2014 College Station GOC Meeting Agenda

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Progress Reports

  • Progress reports by Aim (add links here)
    1. Literature Annotation Annotation Advocacy
    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


  • 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. We will start in N127 in the NMR wing.

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, Val
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 extend 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. We should also go over proposed refactoring of MF. Paul T, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Paola, Mary, Val
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. File:GOCmiRNA2014.pdf Please add information to the wiki miRNA guidelines Paul T, Chris, Heiko, Seth, Tony, Huaiyu, Mary, Val 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 Outreach: website & multimedia bootcamp - Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. Video tutorial ideas. Also, bring your questions about editing content on the GO (Drupal) website. Paul T, Suzi, Jane, Chris, Heiko, Seth, David H, David O-S, Tanya, Paola, Mary Rachael, Rama, Suzi, Moni, Val 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, Val
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, Val

Sunday 16 March - Community relations and Annotation Production

Breakfast on your own

8:30 Start

Room 129: AgriLife Building. See Logistics page

  • Welcome and introductions File:WelcomeMar2014.pptx
    • A gentle reminder if each MOD/DB could please email round when they have new curators.
  • Goals for meeting, and Consortium priorities (PI's)
Community and Outreach
  • Website | Slides available here.
    • Test drive the new GOC website at http://beta.geneontology.org
    • Content status (Moni)
    • Report on Outreach & Multimedia breakout group: video tutorials, adding content. (Moni)
    • New documentation pages in Drupal (Chris, Seth)
    • Exports of GO, retiring GO full (Chris, Seth)
    • Tools Registry (Chris)
      • How to find tools
      • How to register tools
  • AmiGO 2 | Slides available here.
    • Beta status (Seth)
    • Production status (Mike)
  • Preview of new QuickGO interface File:New QuickGO.pptx

10:30 - 11:00 Break

  • GO term enrichment analysis (Chris)
  • jsPAINT status (Suzi)
    Explore the jsPAINT beta version at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/phylo_graph
  • 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 and infrastructure

3:30 - 3:45 pm Break

  • Adoption of Protein2GO
    • Summary of plans for upgrading Protein2GO for non-protein identifiers (Tony)
    • non-protein identifiers (Kimberly)
    • MiRNA annotation (Ruth)

5:30 Group Photo

7PM Conference Dinner

Veritas. Shuttle is available but it's also walking distance

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

Breakfast on your own

8:30 Start

Room 129: AgriLife Building. See Logistics page

10:30 - 11:00 Break

  • Ontology development - Modeling
    • Biochemical Pathways using has_part.(David H)
    • DNA replication (Tanya)
    • Multi-organism BP/CC annotation model (David OS)

12:30 - 2:00 pm Lunch

  • Review SAB presentations - part I
    • Community (Paul S., Moni, Seth, Rama)
    • Annotation (Mike, Rama, Pascale)

3:30 - 3:45 pm Break

  • Review SAB presentations - part II
    • Ontologies (Suzi, Chris, David H, Tanya, Jane, David OS)
    • Common Annotation Framework (Paul T., Chris, Kimberly, Seth)

7 PM SAB / GOC Council Dinner

The SAB Dinner will be at the Republic, which is 0.5 miles from the Hyatt Place. Note that Google maps puts the pin slightly off the correct location (but in the correct complex).

Tuesday 18 March - SAB meeting

ILSB 3147 See Logistics page

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

Group Photo