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Is Vocabulary available for OMOP_CDM_v6?

(Yun Mai) #1

The OMOP CDM at OHDSI github released now is version 6. The vocabulary on ATHENA now is for version CDM version 4 and 5. Is any Vocabulary available for OMOP_CDM_v6? Should I use Vocabulary v5 for CDM v6 if I want to build CDM v6?
Thank you so much for your help in advance.

(Anna Karenina) #2

Hello @yunmai,

You can use the v5 vocabularies from Athena for building CDM v6, the structure of vocabulary tables has not changed.

(Yun Mai) #3

Hi @rookie_crewkie,

Thank you for your reply. I compared the fields in the same table between v5 and v6 and found that the structure is the same. I noticed there were two tables, cohort_definition and attribute_definition, in standard vocabularies of CDM v5 but not in v6. I wasn’t sure the content in the vocabulary is compatible between v5 and v6 and wasn’t sure if I can use the vocabularies for v6 that is explicitly for v5.

Now I will go ahead to load the vocabulary to the database. Thanks.

(Anna Karenina) #4


The vocabulary data you get from Athena do not include anything for cohort_definition and attribute_definition tables, so you’ll be able to load it just fine. The only quirky thing I recall was that vocabulary.vocabulary_reference field is required (in docs) but vocabulary data had a couple of records with NULL values; but I think it was fixed long time ago.