Pat, (01)
Thanks for the pointers to the work in biology and neuroscience. (02)
PC> Check out the BIRN ontology effort:
>
> http://nbirn.net/research/ontology/index.shtm (03)
This work is useful, but I'd like to point out that it is being
used as *terminology*, not as formal ontology. That distinction
is important because many of the claims for the value of ontology
really consist of renaming the much older field of *terminology* (04)
The terminologists have proved the value of their work for over
a century in every branch of science. They are also essential
for translation in multilingual organizations such as the UN,
the Canadian Parliament, and the European Union. (05)
When the terminologies are enhanced with OWL, they have very
few axioms beyond a type hierarchy and a few simple attributes.
They are mainly an aid to consensus in human use and information
retrieval rather than detailed reasoning. (06)
I have no objections to such usage. But I would emphasize that
it does not justify claims that the growth of ontologies shows
that they are using detailed axiomatizations and reasoning. (07)
Following are some quotations from their web sites. (08)
John
_________________________________________________________________ (09)
From https://xwiki.nbirn.org:8443/xwiki/bin/view/+BIRN-OTF-Public/Home (010)
> A controlled terminology is a fundamental requirement for assuring the
> inter-operability of the unique and diverse knowledge sources that
make up
> BIRN's shared environment. In order to enhance collaboration across
BIRN's
> open, fluid, and diverse infrastructure, we have adopted structured
procedures
> to support enhanced interoperability... (011)
Note their list of sources, which include the less formal terminologies: (012)
> BIRN knowledge sources originally included the UMLS, Gene Ontology
> (GO), Logical Observations Identifiers Names and Codes (LOINC),
> Systematized Nomenclature of Medicine Ontology (SNOMED), and
> NeuroNames. Mapping between these sources is provided by UMLS. (013)
Later in that site: (014)
> NeuroLex also includes detailed concepts for describing experimental
> techniques and instruments typically employed to carry out
> neuroscientific studies, as well as concepts for describing digital
> resources being created throughout the neuroscience community. (015)
Again, I'll admit that's probably useful, but I seriously doubt that
anyone has axiomatized their experimental techniques and instruments. (016)
> ... the Neuroscience Information Framework is working with
> neuroscientists and others who have created terminology resources
> for neuroscience to incorporate them into the NIF. (017)
From http://nbirn.net/research/ontology/ontology_neuronames.shtm (018)
> NeuroNames, the nomenclature component of the software called
> BrainInfo, is not really an ontology. It is a collection of about
> 15000 terms, 2000 of which are acronyms. It allows a complete
> description of the primate brain in terms of about 900 structures
> (approximately 580 primary volumetric structures, 130 superstructures
> and 180 superficial structures). These terms form a hierarchy defined
> by a “volumetric substructure” relationship. Each term denoting a
> volumetric structure is also related to a set of terms that denote
> the “superficial features” of the structure. Although not a part of
> NeuroNames per se, each term has an implicit mapping to a primate
> brain atlas region—however, it is unclear that this mapping from
> the term to coordinates can be automatically recovered at this time. (019)
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