RE: SBML L2v2 specification vote #4: References to controlled vocabularies
20 Dec '05 15:11
lenov> Maybe. But one of the reasons we felt we had to use
lenov> SBO within SBML was precisely the continuous versus
lenov> discrete problem (I assume you meant continuous
lenov> when you said "determinitic"). In the current SBML,
lenov> there is nothing that tells-us if a formula has to
lenov> be understood as a discrete or continuous
lenov> formulation. Since all kineticLaws provide
lenov> substance/time, I can read all of them in a
lenov> discrete simulator, and into problems if they were
lenov> expressing contiuous mass-action laws.
I know you know the following too, so I'm writing this only
to remind everyone of another motivation for the
introduction of CV references:
Some software tools provide users with a pull-down list of
rate laws, from which the user can select what they want for
a given reaction. The tool then writes out the appropriate
math expression into the model. Those tools would like a
way to go in the reverse direction, from rate law to name.
Currently there's no systematic way of supporting this in
SBML, because it requires some sort of additional annotation
beyond the math of the kinetic expression.