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Issue 40: Updates for drugFromSource to support drug combinations #41

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merged 8 commits into from
May 8, 2024

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@apriltuesday apriltuesday commented Apr 24, 2024

Closes #40. Tests won't pass until the OT PGx schema is updated, but here is a test run with validation commented out.

Git struggles with the expected test output diff, this is slightly better. Example evidence string from the test:

{
  "datasourceId": "pharmgkb",
  "datasourceVersion": "2023-03-23",
  "datatypeId": "clinical_annotation",
  "studyId": "1447979749",
  "evidenceLevel": "1A",
  "literature": ["29126871", "28606620", "27898234", "27898234", "25981758", "27805836", "27805836", "29327948", "29451946", "28325531", "27334259", "24973281", "24973281", "24973281", "27298017"],
  "genotype": "CTT/del",
  "genotypeAnnotationText": "Patients with cystic fibrosis and the rs113993960 CTT/del genotype (one copy of the CFTR F508del variant) may experience a limited benefit from treatment with the combination drug of ivacaftor/lumacaftor, as shown by improvement in sweat chloride concentrations CFQ-R questionnaire scores when compared to treatment with placebo. However, ppFEV1, BMI or body weight did not show a significant improvement following ivacaftor/lumacaftor treatment. This genotype is not an indication for use of the combination drug of ivacaftor/lumacaftor according to the FDA-approved drug label for this drug combination. Other genetic and clinical factors may also influence response to ivacaftor/lumacaftor.",
  "drugsFromSource": [
    "ivacaftor",
    "lumacaftor"
  ],
  "pgxCategory": "efficacy",
  "phenotypeText": "Cystic Fibrosis",
  "phenotypeFromSourceId": "MONDO_0009061",
  "genotypeId": "21_5010011_CCTT_C,CCTT",
  "variantRsId": "rs113993960"
}

FYI @DSuveges @ireneisdoomed

@apriltuesday apriltuesday marked this pull request as ready for review April 24, 2024 14:59
@apriltuesday apriltuesday requested a review from tcezard April 24, 2024 14:59
@apriltuesday apriltuesday self-assigned this Apr 24, 2024
opentargets_pharmgkb/pandas_utils.py Outdated Show resolved Hide resolved
opentargets_pharmgkb/evidence_generation.py Outdated Show resolved Hide resolved
@apriltuesday apriltuesday requested a review from tcezard May 7, 2024 16:36
@apriltuesday apriltuesday merged commit b43f03d into EBIvariation:main May 8, 2024
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@apriltuesday apriltuesday deleted the issue-40 branch May 8, 2024 08:08
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Updates for drugFromSource and drugFromSourceId to support drug combinations
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