Crop Plant Trait Ontology Workshop Agenda

Dates: Sept 13-15th, 2012 (Thursday through Saturday)

Location: Oregon State University

Return to the main Crop_Plant_Trait_Ontology_Workshop_OSU_2012 page

Weds Sept. 12th, 6-8pm

Dinner on your own those who arrive early

Snack and refreshments will be available at Finley Hall or Arnold dining center will be open until 7pm

Thursday September 13

Location: CH2M Hill Alumni Center Williamette Room

The wireless internet username and password is:

Login User: 25Sept8

Password: shakyDove

* 8:00- 9am Continental Breakfast in Williamette Room

• 9:00- 9:15 Welcome and Introduction - Pankaj Jaiswal, OSU

• 9:15- 9:30 Ruth Bastow: Insights and follow-up from EBI Crop Ontology Meeting

• 9:30- 10:00 Melissa Haendel; "Introduction to Ontologies"

• 10:00- 10:30 The Plant Ontology and the Trait Ontology- Laurel Cooper, OSU

* 10:30- 10:45 coffee break

• 10:45- 11:00 Elizabeth Arnaud, Bioversity /GCP

• 11:00- 11:15 Naama Menda- Sol Genomics Network

• 11:15- 11:30 Rex Nelson- SoyBase

• 11:30- 11:45 Mary Schaeffer- MaizeGDB

• 11:45- 12:00 0pen time for questions and discussion

* 12:00- 1:00 Lunch: Soup and Salad Buffet; Elle/Burlingham Room #111

• 1:00- 1:10 Bob Benson, Syngenta traits

• 1:10- 1:20 Sharon Lewis; Syngenta- Information governance

• 1:20- 1:30 Alice Clara Augustine, Monsanto

• 1:30- 1:40 Sonia Dias- Trait Information Portal, PGR secure

• 1:40- 1:50 Pawel Krajewski, transPLANT

• 1:50- 2:00 Jacques Legouis; INRA, France

• 2:00- 2:10 Cyril Pommier, INRA France; Ephesis

• 2:10- 2:20- John Doonan, UK Phenomics Center

• 2:20- 2:30- Dan Bolser, EBI, Ensemble, potato genomics

• 2:30- 2:40 Reinhard Simon, CIP

* 2:40- 3:00 coffee break

• 3:00- 3:10- Victoria Blake, USDA, ARS, CA GrainGenes

• 3:10- 3:20 Luke Ramsay, Barley traits

• 3:20- 3:30 C Tom Hash, ICRISAT, sorghum

• 3:30- 3:40 Ken McNally, IRRI

• 3:40- 3:50 Michael Dingkuhn, IRRI

• 3:50- 4:00 Sunita Kumari, KBase

• 4:00- 4:30 Justin Preece, OSU - Plant Ontology Tools for Annotation:

• Semantic Image Annotator (SIA)
• Plant Annotation Wiki
• PO Web Services

• 4:30- 5:00 Open time for questions and discussion

* 5:00- 6:00 break, free time

* 6:00- 7:00 Pizza dinner- Elle/Burlingham Room #111

* 7:00 to 9:00pm 'Hands-on' Ontology Session

Requesting terms using the SourceForge trackers

Please see the link: How to use the Source Forge tracker

Before using the PO Source Forge tracker you should:

1. Register (create a login)
2. Log in to your account
3. Search the tracker for existing items on the same topic

Friday September 14

* 8:00- 9am Continental Breakfast in Williamette Room

9:00- 9:20 TBA

9:20- 9:30 Sushma Naithani, OSU Horticulture

9:30-9:40 Laurent DeLuc, OSU Horticulture, grape research

* 9:40- 10:00 coffee break

• 10:00- 11:00 Creating the 'CROP Initiative' (Common Reference Ontologies for Plants)
  • Pankaj: Introduction
  • Barry Smith: Webex presentation
    • List of Ontologies
    • OBO Foundry website
    • Background reading on the OBO Foundry

11:00- 12:00 discussion

* 12:00-1:00 Lunch: Assorted Wraps with Soup and Salad; Elle/Burlingham Room #111

1:00- 1:15 breakout groups are organized and task is explained

1:15- 2:45 breakout group session: "Find your trait of Interest"

* 2:45- 3:00 coffee break

3:00- 3:30- breakout groups report on progress, discussion

3:30- 5:00 breakout groups

5:00- 5:30 breakout groups report on progress, discussion

* 5:30- 6:30 break, free time

* 6:30- 9:00 Dinner and Social -Elle/Burlingham Room #111

Saturday September 15

* 8:00- 9am Continental Breakfast in Williamette Room

9:00- 9:30 Biological examples and ontology applications; Pankaj Jaiswal, OSU

9:30- 10:30 Breakout groups and group discussion

* 10:30- 10:45 Coffee break

10:45 Summary and conclusions

Wrap and to-do lists for follow-up

12:00 Boxed Lunches