#105 Flux / rate

[Anonymous]

Hi Nick,

this is Wolf (Wolfram Liebermeister). I would like to have an SBO for "reaction rate"; i.e., not a specific rate law, but a term for the rate as a quantity. Ideally, i would like two terms: one that measures rates as amounts per time (which is the convention adaopted in sbml) and another one that measures rates a concentration per time (which is a bit more pratical in certain situations). I do not really know where to put this in the hierarchy. maybe reaction rates would deserve a branch of their own within "quantitative systems description parameter"?
A last comment: some people use "metabolic flux" and "reaction rate" synonymously, some distinguish between steady-state situations ("flux") and general situations ("rate"). I don't have a clear preference; but this worthwhile taking into account.

Thank you and best regards!
Wolf (wolfram.liebermeister@gmail.com)

[Nicolas Le Novère]

While we are at it, we should have a term for "extent of reaction", which the chemical term with a symbol (dzeta). http://en.wikipedia.org/wiki/Extent_of_reaction
the rate of a reaction is then the time derivative of the extent

[Nick Juty]

I have created a few terms that I hope will be satisfactory. The general structure:
quantitative systems description parameter (SBO:0000545)
--| reaction parameter (new - SBO:0000613)
--|--| rate of reaction (new - SBO:0000612)
--|--|--| rate of reaction (concentration) (new - SBO:0000614)
--|--|--| rate of reaction (amount) (new - SBO:0000615)
--|--| extent of reaction (new - SBO:0000616)

Please feel free to suggest improvements those entries (eg. http://www.ebi.ac.uk/sbo/main/SBO:0000612).

And thanks for your suggestions.