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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