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Fw: OWL usage

From: Matt Halstead <matt.halstead@auckland.ac.nz>
Date: Wed, 24 Sep 2003 16:16:35 +1200
Message-ID: <007b01c38252$a4b01c40$87d0d882@bioeng.auckland.ac.nz>
To: <public-webont-comments@w3.org>
Cc: "Joanne Luciano" <jluciano@predmed.com>, "Ian Horrocks" <horrocks@cs.man.ac.uk>, "Phillip Lord" <p.lord@russet.org.uk>

In response to a request from Ian Horrocks, via Philip Lord(see thread at
end of email), I have described the main aspects for the adoption of OWL in
our work

What we are doing :

We have developed(and are still evolving) a representation language for the
mathematical modelling of biological systems.  Two resources for information
about this are :

1) CellML main site - http://www.cellml.org/

2) IUPS Physiome project -
http://www.bioeng.auckland.ac.nz/physiome/physiome.php

Both these aspects of our work will benefit from a formal semantic
representation.  For the first domain, semantic representation languages
help us to provide a formal metamodel description of our language, and
therefore a more structured environment and toolset in which to evolve it.
If you get into the spec for CellML at all, it's pretty obvious that
constructs such as 'reaction' need to be pushed into a different level and
also semantic relationship than they currently are in the base language.
Within the second domain, i.e. the IUPS Physiome project, it is obvious how
a formalization of the concepts there would benefit the project, especially
as we integrate Physiome data into toolsets and the modelling language
itself.

Why we chose OWL :

- Based on description logics, which we feel is a natural way for us to
describe our concepts and relations.

- Extends RDF/RDF-S, which we are already using in CellML.  Sidenote : I am
particularly pleased to see the RDFS(FA) branch that the Manchester group
have formed.

- Is focused on machine operability - i.e. computationally attractive for
developing or integrating reasoning tools, interpretation into exchange
syntaxes that we already know how to process at various levels.

- People do seem to be building tools around it that we use.

- Promotes ontology integration and sharing - in this context we will be
working closely with BioPAX to integrate their domain of biochemical
pathways with ours on mathematical modelling of biological systems.  We are
starting similar initiatives with other groups, so OWL provides a common
interpretation and communication language for us at many levels, not just
databases.

Where are we at with OWL :

- Still comparing the language architecture of OWL with that of OMG's
levelled architecture that includes the MOF.  The viewpoint here is from the
software design perspective, I'm not suggesting we are looking at OMG for
semantic representation, but do value their perspective on modelling
language architectures for software development.

- Trying to think how one can move "elegantly" through the levels
IDE(Modelling tools) <-> OWL AS+S <-> RDF/XML - i.e. the exchange form of
OWL is useful for between application data exchange, but seems very messy in
terms of this need to break frames down into triples to interpret it and
then build them back up again.

- Exporting OWL from bioengineering modelling tools that we are developing
for users to more easily design and define mathematical models of biological
systems.  These tools aren't currently ready to be released - but they will
be open source when they are.

I hope this helps,

regards
Matt Halstead

Bioengineering Institute
Faculty of Engineering
University of Auckland
Private Bag 92019
Auckland
New Zealand


----- Original Message ----- 
From: "Phillip Lord" <p.lord@russet.org.uk>
To: <matt.halstead@auckland.ac.nz>; "Joanne Luciano" <jluciano@predmed.com>
Cc: "Ian Horrocks" <horrocks@cs.man.ac.uk>
Sent: Wednesday, September 24, 2003 1:50 AM
Subject: OWL usage


>
>
>
> Matt, Joanne
>
>
> >From your respective talks at bio ontologies this year, I know that
> both of your groups are using, or are starting to use OWL within your
> projects.
>
> I'm forwarding a request from Jim Hendler, via Ian Horrocks, who are
> both members of the web ontology W3C group. They are trying to keep up
> with who is using OWL, and for what. An important part of the W3C
> process is having solid examples of where people are using
> the technology. They would be very grateful if you could forward a
> short message explaining what you are doing with OWL to their mailing
> list described below.
>
> Cheers
>
> Phil
>
>
>
>
> >>>>> "Ian" == Ian Horrocks <horrocks@cs.man.ac.uk> writes:
>
>   Ian> It would be helpful if you or anyone you know who is using OWL
>   Ian> would post a brief message to public-webont-comments@w3.org
>   Ian> with a pointer or short explanation of the application.
>
>   Ian> Thanks,
>
>   Ian> Ian
>
>   Ian> From: Jim Hendler <hendler@cs.umd.edu> Subject: WOWG: Time to
>   Ian> collect implementation info again!  To: webont
>   Ian> <www-webont-wg@w3.org> Date: Wed, 17 Sep 2003 11:21:11 -0400
>   Ian> Resent-From: www-webont-wg@w3.org
>
>
>   Ian> Everyone -
>   Ian>   this is REALLY important -- I've been running into more and
>   Ian>   more
>   Ian> people who are actually using OWL and not telling anyone about
>   Ian> it -- I would like everyone in the WG to find someone you know
>   Ian> using OWL and tell them to send mail to
>   Ian> public-webont-comments@w3.org with a pointer to their
>   Ian> application.  Then ask them to do the same...
>   Ian>   Seriously, the W3C AC is currently being very tough on
>   Ian>   Proposed
>   Ian> Recommendations, and I think our showing just how many people
>   Ian> are really using OWL at this point will help a tremendous
>   Ian> amount.
>   Ian>   We must all spread the word that people shouldn't just be
>   Ian>   using OWL,
>   Ian> but also letting us know that they are!
>   Ian>   -JH
>
> -- 
> Phillip Lord, Phone: +44 (0) 161 275 7821
> PostDoctoral Research Associate,        Email: p.lord@russet.org.uk
> Department of Computer Science          http://www.russet.org.uk
> Kilburn Building                        http://www.cs.man.ac.uk/~phillord
> University of Manchester
> Oxford Road
> Manchester
> M13 9PL
>
Received on Wednesday, 24 September 2003 00:19:03 GMT

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