OHDSI Home | Forums | Wiki | Github

Adapting Common Data Model to Animal Health Records in Veterinary Practices

Implementers
#41

Hi Steve,

We (Chris Brandt, Allison Zwingen both at UC Davis, and Joe Strecker at CSU) have been meeting twice monthly on these CDM issues. Chris/Allison has proposed implementing support for breed and species in two places within our version of the OMOP CDM - based on version 5.2 with the following modifications:

  1. We added species and breed fields in the person table, along with foreign keys to a new owner table. This keeps patient demographics contained in one table instead of creating a new Animal table. Obviously ATLAS and other OHDSI tools can’t see these fields. However, our veterinary specific applications can use these fields without having to include #2 below to simplify SQL construction.

  2. We added species and breed in the observation table not tied to a visit_occurrence_id. The observation_concept_id are SNOMED concepts already in the standard vocabulary. So ATLAS and other existing OHDSI tools can use this information, thus providing a backwards compatibility. One secondary benefit of storing breed information in the observation table is we can support multiple-breed patients. For example a EHR documented “German Sheppard/Cross” can register two concepts in the observation table - one for “German Sheppard” and a second “Mixed breed dog”. This use case came up when we wanted to only include pure breeds in a query.

The above is going into production at Tufts Cummings Veterinary School next week. We have over 340,000 patients and over 816,000 visits.

I’m also in the process of integrating ongoing research data - case reports (surveys) from REDCap - into our CDM as part of our expanding implementation of OMOP CDM to support veterinary research.

Are you a member of the CTSI OneHealth Alliance (COHA)?

  • MK
1 Like
#43

Hi Steve,

Are you already using this CDM vet?

#44

Hi steve…
i really appreciate your effort. you are doing great job.As someone who is intreseted in pets and want to knows about pet diseases and health you can visit this website Dog Health - The Veterinary Student

#46

As of late last year, I read that the community is starting to consider moving the Race and Ethnicity columns to the Observation table as it is becoming increasingly common that 1 person reports multiple values in both of these fields (and that the additional values are collected!)

https://forums.ohdsi.org/t/race-and-ethnicity-in-the-omop-cdm/

Given this conversation, I wonder if we could treat the idea of “Breed” similarly as often times more than 1 breed is reported (mixed breed dog for example), and the reported breed can change over time. It seems like it would make sense to enter this information as Observations. This also avoids the need for the veterinary community to create something outside of the CDM which may be implemented differently across the organizations.

In terms of edits to the Person table, I think it would make sense to add a Species column to the CDM. For organizations with only human persons, it would be easy to populate the column with a concept for human, but for other organizations it allows the flexibility to add patients of all species. In terms of software edits, the Species column could be added to Atlas and used to define a cohort.

#47

@KSimon:

Looks like there are two different problems you are trying to solve:

  1. Species information, which is missing at the OMOP CDM.
  2. Breed information within a species, which you want to handle like human races.

For 1, you are right. It would be an OMOP CDM Expansion (extra tables and fields that won’t make it into the general model, but is supported for those who might need it). Just add something like “species_concept_id” and people will stop making it up. @clairblacketer will help you. The vocabulary should be there already.

For 2, the discussion might indeed be similar. But you know better. Obviously, the breed cannot change, since it is laid down in the genes. If it does in the data then it is probably just an update of the existing information. I don’t know if you have a use case where the “change” of breed is something you are studying. You tell us. If not, I would not bother with making it complicated.

For humans, race is not just biological, but as much a socioeconomical concept that is somehow both self-assigned and determined by the society you are living in. A change in race could mean a new awareness or identity of the holder. Animals cannot have those. So, I think the analogy is not that useful.

t