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RE: Multi-layered Knowledge Representations for Healthcare (was RE: An argument for bridging information models and ontologies at the syntactic level)

From: Olasov, Ben <olasov@medicine.ucsf.edu>
Date: Fri, 25 Jul 2008 18:43:14 -0700
Message-ID: <16779E5DA610CF4BBCE391F0A64C78CF05AC3956@EXVS06.net.ucsf.edu>
To: "Pat Hayes" <phayes@ihmc.us>
cc: dan.russler@oracle.com, "Samson Tu" <swt@stanford.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, "Elkin, Peter L., M.D." <Elkin.Peter@mayo.edu>, public-semweb-lifesci@w3.org, public-hcls-coi@w3.org



> -----Original Message-----
> From: Pat Hayes [mailto:phayes@ihmc.us]
> Sent: Thu 7/24/2008 9:32 PM
> To: Olasov, Ben
> Cc: dan.russler@oracle.com; Samson Tu; Kashyap, Vipul; Elkin, Peter L., M.D.; public-semweb-lifesci@w3.org; public-hcls-coi@w3.org
> Subject: RE: Multi-layered Knowledge Representations for Healthcare (was  RE: An argument for bridging information models and ontologies at the  syntactic level)
>  
> At 3:53 PM -0700 7/24/08, Olasov, Ben wrote:
> >  > From: public-semweb-lifesci-request@w3.org on behalf of Dan Russler
> >>
> >>  Hi Samson,
> >>
> >>  If "denote" = "describe" in your sentence, then I withdraw my objection.
> >
> >But "denote" /= "describe".  These two words
> >were intended to be, and are, used differently.
> >Consider the sentence, "The matrix P contains
> >the entries pij, denoting the probability that
> >for a speaker object i is associated with sound
> >j.".  The word "denoting" functions here in the
> >sense of "marking" or "signifying".  The word
> >"describing" has no equivalent sense that would
> >enable it to be substituted for "denoting" in
> >this sentence.
>
> Indeed. And leaving ordinary English aside for a
> moment, the formal meanings of 'denote' and
> 'describe' as used when discussing semantics of
> formalized descriptions in logics and cognate
> notations are not the same. Names denote things,
> and descriptions - typically, extended
> collections of sentences - describe them. 

That's a crisp way of putting it, thanks.

> They do so by virtue of the names in the sentences
> denoting the things being described, but the two
> notions are distinct. In particular, denotation
> does not require description. If I say, pointing
> into the sky, "Look at that!" then my word "that"
> denotes something I am pointing to. It does not,
> however, describe it. Indeed, the thing denoted
> may, like the Golux's hat, be indescribable.
>
> >
> >I think we need to be very careful about
> >assumptions of denotational equivalence,
> >especially when the words under consideration
> >are the very ones that make the idea of
> >denotational equivalence possible and useful in
> >the first place.
>
> I agree.
>
> Pat Hayes
>
> >
> >>  My concern is that the term "class" as used in UML doesn't seem to mean
> >>  the same thing as you are describing for a class in OWL. For instance, I
> >>  don't see the same concept of "resource" in the definition of class in UML.
> >>
> >>  A UML static diagram is just a symbolic method of displaying a set of
> >>  related assertions, i.e. attribute assertions, association assertions,
> >>  and state transition (behavior) assertions. The semantic interpretation
> >>  of what the class means comes not only from the text definition of the
> >>  "class symbol," but also from inferences made from the entire network of
> >>  attributes, associations, and state transitions.
> >>
> >>  To infer from a UML class more than is implied by the the above
> >>  statement is incorrect.
> >>
> >>  If we can agree on that, then we can better evaluate the equivalent and
> >>  non-equivalent semantics of OWL and the other methods for organizing
> >>  sets of assertions.
> >>
> >>  Dan
> >>
> >>  Samson Tu wrote:
> >>
> >>  >
> >>  >
> >>  > Dan Russler wrote:
> >>  >
> >>  >> Hi Samson,
> >>  >>
> >>  >> We are getting closer.
> >>  >>
> >>  >> 1) In the reference you site..."A class is the descriptor for a set"...
> >>  >>
> >>  >> 2) Earlier, you stated that "semantics of a class as denoting a set
> >>  >> of instances."
> >>  >>
> >>  >> I believe these two statements represent the "apples" and "oranges"
> >>  >> you referenced:
> >>  >>
> >>  >> Statement 1) is the traditional "a class describes the attributes and
> >>  >> associations for a concept that are common to a set of instances."
> >>  >> Statement 2) is better described by your population example.
> >>  >>
> >>  >> I wasn't objecting to 1) . I was objecting to your seeming to
> >>  >> confusie the 2) with 1).
> >>  >>
> >>  >> However, if you claim that "denote" means the same thing as
> >>  >> "describe," then I would agree with you instead of objecting to your
> >>  >> assertion.
> >>  >>
> >>  >> To be a little clearer....The definitions in a set of dictionaries
> >>  >> all "describe" the meaning of the word "farmer." However, the word
> >>  >> "farmer" in a dictionary does not "denote" the set of instances of
> >>  >> farmers in the world. Same with a UML class titled "farmer."
> >  > >
> >>  > Dan,
> >>  >
> >>  > Yes, I am claiming that "denote" means the same thing as "describe" in
> >>  > my intended usage of the English words.
> >>  >
> >>  > We are talking about the semantics of "class." The class "farmer" is
> >>  > not the same thing as the dictionary word "farmer." Some people say
> >>  > that UML is just a graphical notation without semantics because it
> >>  > does try to make its meaning of the word "class" very clear. In
> >>  > logic-based knowledge representation languages, the set-theoretic
> >>  > semantics of class is widely used.
> >>  >
> >>  > The OWL Reference[1] put it this way:
> >>  >
> >>  > Classes provide an abstraction mechanism for grouping resources with
> >>  > similar characteristics. Like RDF classes, every OWL class is
> >>  > associated with a set of individuals, called the class extension. The
> >>  > individuals in the class extension are called the instances of the class.
> >>  >
> >>  > OKBC [2] p. 6 put it even more baldly:
> >>  >
> >>  > A class is a set of entities. Each of the entities in a class is said
> >>  > to be an instance of the class.
> >>  >
> >>  > In logical term, a class is a unary predicate satisfied by all of its
> >>  > instances. Dictionary definitions of words are not involved.
> >>  >
> >>  > [1] http://www.w3.org/TR/owl-ref/#Class
> >>  > [2] http://www.ai.sri.com/~okbc/okbc-2-0-3.pdf
> >>  >
> >>  >--
> >>  >---------
> >>  >Samson Tu                                   email: swt@stanford.edu
> >>  >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
> >
> >Ben
>
>
> -- 
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Received on Saturday, 26 July 2008 01:44:22 GMT

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