>> Answer #4: Let's examine this from the perspective of
>> an application in today's SBML world, without sboTerm
>> in existence. What would an application do if it could
>> not read the kinetic law definition? It could
>> interpret the SBML to some extent (e.g., it could read
>> out the reactants, products and modifiers in a
>> reaction) and perform some manipulations (maybe?), but
>> there is a risk that anything it does would be suspect
>> because the tool is not intepreting the full model. In
>> the end, it could not hope to be a fully compliant SBML
>> application because it can't interpret the kinetics.
lenov> IMHO it is untrue. It is perfectly acceptable to
lenov> have SBML files without kineticLaw. SBML coming
lenov> from KEGG, Reactome or *cyc are valid SBML files.
lenov> In addition, if you have all the reactants,
lenov> products and the stoichiometry, you can already do
lenov> a lot of numerical analysis of the models (although
lenov> not time-series). The models would not be
lenov> MIRIAM-compliant, and they would certainly not be
lenov> acceptable in BioModels DB. But they would be valid
Yes, strictly speaking, you're right; sorry for writing it
the way I did. When I wrote "compliant", I was thinking of
the SBML Test Suite and the idea (discussed on and off) of
having a prescribed procedure for validating an
application's handling and coverage of SBML. Such tested
applications would be branded "SBML compliance tested", and
allowed to use the corresponding icon/logo.
>> Likewise, in an sboTerm world, the application could
>> perform some manipulations (maybe) but it could not be
>> a fully compliant SBML application because it did not
>> have the ability to interpret the kinetics.
lenov> I do not agree. If you have the adequate sboTerms
lenov> on the speciesReferences, the local parameters and
lenov> the kineticLaw (whatever the math element is), you
lenov> can inerpret the kinetics in some cases.
Well, this is a funny situation. What you say is true, but
it also touches on the other question of what's
authoritative in a model. If the kinetic law definitions
are authoritative, yet an application can't read them, then
the application would not be able to interpret the kinetics
based on the authoritative definition in the model. What
are the implications of this?