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monarch-initiative / loinc2hpo

Java library to map LOINC-encoded test results to Human Phenotype Ontology
http://loinc2hpo.readthedocs.io/en/latest/
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glucoseAbnormal.fhir #138

Closed pnrobinson closed 2 years ago

pnrobinson commented 2 years ago

I do not think the following is valid FHIR because the LOINC test is quantitative and but the interpretation is "Abnormal" (which could be high or low).

https://github.com/monarch-initiative/loinc2hpo/blob/develop/loinc2hpo-fhir/src/test/resources/json/glucoseAbnormal.fhir

In principle, we could annotate this with Abnormal blood glucose concentration HP:0011015 But I am not sure this is valid FHIR? @kingmanzhang @iimpulse

kingmanzhang commented 2 years ago

It is a corner case that I can confirm it happens in real world but rarely. I see it as a "valid" FHIR as it will occur if the source data used "abnormal" instead of "high" or "low". Whether we want to include it as a demo case or not is not a critical decision in my mind, so either decision seems reasonable to me.

pnrobinson commented 2 years ago

fixed -- we should probably not allow invalid data to pass through unnoticed.