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RE: blog: semantic dissonance in uniprot

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Mon, 30 Mar 2009 12:11:48 -0400
Message-ID: <AB349814F1ECB143A5D4CD29C7A6456903AADEF2@CCSEXB10.CUNET.CARLETON.CA>
To: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Mark,
 It's clear that the declaration and accurate description of domain
terminology is essential. In the hands of curators or other KA
approaches, this creates structural knowledge. Linked data efforts need
ontologies for typing. The SADI framework requires its associated
services to do this *explicitly*, before one goes about the process of
discovery with arbitrary data and services (although it's unclear from
your website whether services are *actually* described in an OWL
document or they just refer to OWL types). Anyways, it's reasoning over
OWL ontologies that gives SADI its *knowledge* discovery capability.
People still have to commit to the corresponding semantics at some
point. Right?

-=Michel=-



> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> lifesci-request@w3.org] On Behalf Of Mark
> Sent: Monday, March 30, 2009 11:49 AM
> To: Bijan Parsia; public-semweb-lifesci
> Subject: Re: blog: semantic dissonance in uniprot
> 
> On Mon, 30 Mar 2009 04:35:08 -0700, Bijan Parsia
> <bparsia@cs.manchester.ac.uk> wrote:
> 
> >>> that many ontologies (including the OBO ontologies and parts of
the
> >>> Neurocommons Knowledge Base / Banff HCLS demo) encode a lot of
> useful
> >>> information just by using classes and property restrictions,
> without
> >>> instances.
> 
> 
> It's a bit of a stretch to suggest that the OBO ontologies define
> property
> restrictions... I certainly wish they would!  :-)
> 
> 
> > "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).
> 
> 
> I actually worry about describing OWL/Ontologies this way - I think it
> creates a mindset that is artificially limiting.  I *do* use this
> analogy
> when I first describe OWL to my students, but then I tell them to
> immediately forget what I said!!  It's important to point-out to them
> the
> distinction between the ontology and the instances, especially when
> both
> are encoded in RDF (which makes it easy to make the mistake of
> shmooshing
> the two concepts together... and there are Semantic Web projects that,
> IMO, make this exact mistake!) but as soon as that distinction is
clear
> I
> want them to stop thinking about the Semantic Web in that way.
> 
> To me, OWL gives us a framework to *interpret* the world, not to
> *define*
> the world.  The fact that we can purposefully create individuals that
> fit
> a particular model is, to my mind, not the point!  I try to get my
> students to think about OWL as a "lens" rather than a "model" - it
> gives
> us a way to impart meaning onto existing data, rather than create data
> that has a particular meaning.
> 
> The CardioSHARE project (http://sadiframework.org) is my attempt to
> create
> a Semantic Web Services framework that "instantiates" this view of the
> world... in SADI/CardioSHARE, ontologies are used for *discovery*, not
> for
> a priori modelling.
> 
> I don't know if this is a *pragmatic* way to look at the Semantic Web,
> but
> I've always been an idealist LOL!  Wish me luck ;-)
> 
> Mark
> 
Received on Monday, 30 March 2009 16:13:02 UTC

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