On Mar 26, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Thu, Mar 26, 2009 at 3:28 AM, Pat Hayes <pha...@ihmc.us> wrote:
Just because it refers to a set of things does not mean I need to
model it by an owl:Class.
No, but if it really is a set, that would be a very good idea.
Actually, I doubt a protein is a set. It seems to me, in Systems
Biology, a protein is an operator working on statistical ensembles,
from which we can derive expectation values and variances.
Um. OK, you obviously know more about this than I do, but I very much
doubt if any ontology notation is capable of expressing what you here
describe.
Well, it was a problem with OWL DL that an class couldnt be an
instance of
another class. I gather this has been fixed (about time) in OWL 2,
There is
obsolutely no logical or fundamental reason why classes should not be
allowed to be in other classes, for examples like this one.
An OWL Full reasoner takes much longer to compute than an OWL DL
reasoner. What good are classes if you don't intend to instantiate?
I was referring to OWL 2, not OWL Full. It is the new version of OWL,
in last call as we write. The DL version of it runs at DL efficiencies
and allows classes of classes, kinda (using punning, it works for most
applications). And BTW, instantiating classes is fast and easy in just
about any formalism. The speed cost comes from the fact that more
expressive languages allow stranger edge cases which have to be
checked by complete reasoners. But all these complexity results are
worst-case, and normal-case behavior is often very different.
Similarly, a typical approach would be to have a class Protein and
an
instance EGFR ("a protein") that refers to a large number of
molecules
scattered all over the globe.
Um.. this seems confused to me, mixing up ideas from mereology with
classes.
A 'large number of molecules scattered all over the globe' sounds
like a
mereological sum. Which is fine, and pretty well axiomatized
already with
off-the-shelf ontologies. BUt there is no point in also having a
class of
these things, since this just confuses sums with classes. What are
the
elements of the class? The sum or the individual molecules? If the
latter,
we don't need the sum; if the former, we don't need the class.
Ensemble operators are not sets. The whole is more than the sum of
its parts.
Well, OK, but then the whole class/property paradigm seems to not
apply. Classes in any DL language _are_ sets.
I agree it makes sense. But to be exact, whats been found in fruit
fly
embyos are molecules of the (same) protein, not the same molecules
of the
protein. If this is important for reasoning (and I bet it will be),
then
your ontology needs to distinguish protein molecules from proteins.
And if
it doesn't, then I'd predict it is going to get its knickers in a
twist.
You may be talking of single molecules, but I am not, so your
confusion does not apply to me.
Im glad to hear it. You did however refer to protein being found in
fruit fly embryos. My point applies whether this protein in the fly is
thought of as molecules or as a compound. The point is that there is
something analogous to a type/token or type/instance distinction here,
that your ontology needs to be sensitive to, if it is to avoid
becoming completely confused. It needs to distinguish the protein-as-
biochemical-type from the protein-as-property-of-pieces-of-matter. The
latter can be found in places: the former cannot.
Pat
Take care
Oliver
--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
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