Getting standard concepts for Snomed codes from GPFP reset

Vocabulary Users
1

Hi there.

I’m trying to get standard concepts for Snomed GP/FP refset.
There are 2 invalid Snomed codes which don’t have mapping to another standard concepts:
http://athena.ohdsi.org/search-terms/terms/4226097
http://athena.ohdsi.org/search-terms/terms/4019848

What is the right way to deal with it?

Kind regards
Alexander

2

Hi @alexander
You can map them by your own finding the replacement with the closest meaning.

http://athena.ohdsi.org/search-terms/terms/4226097 can be mapped to Viral exanthem

http://athena.ohdsi.org/search-terms/terms/4019848 can be mapped to Death of relative

3

Two comments:

  1. I wish Athena web viewer would show the value for invalid. Exactly the letter from the field in the concept table. It only says invalid but there are subtypes

Well, it is internal SNOMED CT issue. Not always they provide “new concept” for a retired concept. There should be no official refset that includes a retired concepts. Better place to post that would be SNOMED.

4

Added: https://github.com/OHDSI/Athena/issues/85.

5

Hello @Vojtech_Huser ,
Can we show “Upgraded” of “Deleted” instead of “Invalid” word?

6

@acumarav
There are several allowable options for invalid_reason. From the discussion above and here I assume that we need the following:

  • invalid_reason IS NULL resulted in ‘Valid’ in the search results and concept page.
  • invalid_reason = ‘D’ resulted in ‘Deprecated’ in the search results and concept page.
  • invalid_reason = ‘U’ resulted in ‘Upgraded’ in the search results and concept page.
  • invalid_reason = ‘R’ resulted in ‘Reused’ in the search results and concept page.

@Christian_Reich @Vojtech_Huser What about filters? Should be specific as well?
image