Re: SBML L2v2 specification vote #4: References to controlled vocabularies
05 Jan '06 11:01
> If you have connectivity to the sboTerm and, (as some suggest) it has to
> have a mathematical translation attached to it so that the symbols are in
> a standard order, then there is no excuse for not writing the mathML.
> If you don't have the connectivity, a <notes> <B>kineticlaw is mass
> action</B></notes> avoids problems of spelling errors that we have
> sometimes seen when using some of the named equations. It is at least as
> informative as the kineticLaws with only sboTerms.
Certainly not. If that was the case, nobody would have created Gene
Ontology, and that would not have become in a few years one of the most
successful achievements of bioinformatics. A notes element with such a
sentence has hardly any semantic content. First of all, no software but
the most advanced text-mining tool can extract the fact that it is dealing
with mass-action (becasue of spelling, encoding, foreign languages etc.).
Second, a biologist tend to use an unconstrained language. In biochemistry
this is even more tricky. 99.999 % of the articles speak of
while they mean "Briggs-Haldane". It is obvious that the modellers would
do the same in the unconstrained annotation.
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