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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Thu, 26 Mar 2009 16:52:01 -0400
Message-ID: <5639badd0903261352v7ec495a9v69cb4c6435c2a451@mail.gmail.com>
To: Pat Hayes <phayes@ihmc.us>
Cc: Mark Wilkinson <markw@illuminae.com>, Phillip Lord <phillip.lord@newcastle.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Pat, All,

On Thu, Mar 26, 2009 at 3:28 AM, Pat Hayes <phayes@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.

> 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?

>> 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.

> 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.

     Take care

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Thursday, 26 March 2009 20:52:38 UTC

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