Re: Merging Databases

On Tue, Jul 21, 2009 at 8:43 PM, Alan Ruttenberg
<alanruttenberg@gmail.com>wrote:

> On Tue, Jul 21, 2009 at 9:22 PM, Pat Hayes<phayes@ihmc.us> wrote:
> > Heres another example. Cyc lists all the chemical elements, and
> cross-links
> > to other such lists in other ontologies using owl:sameAs. But the Cyc
> > ontology says that an element is the set (class) of all pieces of the
> pure
> > element, so that for example sodium in Cyc has a member which is the lump
> of
> > pure metallic sodium I keep safely under glycerin in a glass bottle on my
> > shelf. This is a clever ontological device which makes a bunch of
> inferences
> > very slick in Cyc, but I bet its not the same *idea* of sodium that most
> > ontologies would agree with. So that sameAs ought to be (and it is
> > understood as meaning) 'same chemical element', but it does not allow
> mutual
> > substitutivity, even if you were to translate those other ontologies into
> > CycL, which nobody is ever likely to do.
>
> My gut reaction is that URIs ought to be names that refer, and that
> sense ought to be conveyed more explicitly as statements. That seems
> to be the basis of the model theory that underlies the semweb
> languages (yes, I realize that there's currently room for 2+ different
> referencings using the same name). I realize that in natural language
> name can carry both sense and reference (or let's just say "more than
> reference" since there seem to be a number of theories of exactly what
> goes on with words). But it seems that it's been at least a hundred
> years that relatively modern philosophers have been hacking away at
> trying to understand exactly what the phenomena are, and how to
> understand them. Should we really try to adopt exactly the same model
> as language, given that we don't really understand it?
>
> In your sodium example, i don't really know what to do with the "idea
> of sodium" being the same or different, but I *can* say that a
> molecule of sodium is not the same sort of thing as a lump of sodium
> metal. They have different physical properties and some things that
> make sense to say about one don't make sense to say about the other
> (like the melting point of xxx is 370.87 K).


For what it's worth, Cyc does not generally consider individual molecules of
a substance to be instances of that substance. For example, "iodine
molecule" (
http://sw.opencyc.org/concept/Mx8Ngh4rwPzt4pwpEbGdrcN5Y29ycB4rvVj8dJwpEbGdrcN5Y29ycA)
is not a subclass of "iodine" (
http://sw.opencyc.org/concept/Mx4rvVj8dJwpEbGdrcN5Y29ycA).

David


>
>
> Now you might say: Well, they are the same *concept*. But what am I to
> do with that? What can I conclude from that statement. Isn't it
> throwing a whole lot under the rug to lump all these sorts of
> relations into any single "same" bucket? And for what good? Google is
> pretty good at bringing all these different sorts of things together
> already - shouldn't the semweb stuff be doing something different?
>
> -Alan
> (who's been reading and puzzling too many days in a row about how
> words relate to ... everything)
>
> > On Jul 21, 2009, at 7:58 PM, Pat Hayes wrote:
> >
> >>
> >> On Jul 21, 2009, at 7:26 PM, Alan Ruttenberg wrote:
> >>
> >>> On Tue, Jul 21, 2009 at 1:23 PM, Toby Inkster<tai@g5n.co.uk> wrote:
> >>>>
> >>>> On Tue, 2009-07-21 at 19:52 +0300, Bernhard Schandl wrote:
> >>>>
> >>>>>> I would say: Never assert sameAs. It's just too big a hammer.
> >>>>>> Instead use a wider palette of relationships to connect entities
> >>>>>> to other ones.
> >>>>>
> >>>>> which ones would you recommend?
> >>>>
> >>>> skos:exactMatch = asserts that the two resources represent the same
> >>>> concept
> >>
> >> Say, refer to the same thing.
> >>
> >>>> , but does not assert that all triples containing the first
> >>>> resource are necessarily true when the second resource is substituted
> >>>> in.
> >>>
> >>> I'm having trouble parsing this one. I don't know what concepts are,
> >>> but they are an odd sort of thing if they can be the same, but can't
> >>> be substituted.
> >>
> >> This is exactly what is needed in many cases. Philosophical terminology
> is
> >> that they have the same referent but not the same sense, and lack of
> >> substitutability reflects the unfortunate but inevitable fact that the
> Web
> >> as a whole is not referentially transparent (yet). More mundane example,
> the
> >> same person might need to be referred to in one way in one context and
> >> differently in another, just because the two social contexts require
> >> different forms of address. (That example from Lynn Stein.)
> >>
> >>> In any case, this isn't much better when the issue I point out is that
> >>> there is a specific relation between e.g. the intervention and the
> >>> drug - that relation is no where near equivalence in any form.
> >>
> >> True, but in cases like this, it is simply a basic conceptual mistake to
> >> be using any kind of loose-sameAs property. rdf:seeAlso would be more
> like
> >> what is needed for linking a drug to an intervention. I agree with you
> about
> >> having a selection of better-thought-out relations rather than just
> using
> >> sameAs as a kind of all-purpose knee-jerk connecting link. Maybe this
> >> "Linked Data" slogan has a rather dumbing-down effect, as it suggests
> that
> >> 'link' is a simple uniform notion that works in all cases.
> >>
> >>>
> >>>> skos:closeMatch = same as exact match, but slightly woolier.
> >>>
> >>> Seems harmless, assuming one doesn't mind whatever one is dealing with
> >>> typed a concept.
> >>> Ditto the broader and narrower relations, which although not to my
> >>> taste  (i don't how to tell when they hold) are certainly better than
> >>> using sameAs.
> >>>
> >>>> owl:equivalentProperty = if {X equivalentProperty Y} and {A X B} then
> >>>> {A Y B}. In other words, the properties can be used completely
> >>>> interchangeably. But perhaps there are other important differences
> >>>> between X and Y, such as their rdfs:label or rdfs:isDefinedBy.
> >>>
> >>> Still near equivalence.
> >>>
> >>>> owl:equivalentClass = if {X equivalentClass Y} then all Xs are Ys and
> >>>> vice versa. Same dealy with owl:equivalentProperty really.
> >>>
> >>> Ditto.
> >>>
> >>>> ovterms:similarTo = a general, all-purpose wimps' predicate. I use
> this
> >>>> extensively.
> >>>
> >>> Under the principal "first do no harm", this seems to work, although I
> >>> note that the intervention (something that happens) isn't similar to
> >>> the drug used in it (something that is consumed when the intervention
> >>> happens).
> >>>
> >>> seeAlso seems pretty harmless and noncommittal.
> >>>
> >>> But better is probably to look more closely at what the entities are
> >>> and then choose a relationship that better expresses how they relate.
> >>> In the case of the intervention, one plausible interpretation is that
> >>> the "intervention" names a class of processes, and that there is a
> >>> subclass of such processes in which the drug participates. (the other
> >>> subclass are those in which a placebo is the participant) This can be
> >>> modeled in OWL.
> >>>
> >>> (My real advice for clinical trial resource is to collaborate with the
> >>> OBI project and use terminology that is being developed for exactly
> >>> that purpose)
> >>>
> >>> In my line of work I start with the OBO Relation ontology,
> >>> http://www.obofoundry.org/ro/ which provides a basic set of well
> >>> documented relations, such as the has_participant relationship.
> >>>
> >>> OWL also provides some relations of beyond equivalences - subclass
> >>> relations are an option, when appropriate, as well as making
> >>> statements that classes overlap - by expressing that the intersection
> >>> of the two is not empty.
> >>>
> >>> That ontology is undergoing some reform, as it should in time. Some of
> >>> the new candidate relations are documented in links from that page. In
> >>> addition it is proposed that that there be class level and instance
> >>> level versions of the relations - the class level relations might
> >>> better a modeling style that would rather avoid using OWL
> >>> restrictions, and fits well with OWL 2 which allows a name(URI) to be
> >>> used as both a class and an instance.
> >>>
> >>> Finally, for those cases where there are more than one URI and they
> >>> *really* mean the same thing - why not try to get the parties who
> >>> minted them to collaborate and retire one of the URIs. If they really
> >>> mean the same thing there should be no harm in either party using the
> >>> other's URI.
> >>
> >> Its not that simple, unfortunately. I'm going to make this issue the
> >> center of my invited talk at ISWC later this year :-)
> >>
> >> Pat
> >>
> >>>
> >>> -Alan
> >>>
> >>>>
> >>>> --
> >>>> Toby A Inkster
> >>>> <mailto:mail@tobyinkster.co.uk>
> >>>> <http://tobyinkster.co.uk>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>
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> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> > ------------------------------------------------------------
> > IHMC                                     (850)434 8903 or (650)494 3973
> > 40 South Alcaniz St.           (850)202 4416   office
> > Pensacola                            (850)202 4440   fax
> > FL 32502                              (850)291 0667   mobile
> > phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes
> >
> >
> >
> >
> >
> >
>
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