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Re: GO as RDF properties

From: Tore Eriksson <tore.eriksson@po.rd.taisho.co.jp>
Date: Fri, 14 Mar 2008 09:53:49 +0900
To: Chris Mungall <cjm@fruitfly.org>
Cc: public-semweb-lifesci@w3.org
Message-Id: <20080314094411.D949.TORE.ERIKSSON@po.rd.taisho.co.jp>

Hi again Chris, sorry for splitting up my answers.

> You could define your own property and link it to the GO class via an  
> annotation property. Here you're just using GO as fancy  
> documentation. This approach would probably be the most in keeping  
> with the BioPAX-y OO type approach above

I don't know much about annotation properties, but I'd like to be able
to use the GO hierarchy when querying, so I assume that this is not an
option.
 
> alternatively you can go down what I guess is more the biopax-obo  
> route; make your reaction a subclass of the GO function, use classes  
> to represent the proteins and chemicals involved, with some kind of  
> participation relation between the participants and the reaction

Interesting. I had to make a conceptual leap here. So you are saying
that I could claim that

:Reaction rdfs:subClassOf GO:GO_0003824 .

That is a clean solution indeed, and it seems that reasoning over it
won't be a problem. I am a little concerned though with the definition
in GO:

"Catalysis of a biochemical reaction at physiological temperatures. In
biologically catalyzed reactions, the reactants are known as substrates,
and the catalysts are naturally occurring macromolecular substances
known as enzymes. Enzymes possess specific binding sites for substrates,
and are usually composed wholly or largely of protein, but RNA that has
catalytic activity (ribozyme) is often also regarded as enzymatic."

It says that GO:0003824 is about the *catalysis* of the reaction - not
the reaction itself. Won't subclassing it lead to some extent of
semantic shift? I guess it might be semantically closer than my proposed
solution though.

Tore

_______________________________________________________________
Tore Eriksson [tore.eriksson ad po.rd.taisho.co.jp]
Received on Friday, 14 March 2008 00:54:31 UTC

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