> 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
ke of
Jackson Labs. PRO is being developed within the framework of the
OBO Foundry, and aims to specify protein entities at the level
mentioned by Chris (accounting for splice variation and
post-translational modification and cleavage). Where appropriate,
PRO will indeed make reference
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
tium), Barry Smith of SUNY
Buffalo, and Judy Blake of Jackson Labs. PRO is being developed
within the framework of the OBO Foundry, and aims to specify
protein entities at the level mentioned by Chris (accounting for
splice variation and post-translational modification and
cleavage). Wher
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
Original Message-
From: [EMAIL PROTECTED]
[mailto:public-semweb-lifesci-
[EMAIL PROTECTED] On Behalf Of Darren Natale
Sent: Thursday, July 19, 2007 11:24 AM
To: Eric Jain
Cc: Alan Ruttenberg; Chris Mungall; Bijan Parsia;
public-semweb-lifesci
hcls
Subject: Re: protein entities (w
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
Darren Natale wrote:
Protein, in this scheme, is the amino acid polymer produced by a
translation process using an mRNA as a template.
This fits about any polypeptide produced by a ribosome.
I'd think that the term 'protein' is reserved for some, but not all
polypeptides (even if we talk
ing the PIs Cathy Wu of
PIR (which is also a member organization of the UniProt Consortium),
Barry Smith of SUNY Buffalo, and Judy Blake of Jackson Labs. PRO is
being developed within the framework of the OBO Foundry, and aims to
specify protein entities at the level mentioned by Chris (ac
the UniProt
Consortium), Barry Smith of SUNY Buffalo, and Judy Blake of Jackson
Labs. PRO is being developed within the framework of the OBO Foundry,
and aims to specify protein entities at the level mentioned by Chris
(accounting for splice variation and post-translational modification
and
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
ation of the UniProt Consortium),
Barry Smith of SUNY Buffalo, and Judy Blake of Jackson Labs. PRO is
being developed within the framework of the OBO Foundry, and aims to
specify protein entities at the level mentioned by Chris (accounting for
splice variation and post-translational modification a
16 matches
Mail list logo
