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Hello Nicholas,

On Mon, 16 Jan 2006 19:58:34 +0000 (GMT)
Nicolas Le Novère <lenov@ebi.ac.uk> wrote:

>
> > This is in my opinion an attempt through the back door to make the
> > sboTerm authoritative by just omitting the Math element in the
> > kinetic law.
>
> No, it is not. It is an issue independant of sboTerm. It is larger
> than that.
>
> > But let me come to the other pro optional argument given by Mike.
> > The kinetic law itself is optional, i.e., we already have the
> > ability to store models which are not 'fully fleshed out'. Since we
> > know already the list of substrates, products and modifiers, from
> > the reaction element
>
> But not the local parameters! So far SBML has been tied to ODE-type
> models. But there is an increasing pressure to make it accept other
> kind of models.
> The ability to store local parameters without a kineticLaw is a
> desirable feature for some quantitative descriptions that are not
> kinetics models per se (particularly if the parameters are properly
> annotated ...).

Any kind of local parameter is associated with a mathematical
expression, be it for 'traditional ODE' modelling, stochastic
modelling, or flux balance analysis. These kinetics can be expressed in
MathML omitting it is not the solution. To overcome the current
restrictions I would suggest kinetic laws for different kind of
modelling, i.e. subtyping. This would also allow two supposedly similar
models to be expressed in one SBML file, e.g. a stochastic model and an
ODE model. Results could than easily obtained from two different types
of integration. I am definitely opposed to removing the contents from
the SBML and putting it in the annotation like the sboTerm. The model
must be interpretable without it the annotation (sboTerm) provides the
context.

>
> SBML is the Systems Biology Markup Language, not ODE-ML. It was very
> clever to restrict its use to one kind of model initially. It was
> certainly seminal in its adoption. But it is a fact that SBML is now
> used by a much wider community.
>
You are absolutely correct. But as I said removing the contents from the
SBML and putting it in an sboTerm can not be the solution.

> In the current situation, the user has the choice between a
> representaiton that one can instantiate in a time-serie simulation
> (with kineticLaw), and a completely qualitative representation
> (without kineticLaw). There is maybe a middle-way.

Yes, as I suggested above. I think we are jumping the gun I am
definitely for enhancing the capabilities of the kinetic law. But
currently this is not even discussed. I think there are more consistent
solutions which will leave the contents in SBML.

>
> We are not advocating for a wild explosion of SBML elements here. But
> on the contrary for simpler SBML models. Even COPASI could read such
> models, even it they would be undetermined. A user would have to
> complete them to run simulations. But this is already the case if
> he/she import a model from Reactome or KEGG.

>
> The problem is that an empty MathML returns "0". It is not undefined.
> One can decide that the following return "0"
>
> <math>
> <apply>
> </apply>
> </math>
>
> while <math /> returns undefined.

I do not see the problem as you correctly pointed out the math lement
can return undefined :)

Let me make one thing clear at the end, I am not against sboTerms.
Actually, I am very much in favor of a controlled vocabulary. The only
problem is that the contents of the SBML file is shifted to the
controlled vocabulary. In the extreme this means we I just would need an
Biomodels ID and no SBML at all:)

Thanks,
Stefan


--
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
Email: shoops@vbi.vt.edu