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Why are concept_name and codes null/empty in vocab file for certain records?


(Selva) #1

Hello Everyone,

I was trying to upload the vocab files (Jan 2020). In addition to the format issues discussed here, am able to see that there is NULL value for concept_name in the concept.csv file.

But we have a NOT-NULL constraint defined in concept table. I found out that the records missing has concept ids 36311145, 35941270,45880107, 1379212 ,8497 which in Athena has NAs . But in csv file it is blank/empty

Though I have updated in the concept.csv files for our use, just thought of reporting.

Issue with recent vocab files - format/length error?
(Christian Reich) #2

8497 is deprecated. We cannot make concepts disappear.
1379212 has a proper concept_name (“Ophthalmic Tablets”), but the concept_code happens to be “NA” Sheer coincidence, has nothing to do with “Not applicable”.
The rest are LOINC and NAACCR Value or Answer codes, which go into the value_as_concept_id field. They are defined as such by the source. We cannot change that. If it were up to us we would not have had those. In the OMOP Standaridized Vocabularies they are flavors of NULL.

Bottom line: Don’t convert “NA” to NULL. Leave it as is.