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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Mon, 30 Mar 2009 12:04:44 -0400
Message-ID: <5639badd0903300904h7de9f514v7fa3c3c30cc6f0d7@mail.gmail.com>
To: Bijan Parsia <bparsia@cs.man.ac.uk>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Bijan, All,

On Mon, Mar 30, 2009 at 11:39 AM, Bijan Parsia <bparsia@cs.man.ac.uk> wrote:
> On 30 Mar 2009, at 16:23, Oliver Ruebenacker wrote:
>>  That is probably the most used phrase in the Semantic Web community.
> And least adhered to?

  Most used as an empty cliche.

> What's your problem with providing application requirements?

  None, but that was not the topic.

>>  I have no idea what that paradigm is.
> http://portal.acm.org/citation.cfm?id=1064.1066&coll=GUIDE&dl=GUIDE&CFID=15151515&CFTOKEN=6184618

  Still no idea.

>>  An ontology should be independent of a particular application.
> First, there's a big difference between being tied to a particular
> application and being informed by intended applications. I sincerely doubt
> the general utility of an ontology designed without *any* thought to the
> class of applications for which it is intended to be used. Advice that is
> not at all informed by the broad characteristics of the applications for
> which the ontology shall be used is worthless.

  Class of applications = Systems Biology applications

> As far as I can tell it's a format converter and visualizer. No ontologies
> needed at a first approximation.

  Uses an ontology to integrate BioPAX and SBML. If you know an
alternate way, you should publish.

     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 16:05:21 UTC

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