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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

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
Received on Monday, 30 March 2009 16:05:21 UTC

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