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Re: GO as RDF properties

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 13 Mar 2008 22:15:02 -0500
Message-Id: <p06230904c3ff9d200144@[192.168.1.2]>
To: Tore Eriksson <tore.eriksson@po.rd.taisho.co.jp>
Cc: Chris Mungall <cjm@fruitfly.org>, public-semweb-lifesci@w3.org

At 9:53 AM +0900 3/14/08, Tore Eriksson wrote:
>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.

Simple languages like OWL and RDF will likely be 
unable to capture the semantic subtlety of the 
notion of a 'a catalysis OF a reaction'.

Not being a chemist, this might be insane, but 
could one not say that a catalysed reaction is in 
fact a different reaction, but one with the same 
reactants and products? After all, many aspects 
of the catalyzed and uncatalyzed reactions are 
very different, so an ontology would seem to need 
to distinguish them.

Just a thought.

Pat Hayes

>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]


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Received on Friday, 14 March 2008 03:15:49 UTC

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