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

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 constructed with input from the Sequence 
Ontology curators.

Eric Jain wrote:
> 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 
>> 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.
> 
> Thanks! And what is a "protein", in this scheme? :-)