Forums

On 22/03/11 12:50, Francois Le Fevre wrote:
> Hello All,
>
> 1.
>
> _*listOfModifiers*_
>
> * for me, if you add multiple modifiers, then they are isozymes,
> * if you want to define a AND relationship, then you have to
> define before a species of type complex/species
> * so here at CEA/Genoscope, we do exactly the same as in
> Manchester :-)_*
> *_

I believe both Manchester and Genoscope are wrong then, except if the FBA
package changes the semantics of the core.

The "modifier" element is born out of the necessity of having all species
symbols used in kineticLaw defined. In kcat*E*S/(Km+S), kcat and Km are
parameters (local or global), S is a reactant. What about E? Later this was
extended to encoding all influences, even if there were no kineticLaws
(e.g. stoichiometric maps).

Representing isozymes in SBGN would require an OR. No doubt about that. You
can have only ONE catalyst per process. The rational when it comes to SBML
is that if you declare two modifiers, they are two pools. Isoenzyme are
part of the same pool as far as the reaction is concerned.

I believe the proper way would be to use a "group". The members of the
group would be the isoenzymes. Of course, that would require to disentangle
the semantic of the "group". We need an attribute "type" on the group, with
the values "class" or "pool".

--
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

____________________________________________________________
To manage your sbml-discuss list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss

For a web interface to the sbml-discuss mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-discuss list,
contact sbml-team@caltech.edu