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Re: blog: semantic dissonance in uniprot

From: Bijan Parsia <bparsia@cs.man.ac.uk>
Date: Mon, 30 Mar 2009 17:13:09 +0100
Message-Id: <42861E13-F099-41B3-845C-FEE1828694D8@cs.man.ac.uk>
To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
On 30 Mar 2009, at 16:49, Mark wrote:

> 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.

We agree. The problem is people rely *too much* on the analogy  
instead of thinking about the points of disanalogy.

[snip]
> To me, OWL gives us a framework to *interpret*

I say "describe" but we seem close.

> 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.

It can be used for the latter as well, of course.

> 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 ;-)

Seems pragmatic to me.

Cheers,
Bijan.
Received on Monday, 30 March 2009 16:09:27 UTC

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