On Mar 31, 2009, at 7:49 AM, Oliver Ruebenacker wrote:
Hello Wacek, All,
On Tue, Mar 31, 2009 at 8:30 AM, Wacek Kusnierczyk
<waclaw.marcin.kusnierc...@idi.ntnu.no> wrote:
i'd agree that having non-integer *molecule numbers* sounds nonsense,
but having non-integer *relative molecule numbers* certainly doesn't.
in any case, the equation
N2O2 -> 2 NO2 + 1/2 O2
is equivalent to
2 N2O2 -> 4 NO2 + O2
and you can always (i guess) avoid non-integer coefficients by
multiplying both sides by a constant.
What about this statement:
"Two grams of hydrogen react with 16 grams of oxygen to 18 grams of
water"
If I were trying to do a professional job of 'ontologizing' this, it
would be a formal rendering of:
Every reaction in which the participants are an amount1 comprising
hydrogen and an amount2 comprising oxygen, is an oxidation reaction in
which the product is an amount3 of water, and the mass of amount2 is
eight times that of amount1, and of amount3 is nine times that of
amount1.
All of which can be expressed, with some tedium, in OWL, perhaps
extended with a little arithmetic on its literal values. To do an
decent job of the notion of 'reaction' would require some work, and
would involve temporal notions, but the bulk of this work has been done.
What would be harder would be describing reactions which take place
slowly and in which one has to speak of the rate at which the product
is created, eg when talking about catalysis. It is not impossible, but
it does get more complicated. But at this point one needs to ask why
one is doing this. If the purpose is to perform quantitative
simulations with full details of chemistry, ontologies are probably
not the best way to proceed.
Pat
Take care
Oliver
--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
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