2014 College Station GOC Meeting Agenda

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Revision as of 18:32, 9 March 2014 by Paul Thomas (talk | contribs) (3:30 - 3:45 pm Break)

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Logistics

Minutes

  • (Add link to google doc here)

Progress Reports

  • Progress reports by Aim (add links here)
    1. Literature Annotation
    2. PAINT Annotation
    3. Common Annotation Framework
    4. Ontologies
    5. Delivery of Annotation and Ontologies to the Community
  • Response to SAB
    1. SAB report from Cambridge April 2013 ( [1])
    2. Our reponse...
  • Questions for SAB

Agenda

  • Assign 'official' note takers, set up Google doc for notes and so everyone can augment, introductions of new people

Saturday 15 March - Pre-Meeting Working Group(s)

Jim will direct pre-meeting working group(s?) to empty classrooms to meet.

Working group schedule
Time Topic Attending
9:30-10:30 CDT Framework - We'll draw up some pictures of the different pieces and how they fit together to get everyone on the same page. We'll discuss where questions still remain. Everyone - Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola, Mary
10:30-12:00 CDT Molecular Modeling Environment - We are now at the stage where we have a working annotation UI available for initial feedback. It connects to the existing LEGO data (stored at present in files under SVN) and thus provides a realistic tool for evaluation. We can also extends these by seeding them with existing GO annotations if a curator wants to work on a particular module. After such seeding a curator can review what's already been annotated and incorporate it into the module. Paul T, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Paola, Mary
1:00-2:00 CDT Integration - We currently have several useful annotation tools for different pieces, but would like to make this more seamless for curators. What code can we share? What signals can we pass? miRNA Annotations - Guidelines for annotation of miRNAs, with specific annotation examples to be provided by attending groups. Please add information to the wiki miRNA guidelines Paul T, Chris, Heiko, Seth, Tony, Huaiyu, Mary Ruth, Rachael, Donghui, Doug, Jennifer, Rama, Kimberly, Huaiyu, Dmitry, Judy
2:00-3:00 CDT Ontology - Sort out how to do multi-species annotation and the overall OWL modeling 2-minute video GO tutorials - Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. Video tutorial ideas Paul T, Suzi, Jane, Chris, Heiko, Seth, David H, David O-S, Tanya, Paola, Mary Rachael, Rama, Suzi, Moni, anyone else who would like to become involved
3:00-4:00 CDT Catalytic activity/Metabolic Process - likely modeling of biochemical pathways in GO, some specifics of EC/GO mapping/interaction, some lingering SF items relating to catalytic activity children and the underlying general problems they revealed Jim, Tanya, David, Chris, Heiko, Peter, Harold, Jane, TAMU experts, Paola, Huaiyu, Mary
4:00-5:00 CDT Roadmap - Milestones and 6-month to year plan for bringing this into eventual production. We can revisit the framework from the morning and revise it based on the day's discussion (for showing at the big meeting the next day) Everyone - Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola, Mary

Sunday 16 March - Community relations and Annotation Production

Breakfast on your own

8:30 Start

  • Welcome and introductions (8:30-8:45)
  • Goals for meeting, and Consortium priorities (PI's, 8:45-9:15)
Community facing
  • Website
    • content status (Moni, 8:30-9:30)
    • New documentation pages in Drupal (Chris, Seth)
    • Exports of GO, retiring GO full - Mike, Chris, Seth
  • Amigo2 (9:30-10)
    • Beta status (Seth)
    • Production status (Mike)

10:30 - 11:00 Break

  • GO term enrichment analysis (Paola, Chris, Paul T., 10-10:15)
  • JS-PAINT status (Seth, Suzi, 10:15-10:30)
  • It would be good if the GOC could take a proactive stance on GO-related papers, by letting journal editors know that GOC members would be happy to review papers that discuss GO.

12:30 - 2:00 pm Lunch

Annotation issues

  • PAINT annotation progress
  • Quality control and consistency (Pascale, Paul T.)
  • Adoption of Protein2GO
    • non-protein identifiers (Kimberly)
    • MiRNA annotation
  • Extended annotation tool (AKA LEGO, ORION)
    • Behavior terms

3:30 - 3:45 pm Break

5:30 Group Photo

Conference Dinner

Monday 17 March - Annotation Infrastructure, Ontology Development, and Planning

Breakfast on your own

8:30 Start

  • Ontology development - Completed work
    • New viral terms with mapping to ViralZone/UniProtKW (Jane)
    • Progress report on transition to OWL (Chris)
    • Overview of cilial and Giardia work (Paola)
    • Update on apoptosis (Paola)
    • Wikipedia links to GO (David OS)

10:30 - 11:00 Break

  • Ontology development - Modeling
    • Biochemical Pathways using has_part.(David H)
      • Glycolysis expanded (are we ready to implement?)
        • Coordinate annotation
      • Molybdopterin cofactor biosynthesis
        • Coordinate annotation
    • DNA replication (Tanya)
    • Multi-organism BP/CC annotation model (David OS)
    • Proposed new structure for extracellular/extraorganismal cc (David OS)
    • Uberon/CL update (Chris)
  • Interaction with other groups (on ubiquitin, Giardia, cilia, Sejal's project on Alzheimer's disease) (David H or Jane)

12:30 - 2:00 pm Lunch

Review SAB presentations

  • Community (Paul S., Moni, Seth, Rama)
  • Annotation (Mike, Rama, Pascale)

3:30 - 3:45 pm Break

  • A gentle reminder if each MOD/DB could please email round when they have new curators.
  • Ontologies (Suzi, Chris, David H, Tanya, Jane, David OS)
  • Common Annotation Framework (Paul T., Chris, Kimberly, Seth)

SAB Dinner

Tuesday 18 March - SAB meeting

8:30 - Presentations of progress

  • Presentations to SAB (~3 hours. Mike, Suzi, Paul S, Paul T)

11:30 - 1:30 pm Lunch

  • SAB discussions privately

1:30 - 3:30 Feedback

  • SAB reports to PIs

3:30 pm End of meeting