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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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Develop #56

Closed kingmanzhang closed 6 years ago

kingmanzhang commented 6 years ago

@pnrobinson Hi Peter, I implemented the features we talked about except creating a pointer to a new hpo file. This can be merged to master if it also runs on your machine. My previous email that said "do not annotate Ord Loinc" expires. You can annotate any LOINC now.

Next step is to create the pointer you talked about. Currently we are using both owl (for Jena) and obo (for annotation). I have refactored to phenol, which appears to be able to parse owl, so I am hoping to do that so that we don't need to always create and use two versions of hpo.

pnrobinson commented 6 years ago

Hi @kingmanzhang I can compile and start with no problem. I am getting an error message that starts 

# malformed loinc codes 0
# loinc codes not found: 50

I will continue to test.

kingmanzhang commented 6 years ago

@pnrobinson For this message and your email, I was able to run the app from my personal laptop. I would suggest checking whether you have used the correct LOINC core table AND/OR restarting the app. Let me know if that does not work.