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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Thu, 26 Mar 2009 17:40:32 -0400
Message-ID: <5639badd0903261440h273ff309r37507224caa6ce7@mail.gmail.com>
To: Matthias Samwald <samwald@gmx.at>
Cc: public-semweb-lifesci <public-semweb-lifesci@w3.org>
     Hello Matthias, All,

On Thu, Mar 26, 2009 at 4:30 PM, Matthias Samwald <samwald@gmx.at> wrote:
>>  I think more useful for Systems Biology is that they participate in
>> the same reactions with the same kinetics.
> But that is a very personal opinion, right? Without doubt, when two classes
> of proteins have the same dispositions and functions (to use BFO - lingo),
> this is a very important thing to know. Nonetheless, if their structures are
> completely different, most biologists would describe them as distinct
> classes of proteins. The notion that any molecule or molecular complex
> should be called "Insulin" just because it has the same effect on regulating
> blood sugar seems quite avantgarde to me.

  If the only reaction you are interested in is the regulation of
blood sugar in the way Insulin does, you would probably not call a
substance Insulin, but perhaps blood sugar regulating hormone, or
Insulin substitute.

  The name Insulin would probably be defined to take into account
other reactions, too, most likely including its transcription, which
would enforce it consisting of amino acids. If another, similar
sequence leads to the same effects, it would probably be called

     Take care

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Thursday, 26 March 2009 21:41:10 UTC

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