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Post-coordinated SNOMED CT concept expression?

Vocabulary Users
#1

Hello all,
I’m wondering how can I express SNOMED CT concept with post-coordination into OMOP CDM v5.
Is there any solution for describing detailed attributes using CDM?
For example, two clinical concepts such as “fracture of femur” and “fracture” have different meaning.
Please give some advice.

Thank you.

Borim

#2

@Borim_Ryu:

This is a wonderful question. Right now, we only allow fully pre-coordinated Concepts that exist in SNOMED. The list is in the vocabulary CONCEPT table. If you want to combine Concepts, you have to put several records into the CONDITION table at the same day.

However, SNOMED is build in a multi-dimensional bases, and all pre-coordinated Concepts have a link to their components. So, “Fracture of femur” is linked to “Fracture” and to “Femur”. But not all combinations exist. So, we could do a couple of things:

  • We create all combinations people need and SNOMED doesn’t have.
  • We put three new fields into CONDITION_OCCURENCE: anatomical_site, pathology, cause
  • We somehow allow different concepts to be combined. Theoretically we have the FACT_RELATIONSHIP table for that, but nobody uses it

Thoughts?

#3

I like #2, but one benefit of #1 is that by creating single concepts, you can put the hierarchy in the concept_ancestor tables (such that a fracture of femur is below fracture of lower limb which is below fracture).

#4

Any more recent thoughts on this? :slight_smile:

#5

Well, what is your use case. Right now, we have Fracture of femur, which has a relationship “Has associated morphology (SNOMED)” to Fracture (Domain Observation) and “Has finding site (SNOMED)” to Bone structure of femur (Domain Spec Anatomic Site). What’s missing?

t