2014 College Station GOC Meeting Agenda: Difference between revisions

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*# Agenda: Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. [http://gocwiki.geneontology.org/index.php/video_tutorial_ideas Video tutorial ideas]
*# Agenda: Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. [http://gocwiki.geneontology.org/index.php/video_tutorial_ideas Video tutorial ideas]


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===Sunday 16 March - Community relations and Annotation Production ===
===Sunday 16 March - Community relations and Annotation Production ===

Revision as of 16:15, 5 March 2014

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.

  • Need to define specific issues we need to resolve in person. Suggest that we try to divide some of these issues into subgroups that can meet in parallel.
  • 9:30am - 12:00pm Molecular Modeling Framework (Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola)
    1. 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.
    2. LEGO? UI - 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.
    3. Ontology - Sort out how to do multi-species annotation and the overall OWL modeling
    4. 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?
    5. 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).
  • 1:00PM-2:30PM Catalytic activity/Metabolic Process (Jim, Tanya, David, Chris, Heiko, Peter, Harold, Jane, TAMU experts, Paola)
    1. Agenda: specifics to follow - 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
  • 2:45PM-3:45PM miRNA Annotations(Ruth, Rachael, Donghui and/or Tanya, Doug, Jennifer, David H......)
    1. Agenda: Guidelines for annotation of miRNAs, with specific annotation examples to be provided by attending groups.
    2. Please add information to the wiki miRNA guidelines
  • 4:00PM-5:00PM, 2-minute video GO tutorials (Rachael, Rama, Suzi, Moni, anyone else who would like to become involved).
    1. Agenda: Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. Video tutorial ideas
Name Organization Nights Required Airport Hotel Name Remote Attending Conference Dinner Dietary constraints

Jim Hu

PortEco/EcoliWiki

n/a

n/a

n/a

N

Y

Lactose intolerant

Paul Sternberg

Caltech-WormBase

3

Hyatt Place

N

Y

Moni Munoz-Torres

BBOP, LBL

5

IAH - Houston Intercontinental

Hyatt Place

N

Y

Jennifer Smith

Rat Genome Database

2

CLL - College Station

Hyatt Place

N

Y

Ruth Lovering

UCL annotation team

4

CLL - College Station

Hyatt Place

N

Y

Kimberly Van Auken

WormBase - Caltech

5

CLL - College Station

Hyatt Place

N

Y

Vegetarian

Tom Hayman

Rat Genome Database

2

CLL - College Station

Hyatt Place

N

Y

Rachael Huntley

UniProt

4

CLL - College Station

N

Y

Vegetarian

Jane Lomax

EMBL-EBI

4

CLL - College Station

Hyatt Place

N

Y

Heiko Dietze

BBOP, LBL

5

IAH - Houston Intercontinental

Hyatt Place

N

Y

Mary Dolan

MGI, JAX

4

CLL - College Station

Hyatt Place

N

Y

Harold Drabkin

MGI, JAX

4

IAH - Houston Intercontinental

Hyatt Place

N

Y

Tanya Berardini

TAIR

5

IAH - Houston Intercontinental

Hyatt Place

N

Y

David Hill

MGI, JAX

5

IAH - Houston Intercontinental

Hyatt Place

N

Y

Doug Howe

ZFIN

3

CLL - College Station

Hyatt Place

N

Y

Karen Christie

MGI, JAX

n/a

Y

N

Rama

Stanford University

3

IAH - Houston Intercontinental

Hyatt Place

Y

Vegan

Selina Dwight

Stanford University

4

AUS Austin

Hyatt Place

N

Y

Petra Fey

dictyBase

3

Hyatt Place

N

Y

Vegetarian

Peter D'Eustachio

NYU - Reactome

3

IAH - Houston Intercontinental

Hilton College Station

N

Y

Suzi Lewis

Lactose intolerant

Paola Roncaglia

EMBL-EBI

3

CLL - College Station

Hyatt Place

N

Y

Valerie Wood

PomBase

CLL - College Station

N

Y

Suzi Aleksander

PortEco/EcoliWiki

n/a

n/a

n/a

N

Shabnam Eslamfam

Texas A&M/OMP

n/a

n/a

n/a

N


edit table

Sunday 16 March - Community relations and Annotation Production

Breakfast on your own

  • Things we'd like to discuss at some point (Jane/Paola):
    • A gentle reminder if each MOD/DB could please email round when they have new curators.
    • 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.

8:30 Start

  • MiRNA annotation
  • MBInfo cross-references
  • Behavior terms

10:30 - 11:00 Break

12:30 - 2:00 pm Lunch

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

  • Exports of GO, retiring GO full - Mike, Chris, Seth
  • 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)
    • 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)

10:30 - 11:00 Break

  • GO enrichment analysis (Paola, Chris, Seth)
  • New documentation pages in Drupal (Chris, Seth)

12:30 - 2:00 pm Lunch

3:30 - 3:45 pm Break

SAB Dinner

Tuesday 18 March - SAB meeting

8:30 - Presentations of progress

  • Presentations to SAB (~3 hours. Judy, 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

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