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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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Issue 36: Improve genotype ID algorithm #37

Closed apriltuesday closed 5 months ago

apriltuesday commented 6 months ago

Closes #36 Also includes the notebook for #21

Example evidence strings for rs72549309 (dbsnp, pgkb)

Reference only:

  "datasourceId": "pharmgkb",
  "datasourceVersion": "2024-04-05",
  "datatypeId": "clinical_annotation",
  "studyId": "1447989678",
  "evidenceLevel": "1A",
  "literature": [
    "10071185",
    "24648345"
  ],
  "genotype": "ATGA/ATGA",
  "genotypeAnnotationText": "The del allele of rs72549309 is assigned no function by CPIC. Patients with the ATGA/ATGA genotype may have increased DPYD activity as compared to those with the ATGA/del or del/del genotypes. Other genetic and clinical factors may also influence catalytic activity of DPYD.",
  "drugFromSource": "fluorouracil",
  "drugFromSourceId": "CHEBI_46345",
  "pgxCategory": "other",
  "genotypeId": "1_97740410_GATGA_GATGA,GATGA",
  "variantRsId": "rs72549309",
  "variantFunctionalConsequenceId": "SO_0002073",
  "targetFromSourceId": "ENSG00000188641"
}

With variant:

{
  "datasourceId": "pharmgkb",
  "datasourceVersion": "2024-04-05",
  "datatypeId": "clinical_annotation",
  "studyId": "1447989678",
  "evidenceLevel": "1A",
  "literature": [
    "10071185",
    "24648345"
  ],
  "genotype": "ATGA/del",
  "genotypeAnnotationText": "The del allele of rs72549309 is assigned no function by CPIC. Patients with the ATGA/del genotype may have decreased DPYD activity as compared to those with the ATGA/ATGA genotype. Other genetic and clinical factors may also influence catalytic activity of DPYD.",
  "drugFromSource": "fluorouracil",
  "drugFromSourceId": "CHEBI_46345",
  "pgxCategory": "other",
  "genotypeId": "1_97740410_GATGA_G,GATGA",
  "variantRsId": "rs72549309",
  "variantFunctionalConsequenceId": "SO_0001589",
  "targetFromSourceId": "ENSG00000188641"
}