search

National-Clinical-Cohort-Collaborative / Data-Ingestion-and-Harmonization

Data Ingestion and Harmonization
41 stars 12 forks source link

OHDSI Vocabulary maps certain procedures in to visit domain. Include these data elements into the visit domain. #124

Closed stephanieshong closed 3 weeks ago

stephanieshong commented 3 months ago

Some procedure codes that map to the visit domain were previously ignored from the source data because we received a specific list of visits via encounter data. The new OMOP vocabulary table version has changed how certain procedure codes (e.g., CPT4, HCPCS) are mapped. Now certain procedure codes can be map to the visit domain, such as visits to a pharmacy or outpatient clinic for a dietary procedure review or management or HCPCS code testing for the presence or absence of COVID. Previously, we ignored these codes, but for consistency, we are now reviewing and including them in the visit_occurrence domain. This may introduce extra noise in the visit domain, but it aligns with the OMOP vocabulary relationship in our translation pipeline.

stephanieshong commented 3 weeks ago

To be consistent with the OMOP vocabulary mapping, procedure codes that maps to visit domain are created in the pipeline. In addition if we see source data that is found in the wrong domain, we move the data to the correct domain.

stephanieshong commented 3 weeks ago

This completes the re-alignment and harmonization of all terminology and vocabulary mapping, as well as domain mapping, using a single version of the OMOP vocabulary tables that is installed on the Enclave. We upgraded the OMOP CDM sites data that might be a vocabulary version or two behind to the latest OMOP standard terms. The domain routing is also performed based on the rules defined in the OMOP concept table. Single version of OMOP vocabulary tables are used to harmonize all incoming N3C data.