Jonathan Rees

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Jonathan Rees works for Science Commons. From 2002 to 2005 he worked in the computational biology group at Millennium Pharmaceuticals.

I'm sorry I haven't been participating much technically. I think the project has great potential, but I am very confused about what the group is for, how it operates, and who controls the agenda and the purse strings (e.g. why grants apparently made to the working group are apparently not being controlled by the working group). I'm making an effort to surface these issues without being too activist. In order to have meaningful dialog and make changes, it's essential to find common ground, such as agreement on goals or current group process, so this is what I'm looking for. Once I can ascertain that BioPAX is an effort worth investing in, I'll be happy to invest.

So here's my agenda:

  1. Get articulation of current process and goals
  2. Lobby for changes if I think administration or goals can be improved to make the effort more effective
  3. Take part in development of the specification

I see the biggest weaknesses of the group as the following:

  • Murky politics
  • Poor process
  • Unclear goals
  • No clear commitment to, or rejection of, semantics and reasoning (or their incarnations as the semantic web and OWL)
  • Little experience in semantics or reasoning
  • Little experience with standards efforts

I may be able to help out with one or more of these, since I have some experience in a few of these areas -- if others are willing to let me meddle.

Of course, sometimes it's better to leave things unexamined. But I don't think this is one of those times.


Detection of activity centers in cellular pathways using transcript profiling.