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Purpose of the vocabulary to vocabulary map


(Micheal ) #1

Hello, guys I’m the person who’s been studying Omop-cdm myself.
I want to ask you why mapping vocabulary to vocabulary such as Snomed to ICD10 or Snomed to Rxnorm and so forth…
I believe Snomed_CT is the most common vocabulary on CDM, then why do they do like this?


(qiongwang) #2

Because the original data is in coded by ICD


(Dmytry Dymshyts) #3

The original data can be stored in different vocabularies, or even as a free text.
We need to have a standard representing the clinical data regardless of what was used in the source.
So, we choose SNOMED for the condition domain (diseases, syndromes).
And build all those mappings from ICD10CM, ICD10, ICD9CM, Read, etc. to SNOMED.

This way when you query CDM data you don’t care about what source was used, you just define the condition using SNOMED concept.
SNOMED also has pretty nice hierarchy. So, defining a condition you can easily find all its subtypes.

Please let me know, if you need more comprehensive explanation.


(Micheal ) #4

Oh, thank you @qiongwang :slight_smile:


(Micheal ) #5

It’s really helpful explanation. I appreciate that @Dymshyts.
Okay another question, then

in this picture, why no.97’s concept_standard field is the ‘Null’? that’s in SNOMED, isn’t that?


(Seng Chan You) #6

It means that this concept id is not standard in OMOP vocabulary system, so you must not use this concept id. Only standard and valid concept id can be used.


(Micheal ) #7

Thank you @SCYou,

What about ‘C’ Classification in standard_concept? I know what that definition means, but I don’t understand what the role is on OMOP.


(Seng Chan You) #8

You can use ‘C’ classification concept ids like other standard concept ids. I don’t know what their expected role is, either… :sweat_smile:


(Doyeop Kim) #9

Classification Concepts (standard_concept = ‘C’) have a hierarchical relationship to Standard Concepts and can therefore be used to query for Standard Concepts using the records of the CONCEPT_ANCESTOR table. However, they themselves cannot appear in the Data Tables.


(Micheal ) #10

Ah, I know what that means now, Thank you @DoyeopKim. :slight_smile:


(Mui Van Zandt) #11

@MichealJeong You should watch the OMOP Vocabulary/CDM tutorial. It will help you answer a lot of the fundamental questions about OMOP and its vocabulary. https://www.ohdsi.org/past-events/2018-tutorials-omop-common-data-model-and-standardized-vocabularies/


(Micheal ) #12

Thank you @mvanzandt I will keep that in mind.


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