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

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? :-)