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Source Code - OMOP CDM Vocabs

vocabularies

(Shinyoung Ju) #1

Hello OHDSI super stars,

Happy 2020.
I had a quick question regarding the OMOP CDM voabularies.
I realized we can view the source codes from which the standardized codes were mapped to using Atlas. Is there a way to view the source codes in Athena as well? I see the list of the codes with concept IDs, but I actually do not see any source codes for each standardized (SNOMED) codes.

Thank you for your help!


(Qi Yang) #2

@byr0sxj

This is extremely simple unless I don’t understand your question. In Athena, the first column is “ID”. The 2nd column “Code” is the source code. For example, for standard concept ID 201826, the SNOMED source code is 44054006 (Type 2 diabetes mellitus).


(Shinyoung Ju) #3

Hi Qi,

Thank you for your reply!
If I understood the OMOP CDM vocabulary system correctly, all the source codes are mapped to SNOMED-CT. If that is the case, how do we know which vocabs were mapped to SNOMED Codes? For instance, if we want to find out what non-standard vocabs (ICD, Medra etc.) are mapped to SNOMED code for Atrial Fibrillation (ID: 313217 and source code: 49436004), where should we look at?

Thank you for your great help!


(Qi Yang) #4

Hi Shinyoung

So what you need to do is to click on the concept name (e.g., Atrial Fibrillation)

and then scroll down in the right panel and find out the section “Standard to Non-standard map (OMOP)”. That lists all the concept ids for other vocabularies. Click on the one you are interested and you will find the original source code.


(Shinyoung Ju) #5

Oh wow! Thank you Qi! I really appreciate your help :slight_smile:
It is very clear to me now!

Best regards,
Mariana


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