resourceType": "Observation",
"id": "dv-63287c9ff7c8d34d272a3d61",
"id": "dv-6737a82bd7c0d2714e4ae580",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
Expand Down Expand Up @@ -333,7 +333,7 @@
"coding": [
{
"system": "https://disease-ontology.org",
"code": "3908",
"code": "DOID:3908",
"display": "Lung Non-small Cell Carcinoma"
}
]
Expand All @@ -350,7 +350,7 @@
]
},
"valueCodeableConcept": {
"text": "C (Case study)"
"text": "B (Clinical evidence)"
}
},
{
Expand All @@ -367,8 +367,8 @@
"coding": [
{
"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
"code": "1424911",
"display": "Dabrafenib"
"code": "1147220",
"display": "Vemurafenib"
}
]
}
Expand All @@ -384,7 +384,7 @@
]
},
"valueCodeableConcept": {
"text": "Supports Resistance"
"text": "Supports Sensitivity/Response"
}
}
],
Expand All @@ -395,7 +395,7 @@
},
{
"system": "https://civicdb.org/evidence",
"value": "91"
"value": "5958"
}
]
}
Expand All @@ -404,7 +404,7 @@
"name": "implication",
"resource": {
"resourceType": "Observation",
"id": "dv-63287c9ff7c8d34d272a40a9",
"id": "dv-6737a82bd7c0d2714e4ae8f5",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
Expand Down Expand Up @@ -452,7 +452,7 @@
"coding": [
{
"system": "https://disease-ontology.org",
"code": "3908",
"code": "DOID:3908",
"display": "Lung Non-small Cell Carcinoma"
}
]
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