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From: Mork, Peter D.S. <pmork@mitre.org>
Date: Fri, 27 Oct 2006 08:18:27 -0400
Message-ID: <224FBC6B814DBD4E9B9E293BE33A10DC0146DC5E@IMCSRV5.MITRE.ORG>
To: "systemsbiology hcls" <public-semweb-lifesci@w3.org>
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


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.





Received on Friday, 27 October 2006 12:31:05 UTC

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