When populating allergy data into the OMOP observation table, we previously used ‘Allergy to …’ concepts. However, many of these have become non-standard concepts.
For example, we used to use ‘Allergy to aspirin’ (concept_id = 4163057) to represent aspirin allergies, but this concept is now non-standard and maps to the standard concept ‘Allergy to drug’.
In such cases, is it best practice to use the drug ingredient (e.g., aspirin) as the value_as_concept_id?
However, some ‘Allergy to …’ concepts are still considered standard — such as ‘Allergy to penicillin’ (concept_id = 4240903). Should we continue to use these standard ‘Allergy to’ concepts directly when available?
Could you please advise on the recommended approach for populating allergy data in this context?
To ensure better data harmonization, concepts that represent allergies have been de-standardized and post-coordinated into ‘Allergy to drug’ (or Allergic disposition in case of non-drug allergy) + causative agent as value.
E.g., in the case of Allergy to aspirin we have the following mapping:
Thus, causative agents (e.g. aspirin) will populate the value_as_concept_id field.
At the same time, SNOMED concepts exist that represent allergies to groups of drugs (e.g., groups of antibiotics: Allergy to penicillin, Allergy to cephalosporine, etc.). There’s no standard concepts for drug groups in RxNorm, so we have no good mapping for them. However, we assume that such allergies may be recorded in patient data, so we keep such concepts standard and pre-coordinated.
