EBIvariation / opentargets-pharmgkb

Pipeline to provide evidence strings for Open Targets from PharmGKB
Apache License 2.0
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Add publications to evidence string #6

Closed apriltuesday closed 1 year ago

apriltuesday commented 1 year ago

Some notes on this:

PMIDs for each clinical annotation are found in the clinical_ann_evidence.tsv file, which contains the following types of evidence:

  1. Variant Drug Annotation, example
  2. Variant Phenotype Annotation, example
  3. Variant Functional Assay Annotation, example
  4. Guideline Annotation, example
  5. Label Annotation, example

The first three have associated PMIDs, the latter two do not (and in the case of drug labels might actually generate their own evidence strings). For now I'll assume we'll use all PMIDs present though it should be easy to filter them in the future if desired.