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Re: Merging Databases

From: Pat Hayes <phayes@ihmc.us>
Date: Tue, 21 Jul 2009 20:22:56 -0500
Cc: Bernhard Schandl <bernhard.schandl@univie.ac.at>, Toby Inkster <tai@g5n.co.uk>, Hugh Glaser <hg@ecs.soton.ac.uk>, Amrapali Zaveri <amrapali.zaveri@gmail.com>, "public-lod@w3.org community" <public-lod@w3.org>, Anja Jentzsch <anja@anjeve.de>, Susie Stephens <susie.stephens@gmail.com>
Message-Id: <FA59F8C2-0631-41B0-A008-9C45F373E38B@ihmc.us>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
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.


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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40 South Alcaniz St.           (850)202 4416   office
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Received on Wednesday, 22 July 2009 01:24:50 UTC

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