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On Tue, 3 Jan 2006, Michael Hucka wrote:

> OK, if I understand your point, you are saying that it
> should be acceptable to have kinetic laws with sboTerms but
> without math filled-in?
>
> It seems to me this would put us in the situation (I think
> it was Ralph Gauges who pointed this out) that it would
> cause all software to be required to understand sboTerms,
> simply because models containing only sboTerm and no math
> would now be considered valid.

No. The same way Reactome does not care about the math. If I can
understand SBO term, fine, the semantics of the model is richer. I
could for instance associate different glyphs to the various reactions
in my pathway database. If I can't understand SBO terms, I still have
the reaction graph.

> lenov> A possible solution would be to put an optional
> lenov> sboTerm on the reaction element. This sboTerm would
> lenov> just be an
>
> I think allowing sboTerms on Reaction would be a fine idea.

Maybe, but thinking further that poses the question of inconsistency
between the sboTerms of reaction and kineticLaw elements. We will have
to put a rule saying that if we export a model with SBO terms in
reaction and kineticLaw, they have to be identical, and if there is a
bogus model with two different SBO terms, the kineticLaw one takes
precedence over the one in reaction.

--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov AIM screen name: nlenovere