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

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=Logistics=
==Dates==
==Dates==
*December 10-13, 2018
*December 10-13, 2018
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== Venue ==
== Venue ==
* Geneva
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 ==
== Hotel ==
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Contact Lourdes to arrange your travel. Give her your preferred flights. Must be on US carrier or code share.
Contact Lourdes to arrange your travel. Give her your preferred flights. Must be on US carrier or code share.


== Agenda ==
 
 
 
= Agenda =


===Sunday December 9===
===Sunday December 9===

Revision as of 18:55, 23 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 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