On Fri, 29 Apr 2005 17:52:42 +0100 (BST)
Nicolas Le Novere <firstname.lastname@example.org> wrote:
> Hugh and yourself are right of course. But I'm not asking how, as a
> modeler, I should avoid that. The answer is just "don't be dumb". My
> problem is as a recipient of the model. I receive the model AS IT
> IS. What can I do with it?
> For the immediat purposes of BioModels and SBMLeditor, such as
> printing the ratelaw, we will just overide everything by the local
> ids. But I'm convinced it is a problem that we should address, and the
> sooner the better.
> For Level2 version2 I propose to follow what is implied by you
> suggestion and PUT ALL THE ID IN THE SAME NAMESPACE, using only the
> "name" when we want to use the same parameter with different local
> values. I know why we create the local namespaces in the first place,
> but retrospectively that was not a good idea.
I strongly agree. For me the understanding was when we agreed for Level
2 to ids and names that ids are computer readable and names are human
readable. This makes it possible to put all ids into the same name
space in Level2 version2. A translation from Level1 is straight forward
move ids to name and generate global ids. Translation from Level2
version1 is similar if no names are used. If names are used, the
change of the id fields should be transparent to a user anyway since
he/she is interested in the names anyway.
> Could SBML users provide examples where that would be a problem
> unfixable by the use of prefixes?
> 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
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility I
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606