2011 USC Meeting Agenda

From GO Wiki
Revision as of 10:36, 17 May 2011 by Paul Thomas (talk | contribs) (Satellite meetings)

Jump to: navigation, search

Minutes: (By hosts of previous meeting: MGI)


Thursday May 19

8:30 Registration

9:00 Welcome; Review of schedule and agenda

  • Introductions.
  • GOC PI announcements

Action Items from Bar Harbor GOC meeting

Move into individual sections?

9:15-5:30 Working Group Reports, plans through 2011, discussion of priorities

9:15 Annotation

(Rama, Emily, Pascale) Progress and Priorities, to encompass:

  1. Annotation Outreach efforts (30 min)
  2. Development of Annotation Guidelines (Geneva, Evidence codes). Suggestions for further guidelines.
  3. Draft on how external groups should display annotation.
  4. Focused annotation efforts by GO Consortium members (Emily)
  5. Proposed improvements to the Annotation web pages
  6. Automated annotation support (QCs, Taxon GO, inferred annotations)

10:15 Annotation deliverables

  1. Discussion of Gene Ontology deliverable, different from the MOD deliverable. (Mike 15 min)
  2. Discussion of policy on restricting taxon to specific GAF files. (Mike)

10:30 Break

11:00 Annotation Extension information

  1. Annotation Extension information (Column 16) (MGI and Val? 30 min)

11:30 Evidence Code Ontology presentation

  1. Marcus 25 minutes
  2. Discussion on the appropriate usage of ECO identifiers in annotation (Rama)

12:15 Community resources and Dissemination (Emily & Rama)

  1. GO Help Rotation. How do share the load. (Rama)

12:30 Lunch

1:30 Overview of the outreach efforts

  1. Overview of the outreach efforts to specific scientific communities for community annotation by the BHF-UCL and TAIR teams as well as the CACAO (Community Assessment of Community Annotation with Ontologies) course by EcoliWiki (Ruth, Tanya and Jim; 10 mins each and 15 mins discussion)
  2. BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth; 15 mins)

2:30 InterPro2GO presentation

(Sarah Burge) (40 min presentation, 10 mins discussion)

  1. Brief summary of the revised guidelines for the GO mapping of InterPro entries.
  2. InterPro evidence requirements, new policy of mapping Domain, Site and Repeat entries, changes in coverage between the old and new approaches, occasions where InterPro is unable to GO map an entry and finally, the automatic checks to prevent taxonomy violations and assignment of redundant terms.

3:20 Break

3:30 Ontology development


  1. Timeline: discuss progress and priorities (10 mins)
  2. Recent projects - notes/accomplishments
    • Transcription factors (Karen; available any time Thursday or Friday morning before noon) (15 mins)
    • Signaling (Becky) (15 mins)
    • Chemicals (Tanya) (15 mins)
    • Software utilities (Reasoners, QC - Chris)
  3. OBO/OWL migration (Chris)
    • Notifications of change (Becky) (15-20 mins).
    • Large-scale changes to the ontology.
      • When a development project is starting up, and when their key changes are released
      • Process for discussion and release of proposed term obsoletions.
  4. Protein complexes (Harold) (15 mins)
    • The scope of GO relative to that of PRO?
    • Should GO capture gene product specific protein complexes, or species-specific protein complexes?
    • Should protein complexes be defined based on function or component information? (Becky and Peter D'E)

Break for the day

Friday May 20

9:00-12:30 Working Group Reports (cont), plans through 2011, discussion of priorities

9:00 Reference Genomes


  1. Timeline: discuss progress and priorities 20 min
  2. Enhancements to PAINT & DB (Paul T) 20 min
  3. Incorporating InterPro motifs into PAINT

10:00 Software - part 1


  1. Timeline: discuss progress and priorities

10:30 Break

11:00 Software

  1. Software status (AmiGO, GOOSE, GOLD, etc. - Seth)

11:45 Review Action items

12:30 Lunch

1:30-5:30 Discussion of the Vision defined in the GOC NIH grant application

(Friday afternoon, Saturday Morning) (This includes presentations of our current efforts and how these will map into the vision. Also what goals are needed to reach the aims stated in the application.)

1:30 Literature-based annotations (Mike, moderator: Rama)

  1. vision (i.e. efficiency, quality and consistency goals)
  2. implementation: what will be necessary to accomplish this goal?
    • prioritization of what organism and genes to be curated
  3. current status/accomplishments
  4. possible metrics

2:00 Biological focus-group annotations (Judy, moderator: Emily)

  1. vision (and entire text-book TOC)
    • implementation: what will be necessary to accomplish this goal?
    • current status/accomplishments
      • New ontologies terms added at recent meetings.
    • possible metrics/milestones

2:45 Phylogenetically-based annotations (Paul T)

    • vision (e.g. dynamically adding a new protein to the right family, versioning with stable IDs for ancestral nodes)
    • implementation: what will be necessary to accomplish this goal.
    • current status/accomplishments
    • possible metrics

3:30 Break

3:45 Common Annotation Framework (Paul S)

    • vision
    • implementation: what will be necessary to accomplish this goal?
    • Current Efforts
      • PomBase community annotation tool (Val)
      • Textpresso, Phenote, PAINT-web, and all the rest...
        • Introduction to GO Curation using Textpresso (Kimberly, 10-15 mins.)
    • metrics and milestones

Break for day

Saturday May 21

9:00-10:45 Discussion of the Vision defined in the GOC NIH grant application

9:00 Ontology development (David)

    • Vision
    • implementation: what will be necessary to accomplish this goal.
    • metrics and milestones

10:00 Community resources and Dissemination (Mike, moderators: Emily & Rama)

    • vision
    • implementation: what will be necessary to accomplish this goal.
    • Monitoring customer satisfaction

10:45 Coffee break

11-noon Wrap up, action items

12:00 lunch and departures or Satellite meeting

Satellite meetings

  1. Cardiac Conduction ontology development workshop (Ruth & David) [1]
    • pre-workshop discussion (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
    • probably straight after main meeting closes on 21st May
    • workshop date not yet set, aiming for Sept-Nov 2011
    • Please let Ruth know if interested in attending workshop/pre-meeting