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Non-standard concepts in the concept Mapping


(Chidam) #1

Hi All,

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?

Please advise

thanks
Chidam


(Chidam) #2

Hi All,

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.

Please advise
regards
Chidam


(Chris Knoll) #3

Yes, only use standard concepts.


(Chidam) #4

Thanks Chris_knoll,

Is there any option, can get standard concepts for non-standard concepts from the vocabulary?

thanks
regards
Chidam


(Alexander Davydov) #5

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.


(Chidam) #6

Thanks Alexdavv,

Thanks a lot. I will get the standard concepts from concept_relationship table.

regards
chidam


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