TODO - Mapping: Procedure Annotations

callahantiff / OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies

http://tiffanycallahan.com/OMOP2OBO_Dashboard

MIT License

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TODO - Mapping: Procedure Annotations #15

Closed callahantiff closed 5 years ago

callahantiff commented 5 years ago

Needed Scripts: verify code to create procedure code mapping

[x] Code to get synonyms, labels, and defs from ontologies (write code to download data)
[x] Similarity code
[ ] Generate mappings
[ ] Verify mappings

Inputs: pandas data frame or results of SQL query Action: maps clinical concepts to different open biomedical ontologies (OBOs) Output: csv file with suggested mappings between condition codes and OBOs

callahantiff commented 5 years ago

Closing: it's unclear exactly how the NCIT ontology, which we are using to map OMOP procedures could be meaningfully integrated with the rest of the KG. Will not prioritize mapping this clinical domain at this time.