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: (room ERB 2519)
    • 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
  • Annotation tools (the following discussions are all interrelated, ordering here is the same as in main agenda)
    • 2:30pm - 3:00pm LEGO group discussion (room ERB 2519)
    • 3:00pm - 4:00pm PAINT group discussion (room NRB 3035)
    • 4:00pm - 5:00pm CAT working group: next steps moving from Protein2GO to free-standing CAT, independent of UniProt (room NRB 3035)

Agenda

Minutes here: https://docs.google.com/document/d/1JuQXt_7zgb_3wkFnsz4Lqqm0gy0UvbH3hBM4unse8FI/edit?pli=1

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

  1. Assign 'official' note takers, set up Google doc for notes and so everyone can augment, introductions of new people
  2. 9:00 - 9:30 am
    • GO-pal transition (GO + Drupal = GO-pal), Seth + Moni
    • GO annotation stats Seth
    • Term enrichment front & center
      • Gold Standard Annotation Sets Rama
      • Biological data interpretation (aka enrichment) Chris
    • Update on tool registry Chris
    • GO analysis gotcha page (e.g. post summary of PLoS article on close/open world?) Suzi
  3. 9:30 - 10:00 am AmiGO 2 Seth
    • Demo with David H David
    • 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..."
  4. 10:00 - 10:30 am Engaging the user community (GO help responsibilities) Suzi
    • A Gene Ontology MOOC (Coursera, EdX, Udacity, etc.) to train and to answer "I want to ..." questions
    • Ideas for dynamic content: e.g. GO help rota responsibilities would include writing blog on latest annotation paper that was discussed, or one of the help questions.
    • GO-FAQ and GO-help Chris

BREAK: 10:30 - 11:00

  1. 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) Rama/Rachael
  2. Tutorial on column 16 Rachael
    • Proposed json file format for GO annotations (up to LEGO-expressivity) Chris

LUNCH: 12:30 - 2:00 pm

2:00 - 3:00 pm

  1. Annotation procedures Val
    • Differences in how we treat annotation propagation the regulation relationship for function and process (implications for Ensembl) implications of not propagating over "regulates" e.g;metaphase anaphase transition (0) regulation of metaphase/anaphase transition (51), if regulation does not propagate (as in Ensembl) other e.gs regulation cell cycle/ regulation of mitotic cell cycle
    • More guidelines about when to precompose/not precompose (especially using during/involved in response to)

BREAK: 3:30 -4:00 pm

4:00 - 5:00 pm

  1. Incorporation of external annotations.Judy
    • 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


Conference Dinner at 5:30 pm Cafe This Way

Saturday 5 Oct - Ontology & Infrastructure

Breakfast on your own

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

  1. Ontology development infrastructure update, transition to OWL, etc. Chris
  2. Ontology developments Judy
    • Updates on content in specific biological domains
      • Neuronal cell components and integration with NIF Paola
      • Apoptosis annotation update Paola
      • Proposed Giardia/unicellular eukaryote cc expansion Paola
      • cell cycle Jane
      • virus project update Becky
      • Uberon/CL/GO developments David OS
    • Update on Cross products- internal and external ontologies David H
    • Molecular Function alignment with Rhea Chris
  3. Biological Modeling (LEGO) Paul T
    • Modular annotation ("lego") progress report Chris
    • Reactome Discussion
      • Automated translation of Reactome & BioPAX to LEGO/OWL Chris
      • Glycolysis example for comparison David H
      • Pathways in GOC, representation and prioritization
      • Relationship between GOC and various pathway representations including wikipathways, using these external definitions to define the starts and ends of slim processes
  4. Annotation Infrastructure Suzi
    • PAINT annotation and tool update Paul T & Suzi
    • Common Annotation Tool update
      • SGD's Migration to Protein2GO Rama
      • Integration of Text Mining Tools with Protein2GO Kimberly
      • CAT: beyond Protein2GO PaulS
  5. Group Picture

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

Sunday 6 Oct - Summary and planning

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