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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Sun, 29 Mar 2009 12:15:38 -0400
Message-ID: <5639badd0903290915ka9904cek543cfcefec780b56@mail.gmail.com>
To: Matthias Samwald <samwald@gmx.at>
Cc: public-semweb-lifesci <public-semweb-lifesci@w3.org>
     Hello Matthias, All,

On Sun, Mar 29, 2009 at 11:13 AM, Matthias Samwald <samwald@gmx.at> wrote:
> Oliver wrote:
>>  As I understand it, an owl:Class is simply something intended to be
>> instantiated. I declare something a class if and only if I intend
>> there to be instances.
> This is how you might choose to use OWL, but it is important to emphasize
> that many ontologies (including the OBO ontologies and parts of the
> Neurocommons Knowledge Base / Banff HCLS demo) encode a lot of useful
> information just by using classes and property restrictions, without
> instances.

  Isn't that the typical way, that ontologies define classes and
properties and users of these ontologies instantiate these classes?

  I am assuming that these classes all make a commitment about what
their instances mean, so users could declares instances and rely on
that commitment to be useful, right?

>> In Systems Biology, as I understand it, EGFR is
>> an instance of class Protein which is subclass of Substance. I don't
>> intend there to be instances of EGFR, so I don't declare it a class.
> Well, that is an arbitrary choice you make here. Is you EGFR protein
> resource specific to a certain species?

  There is a whole family of operators: (1) specific to a species
(e.g. human EGFR) versus not (2) specific to a cellular location (e.g.
EGFR in cytosol) versus not (3) specific to a certain set of
post-translational modifications (e.g. phospho-EGFR) versus not

> Maybe they want to refer to a certain subclass of EGRF out there, e.g.,
> those from a certain species?

  I don't see a way to define those as instances of EGFR in a way that
makes sense. For example, if human EGFR is an instance of EGFR, what
are mammalian EGFR, or phospho-EGFR, or human phospho-EGFR?

> Why do you say that it is 'probably' a
> mistake? Why? And why are you not certain?

  Since I don't intend instances, I make no commitment what these
instances mean, so any one creating instances must rely on a
commitment made elsewhere, not by me. I can not imagine a commitment
that makes sense, but maybe that is just my limited imagination and
maybe some clever person somewhere found a way to define meaningful
instances, but then it will be probably impractical to communicate the
meaning to others.

     Take care

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Sunday, 29 March 2009 16:16:20 UTC

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