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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 26 Mar 2009 10:16:31 -0500
Cc: Oliver Ruebenacker <curoli@gmail.com>, Mark Wilkinson <markw@illuminae.com>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <4874E130-300A-4EDD-A254-A79AA7BACA7B@ihmc.us>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>

On Mar 26, 2009, at 7:20 AM, Phillip Lord wrote:

> Oliver Ruebenacker <curoli@gmail.com> writes:
>>     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
>>
>>  Clear enough?
>
>
> So insulin is not a protein, wheras a dipeptide is?
>
> Besides which, the issue being discussed here is one of equality. When
> are two proteins the same protein?

TWO proteins are never the same protein. Two mangelwurzels are never  
the same mangelwurzel, either. What 'same' means, is that there is ONE  
thing with two names. Being the same as is never a relationship  
between two different things.

Pat

>
> Phil
>
>
>
>

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Received on Thursday, 26 March 2009 15:17:50 UTC

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