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Standard OMOP SNOMED codes not found in SNOMED browser

@Dymshyts,

The following concept_ids are standard concepts, however their concept_code and concept_name are not found in the US or International SNOMED browser: 44808521, 44790759, 44790758. Any idea?

Another question is why these codes have valid_end_dates that are before the valid_start_date (I’m not using the very most recent version of the concept table so this may be fixed already). In fact, in my version, there are 1.9M concepts where valid_end_date occurs prior to valid_start_date, 891K are STANDARD concepts.

select count(*) from concept where valid_end_date < valid_start_date and standard_concept = ‘S’;

@MPhilofsky:

While Dima is on vacation: they are British SNOMED Concepts. We need them for mapping of the vocabularies used in the UK.

@mgkahn:

You need a time machine to use the vocabularies, didn’t you know? :smile:

Not sure what you got, there. That count returns 0 for me. Maybe during loading 1999 got incorrectly loaded as 2099?

Happy New Year.

@Christian_Reich,

Ah, makes sense. An improvement to the vocabularies would be to distinguish the different versions of SNOMED. I’ll add it as a git hub issue.

@MPhilofsky:

Happy New Year.

Yeah, we were thinking about that. Problem is we don’t have a straightforward place for that information:

  • Can’t put it in vocabulary_id, becase we’d have to split SNOMED into SNOMED_UK, SNOMED_US, SNOMED_AUS and SNOMED_INT. And potentially more SNOMEDs. That would break 30% of all queries in the community. And most people don’t care where a SNOMED Concept comes from. And they are all interlinked through CONCEPT_RELATIONSHIP or CONCEPT_ANCESTOR records.
  • Can’t put them in concept_class_id, because those are set by SNOMED itself.
  • We could add a CONCEPT_RELATIONSHIP “Comes from” record linking them to a Concept SNOMED_UK etc. CONCET record. But that is extremely ugly, because vocabularies are indicated through the vocabulary_id field, and now we’d be adding another method of doing that.

So, we couldn’t figure out a solution and left it as is.

t