Geneva ontology editors meeting- Dec 10-13, 2018 - Logistics: Difference between revisions

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= Agenda =
= Agenda =


===Sunday December 9===
https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit
* 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 ==
== Participants ==

Revision as of 21:26, 25 October 2018

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
  • B building ('bâtiment'), 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

https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit

Participants

Ontology Group

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

Software Group

  • Chris Mungall - Berkeley
  • Ben Good- Berkeley
  • Jim Balhoff - Berkeley (RENCI UNC)

External Curators

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