#132 G protein-coupled receptor logical definition broken

[Nicolas Matentzoglu]

The definition of
http://purl.obolibrary.org/obo/PR_000030035
'has function' some 'G protein-coupled receptor activity’
protein and ('has function' some 'G protein-coupled receptor activity’)

is problematic because 'G protein-coupled receptor activity' is classified as a process, while the 'has function' relationship only allows functions as a range, which, contrary to intuition, is, according to BFO, a realisable entity and therefore a continuant. This caused a clash, rendering the above class unsatisfiable.

I have attached a picture of the logical explanation.

[David Osumi-Sutherland]

PR should use capable_of (RO_0002215) instead of has_function here. This will align with GO.

[Darren Natale]

I find the classification of functions as realizable entities and continuants perfectly reasonable. The problem you see actually is an effect of someone's unfortunate decision to class GO MFs as processes. I know there was some talk of this but didn't know it went into effect. Then again, did it? That relation is not asserted at all within the GO hierarchy, so it must be asserted outside of GO itself. Interestingly, it means that there are no targets for has_function in GO. Unintuitive indeed. Will look into it.

[Darren Natale]

Oops, didn't see David's response. I think capable_of will do. We'll make the switch for this and others.

[David Osumi-Sutherland]

Oops, didn't see David's response. I think capable_of will do. We'll make the switch for this and others.

Excellent.

BTW - the classification of GO MF under BFO:occurrent + many uses of capable_of should be visisble in go-plus.owl

[Darren Natale]

Good to know. I couldn't find it indicated in Ontobee.