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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Sun, 29 Mar 2009 22:35:09 -0500
Cc: Matthias Samwald <samwald@gmx.at>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
Message-Id: <9EE06444-5D9C-418D-BBEF-72128D527D4F@ihmc.us>
To: Oliver Ruebenacker <curoli@gmail.com>

On Mar 29, 2009, at 11:15 AM, Oliver Ruebenacker wrote:

>     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?

As I have been taken to task (offline) for agreeing with you, allow me  
to intercede. On this point, I think everyone is right. Yes, classes  
are things that have, or can have, instances, and that is all that a  
class is, in effect. (RDFS makes this quite explicit by _defining_  
classes to be things in the range of the rdf:type property.) On the  
other hand, it is certainly correct that ontologies can say a lot  
about classes without ever mentioning instances. On the other hand, it  
is also the case that, were someone to (not unreasonably) wish to  
connect such classes with their instances, the resulting conclusions  
should be correct, and if they were not, then this would be a serious  
critique of the ontology.

Pat Hayes

>>> 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

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Received on Monday, 30 March 2009 03:36:25 UTC

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