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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Sat, 28 Mar 2009 23:10:05 -0500
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <7934FF54-71DA-4CB7-A398-AD5576CA8C63@ihmc.us>
To: Oliver Ruebenacker <curoli@gmail.com>

On Mar 28, 2009, at 3:52 PM, Oliver Ruebenacker wrote:

>     Hello Pat, All,
> On Sat, Mar 28, 2009 at 4:32 PM, Pat Hayes <phayes@ihmc.us> wrote:
>> On Mar 28, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
>>>  Why not? I don't see any fundamental problem.
>> Well, the very idea of a statistical ensemble is way more  
>> complicated than
>> anything any ontology language semantics is able to deal with. You  
>> would
>> need at least arithmetic to describe this, surely.(?)
>  Arithmetic can be described by ontologies.

Not full arithmetic, because of Goedel's incompleteness theorem. You  
might manage with Peano arithmetic, but I doubt it. I suspect you  
would need at least complex analysis.

> But for starters, before
> we have an ontology that describes all this, let us have one that is
> at least compatible with this.

A much more reasonable aim, indeed, although not one I can pursue very  
far as I know virtually nothing about statistical ensembles or the  
general area you are describing.

>> We humans do this all the time, yes, and not just in technical  
>> areas but
>> also in daily life. But machines are not very good at this kind of
>> cross-domain elision. In fact, they can hardly do it at all. Notice  
>> that if
>> this kind of reasoning were ubiquitous, sameAs would be close to
>> meaningless.
>  Obviously, being the same as is different from being isomorphic to.
>> I understand. However, speaking now as an ontology engineer, I  
>> would not
>> advise anyone to attempt to formalize all this in anything remotely  
>> like OWL
>> or even full first-order logic.
>  What would you do?

I wouldn't. Its far too complicated and too far from existing ontology  
work. Statistical ensembles are just way outside the state of the  
logical-formalizing art, I would guess. If you can cite any work,  
however, I'd be delighted to be proved wrong.


>     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

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Received on Sunday, 29 March 2009 04:11:17 UTC

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