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Re: blog: semantic dissonance in uniprot

From: Mark <markw@illuminae.com>
Date: Mon, 30 Mar 2009 08:49:09 -0700
To: "Bijan Parsia" <bparsia@cs.manchester.ac.uk>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
Message-ID: <op.url3j7w0deqt07@littlesony>
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 15:49:47 UTC

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