I am working on a project involving the OMOP common data model and I am attempting to map BI-RADS related terms such as Background Parenchymal Enhancement (BPE) to SNOMED CT terms.
Hello @zkhan! Thanks for your question. Unfortunately, we don’t have such a concept at the moment. You can create a GitHub issue here, and we will consider adding it in the OMOP Extension during the next release.
In the meantime, you can create and use 2 bill+ standard concepts locally.
I work with data from echos and other medical devices that do not have a good concept mapping within SNOMED, LOINC, and other standard vocabularies. If you need to get your data into an OMOP database to start working with it and do not need necessarily to use OHDSI tools - one option is to go ahead and create a custom vocabulary to cover these unsupported concepts and then work through the standards group to get those data elements supported. I am taking this approach for some device data as well as covering data from pre-hospital patient care records from emergency medical services.
You should create a custom vocabulary and populate all the necessary fields:
concept_id, concept_code, concept_name, concept_class_id, standard_concept, invalid_reason, domain_id, vocabulary_id.
Rules for populating:
Assign ‘concept_id’ values starting from 2,000,000,000.
Set ‘standard_concept’ to ‘S’ and leave ‘invalid_reason’ as NULL.
The ‘vocabulary_id’ should be the name of your custom vocabulary.
You can fill all the other fields in the way you need.
Map to these concepts in the same way you typically map to OMOP concepts. The usage remains the same.
However, concept_ids created by OHDSI users ALWAYS have standard_concept is NULL because these OHDSI user created concepts will be mapped to standard concept_ids!