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?
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
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!
Following up on this thread since I’m attempting to map CUIs to OMOP concepts using each CUI’s source identifier (the “CODE” column). However, I have come across a handful of instances where certain source identifiers are not captured as source codes in concept records.
Please refer to the examples below. I understand the second one is a bit trickier to map, so using the first one as a case study makes more sense.
Is there something I am missing in the mapping process? If this is the correct approach, is there any way to address this issue?
