Currently we are migrating our EMR data to OMOP. In the drugs mapping,
If i map non-standard and invalid concepts, Can i see that non-standard concept with person count in Achillies report? and record count in search result?
Example, our EMR data, we have drug ordered Warfarin Sodium, We search this description in the athena, we found most suitable 4270619 Warfarin Sodium in SNOMED, but it is non-standard concept.
After running the achilles command, this 4270619 Warfarin Sodium shows count zero in achillies report and Atlas search record count also zero.
So, i need to use only standard concepts? or i need to change any code in webapi/atlas to see this count also in the atlas.
Sure, you can use mappings. Use the concept_relationship table and valid (invalid_reason IS NULL) record with ‘Maps to’ relationship_id which always brings you to the Standard concept. So, the mentioned SNOMED substance is mapped to the Standard RxNorm Ingredient.
Hi Chris_Knoll,
I am pretty new to the OMOP CDM and have a question in regard to this topic here. We are currently using the OMOP CDM with standard vocabs and non-standard ones - to be precise ICD10GM. There are mappings to SNOMED in both directions (‘Mapped from’ and ‘Maps to’). Searching for a specific ICD10GM code in Atlas works fine. Unfortunately, the record count is zero. Is this behaviour expectable or am I missing something? This pull request sounds like it should be already integrated so far (Get record counts for non-standard concepts by anthonysena · Pull Request #1725 · OHDSI/Atlas · GitHub). We are on WebAPI version 2.7.2. If you need more information to answer, please let me know
The record count is zero because as of version 2.7.X, we don’t calculate row counts for non-standard concepts. So, those non-standard concepts will be zero.
For version 2.8.x, we have expanded the reporting to include non-standard concepts, so you’ll see non-zeros for records in your data in those cases.