GO 18th Consortium Meeting: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 1: Line 1:
==September 23-24th, 2007 Princeton, New Jersey==
==September 23-24th, 2007 Princeton, New Jersey==
==Draft Schedule==
Sept. 12, 2007


===Progress Reports===
===Progress Reports===

Revision as of 08:26, 12 September 2007

September 23-24th, 2007 Princeton, New Jersey

Draft Schedule

Sept. 12, 2007

Progress Reports

These could be the same as for SAB morning reports

Aim 1

We will maintain comprehensive, logically rigorous and biologically accurate ontologies Suzi Lewis - Moderator/PI Lead.

  1. Ontology Development - Biological Content
Midori Harris and David Hill reporting
  1. Ontology structure
Chris Mungall reporting

Aim 2

We will comprehensively annotate reference genomes in as complete detail as possible. Judy Blake - Moderator/PI lead.

  1. Reference Genome Project
Rex Chisholm and Pascal Gaudet reporting

Aim 3

Michael Ashburner - Moderator/PI lead.

  1. Annotation Outreach
Jen Deegan reporting

Aim 4

Mike Cherry - Moderator/PI lead.

  1. Production Systems
Ben Hitz? reporting
  1. AmiGO working group
Amelia Ireland reporting

Afternoon, Sunday, Sept 23, 2007

We especially have agreed to discuss protein complexes and the intersection with Reactome annotations. Peter D'Eustachio (Reactome) will be able to join us only for the afternoon.

Topics for Discussion

  1. Representation and Annotation of Protein Complexes

Brainstorming on Topics for upcoming 18th meeting

  1. Delineating, and isolating, the different categories of "slims" and their usage. See Taxon_Main_Page for more discussion.
  2. The scope of 'binding' terms in the function ontology:
    1. How granular should terms be?
    2. Should there be terms for substrate origin (e.g. "viral protein binding")? See SF 1674020.
  3. Discuss how we are going to handle regulates and relationships between regulation terms (DPH)
    1. Does regulates always mean the same thing in GO?
    2. Can/should regulation be broken down into parts, or should it be a collection of types?
  4. What is the plan for implementing 'regulates' relationship in live GO?
    1. Will we have two GO implementations operating at once?
    2. How will we notify and time the change-over?...this is a big deal
  5. Discuss whether GO can add a has_part relationship (mah, krc)
  6. Annotation: Discuss situations where the 'contributes_to' qualifier should and should not be used (mah for vw)
  7. Taxon-GO links.
  8. Discuss the disjoint relationships/tags in the GO BP ontology.(dph)
  9. annotation of protein complexes; "use" of IPI protein binding to track physical interactions; collab. with Reactome
    1. This needs to be scheduled for Sunday afternoon as Peter D'Eustachio can attend then.
  10. Discuss ISS evidence code extensions from orthology
  11. Finalizing the format for cross-product information for the new column 16 of the gene association file - could this column also include information on the 'target' of a protein's activity?

GOC and Staff issues

  • The PIs should consider options for the future of the GO Editorial Office (GOEO). Affiliation with EBI has numerous advantages (for both GO and EBI), but all four GOEO staff will reach the 9-year limit by the end of the current NIH grant period.
(added at Michael's request)
  • Annotation Outreach and User Support have been, at least temporarily, combined. Do we need some rearrangement in this area? Comment submitted to go-top "it might make more sense to have groups: Content, Annotation and Public Relations. I really agreed with the PR point, as many of the outreach and advocacy tasks overlap, and it would be much easier to work together on them." and on another poing, "it would make far more sense if there was an annotation working group that maybe had reference genomes and the evidence codes committee as subgroups. Then there could also be a subgroup that could act as a discussion forum on general annotation issues and could write documentation as agreements were reached. This documentation could include the SOPs. In this structure the discussion committee would be chaired by an annotator..." or perhaps two annotators from different MOD groups.

Resources

Action Items from last GOC meeting

Action Items from Jan 2007GOC meeting held in Cambridge, UK http://www.geneontology.org/GO.meetings.shtml?all#consort

2007 Progress Report

2007 Progress Reportfor NHGRI due Jan. 1, 2008