OHDSI Home | Forums | Wiki | Github

How to get Non-standard to Standard map (OMOP) information


(Youngmi Han) #1

In KCD7, A00.0 is OMOP code 42483628, which is nonstandard, and this OMOP code[42483628] can not be used in CDM.
But Looking at the details of the A00.0 code in Athena, there is Non-standard to Standard map (OMOP) information, and the Non-standard to Standard map (OMOP) code for A00.0 is 4344638.
In the above example, I think the standard OMOP code for A00.0 of KCD7 is 4344638.

So, I have two questions about concept ID mapping for KCD7.

1.As in A00.0 -> 42483628 -> 4344638,
I think there is relationship information between a nonstandard code [42483628]
and a Non-standard to Standard map (OMOP) code information [4344638] for source code A00.0 in some place of the vocabulary internal files (CONCEPT.csv, CONCEPT_ANCESTOR.csv, CONCEPT_CLASS.csv, CONCEPT_RELATIONSHIP.csv, CONCEPT_SYNONYM.csv, DOMAIN.csv, DRUG_STRENGTH.csv, RELATIONSHIP.csv, RELATIONSHIP.csv, RELATIONSHIP.csv) , VOCABULARY.csv). If possible, please let me know a way to find the relationship.

  1. If there is a method to download non-standard to standard map (OMOP) codes for some source codes (KCD, or EDI, etc) like A00.0 -> 4344638, I would like to know it.

I believe this will be very helpful to map the standardized concept ID.

Thank you in advance.

Youngmi


#2

Hello @maryhan01,

There was another thread with a similar question answered. Also, you might find some answers in the Book of OHDSI, which covers the vocabulary topic (as long as many others) in great detail.
Hope it helps.


(Youngmi Han) #3

Thank you so much.
I am a very beginner in omop cdm. I’ll check the book of ohdsi.

Please let me know which chapter I have to read.

Youngmi


#4

@maryhan01,

I’d recommend chapter 5 for the overall description of vocabulary standardization approach. The link above specifically points to 5.3 (‘Relationships’).
Good luck!


t