Mapping Microbiology Susceptibility into OMOP CDM4 Observations

@HeideNei:

Precisely. The current situation is confusing.

I don’t think lab reports anything in a standard fashion except LOINC. And that has the organisms in the measurement, e.g. Streptococcus pneumoniae DNA [Presence] by NAA with non-probe detection in Positive blood culture. The result is either Detected or Not detected.

And that’s how it should be. The Measurement represents the specific tests, the value is either numerical+unit or a categorical yes/no.

Remember: There are all sorts of ways how to test for strep: agglutination, antibody presence, PCR, etc. They don’t easily allow reversing like you suggest: PCR?-Strep/Staph/Meningo etc. They are all different tests of their own kind.

So, in EAV whether we say “Blood culture”?-“Strep” or “Strep in blood culture?”-“Yes” makes no substantial difference. We should just stick to the existing convention.