ICD diagnosis codes sometimes have an OMOP code with a different domain than the mapped OMOP code - how to handle?

Vocabulary Users
1

Trying to understand how to ETL ICD diagnosis codes into OMOP. Many have a domain_id that is not Condition, which I understand. However, what happens when the domain_id IS Condition, but its mappings to a “standard concept” are NOT Condition?

Options:

  1. Add a row only in the domain of the standard concept mapping (e.g., Observation).
  2. Add a row in both the domain of the standard concept mapping AND the domain of the source concept_id (e.g., Condition). Presumably then the concept_id in this row would be 0.

The latter acknowledges that the source data had a row in a domain even though no standard mapping exists, though the former is more compact. Which is correct?

Thanks,
Jeff Klann

2

@jklann:

You are right. But this is wrong. The domain of the ICDs has to match their mapped Standard Concepts counterpart. Will fix. Not clear what happened.

3

On domains for mapped concepts, I suspect it is #1 (row only in the standard concept’s table), but I await more sage advice.

4

Christian and George are right. You add only one row to a CDM table that corresponds to a standard concept’s domain.
I’m guessing we’ve never got to massive domain change in ICD as people are used to seeing them as conditions. Sure enough, they should match SNOMED domains.

5

This (and many other problems) could be part of our “code pieces” in the CDM github here: https://github.com/OHDSI/CommonDataModel/tree/master/CodeExcerpts

In our ETL, we try in stage1 to map everthing to the source value and then do the maps-to step. in stage2

I think the ETL code from stage1 to stage2 can be “standardized” for diagnoses coming in as ICD9 or ICD10. And can be a code-excerpt contribution.

This is a call to the community to think about their CodeExcerpts that they would like to contribute. Jeff, consider please sharing your experience with the ICD data loading. Perhaps via CodeExcerpts.