ETL Mapping LOINC vocabulary on OMOP Common Data Model

Question

I am working on the lab test values mapping (MEASUREMENT table of the OMOP CDM). My local mapping table (handmade) has my measurement name (in French) and the associated LOINC code.

The LOINC vocabulary has been loaded from Athena (OHDSI community tool) https://athena.ohdsi.org/search-terms/

I load my local concepts into the CONCEPT table, then use an SQL query to associate the equivalent LOINC concept_id (from concept_code mapping/LOINC source codes). I realise that the link is not made on the LOINC concept_code.

Indeed, when I filter the CONCEPT table on a LOINC concept_code (ex 34714-6) I find no result.

select * 
from omop.concept 
where concept_code in ('34714-6');

When I filter on the corresponding concept_id (3032080) I find the result with the desired concept_code.

select * 
from omop.concept 
where concept_id in ('3032080');

I have tested concept_code like '34714__' which returns the expected line. This is not due to the encoding because when I copy/paste the resulting concept_code (filtering on concept_id = ‘3032080’) into my query concept_code in ('34714-6') I get the same problem.

However other LOINC codes work:

select * 
from omop.concept 
where concept_code in ('14646-4');

When I check what symbol exacty is being used :

select ASCII(substr(concept_code,1,1))
    ,ASCII(substr(concept_code,2,1))
    ,ASCII(substr(concept_code,3,1))
    ,ASCII(substr(concept_code,4,1))
    ,ASCII(substr(concept_code,5,1))
    ,ASCII(substr(concept_code,6,1))
    ,ASCII(substr(concept_code,7,1))
from omop.concept
where concept_id = 3032080 ;

I also checked/removed the whitespaces.

The same process works on drugs (concept_code from ATC).

Can you tell me where this error comes from?

Thank you for your help.

Answer 1

please check that you're using the latest sql-client and JDBC driver versions