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Re: blog: semantic dissonance in uniprot

From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>
Date: Wed, 25 Mar 2009 21:20:49 +0100
Message-ID: <49CA9221.1010202@idi.ntnu.no>
To: Oliver Ruebenacker <curoli@gmail.com>
CC: Phillip Lord <phillip.lord@newcastle.ac.uk>, Mark Wilkinson <markw@illuminae.com>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Oliver Ruebenacker wrote:
>      Hello Philip, All,
>
> On Wed, Mar 25, 2009 at 1:05 PM, Phillip Lord
> <phillip.lord@newcastle.ac.uk> wrote:
>   
>> My own feeling is that it's biology which wove the web; we're just
>> caught in the middle. What role for the web and semantics? Well, I think
>> we need a coordinated, controlled and defined way of expressing our
>> mutual confusion. I'd love to have a clear definition of gene (or
>> protein). In it's absence, a good way of expressing "err..." is probably
>> the best we can do.
>>     
>
>   I don't know whether the BioPAX Level 2 definition of protein is the
> most useful one, but at least it sounds clear to me:
>
>   protein = anything containing exactly one polypeptide chain
>   

hmm, so a mixture of all sorts of substances, incidentally *containing*
exactly one polypeptide chain, would be a protein?  a box *containing*
exactly one polypeptide chain would be a protein? 

clear enough, really?  i think the following, taken from stryer's
biochemistry, 5e p. 41, is more resonable:

"Proteins are linear polymers built of monomer units called amino acids."

vQ
Received on Wednesday, 25 March 2009 20:22:15 UTC

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