On Mar 25, 2009, at 12:30 PM, Oliver Ruebenacker wrote:
Hello Mark, All,
On Wed, Mar 25, 2009 at 1:13 PM, Mark Wilkinson
<ma...@illuminae.com> wrote:
Well, the statement would *imply* that it is... so given that the
individual
"embryo" that was referred to as a uniprot tissue is the same
individual
"embryo" that the plant ontology was talking about, we can therefore
conclude that (as Ben pointed-out) that this particular fly embryo is
somehow embedded in some particular plant seed endosperm.
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.
I can also have an owl:Class Population and
an instance of it populationOfTheUS, which would be an instance, not
an owl:Class, although it seems to correspond to a set of people.
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.
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.
The statements from UniProt, as I understand them, make perfect
sense: there is a protein that has been isolated from that plant, and
can also be found in fruit fly embryos. I don't have the knowledge to
check whether it is true, but it seems to make sense to me.
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.
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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