Re: SBML L2v2 specification vote #4: References to controlled vocabularies
02 Jan '06 22:23
bshapiro> Concise question: Do we make the math term
bshapiro> optional in kineticLaw? [note: this has not
bshapiro> been "officially" proposed]
I think this is a reasonable idea. (It is also consistent
with what some people like Nicholas Allen have argued for in
the past, which is to make everything optional.) If there
are no objections and if there are no technical problems
with this change, I'd like to suggest we go ahead and do a
survey for this as well, for SBML L2v2.
On the following point:
bshapiro> Cons: people would try to reconstruct the full
bshapiro> equation using the sbo terms in the reaction and
bshapiro> parameters, even when the math field is present
bshapiro> and should take precedence over the sbo terms.
I think the "cons" is reduced if the spec defines some rules
of treatment. Some apps will do what you describe above
anyway, of course, but at least we can define the behaviors
that are intended, and thus conformant.
All that said, however, I'm not sure this change will help
with the sboterm situation. In my next posting, I'll
describe some proposed behaviors which I think are
independent of this issue.