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

Data Ingestion and Harmonization
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Assess the current state of OMOP pipeline with non-standard concepts prior to OMOP pipeline updates #119

Closed stephanieshong closed 10 months ago

stephanieshong commented 11 months ago

DI&H issues team requested the current state report of this issue prior to making the updates in OMOP pipeline.

stephanieshong commented 11 months ago

I added the initial percent count of concept ids with non-standard concepts found in each OMOP domains. passing the rest of the query to Yvette to perform the final assessment of how much is rescued by re-mapping to "Maps to" concept. Percent of non-standard concepts found in the OMOP CDM sites can be found here: https://unite.nih.gov/workspace/data-integration/dataset/preview/ri.foundry.main.dataset.51f53c7b-f608-4c6b-b765-0c4a6a006cc4/sh%2Fomop-non-standard-concepts report items are in this contour: https://unite.nih.gov/workspace/contour-app/ri.contour.main.analysis.6422ad33-c39d-492a-b0a9-5495536b672a/path/ri.contour.main.ref.d489b015-b137-4608-958c-f6f100135189/board?viewMode=edit

stephanieshong commented 11 months ago

assigning remaining items to @Yvette

stephanieshong commented 10 months ago

We are rescuing deprecated or null concepts using the following relationship_ids 'Maps to', 'RxNorm is a', 'Concept same as to', 'Concept replaced by', 'Concept poss_eq to'.

stephanieshong commented 10 months ago

generated the new xwalk map using the relationship ids above. Passed on the logic for Yvette to insert the newly mapped data as well as the concept data unable to rescue.

stephanieshong commented 10 months ago

Reviewed code for condition_occurrence today with Yvette.