Re: SBML L2v2 specification vote #4: References to controlled vocabularies
21 Dec '05 02:04
>Some software tools provide users with a pull-down list of
>rate laws, from which the user can select what they want for
>a given reaction. The tool then writes out the appropriate
>math expression into the model. Those tools would like a
>way to go in the reverse direction, from rate law to name.
>Currently there's no systematic way of supporting this in
>SBML, because it requires some sort of additional annotation
>beyond the math of the kinetic expression.
Thanks for clearifying some of the points and I do agree with most of
them, but I think what you wrote above is somewhat dangerous since it
seems to me that this would encourage people to write software that is
not fully SBML compliant. While I think it is perfectly OK for program
authors to do so, I also think that it should not be encouraged.
Maybe I am missing some point here, but in order to go in the reverse
direction, you would have to check if the formula corresponds to any of
your built in functions which basically is the same as doing a
consistency check on the sboTerm and the given formula. So if tools now
just take the sboTerm and substitute one of their built in equations,
they essentially ignore the formula which makes those tools "SBML
uncompliant" to some extent. If the tools have the capability to do
consistency checks for sboTerms, they actually do not need the sboTerm
any longer since they might just as well check if the the formula
corresponds to one of their built in functions. So in this case the
sboTerm on the kineticLaw is superfluous.
So if you encourage people to do this, you basically encourage them to
write software that is not fully SBML compliant, right?
You also mentioned that you would allow a kineticLaw to just have an
sboTerm, so I guess since the formula attribute is not optional it would
have to be an empty string, right?