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Re: ontology specs for self-publishing experiment

From: William Bug <William.Bug@DrexelMed.edu>
Date: Fri, 7 Jul 2006 04:00:25 -0400
Message-Id: <18F059EC-47B3-4960-8A36-CB5F10A08E6B@DrexelMed.edu>
Cc: Tim Clark <twclark@nmr.mgh.harvard.edu>, Trish Whetzel <whetzel@pcbi.upenn.edu>
To: w3c semweb hcls <public-semweb-lifesci@w3.org>

On Jul 6, 2006, at 12:55 PM, William Bug wrote:

> In the context of the comment above, this is being addressed by  
> trying to establish a foundational ontology for biomedical reality  
> and an ontology of relations ([]).  I realize we went through this  
> debate of the foundational ontology a few weeks back, but a fairly  
> specific path is already being followed by the folks working on the  
> OBO Foundry


Ooops.

In my haste, juggling this with 3 other parallel tasks in the lab  
this afternoon, I missed the references here, though I expect many on  
this list are aware of what I'm referring to.


Relations in biomedical ontologies
Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand  
Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector  and  
Cornelius Rosse
Genome Biology 2005, 6:R46     doi:10.1186/gb-2005-6-5-r46
http://genomebiology.com/2005/6/5/R46

Basic Formal Ontology (SNAP/SPAN)
http://ontology.buffalo.edu/bfo/

Biodynamic Ontology
http://ontology.buffalo.edu/medo/biodynamic.pdf

The Ontology of Biomedical Reality
http://ontology.buffalo.edu/medo/biomedo.htm


Please note the unifying factor for all of the above - beyond the  
formalisms presented - is Dr. Barry Smith (http:// 
ontology.buffalo.edu/smith/).

Despite the debates that continue on this topic, over the past 2  
years, this body of work has had a very powerful influence over a  
wide swarth of work in large-scale, field-wide, biomedical KR/KD, so  
it's worth keeping it on our radar. I would stress this influence  
extends well beyond the realm of creating explicit, formal  
ontological frameworks to support complex, automated reasoning but is  
targeting much more basic levels of formal semantic representation -  
such as semantically-based, biomedical data integration - I believe  
to be directly relevant to several of the discussion threads across  
the W3C SW HCLSIG lists.

Cheers,
Bill


Bill Bug
Senior Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu







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Received on Friday, 7 July 2006 08:05:07 GMT

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