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Re: owl:sameAs - Is it used in a right way?

From: Jim McCusker <mccusj@rpi.edu>
Date: Sat, 16 Mar 2013 14:12:18 -0400
Message-ID: <CAAtgn=SH4B9HLccL_iMuW1nMijTfJBV-=VxBK1ee74UY1iPF2g@mail.gmail.com>
To: John Madden <john.madden@duke.edu>
Cc: Umutcan ŞİMŞEK <s.umutcan@gmail.com>, David Booth <david@dbooth.org>, Jeremy J Carroll <jjc@syapse.com>, Kingsley Idehen <kidehen@openlinksw.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
I see Nanopublications as providing a framework for modality. They, of
course, use named graphs to do this, but they provide a way to express
attribution and justification in a consistent manner. http://nanopub.org

On Sat, Mar 16, 2013 at 12:59 PM, John Madden <john.madden@duke.edu> wrote:

> Medical records are filled with modal assertions:
> Possibly P(x)
>  I believe that P(x)
> Jim believes P(x) (whereas e..g. perhaps David, Umutcan, Jeremy and I
> don't).
> At 5:00 pm today P(x)
>  I disavow P(x)
> It is extremely unlikely that P(x)
> I know that P(x)
>  I regret that P(x)
> I am reponsible for bringing about P(x) (!!!!)
> and these are typically the most "interesting" (in the sense of having
> practical medical consequences) statements in medical records.
> OWL logic (out-of-the-box) does not include support for modal reasoning of
> arbitrary kind (and there are a countless number of kinds). Put another
> way, OWL out-of-the-box has a commitment to one particular modality. So we
> don't expect an OWL reasoner to reason with arbitrary modal assertions; in
> fact, we don't expect the OWL language necessarily to even be competent to
> express multiple, arbitrary modalities, out-of-the box. It just isn't part
> of the native language.
> I agree with Jim and others that if you want to use OWL, you must let OWL
> be OWL. We should reason locally with it, accepting its limitations. One
> such limitation is that if you choose to reason with owl:sameAs, under OWL
> rules (i.e under OWL modality), you have situated yourself within a
> universe, consisting of a set of possible worlds related to each other in a
> particular way (to cast it that way), in which the resources referenced
> really are the same resource in all relevant respects—where "relevant"
> means relevant to your considerations: considerations that are not part of
> OWL, but of which OWL inference rules are perforce a subset.
> If you are in doubt whether you can buy into that, then you just shouldn't
> include those particular triples—or else not use OWL (out-of-the box, or
> perhaps at all) to reason. (Maybe "reason" some other way, maybe "manually"
> by using your noggin while inspecting the triples or some insight-provoking
> representation thereof.) Or better and in addition, you should simply
> consider the result of any OWL reasoning exercise as a kind of
> experiment—not "truth" simpliciter, but just a way of informing yourself
> about the implications of situating yourself within some set of possible
> worlds under OWL modality, given that you provisionally accept certain
> assertions as facts.
> In my long-held opinion, where clinical records are concerned "local" and
> "(OWL-)relevant" would often mean pre-selecting a pretty darned small set
> of "wild-type" triples, by which I mean triples culled from sundry sources
> in the jungle of the Semantic Web: a few dozen? a few hundred? Maybe. Maybe
> more or less, depending on what it is you hope to accomplish when you press
> the fateful button labeled "INFER".
> Of course, it's possible to fiat-define as many modal predicates as you
> want, and to use them to navigate through the jungle; but not to
> automagically reason with them. Fiat predicates like <asserts> (with domain
> e.g. foaf:Person and range e.g. trix:graph; thank you Jeremy) could very
> useful for pre-navigating among graph fragments to select the ones with
> which you care to populate your particular world(s).
> John
> On Mar 16, 2013, at 1:08 AM, Jim McCusker <mccusj@rpi.edu> wrote:
> David,
> The problem with this is that by definition, URIs ALWAYS denote the same
> resource. If there is doubt that you might be denoting something other than
> what a resource is, you should be defining your own resource.
> Jim
> On Sat, Mar 16, 2013 at 12:35 AM, David Booth <david@dbooth.org> wrote:
>> Hi Umutcan,
>> You have indeed stumbled on a deep question, and I think Jeremy's
>> suggestion is exactly right.  This paper on "Resource Identity and Semantic
>> Extensions:
>> Making Sense of Ambiguity" illustrates how owl:sameAs works in RDF
>> semantics:
>> http://dbooth.org/2010/**ambiguity/paper.html#sameAs<http://dbooth.org/2010/ambiguity/paper.html#sameAs>
>> There are two keys to understanding owl:sameAs.  One is to answer the
>> question: what RDF graph are you considering?  The other is to understand
>> that the same URI may denote different things in different RDF graphs.  It
>> is only when RDF statements are in the *same* graph that the RDF semantics
>> requires the URI to denote the same resource.  That is why the question of
>> what graph you are considering is crucial, and why Jeremy suggested keeping
>> the different perspectives in different graphs.
>> FYI, the above paper also explains how you can "split" the identity of an
>> RDF resource if you need to merge RDF graphs that use the same URI in
>> contradictory ways.
>> David
>> On 03/15/2013 02:29 PM, Jeremy J Carroll wrote:
>>> I did not find this a rookie question at all.
>>> This seems to get to the heart of some of the real difficult issues in
>>> Semantic Web.
>>> My perspective is different from yours, and a resource description that
>>> I author is a description of the resource from my perspective; a resource
>>> description that you author is a description from your perspective.
>>> If I have some detailed application that depends in some subtle way on
>>> my description, I may want to ignore your version; on the other hand, a
>>> third party might want to use both of our points of view.
>>> One way of tacking this problem is to have three graphs for this case:
>>> Gj, Gu, G=
>>> Gj contains triples describing my point of view
>>> Gu contains triples describing your point of view
>>> G= contains the owl:sameAs triples
>>> Then, in some application contexts, we use Gj, sometimes Gu, and
>>> sometimes all three.
>>> Jeremy
>>> On Mar 15, 2013, at 11:02 AM, Umutcan ŞİMŞEK <s.umutcan@gmail.com>
>>> wrote:
>>>  Thanks for the quick answer : )
>>>> So this issue is that subjective for contexts which allows to use
>>>> owl:sameAs to link resources  if they are not semantically even a little
>>>> bit related in real world?
>>>> Sorry if I'm asking too basic questions. I'm still a rookie at this :D
>>>> Umutcan
>>>> On 15-03-2013 19:38, Kingsley Idehen wrote:
>>>>> On 3/15/13 1:05 PM, Umutcan ŞİMŞEK wrote:
>>>>>> My question is, does LODD use owl:sameAs properly? For instance, are
>>>>>> those two resources, dbpedia:Metamizole and drugbank:DB04817 (code for
>>>>>> Metamizole), really identical? Or am I getting the word "property" in the
>>>>>> paper wrong?
>>>>> The question is always about: do those URIs denote the same thing? Put
>>>>> differently, do the two URIs have a common referent?
>>>>> ## Turtle ##
>>>>> <#i> owl:sameAs <#you>.
>>>>> ## End ##
>>>>> That's a relation in the form of a 3-tuple based statement that
>>>>> carries entailment consequences for a reasoner that understand the relation
>>>>> semantics. Through some "context lenses" the statement above could be
>>>>> accurate, in others totally inaccurate.
>>>>> Conclusion, beauty lies eternally in the eyes of the beholder :-)
> --
> Jim McCusker
> Programmer Analyst
> Krauthammer Lab, Pathology Informatics
> Yale School of Medicine
> james.mccusker@yale.edu | (203) 785-4436
> http://krauthammerlab.med.yale.edu
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@cs.rpi.edu
> http://tw.rpi.edu

Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-4436

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
Received on Saturday, 16 March 2013 18:13:02 UTC

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