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OCTRI / fhir2hpo

Library for converting FHIR messages to HPO
MIT License
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Noninterpretable loincs #15

Closed aeyates closed 6 years ago

aeyates commented 6 years ago

This implements an additional tab-delimited file for storing information on LOINCs that should not be converted to HPO terms. Optionally the row can contain a reason it should not be interpreted. When a conversion of one of these LOINCs is requested, it will fail with a NonInterpretableLoincException. This will distinguish it from LoincNotAnnotatedException.

pnrobinson commented 6 years ago

I would agree that it is good to denote that this is used as a Q/C parameter in the file. It might become useful later on...

aeyates commented 6 years ago

I added the unspecified_specimens list to the noninterpretable-annotations file. I used the LOINC scale "Qn" for all annotations rather than look them up, since our algorithm doesn't use this. Will need to fix this later. I ran through all the sandboxes, but it didn't change statistics much since most of the LOINCs are not exercised.