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phenoscape / ubeRsim

R package for computing semantic similarity metrics using online or offline Ubergraph
MIT License
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Would modified mutual exclusivity functions be appropriate to add here? #2

Open hlapp opened 1 year ago

hlapp commented 1 year ago

Would modified mutual exclusivity functions be appropriate to add here? Currently mutual exclusivity is returned based on evidence from studies in the KB but could potential query a user defined dataset. The optional quality_opposites parameter for mutually exclusivity will be user specified, so opening the overall function to other datasets might make sense.

Originally posted by @wdahdul in https://github.com/phenoscape/TraitFest-2023/issues/20#issuecomment-1402041430

hlapp commented 1 year ago

@wdahdul it's not impossible to add this in some way to ubeRsim, but we'd first need to understand a lot better how we would want to define this.

More specifically, for Rphenoscape mutual exclusivity is determined for phenotypes in the KB. Phenotypes could be in Ubergraph, but presumably only from pre-composed named classes in requisite phenotype ontologies (such as HPO or MP), and not as the anonymous class expressions we use for annotating natural trait data.

Though perhaps it's time to create a pre-composed phenotype ontology for natural trait data as well. Or try to add our phenotypes to one that's already being developed (OBA? UBERPHENO?). (Thoughts @balhoff ?)

Originally posted by @hlapp in https://github.com/phenoscape/TraitFest-2023/issues/20#issuecomment-1407497572

balhoff commented 1 year ago

@hlapp I think OBA fits the bill.