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EBIvariation / opentargets-pharmgkb

Pipeline to provide evidence strings for Open Targets from PharmGKB
Apache License 2.0
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Named alleles #33

Closed apriltuesday closed 8 months ago

apriltuesday commented 8 months ago

Better diff of test output here

Example named-allele evidence:

{
  "datasourceId": "pharmgkb",
  "datasourceVersion": "2024-01-05",
  "datatypeId": "clinical_annotation",
  "studyId": "1448104189",
  "evidenceLevel": "2A",
  "literature": [
    "16338275",
    "17329992",
    "26389554",
    "26389554",
    "27286724",
    "17178267",
    "17502774",
    "17502774",
    "21589866",
    "28723731",
    "28723731",
    "32302325"
  ],
  "genotype": "*6",
  "genotypeAnnotationText": "Patients carrying the CYP2B6*6 allele in combination with a normal or decreased function allele may have decreased clearance of methadone as compared to patients with two normal function alleles. However, conflicting evidence has been reported. Other genetic and clinical factors may also affect methadone metabolism. This annotation only covers the pharmacokinetic relationship between CYP2B6 and methadone and does not include evidence about clinical outcomes.",
  "directionality": "Decreased function",
  "drugFromSource": "methadone",
  "drugFromSourceId": "CHEBI_6807",
  "pgxCategory": "metabolism/pk",
  "phenotypeText": "Heroin Dependence",
  "phenotypeFromSourceId": "EFO_0004240",
  "haplotypeId": "CYP2B6*6",
  "haplotypeFromSourceId": "PA165818762",
  "targetFromSourceId": "ENSG00000197408"
}
apriltuesday commented 8 months ago

Updates to schema as per this thread