This is not a pre-coordination issue, but a data granularity issue. ETL is free to map to all the variety of specific LOINC / SNOMED tests. A researcher is free to exclude the generic Measurement concepts from the analysis.
The only reason such pre-coordinated concepts exists is the SNOMED, that created them. Then we placed them to the appropriate place in the hierarchy.
But, when the source data is not granular enough and ETL basically doesn’t know what testing method was, it might (and probably should) be mapped to generic concepts with no matter how value is stored (separately or in a pre-coordinated way). SNOMED normally provides only pre-coordinated options, but for COVID we did generic: Measurement of severe acute respiratory syndrome coronavirus 2.
The reason was: to organize the COVID concepts in the hierarchy and to provide a way to store the results of the unknown testing method.
I think the possibility of choice is better than wrong mapping that usually happens. Let’s say HIV negative or Finding of HIV status might be wrongly used for this purpose on the reason that user doesn’t even realise that both stand for antibody testing.
This concept-set should only include 2019 novel coronavirus detected concept. Can you please check?
The reasons why we used this concept in both narrow and broad definitions during the study-a-thon were uncertainty about how data was coded and ETLed on that point together with unavailability of Ab testing and low availability of antigen tests. I’d agree that narrow definition should be reassessed during the time and should include just most reliable testing methods (PCR and, possibly, Ab).
- Mapping should be such granular as possible (as it always supposed to be);
- We have a bunch of pre-coordinated concepts in SNOMED. Just look into the descendants of Virus present, Virus not detected, Bacteria present, etc. One of the possible solutions is to remap and split them to generic Measurement concept (that are simply doesn’t exist yet, except for COVID ) + maps to value. As far as I know, the only reason that stopped us is the unavailability of analytical methods to use the concept_id/value_as_concept_id combinations as covariates.
The same might be applied in the other Domains:
@Vojtech_Huser @Christian_Reich, @Dymshyts, @mik, @aostropolets your thoughts, please.