See, for example,

Mungall et al., “Integrating phenotype ontologies across multiple
species”, Genome
Biology 2010, 11:R2 doi:10.1186/gb-2010-11-1-r2)

Ward Blondé et al.  "Reasoning with bio-ontologies: using relational
closure rules to enable practical querying", Bioinformatics (2011)
doi: 10.1093/bioinformatics/btr164

Calder, et al. "Machine Reasoning about Anomalous Sensor Data"
http://dx.doi.org/10.1016/j.ecoinf.2009.08.007 or in manuscript form
at http://efg.cs.umb.edu/pubs/SensorDataReasoning.pdf

...

OK, so  maybe these knowledge domains are all hypothesis-driven
sciences (i.e.,  sciences), and <whatever dsw is modelling> is not.
But that would be sad.

Bob
p.s. I had almost finished something else on this thread when Hilmar
beat me to the punch. But here's a slightly different expression of
his point:

It turns out that the differences between instances and classes is
mainly important in contexts in which you have declaimed interest,
namely reasoning.  In the RDF/RDFS/OWL stack, enforcing a distinction
between classes and instances only occurs pretty high up in the stack,
when one desires an OWL variant that will offer guarantees that
reasoners will finish any inference they are asked to verify,
preferably in less than exponential time . I guess, but am not
certain, that even in an LOD context, if data are described with an
OWL ontology that is known to be intractable, e.g. not in OWL DL, that
it is possible to design SPARQL queries that will never complete. In
fact, I believe that even with tractable ontologies, there are SPARQL
queries that are fundamentally exponential in the number of variables.

p.p.s. Irrelevant, but equivalent, aside about mathematics. At the
turn of the 20th century, Whitehead and Russell tried (and failed) to
show that everything about numbers could be logically derived from an
axiomatic description of the natural numbers (i.e. non-negative
integers). It was later shown to be the case that you must include in
your logical foundations something deeper, namely the ability to have
sets that are elements of other sets (roughly, classes that are
individuals in other classes.).  Without this, and starting only with
the natural numbers, you can logically derive all rational numbers
(fractions) and their arithmetic properties, and even all the
irrational numbers that are are the solutions of polynomial equations
with integer coefficients ("algebraic numbers") such as sqrt(2), and
even solutions of the polynomials that have coefficients that are
algebraic numbers.  But without introducing the notion of the set of
subsets of a set, you cannot logically derive the all the interesting
transcendental numbers (i.e. those which are not the roots of
polynomials), such as e and pi.  So if you love calculus, you better
not insist on  distinguishing instances from classes. But if you are
content with polynomials, you can probably be ontologically sloppy.
Or, if you don't care about logical foundations of your science, you
can forget about the whole thing. :-)

On Tue, May 3, 2011 at 11:51 PM, Steve Baskauf
<steve.baskauf@vanderbilt.edu> wrote: