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Non-standard concepts in the concept Mapping

Vocabulary Users
#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

#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

#3

Yes, only use standard concepts.

#4

Thanks Chris_knoll,

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

thanks
regards
Chidam

#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.

#6

Thanks Alexdavv,

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

regards
chidam

#7

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 :slight_smile:

Thank you in advance
Kind regards,
Mirko

#8

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.

#9

Thank you very much for the fast reply!

t