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David, Judy, Suzi, Paul S, Paul T, Chris, Jane, Pascale, Kara

Discussion topics


  • Updating annotation documentation
  • Set a date for a regular conf call every other Monday to reduce Doodle polls
  • Working on 'chain of evidence' (need a better name for this - includes much more than chain of evidence - context, background info, multiple annotation inference etc).

Evidence Proposal

Ref Genome

  • Discussing how to set priorities for ref genome - tree annotations for specific families. Scalable? Could do a few hundred trees before grant.
  • Biocuration meeting next week.

Possible paper (Kara)

I was asked to do a write-up on PPOD in for a chapter on inferring evolutionary relationships in Current Protocols in Bioinformatics (, due November 15.

However, it occurred to me that we could instead use this as a forum for the phylogenetic-based annotation, specifically the Annotation Tracker that we have been working on, which can end up as a really handy portal to this project for the general community (in addition to us using this as an internal tool). To do this, we'd need to:

1) be comfortable rolling this out in production to the general public. This would just require a little clean-up (eg hiding the "Not in DB" fields), and adding some additional info to make it more useful to general users.

2) provide a way for users to query the phylotree pages in a useful way. One idea: from the Gene Product Search Results, we just add a link under the Ref Genome line that links to the correct phylotree page.

Note that, at least at this point, we don't expect this to be the main face of the project, rather it would be at least one hook in for people to explicitly see the phylogenetic-based annotations in one place, can see our progress, etc.

  • Hold off until we have a better idea how users can navigate tree-inferred annotations
  • ACTIOM: load ancestral annots into labs

Ontology Development

  • Ruth emailed to request some ontology development meetings - Judy will forward email
  • GOCHE completion - in time for grant? Paper probably be finished in time for renewal in Jan 2011, implementation some time later.
  • Becky started on Friday - working on signaling
  • BP x BP cross-products to be implemented soon (processes involved in other processes)
  • Taxon paper should be published by now - BMC Bioinformatics


  • AmiGO 1.8 out soon
  • OBO-Edit 2.1 - addresses outstanding bugs. There will be another maintenance release - 2.2 - before freeze.
  • Have money for 3 one-year positions - Berkeley position filled, two still available at Stanford.