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Published 20 hours ago • verified publisher icon OHDSI

Create the mechanism to keep the vocabulary list up to date

Open TatianaSkugarevskaya opened this issue 2 years ago • 3 comments

Recently we have found out that there is a vocabulary in the Athena download list that has been deleted from the VOCABULARY table and deprecated in the concept (HGNC - Human Gene Nomenclature (European Bioinformatics Institute)). Since this is not supported any more, does not have concepts , it technically 'does not exist' in OMOP. It would be good to find an approach for keeping the Athena vocabulary list up-to-date. HGNC https://github.com/OHDSI/Vocabulary-v5.0/blob/5834f9f149f86598f26a8ee8724185d4fa55ed3d/working/manual_changes/2021/2021-10-20.sql#L1

TatianaSkugarevskaya avatar Dec 02 '22 12:12 TatianaSkugarevskaya

This is connected to this vocabulary issue - we have to remove this entry from the vocabulary_conversion table, which in turn is connected to #278 ....

mik-ohdsi avatar Dec 06 '22 22:12 mik-ohdsi

we have to remove this entry from the vocabulary_conversion table

It was removed within the commit @TatianaSkugarevskaya is referring to.

Alexdavv avatar Dec 09 '22 11:12 Alexdavv

to be precise, this is not an Athena issue but rather an issue on vocabulary maintenance, in which if there is not one concept for a given vocabulary ID on distribution to Athena, the vocabulary ID should be retired (deprecated).

mik-ohdsi avatar Jun 09 '23 07:06 mik-ohdsi