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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

-- 
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
Received on Sunday, 29 March 2009 16:16:20 UTC

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