RE: protein entities (was Re: Rules (was Re: Ambiguous names. was: Re: URL +1, LSID -1)

> 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.

Independent of whether there is a (known) difference in function,
chemistry (and circumstance) defines function. Any chemical modification
results in a different biochemical entity with potentially different
function. Proteins and their "version" derivatives are no exception. The
relationship between them is that they participate in a chemical
process, but they are fundamentally different entities.

Cheers,

-=Michel=-
 

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-
> request@w3.org] 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 (was 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) protein and the sub-length parts of proteins
> (commonly called domains by protein scientists, unfortunately).  The
> term "whole protein" is somewhat of a placeholder; it is used to
signify
> the evolutionary classes (families) of full-length proteins as opposed
> to the evolutionary classes of domains.  Sequence form is again a
> placeholder term used to denote the initial translation product from
an
> mRNA, which itself might be based on a "normal" gene or a mutant
> thereof, or which might be one of several possible alternatively
spliced
> transcripts from the normal or mutant gene.  The cleaved or modified
> product is a further breakdown of those initial translation products,
> and allows one to 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.
> 
> Eric Jain wrote:
> > 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
> >> 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 cleavage). Where appropriate, PRO will indeed make reference to
> >> both other ontologies and to UniProt Knowledgebase (UniProtKB)
> >> records. Furthermore, we are also undertaking the "wildly
ambitious"
> >> job of representing broader, more-inclusive classes of similar
> >> proteins based on evolutionary relatedness.
> >>
> >> A further description of PRO (with examples and link to a paper)
can
> >> be found at http://pir.georgetown.edu/pro
> >
> > This will no doubt be interesting to quite a few people here! For
the
> > sake of this discussion, could you elaborate a bit more on how the
> > different concepts in PRO are defined, i.e. what is a "protein",
"whole
> > protein", "sequence form" and "cleaved and/or modified product"?
>

Received on Thursday, 19 July 2007 19:57:30 UTC