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Re: blog: semantic dissonance in uniprot

From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>
Date: Thu, 26 Mar 2009 16:59:20 +0100
Message-ID: <49CBA658.2010509@idi.ntnu.no>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>
CC: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Phillip Lord wrote:
> Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no> writes:
>   
>>>>   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
>>>>
>>>>   Clear enough?
>>>>     
>>>>         
>>> So insulin is not a protein, wheras a dipeptide is?
>>>   
>>>       
>> indeed;  insulin is a protein complex, and a dipeptide, following this
>> and other similar definitions, is a protein.
>>
>>     
>
> Insulin is two polypeptide changes so following this definition is not a
> protein. 
>   

that's what i was saying:  that it is a protein complex, specifically,
an aggregate of two polypeptide chains. 

it may sound revolutionary to you that insulin is not a protein, since
insulin is typically called a 'protein'.  but, provided one accepts a
definition like the one above, there is nothing wrong in saying that
insulin is not a protein.

i didn't say i supported the definition from biopax, though.  the one i
found in stryer's biochemistry seemed to concord with it (modulo the
somewhat unfortunate 'contains'), but i don't think those authors would
insist that insulin is not a protein, and that any dipeptide is a
protein;  biopaxers seem to do that.

i agree, of course, that insisting on definitions that are
counterintuitive to what experts in the field are used to think is not a
good idea.

vQ
Received on Thursday, 26 March 2009 16:00:10 UTC

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