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Re: [Obo-phenotype] quality and realizable entity
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From: Alan R. <ala...@gm...> - 2008-11-19 13:32:55
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On Tue, Nov 18, 2008 at 7:53 PM, Samson Tu <sw...@st...> wrote: > Thanks. For now, I've added the terms I need as direct children of > specifically_dependent_continuant. > > It seems to me that whether a phenotype trait is always expressed or is a > "disposition" depends on specific empirical contexts. I suspect that it's > not a good idea to pre-judge that in the ontology. I don't think that's the issue. Or at least not all of it. Realizable entities are about potentials, capabilities. Learning that the capability exists is empirical, but is the normal sort of thing we learn in studying. If it happens all the time, then certainly the bearer has the potential. And nothing happens all the time. But to focus the discussion, could you give a concrete case of the sort of thing that worries you - some particular phenotype trait that exemplifies a case where you think a choice would be problematic? Regards, Alan > > Samson > > Alan Ruttenberg wrote: >> >> It's been noticed, but not yet addressed. >> >> https://sourceforge.net/tracker2/?func=detail&aid=1675411&group_id=76834&atid=595654 >> -Alan >> >> On Mon, Nov 17, 2008 at 6:15 PM, Samson Tu <sw...@st...> wrote: >> >>> >>> Hi, >>> >>> In the BFO, quality and disposition are mutually exclusive. >>> >>> The definition of quality is >>> >>> Definition: A specifically dependent continuant >>> [snap:SpecificallyDependentContinuant] that is exhibited if it >>> inheres in >>> an entity or entities at all (a categorical property). >>> >>> The definition of realizable_entity (of which disposition is a subclass) >>> >>> Definition: A specifically dependent continuant >>> [snap:SpecificallyDependentContinuant] that inheres in continuant >>> [snap:Continuant] entities and are not exhibited in full at every time >>> in which it inheres in an entity or group of entities. The exhibition or >>> actualization of a realizable entity is a particular manifestation, >>> functioning or process that occurs under certain circumstances. >>> >>> The qualities enumerated in the PATO quality class hierarchy, however, >>> have no inherent reason to be exhibited whenever it inheres in an >>> entity. Thus, for example, if we use PATO qualities to describe >>> phenotypes during developmental processes, where the phenotypes are best >>> seen as dispositions (exhibited under certain circumstances), we end up >>> with an inconsistent ontology. Does it mean that we want to describe >>> dispositions (e.g., diseases) as composition of qualities with some >>> structures or processes, we need to define a separate "disposition >>> quality" hierarchy? >>> >>> I can't believe that this issue has not come up before. Am I missing >>> something? >>> >>> Thank you. >>> >>> With best regards, >>> Samson >>> >>> -- >>> Samson Tu email: sw...@st... >>> Senior Research Scientist web: www.stanford.edu/~swt/ >>> Center for Biomedical Informatics Research phone: 1-650-725-3391 >>> Stanford University fax: 1-650-725-7944 >>> >>> >>> ------------------------------------------------------------------------- >>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>> challenge >>> Build the coolest Linux based applications with Moblin SDK & win great >>> prizes >>> Grand prize is a trip for two to an Open Source event anywhere in the >>> world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> _______________________________________________ >>> Obo-phenotype mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-phenotype >>> >>> > > -- > Samson Tu email: sw...@st... Senior > Research Scientist web: www.stanford.edu/~swt/ > Center for Biomedical Informatics Research phone: 1-650-725-3391 > Stanford University fax: 1-650-725-7944 > > |