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Re: blog: semantic dissonance in uniprot

From: Matthias Samwald <samwald@gmx.at>
Date: Sun, 29 Mar 2009 17:13:09 +0200
Message-ID: <A0B02511C1B440ABB5C9F5EA34762120@ms>
To: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>

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 

> 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?

> If some one else wants to declare instances of EGFR, that's their
> responsibility and it is probably a mistake.

Maybe they want to refer to a certain subclass of EGRF out there, e.g., 
those from a certain species? Why do you say that it is 'probably' a 
mistake? Why? And why are you not certain?

 -- Matthias 
Received on Sunday, 29 March 2009 15:13:52 UTC

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