Geneva ontology editors meeting- Dec 10-13, 2018 - Logistics
Logistics
Dates
- December 10-13, 2018
- ARRIVAL: Dec 8th (Fly from US on Friday Dec 7th)
- DEPARTURE: Friday Dec 14th
Venue
HEG (Haute Ecole de Gestion de Geneve), Carouge (Geneve) Campus de Battelle: https://goo.gl/maps/k93FWVUxdv42 Bâtiment B, Room B5.18 Rue de la Tambourine 17 1227 Carouge
https://www.hesge.ch/heg/sites/default/files/documents/plan-acces-heg.pdf
Public transportation
- Tram lines 18 et 12 : "Carouge (Rondeau)" stop
- Tram 18 is also connected from the train station ("Gare Cornavin")
- Bus 44 or 45 : "Grange-Collomb" stop
Hotel
Travel
Contact Lourdes to arrange your travel. Give her your preferred flights. Must be on US carrier or code share.
Agenda
Sunday December 9
- Planning and discussion
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
- Chris Mungall - Berkeley
- Ben Good- Berkeley
- Jim Balhoff - Berkeley (RENCI UNC)
External Curators
- Peter D-Eustachio Reactome
- Alan Bridges Rhea
- Anne Morgat