Re: SBML L2v2 specification vote #4: References to controlled vocabularies
20 Dec '05 23:55
bshapiro> Its not just the reaction that needs to have the
bshapiro> correct SBO term: don't all of the appropriate
bshapiro> parameter values also need to have corresponding
bshapiro> (correct) SBO Terms (or some equivalent
bshapiro> information) for the kinetic law to be fully
bshapiro> specified independent of the math fields?
But, won't a parameter declared as (e.g.) "rate constant for
first-order mass action" remain the same no matter if the
kinetic law itself is changed? Or (e.g.) "Michaelis
constant"?
bshapiro> So we can't just ignore the kineticLaw if
bshapiro> there is an SBO term, we have to read the
bshapiro> parameter values and figure out where the go in
bshapiro> the reaction specified by the SBO term.
I thought of this when I was writing my other message, but
decided it seemed like the meanings of the quantities and
other elements of a model would stay the same despite that a
change in a formula may change how they are *used*. This
assumption may be incorrect. I'd like to see a case example
if so.