monarch-initiative / oncoexporter

A package to convert cancer data to GA4GH phenopacket
https://monarch-initiative.github.io/oncoexporter
MIT License
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Mapping stages from disease table in CDA #30

Open pnrobinson opened 1 year ago

pnrobinson commented 1 year ago
  1. See file OpDiagnosisMapper
  2. Create TSV file with Stage terms (e.g. https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C27966) -- limit to "generic" stage terms such as Stage III.
  3. Consider how to model this with the MapEntry class -- do we need a class hierarchy (because right now the labels of the "neoplasm_types.tsv" file are hard coded)
  4. Add this to OpDiagnosisMapper and then add the Stage to the Disease entry in Phenopacket.
ielis commented 10 months ago

Update, the stage mapping is the sole responsibility of oncoexporter.cda.mapper.OpDiseaseStageMapper.