Re: SBML L2v2 specification vote #4: References to controlled vocabularies
20 Dec '05 20:18
Its not just the reaction that needs to have the correct SBO term:
don't all of the appropriate parameter values also need to have
corresponding (correct) SBO Terms (or some equivalent information)
for the kinetic law to be fully specified independent of the math
fields? And the parameter values part of the "kineticLaw" field. So
we can't just ignore the kineticLaw if there is an SBO term, we have
to read the parameter values and figure out where the go in the
reaction specified by the SBO term.
On Dec 20, 2005, at 7:56 PM, Michael Hucka wrote:
> RG> [...] (Can there be a kineticLaw without a formula?
> RG> Since the math field is not optional, can it be
> RG> empty?)
> KineticLaw is optional (which is why the math field is not).
> See http://sbml.org/specifications/sbml-level-2/version-1/html/sbml-
> RG> I think it should only be allowed to use the sboTerm
> RG> to simulate the model if there is not formula present.
> RG> [...]
> RG> I think that it is very important to state which is
> RG> the correct behavior in case of potentialy
> RG> contradicting information because only one behavior
> RG> can be correct here. And since it is not trivial to
> RG> make a consistency check in this case, I think we
> RG> should state that it is wrong to use the sboTerm to
> RG> simulate the model if there is an equation present?
> I think you're right that the issue exists.
> Your suggestion is an interesting idea. It would be a
> stronger version of the guidelines I wrote about earlier
> Do we need to put this question to a separate vote?