Classify `onset` patterns?

[matentzn]

How will we get the onset pattern to reason properly?

disease_onset.yaml

text: "'onset' and 'inheres in' some %s"

manually asserting onset terms under “trait”, or somehow get Peter to agree onset should be a quality? Right now the disease onset terms dangle around up top with no connection to the rest.

Also, HP is not imported into OBO yet. I feel this is a case where we should manually create a "onset trait" term in OBA and use that in the pattern instead of HPO.

[dosumis]

We're using a sub-ontology of HP here - the clinical modifier branch. This does not refer to phenotypes. I think it is reasonable to consider the terms under clinical course to be qualities.

[matentzn]

But technically, who will consider that? Peter wont take that axioms easily (onset subclass of pato:quality), and we have decided not to do axiom injection..

[dosumis]

So we ignore a perfectly good set of terms in HPO that work well for our use cases? Seems suboptimal

[matentzn]

I guess we also want to align HPO with COB, and we will align the modifier branch separately from the phenotype branch. This upper alignment could take care of this alignment as well?

[matentzn]

Is a clinical modifier a PATO quality?