October 30,2005: Now that this isn't a level 2 proposal, I don't consider it a real level 3 proposal either, more a catalog of issues and a starting point. In important ways this proposal tried to be backwards compatible due to it being proposed as a level 2 replacement. It is now my opinion that any effort towards backwards compatibility should be low priority.
My priority for level 3 is in making the terms well defined, and to leverage OWL as best possible, to maximize the ability of a client to blindly merge BioPAX data from a number of different sources and have it work together in a sensible way.
A fairly radical rewrite of the current level 2 proposal. There is some documentation in the comments in the owl project. More will appear on this page soon. Views stated are emphatically my own though various ideas are influenced by discussions with Jonathan, Imre, Matthias, Emek, Gary, Dan, Joanne and Chris.
State_Proposal_Discussion_July_2005/alanr-level-2-or-3.tar.gz
Discussion (in no particlar order, for the moment. Undergoing rapid edits). Please feel free to add your comments to these pages, but I would appreciate if you would not change the underlying text (except to clean up the typos, etc.) and leave your name with your comments.