obo-relations
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oborel
RO includes quality from both PATO and BFO
RO includes PATO:morphology as a direct subclass of BFO:quality and also
morphology as a subclass of physical object quality which is a subclass of PATO
quality. I think it would be good to commit to one of the other. I have weak
preference for BFO:quality.
Original issue reported on code.google.com by [email protected] on 3 Jun 2015 at 11:28
Unfortunately PATO cannot commit it BFO quality so long as BFO outlaws QoPs.
PATO:quality is more general than BFO:quality. There is an argument for
relabeling PATO:quality, but the PATO people would say PATO was there first
(indeed, the original PATO with QoPs was co-developed and approved by Barry)
The compromise is to use 'obo foundry unique label'. Unfortunately, only 4
people in world have Protege configured to view this, and there is I would
estimate exactly 0 tools that are not Protege that are even capable of
supporting OFUL.
Another option would be to relabel BFO quality, something like 'quality (sensu
BFO)' or 'quality proper' (taking a leaf from the FMA).
Anyway this may be better as a ticket on the PATO tracker, RO will do what PATO
does...
Original comment by [email protected] on 3 Jun 2015 at 11:38
and it seems the two Qs are siblings rather than parent/child
Just FYI, purists may look at some parts of PATO and make an argument that some
classes are dispositions not qualities. I'm sympathetic to this but it's often
a fuzzy line (even colors can be argued to be dispositions). This somewhat
argues for PATO relinquishing the label 'quality' and going with something more
general... but that's for the PATO tracker
Original comment by [email protected] on 3 Jun 2015 at 11:41
@matentzn happy to look into this, but this is honestly beyond my admittedly limited knowledge >.< Happy to put this on the tech board and go through what needs to be done on a Monday sprint?
The action item is:
Add QC check for preventing punning of annotation and object properties. We would want this check in all ontologies, and its a good problem for Anita to look into. We can discuss on Monday.
My comment has nothing to do with this ticket must have been a mix up.. Sorry.
@cmungall can we remove the PATO->BFO assumptions in RO? Shouldnt this come from PATO itself?