Re: Proposal: simple mechanism for referencing rate laws
21 Jul '05 14:13
> True, the URI must provide the ordering of the kinetic parameters in the
> reaction rate law and the SBML model file must adhere to that ordering.
> Or, the kinetic constants themselves must be given a URL/URI that
> describes what it means (kcat, Km, Hill constant, etc).
This is not a problem and your second sentence actually describes what
we'll do with SBO. Each term of the rate-law controlled vocabulary will be
linked to terms of the parameter and species role vocabularies. Let's say
the term "Briggs-Haldane equation" defines "kp * Et * S / ( Km + S )", it
would be linked to the terms "Michaelis constant" defining "Km",
"substrate", defining "S" and "catalyst" defining "Et".
The problem is to understand that the global parameter of id XZKJ76gS,
linked to the SBO term "Michaelis constant" is actually the Km of our
reaction, and not the parameter of id foobar1223, also linked to the term
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