Merge pull request #184 from opentargets/il-pgx

feat(pgx): add haplotypeId
opentargets · Jan 23, 2024 · 6973c68 · 6973c68
2 parents cc9b929 + 04e5816
commit 6973c68
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Showing 2 changed files with 16 additions and 4 deletions.
diff --git a/pydantic_models/pharmacogenomics.py b/pydantic_models/pharmacogenomics.py
@@ -50,6 +50,10 @@ class Pharmacogenomics(BaseModel):
     literature: List[str] = Field(
         description="List of PMIDs of supporting publications.",
     )
+    haplotypeId: Optional[str] = Field(
+        description="Combination of genetic variants that constitute a particular allele of a gene.",
+        examples=["CYP2C9*3"],
+    )
     genotypeId: Optional[str] = Field(
         description="VCF-style (chr_pos_ref_allele1,allele2) identifier of genotype; computed as described here: https://github.com/apriltuesday/opentargets-pharmgkb/tree/issue-18#variant-coordinate-computation.",
         examples=[
@@ -109,7 +113,7 @@ class Config:
 
 
 def main() -> None:
-    with open("pharmacogenomics.json", "wt") as f:
+    with open("schemas/pharmacogenomics.json", "wt") as f:
         f.write(Pharmacogenomics.schema_json(indent=2))
         f.write('\n')
 

diff --git a/schemas/pharmacogenomics.json b/schemas/pharmacogenomics.json
@@ -49,6 +49,14 @@
         "type": "string"
       }
     },
+    "haplotypeId": {
+      "title": "Haplotypeid",
+      "description": "Combination of genetic variants that constitute a particular allele of a gene.",
+      "examples": [
+        "CYP2C9*3"
+      ],
+      "type": "string"
+    },
     "genotypeId": {
       "title": "Genotypeid",
       "description": "VCF-style (chr_pos_ref_allele1,allele2) identifier of genotype; computed as described here: https://github.com/apriltuesday/opentargets-pharmgkb/tree/issue-18#variant-coordinate-computation.",
@@ -89,7 +97,7 @@
     },
     "genotype": {
       "title": "Genotype",
-      "description": "Genotype string",
+      "description": "Genotype string.",
       "examples": [
         "(CA)16/(CA)17",
         "TA",
@@ -107,15 +115,15 @@
     },
     "drugFromSource": {
       "title": "Drugfromsource",
-      "description": "Drug name",
+      "description": "Drug name.",
       "examples": [
         "succinylcholine"
       ],
       "type": "string"
     },
     "drugId": {
       "title": "Drugid",
-      "description": "CHEBI ID of drug, mapped through OLS",
+      "description": "CHEBI ID of drug, mapped through OLS.",
       "pattern": "^CHEBI_\\d+$",
       "examples": [
         "CHEBI_45652"