> Many post-translational modifications like glycosylation
> (http://www.functionalglycomics.org/static/index.shtml)in proteins
> fundamentally change the (functional) 'nature' of the protein (as also
the
> molecular structure of the protein in case of glycosylation through
> addition of sugar cha
> An interesting issue, one of identity. What determines the identity
of
> a molecule, a protein in this case?
I strongly believe that the identity of a molecule is only dependent on
its physical (chemical) composition.
> If you have a protein that becomes
> phosphorylated, is the phosphoryla
Quite a nice example! These are the sorts of issues that we must
contend with while creating the PRO framework. In fact, this addresses
another issue of scope; that is, whether or not (in the long or short
term) to also account for homodimers, trimers, and so on (currently, GO
handles heter
Original message
>Date: Thu, 19 Jul 2007 16:29:18 -0400
>From: Michel_Dumontier <[EMAIL PROTECTED]>
>Subject: RE: protein entities (was Re: Rules (was Re: Ambiguous names. was:
>Re: URL +1, LSID -1)
>To: Darren Natale <[EMAIL PROTECTED]>, Michel_Dumont
If I may put forward a key protein in Alzheimer disease as an example
that we are grappling with, there is full-length APP (which itself
has a number of forms as well as mutations); various peptides derived
from cleavage of APP; and then multimeric forms of the peptides,
particularly Abet
Michel_Dumontier wrote:
Darren,
Also, while we recognize
that there are different qualities that can be ascribed to a basically
identical biochemical entity in different structural conformations or
states of ligand binding, we are not attempting (at least in the
beginning) to describe these st
Darren,
> Also, while we recognize
> that there are different qualities that can be ascribed to a basically
> identical biochemical entity in different structural conformations or
> states of ligand binding, we are not attempting (at least in the
> beginning) to describe these structural conforma
Michel_Dumontier wrote:
Sequence form is again a placeholder term ...
... distinguish between a phosphorylated version of a
protein and the non-phosphorylated version (as an example). The need
for the latter derives from the fact that the two versions might have
different functions.
Inde
as Re: Rules (was Re: Ambiguous names.
was: Re: URL +1, LSID -1)
We don't yet have formal definitions for many of the classes and
relations (the effort only began in earnest a few months ago). But,
basically, there is a distinction made between the full-length (in
terms
of amino acid sequence) p
9, 2007 11:24 AM
> To: Eric Jain
> Cc: Alan Ruttenberg; Chris Mungall; Bijan Parsia;
public-semweb-lifesci
> hcls
> Subject: Re: protein entities (was Re: Rules (was Re: Ambiguous names.
> was: Re: URL +1, LSID -1)
>
>
> We don't yet have formal definitions for many of t
We don't yet have formal definitions for many of the classes and
relations (the effort only began in earnest a few months ago). But,
basically, there is a distinction made between the full-length (in terms
of amino acid sequence) protein and the sub-length parts of proteins
(commonly called
Protein, in this scheme, is the amino acid polymer produced by a
translation process using an mRNA as a template. I suppose this
excludes peptides (also amino acid polymers) that are produced
non-ribosomally, but perhaps that is okay for the time being. The
precise definition will be constr
Darren Natale wrote:
We don't yet have formal definitions for many of the classes and
relations (the effort only began in earnest a few months ago). But,
basically, there is a distinction made between the full-length (in terms
of amino acid sequence) protein and the sub-length parts of protei
Darren Natale wrote:
We recently began a new Protein Ontology (PRO) effort geared precisely
toward the formal definition of the "smaller entities" referred to by
Alan. By "we" I mean the PRO Consortium, comprising the PIs Cathy Wu of
PIR (which is also a member organization of the UniProt Con
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