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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Wed, 25 Mar 2009 13:30:58 -0400
Message-ID: <5639badd0903251030j609847eavbf5196f1198aea7e@mail.gmail.com>
To: Mark Wilkinson <markw@illuminae.com>
Cc: Phillip Lord <phillip.lord@newcastle.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Mark, All,

On Wed, Mar 25, 2009 at 1:13 PM, Mark Wilkinson <markw@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. 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.
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.

  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.

     Take care

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Wednesday, 25 March 2009 17:31:32 UTC

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