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Vocabulary ICD - non standard Codes

(Chidam) #1

Hello All,

Currently we are migrating our source EMR data to OMOP CDM. Our diagnosis is in ICD codes.
When we check the concept_code in the Concept table, same concept exist in the concept table but it is non standard.

I want to use the same concept, also want to see that concept count in the ATLAS. Can you please advise? In my vocabulary table can i change that concept Standard_Concept flag to ‘S’ ?
or is there any other way?


(Chris Knoll) #2

In reality, you can do anything you want, but, you should really strive to put your data into the standardized forms. This means that each of your ICD9 codes get mapped over to the standard concepts using the CONCEPT_RELATIONSHIP table, using the ‘Maps to’ relationship.

This is a very complicated topic to educate you on a forum thread about how mapping is implemented in your ETL, but you should be able to find threads that point you to tutorial videos on how this is done. There may be other questions on the forums that have this type of questions, you should search for.

In any event, you should not make your own local updates to the vocabulary to make it ‘work for you’: when you have other issues related to vocabulary, no one will be able to help you because your vocabulary is modified and no one will be able to give you an guidance based on your changes. They define standard concepts for very good reasons.

(Chidam) #3

Hi Chris,

Thanks for your reply.

Yes, agree. We implemented standard concepts in ATLAS.
Example, Our EMR system have concept O80 - Single Spontaneous delivery ICD10 code, but this is non-standard code. When we map the data, we use the relationship table, and Maps to relationship column, we use 48782003 -Delivery normal snomed standard concept.

But the issue, end users don’t know this new standard concept name. They always search O80 concept in the ATLAS and not getting any count.

How to handle this? please advise.


(Chris Knoll) #4

I think there was a change with Achilles to populate source concept counts in the achilles_results tables, and those values will be returned to the Atlas UI in the 2.8 release. So stand by for the next release and see if that will give you what you need.

(Chidam) #5

Thanks Chris


(Purvi Mehta) #6

Hi Chidam,

Late to the discussion but not sure what you mean as a “non-standard” code. Did you mean a non-billable code?

(Don Torok) #7

As Chris says above, ‘This (mapping to standard concepts) is a very complicated topic to educate you on a forum thread about how mapping is implemented in your ETL’.

Suggest you look at The Book of Ohdsi or if you prefer a video, https://www.youtube.com/watch?v=vHMkBaHJrDA&t=7884s