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? :-)
