- From: Pat Hayes <phayes@ihmc.us>
- Date: Wed, 1 Apr 2009 16:09:45 -0500
- To: Oliver Ruebenacker <curoli@gmail.com>
- Cc: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>, Matthias Samwald <samwald@gmx.at>, Phillip Lord <phillip.lord@newcastle.ac.uk>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
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.Kusnierczyk@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 > > > ------------------------------------------------------------ IHMC (850)434 8903 or (650)494 3973 40 South Alcaniz St. (850)202 4416 office Pensacola (850)202 4440 fax FL 32502 (850)291 0667 mobile phayesAT-SIGNihmc.us http://www.ihmc.us/users/phayes
Received on Wednesday, 1 April 2009 21:11:33 UTC