Geneva ontology editors meeting (Dec 10-13, 2018) - potential agenda topics

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Dates

  • December 10-13, 2018

Venue

  • Geneva

Hotel

Travel

Agenda

Monday December 10

  • 9:00am-10:30am: Use a pre-generated spreadsheet to add missing xrefs across MFs- strategize and prioritize,
  • 10:30am- 10:45am: coffee break
  • 10:45am- 12:00pm: Data flow and updating. Design a strategy to keep the resources in synch and appoint key personnel as contact points for data exchange.
  • 12:00pm - 1:00pm: lunch
  • 1:00pm-3:00pm: curators work to add missing xrefs
  • 3:00pm- 3:15pm: break
  • 3:15pm-4:15pm: Address the issue of automatically adding definitions to GO. Can we harvest Rhea reaction descriptions to automatically populate GO defs. What happens when Rhea reactions change? Do they ever change?
  • 4:15pm-5:00pm: Discuss a strategy to handle reaction directionality. Do we want to have all reactions point to the generic bidirectional reactions in Rhea, or are there some that we can restrict through cross-reference to the directional reaction. Plan a strategy to find these.

Tuesday December 11

  • 9:00am-10:30am: Update reaction xrefs, continued.
  • 10:30am- 10:45am: coffee break
  • 10:45am-12:00pm: Automated classification of reactions based on reactants. ‘Currency’ participants, other types of participants. Discuss Rhea generic chemicals. Do we need reactant pools?
  • 12:00am- 1:00pm: lunch
  • 1:00pm- 3:00pm: QC methods for automatic classification of reactions based on participants.
  • 3:00pm-3:15pm: break
  • 3:15pm- 5:00pm: QC Reactome-GO-Rhea xrefs

Wednesday December 12

  • 9:00am- 10:30am: From Reactions to pathways. Examine imports of Reactome pathways into GO-CAM models. Test reasoning going from functions to processes.
  • 10:30am-10:45am: coffee break
  • 10:45am-12:00pm: Discuss issues identified in the morning session.
  • 12:00pm- 1:00pm: lunch
  • 1:00pm- 3:00pm: Identify pathways for modeling in GO-CAM
  • 3:00pm- 5:00pm: Create template models. Compare to Reactome imports.

Thursday December 13

  • 9:00am-10:30am: Create guidelines for GO-CAM models and biochemical pathways. Create models according to guidelines.
  • 10:30am-10:45am: coffee break
  • 10:45am-12:00pm: Test model reasoning: annotations and inferences
  • 12:00pm-1:00pm: lunch
  • 1:00pm-3:00pm: Create documentation for GO-CAM model biochemical pathway work flow.
  • 3:00pm-3:15pm: break
  • 3:15pm-5:00pm: general ontology developer’s discussion of priorities, GH tickets workflow etc.

Friday December 14, Departure

Participants

Ontology Group

  • David Hill MGI
  • Harold Drabkin MGI
  • Kimberly Van Auken WormBase
  • Pascale Gaudet SIB
  • Paul Thomas USC
  • Huaiyu Mi USC

Software Group

  • Ben Good- Berkeley
  • Jim Balhoff - Berkeley

External Curators

  • Peter D-Eustachio Reactome
  • Alan Bridges Rhea
  • Anne Morgat