I am relatively new to the OMOP CDM and am currently designing the ETL process for our data at the moment. I would like to transform our blood culture results. However, I am not quite sure about the CDM table that the results should be added to.
The problem I have is as follows:
As I understand it, the microbiology results (if there is an organism present and if so, which one) should be part of the measurement table as the observation table user guide states the following: “If the generation clinical facts requires a standardized testing such as lab testing or imaging and leads to a standardized result, the data item is recorded in the MEASUREMENT table.” I would then store the organism in value_as_concept_id or the concept 9190 (Not detected) if no organism was detected.
However, my problem is that less than 20% of the organisms present in our data can be mapped to the Meas Value domain. The rest didn’t have a match in this domain but in the observation domain instead. And it would also be possible to map all the organisms that I mapped to the Meas Value domain to the Observation domain. In other words, the vocabulary used for the Meas Value domain (LOINC) is not complete at all, but the vocabulary used for the Observation domain (SNOMED) is almost complete.
Having the data mapped to two different vocabularies does not seem appropriate when I could just map everything to SNOMED which is in the observation domain.
Now I am wondering what is the preferred way to handle this situation.
- Using the measurement table, mapping everything to the observation domain
- Using the observation table, mapping everything to the observation domain
- Using the measurement table, mapping as much as possible to the Meas Value domain and the rest to the observation domain and having mixed terminologies for the organisms
- Split the data in the measurement and observation tables based on the domain to which the data can be mapped
Thank you very much for your help and opinion on this topic!