This is a post very similar to an old topic. We’ve been looking at how to model cultures in OMOP. In my opinion there are two options:
- Adopting a table similar to PEDSnet called measurement_organism.
- Creating a new relationship.
For option 2, it would store susceptibility information in the measurement table and organism information in the observation table; however, there isn’t a relationship to connect the two, like a ‘organism tested’ and ‘antibiotic tested’ relationship.
For example, if we are testing Cefuroxime susceptibility (concept_id= 3042086) on streptococcus pneumoniae (concept_id=4321152), for both approaches there would be one measurement row for the test where measurment_concept_id=3042086 and the value_concept_id would be one of three possible values: Susceptible (4038110), Indeterminate (4219043), or Resistant (4148441).
I’m thinking option 2 is the way to go, but we’d need a new relationship to connect the test to the organism. I’m ignoring MIC values in this case where there would be another row in the measurement table added.
The other thing we would want to consider is how either decision (of course after the CDM/Vocab WG reviews) would affect Atlas. Right now, it doesn’t seem that relationships are part of Atlas. Calling out @Chris_Knoll on his input on the application side.