RE: SBML L2v2 specification vote #4: References to controlled vocabularies
21 Dec '05 11:02
I think a lot of these questions can be clarified by viewing the sboTerm
as a type, and kineticLaws are data which may be typed or untyped.
If the kineticLaw is untyped, then you simply have a mathML expression,
all you can check is whether the formula is well-formed.
If it is typed then you have the ability to add consistency checks, such
as determining whether the kineticLaw really belongs to the sboTerm type.
Note that this may be difficult to determine in practice, since many
equivalent algebraic forms can exist for an sboTerm. So what the sboTerm
should do is define a canonical representation into which any
kineticFormula of that type can be transformed algebraically
Therefore, the ability to detect inconsistencies between the sboTerm and
the kineticFormula is very important. It basically allows one to perform
type-checking on mathematical formulas beyond the well-formedness of the
>> RG> [...] (Can there be a kineticLaw without a formula?
>> RG> Since the math field is not optional, can it be
>> RG> empty?)
>> KineticLaw is optional (which is why the math field is not).
> Yes but the sboTerm is in kineticLaw. So the question is could-we have a
> kineticLaw with just an sboTerm and no math element? The answer is no.
> An empty math element. The answer is yes, but then there is an
> inconsistency between the mathML provided by the sboTerm and the one
> provided by the kineticLaw. Back to the starting point.
> Nicolas LE NOVÈRE, Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
> Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676