OHDSI Home | Forums | Wiki | Github

Mapping from OHDSI concept id to UMLS concept id


(Miao Chen) #1

Hi,

I have a question about how I can map an OHDSI concept id to a UMLS concept. What I know is (learned from the recent OHDSI tutorial), given a concept name, I can retrieve its OHDSI concept id from the concept table and also find its ID in the source vocabulary ( e.g. a LOINC vocabulary id), and then I can retrieve this source concept id in the UMLS database to get its UMLS id.

This would mean multiple joins. Is there some table in OHDSI that has the mapping from OHDSI concept id to UMLS concept id directly?

Thanks for your help.

Miao


(Dmytry Dymshyts) #2

Hi @mchen
There’s no standard OHDSI Vocabulary table related to UMLS.
You can install UMLS on your instance.
Here is a code we use for this purpose (postgreSQL)

Then “code” column from MRCONSO table corresponds to concept_code
“SAB” column from MRCONSO corresponds to vocabulary_id
sab = ‘SNOMEDCT_US’ corresponds to vocabulary_id= ‘SNOMED’
sab = ‘RXNORM’ corresponds to vocabulary_id= ‘RxNorm’
sab = ‘LNC’ corresponds to vocabulary_id= ‘LOINC’
and so on, you can find what different SAB mean in UMLS documentation.
So you need only one join :slight_smile:


(Miao Chen) #3

Hi @Dymshyts thanks a lot for your quick reply and the query example. It’s good to know there is a table with this OMOP id and source vocabulary information!


t