From: Robert S. <rob...@ma...> - 2010-07-27 19:37:04
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David captures my point very well. Just as David has sensible repeatable measures for his exsample, I can think of several for "patients in the Long Island Jewish North Shore Hospital ". I'd hope that my classes had repeatably measurable attributes. The normalisation methodology is purely an engineering approach that manages the production of multiple inheritance -- it is no more than that. As David says, the status of the primitive and defined types has no difference in terms of their realness. Robert. At 18:25 27/07/2010, David Osumi-Sutherland wrote: >On 27 Jul 2010, at 17:19, Barry Smith wrote: > > > At 11:40 AM 7/27/2010, Robert Stevens wrote: > > > >>> <snip> > >> > >> > >> > >>> It is clear that many application ontologies will need to include, > >>> in > >>> addition to representations of universals (types, kinds, whatever > >>> you > >>> prefer to call them), also representations of defined classes. The > >>> (heuristic) proposal is (1) that single inheritance holds for the > >>> former, but not for the latter and (2) that is_a links should be > >>> asserted for the former and inferred from the latter. This coheres > >>> well, I think, with Alan's ideas on normalization. > >>> BS > >> > >> Are defined classes in OWL not universals (or whatever)? > > > > The idea is that there are certain repeatable features (e.g. charge > > of an electron, influenza), which reference ontologies (in the ideal > > case) should represent. We call these 'universals', because the word > > is sufficiently toxic that it is unlikely to be purloined (in the way > > of 'class') for multiple other uses. > > > > Given these repeatable features we can create terms representing many > > defined classes, e.g. the class of influenza patients in the Long > > Island Jewish North Shore Hospital System > >This makes it sound like the distinction between Universals and >defined classes is clear enough to be useful. In my experience it is >not. > >Imagine a single instance of a fly sensory organ - a small bristle on >the edge of a wing. > >This bristle is variously and usefully classified by scientists >according to: its function (it is both chemosensory and >mechanosensory); the shape and structure of its cuticular >specialization (a socketed bristle with a terminal pore), by the >number of neurons whose dendrites terminate in it (5), by its >location (the dorsal wing margin), by its developmental origin and >pathway. In future it may be classified according to the chemosensory >genes its neurons express... > >Which one of these classifications is the Universal? As far as I can >see, different classifications are useful depending on the questions a >scientist is interested in. If Universals are simply the subjects of >scientific discourse - the things that scientists make assertions >about - then this could apply to 'mechanosensory organ', wing margin >sensillum, bristle, bristle with pore, socketed bristle... > >I haven't found it very productive to get a bunch of ontologists and >scientists together to agonise over how we can make a single >inheritance hierarchy of 'univerals' for some domain of biology. Even >if we arbitrarily pick, say 'structure' as a single 'axis of >classification', there's no reason to believe there will not be many >useful ways to classify something structurally. > >What I have found to be very practical is to list all of the ways that >scientists want to classify something, and then try to automate as >much of this classification as possible using defined classes (e.g.- >wing margin bristle EquivalentTo: bristle and part_of some wing >margin). I'd happy be to automate all classification in this way and >assert no classification at all. The choice between automated >classification using defined classes and asserted classification then >comes down to the practical question of what we can easily formalize. >The asserted classification is not necessarily more important or less >arbitrary. It's just what's left. > >Now, is the ontology I maintain an application ontology simply because >of my use of defined classes? What reason is there to believe that >any of the ontologies that are now full OBO foundry members can >reflect scientifically useful classification within their domains and >be single inheritance asserted classifications with little or no use >of defined classes? If there is no reason to believe this, are these >all actually application ontologies? > >You might have guessed by now that I'm pretty skeptical that the >distinctions between Universal and defined class and between >application and reference ontologies are clear enough to be useful. >I'm happy to say that we should avoid filling our ontologies with >obviously contingent and arbitrary classes and if that is all that is >meant by 'Universal' then I'm fine with it. But I still haven't >heard any convincing theoretical arguments for why we might expect >that good classification consists of single inheritance hierarchies of >'universals' or for that clearly differentiates universals from >defined classes. Practically, I can say from experience that an >approach to ontology building that places great emphasis on judging >what counts as a universal and finding ways to construct single >inheritance hierarchies with these is highly unproductive. > >- David > > > > >> Is this kind of technique only to be used in application ontologies? > > > > We are attempting not to lay down the law too narrowly on this and > > many related questions until we know what works best in practice; > > however we anticipate that application ontologies will likely include > > many representations of defined classes, while reference ontologies > > will likely include few. > > > >> So, not in GO? Does multiple inheritance still need to be removed > >> from reference ontologies? > > > > Efforts along these lines for GO are underway. Experimentally > > BS > > > > > >> Robert. > >> > >> > >> > >> > >> > >>>> Barry Smith <phi...@bu...> writes: > >>>>> Here, too, we are broadly in agreement -- the GO itself is > >>>>> attempting > >>>>> to realize a modified version of your proposals here, namely to > >>>>> have > >>>>> an asserted single inheritance hierarchy and to infer the rest. > >>>> > >>>> > >>>> > >>>> ------------------------------------------------------------------- > >>> ----------- > >>>> The Palm PDK Hot Apps Program offers developers who use the > >>>> Plug-In Development Kit to bring their C/C++ apps to Palm for a > >>>> share > >>>> of $1 Million in cash or HP Products. Visit us here for more > >>>> details: > >>>> http://ad.doubleclick.net/clk;226879339;13503038;l? > >>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/ > >>>> _______________________________________________ > >>>> Obo-discuss mailing list > >>>> Obo...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss > >>> > >>> > >>> > >>> ------------------------------------------------------------------- > >> ----------- > >>> The Palm PDK Hot Apps Program offers developers who use the > >>> Plug-In Development Kit to bring their C/C++ apps to Palm for a > >>> share > >>> of $1 Million in cash or HP Products. Visit us here for more > >>> details: > >>> http://ad.doubleclick.net/clk;226879339;13503038;l? > >>> http://clk.atdmt.com/CRS/go/247765532/direct/01/ > >>> _______________________________________________ > >>> Obo-discuss mailing list > >>> Obo...@li... > >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss > >> > >> > >> > ------------------------------------------------------------------------------ > >> The Palm PDK Hot Apps Program offers developers who use the > >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share > >> of $1 Million in cash or HP Products. Visit us here for more details: > >> http://ad.doubleclick.net/clk;226879339;13503038;l? > >> http://clk.atdmt.com/CRS/go/247765532/direct/01/ > >> _______________________________________________ > >> Obo-discuss mailing list > >> Obo...@li... > >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > > > > > > > ------------------------------------------------------------------------------ > > The Palm PDK Hot Apps Program offers developers who use the > > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > > of $1 Million in cash or HP Products. Visit us here for more details: > > http://ad.doubleclick.net/clk;226879339;13503038;l? > > http://clk.atdmt.com/CRS/go/247765532/direct/01/ > > _______________________________________________ > > Obo-discuss mailing list > > Obo...@li... > > https://lists.sourceforge.net/lists/listinfo/obo-discuss > >David Osumi-Sutherland, PhD >Ontologist / Curator >Virtual Fly Brain / FlyBase >Department of Genetics >University of Cambridge >Downing Street >Cambridge, CB2 3EH >UK >+44 (0)1223 333 963 > > > > >------------------------------------------------------------------------------ >The Palm PDK Hot Apps Program offers developers who use the >Plug-In Development Kit to bring their C/C++ apps to Palm for a share >of $1 Million in cash or HP Products. Visit us here for more details: >http://ad.doubleclick.net/clk;226879339;13503038;l? >http://clk.atdmt.com/CRS/go/247765532/direct/01/ >_______________________________________________ >Obo-discuss mailing list >Obo...@li... >https://lists.sourceforge.net/lists/listinfo/obo-discuss |