I have an ETL problem, and would like to know if anyone has addressed this issue.
We are trying to map microbiology susceptibility. I have an isolate (tissue sample), an antibiotic and a result. My question is how to fit this into OMOP 4 Observation table.
For the observation type, we typically put in a generic term such as ‘Observation from EMR’. However it might be possible to find a ‘non standard’ concept that would indicate this is a ‘Microbiology susceptibility’ observation.
The problem is that there are still three items to map. The tissue sample, the antibiotic and the result, but only have the observation concept id and value as concept id fields. It seems that the result of the test should go into value as concept_id ( positive/negative … ). So where to put the tissue sample and antibiotic?
If anyone that has addressed this problem I would appreciate your input.