Re: SBML L2v2 specification vote #4: References to controlled vocabularies
21 Dec '05 02:18
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?
MH>But, won't a parameter declared as (e.g.) "rate constant for
MH>first-order mass action" remain the same no matter if the
MH>kinetic law itself is changed? Or (e.g.) "Michaelis
MH>constant"?
But the name is OPTIONAL in the spec. There is nothing to say that
the parameter must be declared with such a meaningfull name (good practice
notes aside). It may be referred to using the id in the KineticLaw. If
there are two or more parameters for the reaction (Ki and Km for example)
- and they have ids of p1 and p2, there is no guarantee that programs
using only the SBO term will be able to do anything with this anyway.
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 they go in
bshapiro> the reaction specified by the SBO term.
MH>I thought of this when I was writing my other message, but
MH>decided it seemed like the meanings of the quantities and
MH>other elements of a model would stay the same despite that a
MH>change in a formula may change how they are *used*. This
MH>assumption may be incorrect. I'd like to see a case example
MH>if so.
Hugh Spence
GSK Scientific Computing and Mathematical Modelling
Medicines Research Centre
Gunnels Wood Road
Stevenage
UK
SG1 2NY
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.
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21 Dec '05 02:18
