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Re: blog: semantic dissonance in uniprot

From: John Madden <john.madden@duke.edu>
Date: Fri, 27 Mar 2009 02:23:59 -0700
Cc: w3c semweb HCLS <public-semweb-lifesci@w3.org>
Message-Id: <3D5449F8-291D-44DF-8C20-28BC3382ED50@duke.edu>
To: Pat Hayes <phayes@ihmc.us>
>
>> So, here's how I'd do this. Introduce a property linking a protein  
>> to  something (which might be anything from a piece of text to a  
>> protein) called sameProteinAs. Its reflexive and transitive but  
>> might not be symmetric (though it probably is when the value is  
>> itself a protein). It is NOT substitutive. It means, roughly, that  
>> its value either is, or has as its main topic, the same protein as  
>> the argument. It is a mixture of sameAs restricted to proteins and  
>> seeAlso restricted to cases where the topic is a single protein.
>
> The "something" to which you link could even just be a blank node,  
> Basically, if I understand you correctly, it's just a hypothetical  
> tertium quid, that you might later abandon or declare to be devoid  
> of any useful meaning. Or perhaps better, it's a collection that  
> collects things that somebody thought were "similar" to each other.  
> So if it's a class or set, it's a set whose intension is defined by  
> some human opinion, not a class that makes any claim on being like a  
> natural kind.

Uh-oh. Rereading your proposal, I see I misinterpreted it. Apologize.

Would this be like a property defined by a rule? e.g.

If (subject type protein) and (object type protein)
	then sameAs
else seeAlso.

or maybe

if (type(subject) equivalentClass type(object))
	then sameAs
else seeAlso.



Received on Friday, 27 March 2009 09:25:58 UTC

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