- From: Darren Natale <dan5@georgetown.edu>
- Date: Thu, 19 Jul 2007 14:22:18 -0400
- To: Eric Jain <Eric.Jain@isb-sib.ch>
- CC: Alan Ruttenberg <alanruttenberg@gmail.com>, Chris Mungall <cjm@fruitfly.org>, Bijan Parsia <bparsia@cs.man.ac.uk>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
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? :-)
Received on Thursday, 19 July 2007 19:14:01 UTC