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Duplicate record in concept_synonym csv from Athena

(David Denton) #1

I have downloaded the vocabulary files a few times in the past couple weeks. Each time, there has been a duplicate record on the concept_synonym table that prevents me from adding the unique constraint as defined in the DDL:

ALTER TABLE cdm.concept_synonym ADD CONSTRAINT uq_concept_synonym UNIQUE (concept_id, concept_synonym_name, language_concept_id);

The offending records are:

row_number concept_id concept_synonym_name language_concept_id
3309007 43534828 PHENIBUT 4180186
3309008 43534828 PHENIBUT 4180186

I’m relatively new to the OMOP data model (just starting to code some ETL using Epic-Caboodle as a source). Am I missing something, or is this an error?

(Anna Ostropolets) #2

Agree that it doesn’t look good. You’d expect multiple records only if language differs (but spelling is the same), which is not the case here. Here the issue is that one of the names contains a space that you can’t see.
Here’s the issue for tracking.