Good evening -
I have been downloading the OMOP standardized vocabularies for the purpose of reloading our source_to_standard table, and it seems to work pretty well. The new vocabulary set had all the COVID-related concepts we were missing. Thank you all for the hard work!
However, I did notice one quirk, the new dataset is missing, for certain vaccines, some of the CPT4 > standard concept mapping that was included in my old dataset.
SELECT * FROM concept_relationship
WHERE (concept_id_1 IN (44816520, 42628616, 42628541, 2213492)) AND relationship_id = 'Maps to
old dataset: 4 rows
new dataset: 0 rows
I did run get a UMLS key and run the Java utility to map the CPT4 codes, which ran without incident.
The front end of Athena has the non-standard > standard mapping for the above concept IDs, which makes me nervous that the problem is my implementation, not a change in business rules > eg https://athena.ohdsi.org/search-terms/terms/2213492
I understand that there’s a lot of discussion around improving the mapping of exactly these codes (that’s not super penetrable for me as a data engineer, not a medical vocabulary expert) Vaccine concept mapping improvement
Really what I’m asking, is the change in the concept_relationship table expected behavior, or is it my implementation of the concept_relationship table?
Thank you for your attention and for everything that you do.