Forums

Nicolas

>What
> is the use of having compartments, species and parameter ids
> in the same
> namespace?
>

Because they are symbols that occur in MathML (L2) or ascii infix (L1)
without any qualification to indicate their type.

consider a model with separate namespaces...:

<parameter id="p"/>
...
<species id="p"/>
...
<kineticLaw>
<math>
<apply>
<times/>
<ci> p </ci>
<ci> p </ci>
</apply>
</math>
</kineticLaw>

which p are the ci elements refering to?

Most tools share the global namespace amoungst all the symbol types.

This is pretty fundamental.

yours
Andrew Finney

> -----Original Message-----
> From: sbml-discuss-bounces@caltech.edu
> [mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of
> Nicolas Le Novère
> Sent: 29 April 2005 22:51
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] parameters and namespaces
>
>
> > Why complicate matters further by adding another special case when
> > interpreting SBML (e.g. SBML L1v1, L1v2, L2v1 allow for local
> > parameters, L2v2 turn local parameter processing off)?
>
> Alternatively, let's keep the parameter system as it is, but
> let's decide
> the ids of the various model components are in different
> namespaces. What
> is the use of having compartments, species and parameter ids
> in the same
> namespace?
>
> In SBMLeditor, we keep record of the different lists, and
> only the metaid
> are file-wide (am-I wrong Nicolas?). I strongly suspect this
> is the case
> of almost all software.
>
> --
> 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
>
>
>