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Re: OWL vs RDF

From: William Bug <William.Bug@DrexelMed.edu>
Date: Fri, 27 Oct 2006 11:33:17 -0700
Message-Id: <08DF3399-80FC-407A-B3EE-696D43E798C0@DrexelMed.edu>
Cc: Chris Mungall <cjm@fruitfly.org>, Barry Smith <phismith@buffalo.edu>, "Mork, Peter D.S." <pmork@mitre.org>, Phillip Lord <phillip.lord@newcastle.ac.uk>, Robert Stevens <robert.stevens@manchester.ac.uk>
To: systemsbiology hcls <public-semweb-lifesci@w3.org>
I completely agree with Peter's point.

As he describes, the only way we'll be able to stay commensurate with  
the multiple neuroanatomical frameworks in use in BIRN (not to  
mention in the community at-large) is to start by deconvolving the  
sometimes contradictory ontological "senses" these resources have pre- 
coordinated into one, and then work to use various OWL mechanisms for  
axiom construction to construct these more complex graphs via a post- 
coordinated mechanism.

The only addition I'd make to Peter's point is the community is still  
working out what the best formal means for specifying "equivalence  
relationships" will be.  In addition to the standard class axioms  
(subClassOf, Complement, Union, Intersection, etc.) and sameAs at the  
instance level, it's clear some of the various ontology merging  
requirements will need to use mechanisms beyond this set of options.   
More info on this effort can be obtained from Chris Mungall and/or  
Barry Smith from NCBO - or the Wikis NCBO is maintaining on these  
issues.  There has been a lot of discussion on this topic both during  
and in the wake of the recent Common Anatomy Reference Ontology  
meeting in Seattle, as well as in the context of the major  
refactoring of the OBI (nee FuGO) community ontology and the BIRN  
BIRNLex ontology.


On Oct 27, 2006, at 5:18 AM, Mork, Peter D.S. wrote:

> I think that even if you are talking about ontology construction,  
> in most cases you need OWL.  It is certain that multiple  
> overlapping ontological structures will be developed.  For example,  
> in BIRN, there is a core ontology describing neuron-anatomical  
> structures.  However, each brain atlas introduces its own set of  
> structures (based, in part, on the available resolution).  One  
> could try to merge these into a single ontology, but that would be  
> poor engineering.  Instead, a new set of axioms can be constructed  
> that define atlas structures in terms of the core BIRN ontology  
> (and vice versa).  This articulation requires class constructors  
> and equivalence relationships.  Moreover, if the source structures  
> are expressed using DL definitions, the inference engine will often  
> be able to identify additional articulation conclusions.
> Peter Mork
> As Phil implies below, if you really just need a formalism for  
> nodes and edges, you don't NEED OWL - in fact, for many types of  
> graphs, you don't need RDF.  On the other hand, if you are clearly  
> going to require a formalism with considerable ontological  
> expressivity, you probably want to give the OWL dialects (and their  
> underlying DLs and the toolsets such as ProtegeOWL  and the Pellet,  
> FACT++, and other reasoners, etc.) serious and in depth consideration.
> Just to be clear, I'm talking here about ontology construction  
> which I consider just a portion of the required task of  
> semantically formal data representation.  For much of the semantic  
> representation we need to do in large scale biological data  
> repositories, RDF alone will clearly be a sufficient first step, so  
> long as we continue to develop effective means of expressing the  
> triplets in the context of the ontologies and extending the  
> ontologies via analysis (as automatic as is feasible) of the  
> triplet repositories.
> Cheers,
> Bill

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
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
Received on Friday, 27 October 2006 18:33:37 UTC

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