Can Leaf query the source codes in an OHDSI CDM dbms?

[artgoldberg]

Hello Nic & Team

As you know, in OHDSI CDMs each clinical dbms record can have a standard concept code and a source concept code. See meta-examples in this list of domains and vocabularies for standard and source codes.

My question is: can Leaf query the source codes in an OHDSI CDM dbms?

Thanks
Arthur

[ndobb]

Hi @artgoldberg,

Thanks for your question! Yes, as Leaf concept WHERE clauses are flexible, Leaf can be configured to use either the OMOP standard concept code or source code (or even incorporate the concept_ancestor table to include descendant coded concepts).

For example, at UW we host one OMOP Leaf instance which happens to use source codes, as can be seen here:

One could instead of course use the standard concept by changing the WHERE clause from:

@.condition_source_value = 'E11.22'

to

@.concept_id = 45595797

which would accomplish the same thing (though you'd likely use different database indexing strategies and so on, depending on your implementation).

Also, in our leaf-scripts repo you can find examples of how we build the concept tree dynamically and assign OMOP WHERE clauses by script as well. (example: https://github.com/uwrit/leaf-scripts/blob/master/omop/5.3/5_vitals.sql#L71).

Best,
-nic

[artgoldberg]

Thanks @ndobb , that's very helpful.