GO 18th Consortium Meeting

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September 25th, 2007 Princeton, New Jersey

Meeting Location
Prospect House - Presidential Dining Room
 Prospect House ]] 
 Washington St
 Princeton, NJ 08544
 (609) 258-3455
 www.princeton.edu/prospecthouse/
Lunch Location: Prospect House - Library 
Dinner - dinner reservations at Mediterra
 Mediterra
 29 Hulfish St 
 Princeton, NJ 08542
 (609) 252-9680
Accomodations
Nassau Inn
 Nassau Inn
 10 Palmer Sq E
 Princeton, NJ 08542
 (609) 921-7500
 www.nassauinn.com

Draft Schedule

Judy 05:38, 12 September 2007 (PDT)Sept. 12, 2007

Sunday morning, September 22, 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

We will support annotation across all organisms. Michael Ashburner - Moderator/PI lead.

  1. Annotation Outreach
Jen Deegan reporting
Aim 4

We will provide our annotations and tools to the research community. Mike Cherry - Moderator/PI lead.

  1. Production Systems
Ben Hitz? reporting
  1. Hub Group
Chris Mungall or Eurie Hong? 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 related to Annotation

  1. annotation of protein complexes; "use" of IPI protein binding to track physical interactions; collab. with Reactome
  2. Discuss ISS evidence code extensions from orthology
  3. 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?

Topics related to Annotation Outreach

  1. Should Annotation Outreach and User Support groups be combined?

Topics related to User Support

Morning, Monday, September 24, 2007

Topics relevant to Ontology Development

  1. Update of regulation terms and relationships: David Hill
    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?
  2. Plan for implemnting 'regulates' relationship in live GO: Chris Mungall
    1. Will we have two GO implementations operationg at once while users catch-up?
    2. How will we notify users about nature and time of change-over ?
  3. Delineating, and isolating, the different categories of "slims" and their usage. See Taxon_Main_Page for more discussion.
  4. 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.
  5. Discuss whether GO can add a has_part relationship (mah, krc)
  6. Discuss the disjoint relationships/tags in the GO BP ontology.(dph)

Afternoon, Monday, September 24, 2007

Topics relevant to GO intersection with other ontologies

  1. Collaboration and cross-products with Cell Type Ontology
  2. Taxon-GO links

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