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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Wed, 1 Apr 2009 16:09:45 -0500
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>
Message-Id: <69A9E1FD-C143-4958-BD55-C1FF76BE79F1@ihmc.us>
To: Oliver Ruebenacker <curoli@gmail.com>

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  

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.


>     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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Received on Wednesday, 1 April 2009 21:11:33 UTC

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