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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Mon, 30 Mar 2009 11:12:44 -0400
Message-ID: <5639badd0903300812s4f11b4fcg7b58ce3a9f8c3e68@mail.gmail.com>
To: Bijan Parsia <bparsia@cs.manchester.ac.uk>
Cc: public-semweb-lifesci <public-semweb-lifesci@w3.org>
     Hello Bijan, All,

On Mon, Mar 30, 2009 at 7:35 AM, Bijan Parsia
<bparsia@cs.manchester.ac.uk> wrote:
>>  Isn't that the typical way, that ontologies define classes and
>> properties and users of these ontologies instantiate these classes?
> Nope. It's "a" way, but it's hardly typical and the way you talk about it is
> seriously misleading.

  Can you name any popular ontology that does not primarily declare
classes and properties?

> "Instantiating classes" suggests something akin to what one does in an
> object oriented programming language. I.e., it suggests that individuals are
> "created" from templates (aka classes). While OWL Classes are used this way
> in KA systems, it requires careful thought (and the intervention, typically
> of a "sanctioning" mechanism which indicates which parts of the description
> are salient for the KA).

  If you do not like the word "instantiate", what word you would use instead?

> So, that's just not a helpful way to think about things in the owl context.
> I myself do use the "TBox=schema; ABox=data" analogy sometimes, but I fear
> that its utility is limited and risk of misinterpretation very high.

  It's not an analogy. It's a typical use.

> Second, there's lots of ways to use ontologies with out having to use
> logical constants (i.e., individuals). Alignment of database schemas comes
> to mind. There you might never lift the database data into the ontology, but
> merely use information from the alignment to rewrite queries.

  You mean, you rewrite queries never to be run? Then, what are you
rewriting them for?

> That's not to say that anyone writes class descriptions intending them to be
> necessarily empty (i.e., unsatisfiable). Just that instance retrieval is one
> task among many.

  I wasn't talking about tasks, but of a pattern I found almost all
ontologies I have seen so far to conform to. Instead of philosophizing
about it, why don't you just show me a popular ontology that does not
fit that pattern?

     Take care

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Monday, 30 March 2009 15:13:24 UTC

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