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Mapping stages from disease table in CDA #30

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pnrobinson opened this issue Nov 21, 2023 · 1 comment
Open

Mapping stages from disease table in CDA #30

pnrobinson opened this issue Nov 21, 2023 · 1 comment

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@pnrobinson
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  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
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ielis commented Feb 2, 2024

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

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