Merge pull request #180 from opentargets/ds_3110_pharmacogenomics_schema

feat: adding new schema for pharmacogenomics
opentargets · Oct 17, 2023 · 7f5ce2d · 7f5ce2d
2 parents 022fabb + 435b8fa
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diff --git a/pydantic_models/pharmacogenomics.py b/pydantic_models/pharmacogenomics.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+"""Generating a JSON schema via Pydantic models."""
+
+from enum import Enum
+from typing import List, Optional
+
+from pydantic import BaseModel, Extra, Field
+
+
+class phenotypeCategory(str, Enum):
+    """Accepted phenotype categories describing pharmacogenomic effect."""
+
+    toxicity = "toxicity"
+    efficacy = "efficacy"
+    dosage = "dosage"
+    metabolism = ("metabolism/pk",)
+    pd = "pd"
+    other = "other"
+
+
+class EvidenceLevel(str, Enum):
+    """Evidence levels class describing the confidence in the assocations."""
+
+    _1a = "1A"
+    _1b = "1B"
+    _2a = "2A"
+    _2b = "2B"
+    _3 = "3"
+    _4 = "4"
+
+
+class Pharmacogenomics(BaseModel):
+    """Pharmacogenomics schema object."""
+
+    datasourceId: str = "pharmgkb"
+    datasourceVersion: str = Field(
+        description="Date of data dump generation.",
+        regex=r"[12]\d{3}-[01][0-9]-[0123][0-9]",
+        examples=["2023-08-05"],
+    )
+    datatypeId: str = "clinical_annotation"
+    studyId: str = Field(
+        description="Clinical Annotation ID in the PharmKGB dataset.",
+        examples=["1449309937"],
+    )
+    evidenceLevel: EvidenceLevel = Field(
+        description="Level of evidence. More info: https://www.pharmgkb.org/page/clinAnnLevels.",
+        examples=["1A"],
+    )
+    literature: List[str] = Field(
+        description="List of PMIDs of supporting publications.",
+    )
+    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=[
+            "19_38499645_GGAG_G,GGAG",
+            "20_54156202_T_C,T",
+            "X_12885540_A_A"
+        ],
+        regex=r"^[0-9YX]{1,2}_\d+_[GATC]+_([GATC]+,)?[GATC]+$",
+    )
+    variantRsId: str = Field(
+        description="RS identifier of the variant.",
+        examples=["rs12354"],
+        regex=r"^rs\d+$",
+    )
+    variantFunctionalConsequenceId: Optional[str] = Field(
+        description="Sequence Ontology term, from VEP.",
+        examples=["SO_0001822"],
+        regex=r"^SO_\d+$",
+    )
+    targetFromSourceId: Optional[str] = Field(
+        description="Ensembl gene identifier.",
+        examples=["ENSG00000196218"],
+        regex=r"^ENSG\d+$",
+    )
+    genotype: str = Field(
+        description="Genotype string.", examples=["(CA)16/(CA)17", "TA", "del/GAG"]
+    )
+    genotypeAnnotationText: str = Field(
+        description="Full annotation string for genotype.",
+        examples=[
+            "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics [...]"
+        ],
+    )
+    drugFromSource: str = Field(description="Drug name.", examples=["succinylcholine"])
+    drugId: Optional[str] = Field(
+        description="CHEBI ID of drug, mapped through OLS.",
+        examples=["CHEBI_45652"],
+        regex=r"^CHEBI_\d+$",
+    )
+    # pgxCategory: phenotypeCategory = Field(
+    pgxCategory: str = Field(
+        description="Pharmacogenomics phenotype category.", examples=["toxicity"]
+    )
+    phenotypeText: Optional[str] = Field(
+        description="Phenotype name.", examples=["Malignant Hyperthermia"]
+    )
+    phenotypeFromSourceId: Optional[str] = Field(
+        description="EFO ID of phenotype, mapped through ZOOMA / OXO.",
+        examples=["Orphanet_423"],
+        regex=r"^NCIT_C\d+$|^Orphanet_\d+$|^GO_\d+$|^HP_\d+$|^EFO_\d+$|^MONDO_\d+$|^DOID_\d+$|^MP_\d+$|^OTAR_\d+$|^PATO_\d+$|^CHEBI_\d+$|^OBI_\d+$|^OGMS_\d+$",
+    )
+
+    class Config:
+        title = "OpenTargets-Pharmacogenomics"
+        extra = Extra.forbid
+        anystr_strip_whitespace = True
+
+
+def main() -> None:
+    with open("pharmacogenomics.json", "wt") as f:
+        f.write(Pharmacogenomics.schema_json(indent=2))
+        f.write('\n')
+
+
+if __name__ == "__main__":
+    main()
diff --git a/schemas/pharmacogenomics.json b/schemas/pharmacogenomics.json
@@ -0,0 +1,178 @@
+{
+  "title": "OpenTargets-Pharmacogenomics",
+  "description": "Pharmacogenomics schema object.",
+  "type": "object",
+  "properties": {
+    "datasourceId": {
+      "title": "Datasourceid",
+      "default": "pharmgkb",
+      "type": "string"
+    },
+    "datasourceVersion": {
+      "title": "Datasourceversion",
+      "description": "Date of data dump generation.",
+      "pattern": "[12]\\d{3}-[01][0-9]-[0123][0-9]",
+      "examples": [
+        "2023-08-05"
+      ],
+      "type": "string"
+    },
+    "datatypeId": {
+      "title": "Datatypeid",
+      "default": "clinical_annotation",
+      "type": "string"
+    },
+    "studyId": {
+      "title": "Studyid",
+      "description": "Clinical Annotation ID in the PharmKGB dataset.",
+      "examples": [
+        "1449309937"
+      ],
+      "type": "string"
+    },
+    "evidenceLevel": {
+      "description": "Level of evidence. More info: https://www.pharmgkb.org/page/clinAnnLevels.",
+      "examples": [
+        "1A"
+      ],
+      "allOf": [
+        {
+          "$ref": "#/definitions/EvidenceLevel"
+        }
+      ]
+    },
+    "literature": {
+      "title": "Literature",
+      "description": "List of PMIDs of supporting publications.",
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "genotypeId": {
+      "title": "Genotypeid",
+      "description": "VCF-style (chr_pos_ref_allele1,allele2) identifier of genotype; computed as described here: https://github.com/apriltuesday/opentargets-pharmgkb/tree/issue-18#variant-coordinate-computation.",
+      "pattern": "^[0-9YX]{1,2}_\\d+_[GATC]+_([GATC]+,)?[GATC]+$",
+      "examples": [
+        "19_38499645_GGAG_G,GGAG",
+        "20_54156202_T_C,T",
+        "X_12885540_A_A"
+      ],
+      "type": "string"
+    },
+    "variantRsId": {
+      "title": "Variantrsid",
+      "description": "RS identifier of the variant.",
+      "pattern": "^rs\\d+$",
+      "examples": [
+        "rs12354"
+      ],
+      "type": "string"
+    },
+    "variantFunctionalConsequenceId": {
+      "title": "Variantfunctionalconsequenceid",
+      "description": "Sequence Ontology term, from VEP.",
+      "pattern": "^SO_\\d+$",
+      "examples": [
+        "SO_0001822"
+      ],
+      "type": "string"
+    },
+    "targetFromSourceId": {
+      "title": "Targetfromsourceid",
+      "description": "Ensembl gene identifier.",
+      "pattern": "^ENSG\\d+$",
+      "examples": [
+        "ENSG00000196218"
+      ],
+      "type": "string"
+    },
+    "genotype": {
+      "title": "Genotype",
+      "description": "Genotype string",
+      "examples": [
+        "(CA)16/(CA)17",
+        "TA",
+        "del/GAG"
+      ],
+      "type": "string"
+    },
+    "genotypeAnnotationText": {
+      "title": "Genotypeannotationtext",
+      "description": "Full annotation string for genotype.",
+      "examples": [
+        "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics [...]"
+      ],
+      "type": "string"
+    },
+    "drugFromSource": {
+      "title": "Drugfromsource",
+      "description": "Drug name",
+      "examples": [
+        "succinylcholine"
+      ],
+      "type": "string"
+    },
+    "drugId": {
+      "title": "Drugid",
+      "description": "CHEBI ID of drug, mapped through OLS",
+      "pattern": "^CHEBI_\\d+$",
+      "examples": [
+        "CHEBI_45652"
+      ],
+      "type": "string"
+    },
+    "pgxCategory": {
+      "title": "Pgxcategory",
+      "description": "Pharmacogenomics phenotype category.",
+      "examples": [
+        "toxicity"
+      ],
+      "type": "string"
+    },
+    "phenotypeText": {
+      "title": "Phenotypetext",
+      "description": "Phenotype name.",
+      "examples": [
+        "Malignant Hyperthermia"
+      ],
+      "type": "string"
+    },
+    "phenotypeFromSourceId": {
+      "title": "Phenotypefromsourceid",
+      "description": "EFO ID of phenotype, mapped through ZOOMA / OXO.",
+      "pattern": "^NCIT_C\\d+$|^Orphanet_\\d+$|^GO_\\d+$|^HP_\\d+$|^EFO_\\d+$|^MONDO_\\d+$|^DOID_\\d+$|^MP_\\d+$|^OTAR_\\d+$|^PATO_\\d+$|^CHEBI_\\d+$|^OBI_\\d+$|^OGMS_\\d+$",
+      "examples": [
+        "Orphanet_423"
+      ],
+      "type": "string"
+    }
+  },
+  "required": [
+    "datasourceVersion",
+    "studyId",
+    "evidenceLevel",
+    "literature",
+    "variantRsId",
+    "genotype",
+    "genotypeAnnotationText",
+    "drugFromSource",
+    "pgxCategory"
+  ],
+  "additionalProperties": false,
+  "definitions": {
+    "EvidenceLevel": {
+      "title": "EvidenceLevel",
+      "description": "Evidence levels class describing the confidence in the assocations.",
+      "enum": [
+        "1A",
+        "1B",
+        "2A",
+        "2B",
+        "3",
+        "4"
+      ],
+      "type": "string"
+    }
+  }
+}