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No Standard concept for Invalid SNOMED code

(Sooraj Lankala) #1


Am working on mapping SNOMED codes (veterinary data) to OMOP standard concepts. Some of these SNOMED source concepts are invalid and I couldn’t find a standard map to these concepts in Athena.
For Ex. Concept Code - 57831000 - [Animal immunization for rabies] (http://athena.ohdsi.org/search-terms/terms/4212619) has no standard concept. Could someone help us on how to proceed for these concepts.


(Christian Reich) #2

What about SNOMED concept_id=42572869 (concept_code=‘344321000009105’) “Animal immunisation for rabies”? It’s a SNOMED Veterinary concept.

(Sooraj Lankala) #3

Thanks for the help. I would like to know if we will be able to find the Non-Standard to Standard mapping to these invalid concepts (Veterinary) so that it would be easy to lookup and automate the mapping process to some extent.

(Christian Reich) #4

Help me understand. What non-standard to standard mappings? Within SNOMED? Usually, SNOMED does that. If they de-duplicate two identical concepts they will provide that link, and we will have that link also. See all those SNOMED concepts where invalid_reason=‘U’. For example, they merged 44810520 “Ultrasonography guided biopsy of lymph node” into 45765586 “Biopsy of lymph node using ultrasound guidance”, making the former concept invalid.

We don’t second-guess SNOMED. If they don’t provide that link between the concepts you are mentioning above we won’t have it either.

What is your use case? What are you trying to do?

(Sooraj Lankala) #5

We have our EHR veterinary source data already encoded in SNOMED and are in the process of standing up our OMOP for proof of concept. We thought we could do it easily using automated ETL scripts but seems there are SNOMED codes which are invalid and do not have ‘Maps to’ relationship.
Ex. http://athena.ohdsi.org/search-terms/terms?query=Protrusion+of+gland+of+third+eyelid&page=1
Could you suggest if there is best way to map SNOMED codes like these to standard concepts.
Here is summary of SNOMED codes we couldn’t map to standard concepts for sample of 2000 records (our ETL scripts are still work in progress and these counts may go down)
Domain Count
Condition 85
Device 3
Drug 11
Measurement 4
Observation 70
Procedure 36
Specimen Anatomic Site 1

(Dmytry Dymshyts) #6

Sometimes SNOMED deprecates concepts without any replacement.
You gave a very good example Protrusion of gland of third eyelid
like what’s a Third eyelid??
This illustrates the idea that some concepts are added there by mistake.

The same with Animal immunization for rabies. Core SNOMED doesn’t want veterinary concepts at all, so no replacements.

You can try to run usagi to get the closest meaning.
Or apply such an algorithm:
map those equal by name
try to map other manually.
and some concepts are just non-sense (like the third eyelid), so you don’t map them at all.

(Chris Knoll) #7


My cat wishes to inform you that his third eyelid is real, and you are formally on notice for your species-isim.


(Dmytry Dymshyts) #8

Please tell your cat, I said sorry and thanks for the information:)
And thus we have the correct concept for this
42599364 351051000009101 Protrusion of nictitating membrane
So, this is also a case of missing links between SNOMED and SNOMED Veterinary. We’ll take a look later whether we can retrieve them

(Sooraj Lankala) #9

Thanks @Dymshyts. Are there any standard concepts to these ? I tried to find in Athena using concept names and their synonyms and couldn’t find a match