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Can deprecated non-standard SNOMED codes be used in OMOP CDM?

Vocabulary Users
#1

Hello,

I am using SNOMED and SNOMED Veterinary codes to map veterinary source codes to a common vocabulary. I am currently mapping breeds and have noticed that they are almost all deprecated (‘Validity’) and non-standard (‘Concept’) within Athena.

A couple examples include: English cocker spaniel and Maine coon cat.

Does anyone know if I can use deprecated/non-standard concept IDs and have them appropriately work within my OMOP CDM (e.g., supported, contain the hierarchical info, etc.)?

If this should be directed to another group, please let me know. I am happy to provide additional details, if needed.

Thank you for your help.
Emma

#2

Hi Emma. I am working with folks at Colorado State Univ and UC Davis veterinary schools as part of the CTSI OneHealth Alliance (COHA) creating a veterinary OMOP warehouses at our 3 respective schools. We do have OMOP mapping for breeds and species we are using for our project.

#3

For example I use:

±-----------±---------------±------------±--------------±-----------------±-----------------±-------------±-----------------±---------------±---------------+
| concept_id | concept_name | domain_id | vocabulary_id | concept_class_id | standard_concept | concept_code | valid_start_date | valid_end_date | invalid_reason |
±-----------±---------------±------------±--------------±-----------------±-----------------±-------------±-----------------±---------------±---------------+
| 4219909 | Maine coon cat | Observation | SNOMED | Organism | S | 81866001 | 1970-01-01 | 2099-12-31 | NULL |
±-----------±---------------±------------±--------------±-----------------±-----------------±-------------±-----------------±---------------±---------------+

It doesn’t appear to be deprecated.

#4

It is in the current version. Will found out what happened.

#5

On Refset tab in the official SNOMED browser it looks like it was “moved” to a different namespace, namely 1000009.

Which IS the veterinary extension, so SNOMED Veterinary vocab just needs to be updated. New standard concept will appear there. Unfortunately, MOVED_TO does not contain a link to an exact code, but maybe refset entries for that new code would contain reverse links?

So changes to make are:

  1. Update SNOMED Veterinary to a new version;
  2. Add deactivation reason metadata to CONCEPT_RELATIONSHIP table. It is contained in the same table “replaced by” links are sourced from.
  3. Try to make automated “Maps to” links following the “MOVED_TO” logic. Even if no refset contain this link, name matching can help. Existence of a MOVED_TO link pointing at 1000009 veterinary namespace should show which concepts to match.
#6

And I thought this is just a big overfed cat.

#7

They’re fluffy, not fat!

#8

Hi Eduard,
Do you know what the process would be to update the SNOMED Veterinary vocabulary download within Athena?
Thanks!

#9

Hi, wanted to add a little background info here if it helps. I’m the director of the Veterinary Terminology Services Lab that is tasked with maintaining the veterinary extension. In 2014 IHTSDO decided to move all veterinary only content out of the International release and into our veterinary extension (VetSCT). A large mass of content was moved in 2014, but they continue to find veterinary content on a regular basis and transfer them to our extension. The breed concepts are one example of this. These transfers do in fact nearly always have references to replacement concepts depending on when the transfer was made. There are a few instances where the content was truly inappropriate and no replacement was created.

Up until a couple of years ago (I apologize, I didn’t note the exact date when this change occured), when concepts were transferred from the International Release (core) to the extension, the core concept was retired and a new extension concept was created to replace it (with an extension identifier). We would then create a historical relationship that related the retired concept to the new extension one (this would be in the historical relationships refsets in the extension data).

A couple of years ago, IHTSDO decided that there was no need to create a new extension identifier, that we could retain the same identifier and just have it move from core to extension. In those cases, there is no need for a historical relationship, as the concept identifier is just moved into our tables with relationships, descriptions etc, in the extension. There are still occasionally incidents where there will be historical relationships however, because occasionally there is already an extension concept that has been created and we allow the core concept to remain retired and create a historical relationship from the retired concept to the extension one.

I hope that information is helpful. And if there’s anything I can do to aid in getting the VetSCT content updated in Pallas/Athena, please let me know. We release updates every April 1 and October 1.

~julie

1 Like
#10

@Alexdavv are there plans to update SNOMED veterinary any time soon? There is a demand

2 Likes
#11

@emmaleof - we had no immediate plans for an update, but we are very open to hear about the use case and will look into how and when we can make it happen. It is no small endeavor though…
If you could explain a little about your project, it would help us a lot to understand the urgency.
thanks ~mik

#12

@mik - At least 4 veterinary schools (UC Davis, Tufts, CSU, and the University of Minnesota have standardized on the OHDSI CDM and tools and are dependent on having up-to-date concepts available within Athena. As we ETL our data, we’re working to map existing concepts to the appropriate SNOMED (+vet) terms. When one isn’t available, we work with @jmgreen at the VTSL to add it. If we don’t have the ability to download these updated concepts with the OHDSI Concept ID, the tools won’t work for us. Unfortunately, none of the changes made since 2019 have been included.

When I requested that SNOMED Veterinary be added to Athena back in 2019, the initial import was incredibly efficient - I had hoped that whatever tools the vocabulary group has for other SNOMED extensions would work for this as well. Perhaps Julie’s comments about how the extension identifier was handled by IHTSDO is contributing to this additional workload.

If there is any way to get this work done, your veterinary colleagues would certainly appreciate it. If there is something that we can do to assist with this process, we’re also happy to explore that effort.

Thanks,
Chris

1 Like
#13

Thank you, Chris, for this reply! We also know that there are additional efforts within the veterinary community that are planning to utilize SNOMED (+vet) terms and OHDSI concepts and tools. @mik and @Alexdavv, please let us know if you need additional information.

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