2013 Bar Harbor GOC Meeting Agenda

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Pre-Meeting Working Groups

Thurs 3 Oct

These pre-meeting working groups will meet at The Jackson Laboratory. Please arrive 30 minutes before the session you wish to attend so you can get a badge and escort.

  • 9:30am - 10:30am Web documentation, Drupal transition (room ERB 1421)
  • 11:00am - 12:00pm Ontology group discussion: OWL/OBO editing workflow (room NRB 3035)
  • 12:00pm - 1:00pm Lunch at Roscoe's
  • 12:50pm - 1:30pm Lab tour (optional; Mark Wanner leading)
  • 1:30pm - 2:30pm Annotation extensions: for those already making c16 annotations and ontology developers; This group will be finalizing what they want to present to the whole GOC during this meeting (room ERB 2519)
  • Annotation tools (the following discussions are interrelated, therefore if you attend one, then plan on attending them all. Attendance only if contributing to all 3)
    • 2:30pm - 3:00pm CAT working group: next steps moving from Protein2GO to free-standing CAT (independent of UniProt)(room ERB 2519)
    • 3:00pm - 4:00pm: LEGO group discussion (room NRB 3035)
    • 4:00pm - 5:00pm PAINT group discussion: This is a working group meeting for those PAINT curators and developers in town on Thur. (room NRB 3035)

Agenda

The SAB report from April 2013 (Cambridge) was very specific and productive [1]. We will be meeting with them again in March 2014 and need to show progress on their useful recommendations. Therefore the focus of this meeting is to identify targeted projects that we can demonstrate to them by completely them in the (roughly) six intervening months. Establishing priorities, point people who will handle coordination, and monthly milestones.

Friday 4 Oct - Annotation Impact & Usability

Breakfast on your own

8:30 start (lunch 12:30-2:00, breaks at 10:30 and 3:30)

  1. GO-pal transition (GO + Drupal = GO-pal), Seth + Moni
    • Term enrichment front & center
      • Gold Standard Annotation Sets (Rama)
    • Other key use cases
      • Scicrunch registry (improvement on neuroLex?)
      • GO analysis gotcha page (PLoS article?)
    • GO stats
  2. Engaging the user community (GO help responsibilities)
    • A Gene Ontology MOOC (Coursera, EdX, Udacity, etc.) to train and to answer "I want to ..." questions
    • Obligatory blog during each rota on latest annotation paper that was discussed
  3. AmiGO (Seth)
    • Timeline for transition to Stanford hosting
    • Filtering feature requests
      • Could we see the major models in the first set, rather than broad taxon groupings?
      • Maybe the "text box" filter should be available without going to "more..."
      • Filters for NOT, contributes to, and colocates
  4. Incorporation of external annotations.
    • Discuss which evidence codes to use for annotation predictions.
    • Discuss strategies for incorporation, including non-MOD IEAs
    • Reactome annotations, their use of ev.codes etc
    • Proposal to integrate protein binding annotations
  5. Annotation workflow (Quality control reports and how to manage them efficiently)
    • Review of Jenkins GAF QC checks and inferences
      • Location of files and what they contain - Heiko
      • Examples from the MGI file and discussion of most efficient ways to deal with reports - David H.
    • With/From column IDs (what is mandatory, how to move this to Jenkins for checking)
    • Tutorial on column 16 (Rachael)
  6. PAINT annotation update (Paul T)
  7. PAINT tool update (Suzi)
  8. Common Annotation Tool update
    1. SGD's Migration to Protein2GO (Rama)
    2. Integration of Text Mining Tools with Protein2GO (Kimberly)

Conference Dinner at 5:30 pm Cafe This Way

Saturday 5 Oct: Ontology)

Breakfast on your own

8:30 start (lunch at 12:30, breaks at 10:30 and 3:30)

  1. Ontology Development (Judy)
    1. Biological content
      1. Neuronal cell components and integration with NIF (Paola)
      2. Apoptosis annotation update (Paola)
      3. Proposed Giardia/unicellular eukaryote cc expansion (Paola)
      4. cell cycle (Jane)
      5. virus project update (Becky)
      6. Uberon/CL/GO developments (David OS)
    2. Update on Cross products- internal and external ontologies (David H)
      1. TermGenie Template Updates
      2. CHEBI - http://www.biomedcentral.com/1471-2164/14/513
      3. Display of external ontologies in AmiGO 2
    3. Transition to OWL update (Chris)
    4. Inference of LEGO diagrams from GO annotations and external sources (Chris)
      1. Reactome Discussion
        1. Automated translation of Reactome & BioPAX to LEGO/OWL (Chris)
        2. Glycolysis example for comparison (David H)
        3. Pathways in GOC
        4. Relationship between GOC and various pathway representations including wikipathways
    5. Proposed json file format for GO annotations (up to LEGO-expressivity) (Chris)
    6. Molecular Function alignment with Rhea (Chris)
    7. Biological data interpretation (aka enrichment) (Chris)
      1. GO-FAQ and GO-help
  2. Group Picture
  3. Biological Usability
    1. LEGO and pathways (Paul T)

Field Trips: Enjoy Acadia National Park. 4:00pm

Sunday 6 Oct (Usability) (NOTE: MIGHT BE ALL MOVED TO SATURDAY)

  1. Action Item review and assignments
  2. Monthly milestones for next 6 months
  3. Future Meetings
    • LEGO Hackathon
    • GOC meeting next Spring (Jim Hu, Paul Thomas) (College Station, Texas) will include SAB meeting
    1. Possibility of an Annotation Camp in the near future (discuss dates/venue)
  4. Papers published and in progress
  5. Wrap Up