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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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add linkages to bridge traits as phenotypes #150

Open nlwashington opened 8 years ago

nlwashington commented 8 years ago

We need to ensure that all traits (from OBA and/or VT) can be reasoned to be subclasses of UPHENO:0001001. This may require a new subclass axiom.

This may be related to #140 and #142.

As suggested by @cmungall, it may be more appropriate to bring in OBA to get at VT.

jmcmurry commented 8 years ago

@cmungall can you comment on degree of difficulty? There are a few open tickets this might resolve.

matentzn commented 6 years ago

Is this still wanted? Are we officially treating traits as phenotypes then?

sbello commented 6 years ago

I would suggest we not treat traits as phenotypes. From the MGI and RGD perspective these are NOT the same thing. The difference is subtle but important. By our definition a trait is a 'measurable or observable characteristic' while a phenotype is a 'measurable or observable characteristic manifested in an organism' basically a phenotype is a manifestation of a trait in an organism or population. So eye color is a trait but blue eyes or dark eyes is a phenotype, We would prefer to not get these concepts mixed up in the cross-species phenotype ontology.

cmungall commented 6 years ago

@sbello if "phenotypes" are subclasses of traits, but in different ontologies, does that satisfy the requirement of not treating them the same? Or did you have a different relationship type in mind?

sbello commented 6 years ago

I'm inclined to say we should use a different relationship but I'm not sure what. I think it would be useful to discuss this on a pheno-editors call at some point.

nicolevasilevsky commented 6 years ago

can you please add this as an agenda item, @sbello? https://docs.google.com/document/d/1WrQanAMuccS-oaoAIb9yWQAd4Rvy3R3mU01v9wHbriM/edit