could you integrate CUIs into parsing?

OHDSI / Criteria2Query

[In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed against OMOP CDM

Apache License 2.0

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could you integrate CUIs into parsing? #12

Closed zhangpn closed 2 years ago

zhangpn commented 5 years ago

I think it'd be helpful to output CUIs or concept codes from UMLS to parsed outputs so that not only terms are marked up but they are also mapped to specific, standardized concepts. This is a very minor point since concept codes are already incorporated into generated queries. Regardless, it would be a "nice to have." thanks.

cgreich commented 5 years ago

@zhangpn: The standardized concepts you are referring to are identified through the concept_ids. CUIs are similar unique identifiers in the UMLS system, but they have different rules: They cross vocabularies. That doesn't work in the OMOP CDM. If you need them for some reason in your use case you may want to join the mrconso table to the CDM CONCEPT table through mrconso.code=concept.concept_code.