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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Sun, 29 Mar 2009 11:48:51 -0400
Message-ID: <5639badd0903290848pb9e434dp9476c8e325aafedc@mail.gmail.com>
To: Pat Hayes <phayes@ihmc.us>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Pat, All,

On Sun, Mar 29, 2009 at 12:10 AM, Pat Hayes <phayes@ihmc.us> wrote:
> On Mar 28, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
>>  Arithmetic can be described by ontologies.
> Not full arithmetic, because of Goedel's incompleteness theorem. You might
> manage with Peano arithmetic, but I doubt it. I suspect you would need at
> least complex analysis.

  Isn't Goedel Incompleteness something that does not apply only to
Math, but to Formal Logic in general? Wouldn't that imply that it is a
concern for ontology building regardless of whether it is about Math
or any other area?

  The way I understand it: It depends on how deep you want to dig. For
example, if you want to talk about the real number one, you could just
declare a symbol for it and define in words that this is the real
number one and rely on every one agreeing what it is and you will not
be confronted with incompleteness. Or you could try to formalize the
definition of real numbers by formalizing field axioms. For example,
you can base real numbers on set theory, and then you have the choice
of naive set theory, which leaves some things undefined, or more
sophisticated approaches, and then you would definitely be concerned
about incompleteness.

>>  What would you do?
> I wouldn't. Its far too complicated and too far from existing ontology work.
> Statistical ensembles are just way outside the state of the
> logical-formalizing art, I would guess. If you can cite any work, however,
> I'd be delighted to be proved wrong.

  Perhaps the question should read: What would you advice to some one
who wants to build an ontology to describe pathways for Systems
Biology purposes?

     Take care

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Sunday, 29 March 2009 15:49:30 UTC

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