A related question regarding choice of vocabulary was posted in June of ’22.
We, too, are wrestling with this situation.
Culture result organisms are supposed to go into Measurement but the only Standard Taxonomy of organism names not cluttered with extraneous information that we’ve found is SNOMED, in the Observation domain.
My take on addressing this problem:
- Changing the domain of SNOMED Organism Concepts to Measurement could be problematic because these concepts may already be widely used in their current domain.
- While we have found concepts in LOINC that initially seem useful, they are Classification concepts, not Standard concepts. Therefore, using them would violate the “Standard Concepts Only” rule.
- The least problematic solution might be to revise the convention to allow the use of SNOMED Observation/Organism concepts for transformations into the Measurement tables.
Is there a current consensus or best practice for handling the issue of choosing vocabulary for culture-result organisms within the context of OMOP 5.4 standards?
If not, perhaps we could come to one now.