GO 18th Consortium Meeting: Difference between revisions

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# Discuss ISS evidence code extensions from orthology
# Discuss ISS evidence code extensions from orthology
# 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?
# 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 and User Support====
# Should Annotation Outreach and User Support groups be combined?
# Is 'help desk' working ok?


===''Morning, Monday, September 24, 2007''===
===''Morning, Monday, September 24, 2007''===
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*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.
*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)
:(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.
* Currently we have several working groups including:
 
Ontology content - to work on the content of the ontology<br>
Annotation-Outreach - to encourage new groups to start annotating <br>
User Advocacy - to help users to learn how to use the GO and to represent user's need to the consortium.<br>
Reference Genomes - to choose genes lists for everyone to work on. <br>
 
1) Would it be a good idea to merge user advocacy and annotation outreach as these have a lot in common? <br>
2) Would it be possible to make a general annotation working group to deal with all issues surrounding annotation? This group could include sub-groups such as the reference genomes group, the evidence code groups and the annotation standard operating procedure group. 
 
 
 
 
 
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==
==Resources==

Revision as of 10:56, 13 September 2007

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


Introduction

  1. Introductions, especially new people
  2. Quick review of any outstanding Action Items from last GOC meeting.

Progress Reports

These reports will review accomplishments to date.
We could use the itemized list of sub-aims from the grant to organize these
 Aim1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.
 Aim2: We will comprehensively annotate reference genomes in as complete detail as possible.
 Aim3: We will support annotation across all organisms.
 Aim4: We will provide our annotations and tools to the research community.
Aim 1- Ontology Development

Suzi Lewis - Moderator/PI Lead.

  1. Ontology Development - Biological Content:::Midori Harris and David Hill reporting
  2. Ontology structure :::Chris Mungall reporting
  3. Ontology_Development wiki site.
Aim 2- Reference Genome Project

Judy Blake - Moderator/PI lead.

  1. Reference Genome Project :: Rex Chisholm and Pascale Gaudet reporting
  2. Reference Genome Annotation Project wiki site.
Aim 3- Annotation across all organisms

Michael Ashburner - Moderator/PI lead.

  1. Annotation Outreach:: Jen Deegan reporting
  2. OBO-Edit working group::John Day-Richter reporting
Aim 4- Providing annotations and tools to Users

Mike Cherry - Moderator/PI lead.

  1. User Advocacy::Eurie Hong reporting
  2. Production Systems :: Ben Hitz? reporting
  3. Web presence working group::? reporting
  4. Hub Group:: Chris Mungall or Eurie Hong? reporting
  5. 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 Ontology Development-1

  1. Update on 'regulates' terms and relationships in GO (David)
  2. Plan for adding 'regulation of' relationship to GO (Chris_
    1. Will we maintain two copies of GO live at once?
    2. How will will notify users of timing and consequences of this change?

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?

Morning, Monday, September 24, 2007


Topics relevant to Ontology Development-2

catch-up?
  1. How will we notify users about nature and time of change-over ?
  2. Delineating, and isolating, the different categories of "slims" and their usage. See Taxon_Main_Page for more discussion.
  3. 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.
  4. Discuss whether GO can add a has_part relationship (mah, krc)

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

Background: Cross_Product_Guide

GOC and Staff issues (this is largely go-top stuff, perhaps a breakfast?)

  • 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)
  • Currently we have several working groups including:

Ontology content - to work on the content of the ontology
Annotation-Outreach - to encourage new groups to start annotating
User Advocacy - to help users to learn how to use the GO and to represent user's need to the consortium.
Reference Genomes - to choose genes lists for everyone to work on.

1) Would it be a good idea to merge user advocacy and annotation outreach as these have a lot in common?
2) Would it be possible to make a general annotation working group to deal with all issues surrounding annotation? This group could include sub-groups such as the reference genomes group, the evidence code groups and the annotation standard operating procedure group.



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