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RE: blog: semantic dissonance in uniprot

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Thu, 2 Apr 2009 11:35:26 -0400
Message-ID: <AB349814F1ECB143A5D4CD29C7A6456903AAE641@CCSEXB10.CUNET.CARLETON.CA>
To: "Egon Willighagen" <egon.willighagen@gmail.com>, "Matthias Samwald" <samwald@gmx.at>
Cc: "Phillip Lord" <phillip.lord@newcastle.ac.uk>, "Oliver Ruebenacker" <curoli@gmail.com>, "Pat Hayes" <phayes@ihmc.us>, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>


> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> lifesci-request@w3.org] On Behalf Of Egon Willighagen
> Sent: Thursday, April 02, 2009 10:57 AM
> To: Matthias Samwald
> Cc: Phillip Lord; Oliver Ruebenacker; Pat Hayes; public-semweb-lifesci
> Subject: Re: blog: semantic dissonance in uniprot
> 
> On Tue, Mar 31, 2009 at 2:09 PM, Matthias Samwald <samwald@gmx.at>
> wrote:
> >>> Reaction equations describe stochastic processes, that's why you
> can
> >>> have non-integer molecule numbers
> >>
> >> I think you can't have non-integer molecule numbers because it
makes
> >> no chemical sense. Half a molecule is a whole molecule of a
> different
> >> kind.
> >
> > You can have reaction equations that look like
> >
> > N2O5 ---> 2 NO2 + 1/2 O2
> >
> > Which means that the number of O2 molecules that would be produced
if
> the
> > equilibrium would be shifted to the absolute right side is 1/2 of
the
> number
> > of molecules of N2O5 that would exist if the equilibrium would be
> shifted to
> > the absolute left. This only makes sense if we interpret reaction
> equations
> > as descriptions of pools of molecules and their stochastic
processes,
> rather
> > than single molecules. Representing reaction equations as processes
> where
> > the participants are single molecules is wrong. In that case, one
> cannot
> > blame OWL if one is running into inconsistencies.
> 
> Actually, I'd say OWL is to blame here... that is, the OWL class was
> not properly defined.

Just to clarify - it's not OWL that's the problem. It's the
representation of Chemistry in a formal logic-based language where it
actually matters what you say and how you say it.

> 
> Reaction Equations are a difficult concept, and depending on the
> context mean different things. This discussions is just caused by
> different meaning people give to Reaction Equation. Very typically,
> you would even mix both types in reaction schemes (e.g. schemes where
> both the overall as well as mechanistic reactions are given), even
> though they refer to different concepts.


In the BioPAX-OBO effort we have begun to address the distinction
between a chemical reaction and a reaction equation. Indeed, it is
useful to make the distinction, as they imply different things.

-=Michel=-

> 
> Egon
> 
> --
> Post-doc @ Uppsala University
> http://chem-bla-ics.blogspot.com/
Received on Thursday, 2 April 2009 15:37:13 UTC

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