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monarch-initiative / owlsim-v3

Ontology Based Profile Matching
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Read phenopackets #28

Open balhoff opened 8 years ago

balhoff commented 8 years ago

Input phenotype profiles for analysis from a phenopacket file.

balhoff commented 8 years ago

@cmungall you mentioned reading a phenopacket in place of existing TSV reading. But the only TSV I can find is ReadMappingsUtil.readPairwiseMappingsFromTsv which seems like it's used to read in a list of individual comparisons to run, rather than phenotype annotations. Is that right? Should a phenopacket be read in along with the ontologies?

cmungall commented 8 years ago

You're right, currently the only way to load the phenotype annotations is as OWL

balhoff commented 8 years ago

Actually I think I was wrong—just came across OWLLoader.loadDataFromTsv, not sure how I missed that before. I'll add loadDataFromPhenoPacket.

balhoff commented 8 years ago

Initial implementation here: https://github.com/balhoff/owlsim-v3/commits/phenopacket-reading

Need to create some test data.