Resolving Issues with Deprecated Concepts in Vocabulary Updates

Vocabulary Users
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Hello OHDSI Community,

I work for IOMED, and we have encountered an issue related to vocabulary versions.

It has been a couple of years since we last updated our vocabulary version (v5.0 28-JAN-22), and recently, with the newest version (V5.0_30-AUG-24) we discovered that numerous concept_ids are deprecated without a designated replacement.

The final step in our update process involves replacing deprecated concepts with their replacements across various OMOP CDM tables (e.g., condition_occurrence_concept_id, drug_concept_id, measurement_concept_id, etc.).To perform this replacement, we use the relationship_id = 'Concept replaces' relationship.

This update works, but upon review, we found that there are still concept_id that remain deprecated and lack a replacement. Thanks to this comment we find that exists another relations that we can used.

But despite considering this new relationships still exists concept_id deprecated without replacement.

One concept_id for example is 73906 - Open wound of wrist with tendon involvement, that has been deprecated, but has no relation of: ‘Concept same_as to’, ‘Concept alt_to to’, ‘Concept poss_eq to’, ‘Concept was_a to’ to a related standard concept.

In this scenario is correct to use another relationship like Maps to o Is a? Is there any hierarchy of relation from the more restrictive to the least. Eg: Concept replaces, Concept poss_eq from, … Is a. ?

We work with multiple OMOP instances, each containing millions of rows pending review and we are seeking guidance on how to address this issue without manually reviewing each concept_id.

Any suggestions or recommendations to solve this process would be greatly appreciated. Thank you!

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@Luis_Leon:

Welcome to the family.

Yeah, SNOMED does that. They deprecate concepts, and sometimes they don’t give you a replacement. The reason could be multiple: they split it into two, they found it wrongly defined, we don’t know. It doesn’t happen that often, but since SNOMED is gigantic you will find those cases regularly, and the longer you wait with the upgrade the more likely it becomes.

We don’t fix SNOMED. We take it as is (with the exception of assigning our domains, which often is slightly different from how they see things). So, if there is no “concept replaced by” relationship there is not much we can offer.

However, if you are coming from source concepts (ICD10 for example) you should be fine. We do fix those mappings. If they used to be mapped to a SNOMED that is now obsolete and no replacement is given we will find the replacement.

Is that your situation? Or do you do de-novo SNOMED mappings? Do you have an example?

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