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Adapting Common Data Model to Animal Health Records in Veterinary Practices


(Waydes) #21

There should not be any human concepts in the veterinary extension from Virginia Tech. The moduleId should be 332351000009108 = Veterinary Terminology Services Laboratory maintained module (core metadata concept) for all the concepts. If there is a discrepancy, please let me know.


(Waydes) #22

I believe the original request to add the Veterinary Extension was sent by Chris Brandt. Just want to make sure you have the correct files. The Veterinary Extension files can be downloaded at:

https://vtsl.vetmed.vt.edu/extension/default.cfm


(Dmytry Dymshyts) #23

Yes,

and yes, we are working on this one

The thing is Veterinary Extension can work as a self-contained vocabulary, so
there are concepts that help to make SNOMED structure, i.e. Attributes (70258002 Ankle joint structure), general concepts that works for human and animals (77386006 Pregnant, 91302008 Sepsis etc).

Also some veterinary terms already exist in Human SNOMED, for example
Organisms: 61839006 Cornish chicken, even viruses that affects animals (71448008 Canine minute virus) etc.

Attached file contains all such a concepts:
common_concepts.xlsx (132.0 KB)


(Waydes) #24

Thanks Dmytry,
The problem with creating a veterinary vocabulary with only the veterinary extension is that many human concepts are used to code animal diseases without any concepts from the veterinary extension. I thought the vocabulary you were creating was just the concepts, relationships and descriptions in the Veterinary Extension. I think a freestanding vocabulary is a great idea. Since VMDB has 15 years and approximately 1.7 million visits codes, I can query the database and provide all the human concepts that have been used for coding from our submissions. Those concepts plus the veterinary extension will provide a self-contained vocabulary and allow for comparing animal and human diseases. That vocabulary should met the needs of anyone interested in coding / transforming animal records. Let me know if that will be helpful.


(Christian Reich) #25

@waydes:

Problem with this approach is that there will be two concepts for Sepsis, one from SNOMED and another one from SNOMED Vet. They really mean the exact same thing. One of our principles is to have only one standard concept per semantic entity per Domain, and the other concepts map to it. If we did it as you suggest we would go into the opposite direction and violate that principle.

The alternative is this: Veterinarians have to use the union of SNOMED and SNOMED Vet for their work. The rest of the community, which is the vast majority, can continue just with SNOMED as if nothing happened. Similar to the US researchers use RxNorm for drugs, and everybody outside has to say where vocabulary_id in ('RxNorm', 'RxNorm Extension') to make use of that combined universe. Works well.

The only downside to that approach is that your colleagues will have certain non-veterinary concepts to deal with, like “Bipolar Disease”. Can they live with that?


(Manlik Kwong) #26

From a SQL, programming perspective either approach is fine. As was said - using “vocabulary_id in (‘RxNorm’,‘RxNorm Extension’)” construct is common. For how folks are using and constructing SQL now, I think one concept principal is the preferred method. It also simplifies the decision logic of choosing which vocabulary to to map the example “Sepsis” to and maintaining the consistency if the query is run on both the human and animal sides. This also impacts on the application side as well - displays one concept choice instead of two and have to display which vocabulary the concept is attached - more screen space required.


(Waydes) #27

Using a union of SNOMED and SNOMED Vet is perfectly acceptable. In fact, that is how VMDB incorporates SNOMED and the veterinary extension. Just to state the obvious since I am a bit of a newbie to OHDSI, to use the CDM, veterinarians would use both the SNOMED vocabulary and the SNOMED veterinary extension vocabulary. If the veterinary vocabulary contains only those with the moduleId for the veterinary extension, then there will not be any duplicate concepts and fits the principles for OHDSI? Is that stated correctly?
Thanks again.


(Christian Reich) #28

Exactly. Thanks guys.


(Dmytry Dymshyts) #29

We found a typo:
there’s concept_code =‘89001000009106’ with description = ‘Cracticus mentalis (oranism)’

  • oranism instead of organism.

Where to report it?


(Ronald Cornet) #30

Hi, not knowing the context, here’s what I did to come up with my below suggestion.
89001000009106, clearly a SNOMED-code.
But not in international release.
Looked at 1000009 here: https://cis.ihtsdotools.org/info/index.html?home=namespaces
This shows it’s VetMed.
Had downloaded that extension, and saw the error was there too (so not a copy-paste error).
So either you approach info@snomed.org, as mentioned on the site mentioned earlier.
Or, contact the owner mentioned in previous versions of the list found here: https://confluence.ihtsdotools.org/download/attachments/6160816/SNOMED_CT_Namespace_Registry%20-%20OFFICIAL%2020141021.pdf?version=1&modificationDate=1426061583000&api=v2&download=true

That gives the answer:
Email: jwilcke@vt.edu

Best, Ronald


(Dmytry Dymshyts) #31

Thanks @ronaldcornet.
I like really like your logic, you act like a detective here:)
We found a bunch of other innaccurracies, so we’ll report them.


(Dmytry Dymshyts) #32

I’m happy to inform that Veterinary Extension is available for download in Athena.
Vocabulary_id =‘SNOMED Veterinary’


(Manlik Kwong) #33

This is great! Thanks for getting the vocabulary setup.


(Waydes) #34

Just want to add my thanks for creating that.


(Dmytry Dymshyts) #35

You’re welcome:)


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