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: 9sept23

Password: squeakyReindeer

Use Conference network and Local DB

* 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 : Media:Bastow_GARNet-9-13-12.pdf

• 9:30- 10:00 Melissa Haendel; "Introduction to Ontologies" Media:Haendel_OHSU-9-13-12.pdf

• 10:00- 10:30 The Plant Ontology and the Trait Ontology- Laurel Cooper, OSU Media:Cooper_PO+TO-9-13-13.pdf

* 10:30- 10:45 coffee break

• 10:45- 11:00 Elizabeth Arnaud, Bioversity /GCP Media:Arnaud_GCP-9-13-12.pdf

• 11:00- 11:15 Naama Menda- Sol Genomics Network Media:Menda_sol-9-13-12.pdf

• 11:15- 11:30 Rex Nelson- SoyBase Media:Nelson_SoyBase-LIS-9-13-12.pdf

• 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 Media:Bensen_syngenta-9-13-12.pdf

• 1:10- 1:20 Sharon Lewis; Syngenta- Information governance Media:Lewis_syngenta-9-13-12.pdf

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

• 1:30- 1:40 Sonia Dias- Trait Information Portal, PGR secure Media:Dias_PGRSecure-9-13-12.pdf

• 1:40- 1:50 Pawel Krajewski, transPLANT Media:Pawel_transPLANT-9-13-12.pdf

• 1:50- 2:00 Jacques Legouis; INRA, France Media:Legouis_INRA-9-13-12.pdf

• 2:00- 2:10 Cyril Pommier, INRA France; Ephesis Media:Pommier_URGI-9-13-12.pdf

• 2:10- 2:20- John Doonan, UK Phenomics Center Media:Doonan_OR_ontology_WS-9-13-12.pdf

• 2:20- 2:30- Dan Bolser, EBI, Ensemble, potato genomics Media:Bolser_CPTO-9-13-12.pdf

• 2:30- 2:40 Reinhard Simon, CIP

* 2:40- 3:00 coffee break

• 3:00- 3:10- Victoria Blake, USDA, ARS, CA GrainGenes Media:Blake_T3-9-13-12.pdf

• 3:10- 3:20 Luke Ramsay, Barley traits Media:Ramsay_Hutton_Institute-9-13-12.pdf

• 3:20- 3:30 C Tom Hash, ICRISAT, sorghum Media:Hash_ICRISAT-9-13-12.pdf

• 3:30- 3:40 Ken McNally, IRRI Media:McNally_ASPIR-9-13-12.pdf

• 3:40- 3:50 Michael Dingkuhn, IRRI Media:Dingkuhn_IRRI_CIRAD-9-13-12.pdf

• 3:50- 4:00 Sunita Kumari, KBase Media:Kumari_Kbase-9-13-12.pdf

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

• 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

Ontology editing: Using OBO Edit- tutorial and practice

• You can download and install OBO-Edit from here: OBO-Edit

Note: the newest version of Mac OS Mountain Lion appears to have a default setting blocking installations from sites other than Apple Apps store. This can be turned off.

Steps to setting up the OBO-Edit after doing download and install:

1. Select "New Ontology"
2. Set up save profile
3. set up a number space using ID Manager
4. Set auto commit text edits
5. Create a root class
6. Create a root relation- part_of
7. Populate the ontology

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- 9:10 Welcome and Announcements

9:10- 9:20 Sushma Naithani, OSU Horticulture Media:Naithani-9-13-12.pdf

9:20-9:30 Laurent DeLuc, OSU Horticulture, grape research Media:Deluc-9-13-12.pdf

9:30-9:40 Pankaj

* 9:50- 10:50 coffee break

• 10:00- 11:00 Creating the 'CROP Initiative' (Common Reference Ontologies for Plants)
  • Pankaj: Introduction
  • Barry Smith: Webex presentation Media:Smith_CROP-9-13-12.pdf
    • slides
    • List of Ontologies
    • OBO Foundry website
    • Background reading on the OBO Foundry

Streaming recording link

Download recording link

11:00- 12:00 discussion

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

1:00- 1:30 Breakout Groups are organized and tasks are explained

1:30- 3:00 Breakout Group Session: "Find your trait of Interest"

• Groups will explore the TO and find out if the traits they are interested in are represented

- Creating name, defining the trait, assigning a place in the hierarchy

- Can also be 'Hands-on' using OBO-Edit

• Breakout Groups:

Quality: Pawel, Luke, Rex, Melissa, Sharon

Yield: Jaques, Mary, Ruth, Tom, Cyril, Michael, Laurel

Stress: Sunita, Sonia, Pankaj, Bob

Anatomy and Morphology: Victoria, Ken, Elizabeth, Alice Clara, Laura

Growth and Develoment: John, Laurent, Naama, Reinhard

Informatics: Justin E, Justin P, Dan, Alok?, Rex

3:00 coffee break and group photo

3:30- 5:00- Breakout Groups report on progress, discussion, questions

fill in details....

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

• 6:00- 6:30 Gathering

* 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 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