I spoke to Barry Smith at the OIC-06 conference in December, and he
mentioned that they are working on a common core for the OBO, but it is
initially planned to be a lot smaller than the FO I have been discussing,
and is not intended to serve as a means of translation among alternative
views. The BFO is a single-inheritance ontology, and is prescriptive and
restricted as to what is allowed at the most abstract levels. (01)
Projects such as OBO, that use core ontologies with only one way of
representing any given concept probably would not work, unless changed
significantly, as the core component of the lattice or hierarchy of
theories, but would have to be mapped to such a hierarchy. I think that the
'disjoint' axioms in BFO would make it incompatible with many other
ontologies, but I think that that problem could be cured by just removing
some of the 'disjoint' assertions (or the partitions) without changing the
actual performance of the ontology in practical applications. This is
something that needs direct investigation - once the practical applications
of the OBO are available for public examination. (02)
Pat (03)
Patrick Cassidy
MICRA, Inc.
908-561-3416
cell: 908-565-4053
cassidy@xxxxxxxxx (04)
> -----Original Message-----
> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx [mailto:ontolog-forum-
> bounces@xxxxxxxxxxxxxxxx] On Behalf Of Elisa Kendall
> Sent: Monday, January 12, 2009 11:49 PM
> To: [ontolog-forum]
> Subject: Re: [ontolog-forum] Next steps in using ontologies as
> standards
>
> The closest thing I'm aware of is Stanford's BioPortal -- see
> http://bmir.stanford.edu/projects/view.php/ncbo.
>
> Elisa
>
> John F. Sowa wrote:
> > John G, Elisa, Ron,
> >
> > JG> I ask because I'm not sure why this group is devoting time
> > > discussing design of a system, when the interested parties
> > > might instead agree on basic goals, pick a system, and start
> > > work? Or else I am missing something.
> >
> > The critical issue is to *relate* different ontologies or the
> > modules from which ontologies can be built to one another and
> > to provide a systematic framework for evaluating them. There
> > are many different ontologies that people can pick, but it is
> > desirable to have a framework for showing how they are related.
> >
> > It is also necessary to include reviews, evaluations, and
> > comments by actual users of any ontology.
> >
> > EK> ... we have customers who want to ensure that certain
> > > ontologies (even "open source" ontologies) that they elect to
> > > depend on are developed and managed in processes similar to
> > > those of typical standards bodies...
> > >
> > > The more important issue I think is one of stewardship --
> > > irrespective of where ontologies "reside" from a linked data
> > > perspective, one would hope that there is a community of interest
> > > that is responsible for evolving and managing that ontology in
> > > a way that others can depend on.
> >
> > That is essential for anything that businesses are going to
> > adopt for any mission critical applications.
> >
> > For relating ontologies and modules, there is no need to "design"
> > a system, since there is (and always has been) a natural system
> > for relating theories: it's called the Lindenbaum lattice, which
> > shows how theories are related to one another as specializations,
> > generalizations, or siblings.
> >
> > Whenever two or more modules are combined to form a larger theory,
> > the result is always a common specialization of the starting modules.
> > Any deletion of an axiom from a theory makes it more generalized;
> > any addition of a nonredundant axiom makes it more specialized.
> > For a brief summary of the lattice of theories and its application,
> > see Sections 2, 3, and 4 of the following paper:
> >
> > http://www.jfsowa.com/logic/theories.htm
> >
> > Since the complete lattice of all conceivable theories is infinite,
> > there are many more than anyone would ever document or implement.
> > Therefore, I suggest the term 'hierarchy of theories' for those
> > that have been documented in the registry.
> >
> > As far as storing the theories, we need something more than
> > a list of links to ontologies scattered across the WWW:
> >
> > 1. Links to web sites have a notoriously short lifetime, and the
> > owners of any given site tend to change or move the contents
> > of any page at unpredictable, usually inconvenient times.
> > Furthermore, the reviews and evaluations should be linked
> > to and from the ontologies.
> >
> > 2. We need policies for version control, reviewing, evaluating,
> > testing, relating, and commenting on ontologies. The policies
> > should also standardize the required metadata for each
> > contributed ontology, the licensing information, etc.
> >
> > 3. The metadata, comments, reviews, and evaluations should be
> > linked to and from the ontologies, but controls are needed
> > to prevent unauthorized modification or deletion of anything.
> >
> > 4. The repository may be virtual, but the methods of version
> > control should ensure that all previous versions of any
> > contributed ontology (and metadata) are available under
> > their original URIs, independently of where they may be
> > physically stored.
> >
> > RW> If someone already has an open repository where the metadata
> > > about an ontology can be uploaded by anyone who wants to and the
> > > community can post comments and create links between ontologies,
> > > then lets all support that.
> >
> > There are many good resources available on the WWW, but I am not
> > aware of anything that comes close to meeting the above criteria
> > for maintaining, evaluating, relating, and organizing an open-ended
> > and growing collection of ontologies. If anyone knows of any such
> > things, please let us know.
> >
> > John Sowa
> >
> >
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