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Hello Nicolas,

As Sven already mentioned this might be done when we have experience
with the use of sboTerms. However, in my opinion the MathML should
always be present since the look up sboTerm -> MathML + parameters can
be done on writing, i.e., sboTerm aware software can communicate with
other. SBML must strive to allow exchange of models on the lowest common
level. It is of no advantage to compress it to a level that it only
can be understood with an external reference database.

In addition, replacing MathML with an sboTerm makes SBML dependent on
something not under SBML's control. I like to point to the heated
discussions in Boston regarding this issue.

The sboTerm at this point in time of its and SBML's evolution only adds
semantic information and not more. If something else is intended we need
to vote for that.

Thanks,
Stefan

On Thu, 22 Dec 2005 13:23:05 +0000 (GMT)
Nicolas Le Novère <lenov@ebi.ac.uk> wrote:

>
> > Here's my point: reactions may include more than one parameter, and
> > we need to identify which parameter is which. For example, suppose
> > we know that a reaction is Michaelis-Menten-Henri, and we know the
> > k1 and the kD. We can not specify this information without giving
> > the entire math field, because even though the kineticlaw is
> > optional, if the kineticLaw is present the math is required, and the
> > parameters are inside of the kinetic law.
>
> Yes. Because of the sboTerms in kinetiocLaw and local parameters, I
> think we should make the math element optional.
>
>
> --
> 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
>
>


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
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