Open cmungall opened 1 year ago
Thanks Chris! We are undertaking a migration of Apollo-SV to the ODK and will be reviewing these and other more "complicated" axioms. See the pull request that Nico created here: https://github.com/ApolloDev/apollo-sv/pull/227
I'd say the resolution of this issue is pending the ODK migration, after which we can review to see what still needs to be fixed. At least with respect to the axioms.
Making definitions more expert friendly is indeed often in tension with ontological precision. In Apollo-SV, we actually used a separate annotation for the expert-friendly version (I think we call the annotation "elucidation" although we were never quite comfortable with it. And I'm not sure we managed to have both for every class that had one or the other).
here is a subset of the symbiosis terms, their text definitions, their logical definitions, and problems
'interspecies interaction between organisms' and (('has occurrent part' some 'multi-organism behavior') and (has_participant min 2 organism))
symbiosis and (('has occurrent part' some 'bodily harm') and (has_participant min 2 organism))
symbiosis and (has_participant some (organism and ('spatially disjoint from' some organism)))
ectosymbiosis and (not (realizes some (homeostasis and ('characteristic of' some organism)))) and ('has part' some 'bodily benefit')
ectosymbiosis and ('has part' some 'bodily benefit') and ('has part' only 'bodily benefit')
'ectosymbiotic commensalism' and (realizes some (function and (('proper part of continuant at all times' some organism) and ('characteristic of' some 'anatomical structure'))))
symbiosis and (has_participant some (organism and ('located in' some organism)))
endosymbiosis and ('has part' some ('bodily harm' and (not ('has part' some 'life-death temporal boundary'))))
'intimate agonism' and ('has part' some ('bodily harm' and ('has part' some 'life-death temporal boundary')))
agonism and (has_participant min 2 (organism and ('colocalizes with' some organism)))
I would be happy to go into each of these in detail, but overall I suspect you do not derive any benefit from these OWL definitions (i.e if you removed them entailments would be effectively unchanged), and they could be removed (the text definitions are excellent and should remain, that's really all you need).
Some general principles I recommend:
Following these would involve simply dropping the OWL definitions
I note that in many of the OWL definitions you are hitting the coreference problem. If you are interested I can point you at some papers where the OWL community attempted to solve this by extending OWL2 with a concept called Description Graphs. But ultimately this effort was a bit pointless.
I'd also recommend keeping the text definitions something that could be understood by an ecologist. This is generally followed except in the cases where you veer into BFO language (inheres, realizing, continuant).