RCN Plant and Trait Ontology Workshop

June 10-11, 2007
Genome Research Center
CSHL Woodbury Campus

Workshop Description

The topic of this workshop is to map the trait descriptors in various Gene Bank (stock center) records to the Trait Ontology(TO) and Plant Ontology (PO), and the result is expected to unite all the plant seed stock datasets world over with a common set of vocabulary to describe the similar phenotypes, traits, anatomy and growth stages.

Workshop Agenda

June 10
Morning
9:00am Introduction
                - TO, PO, EO ontology
                - PATO  
                - Ontology-to-ontology mappings

11:00am Discussion
                - How the participants value this work and how they would like this work to move forward for a worldwide acceptance of ontology standards and descriptors
                - Presentations from GRIN and GCP on their use of trait descriptors  

12:30pm Lunch

Afternoon
1:30pm Hands-on session
                - Demo and use OBO-Edit
                - Evaluating and validating the mapping files
                - Add TO, PO and EO terms and synonyms if necessay
                - Modify species-specific TOs if required
                - Discussion

7:00pm Dinner

June 11
Morning
9:00am Hands-on session
                - Continue from June 10 afternoon
                - Ontology mapping and association annotation
                - Strategies on implementing the ontology mapping and association in participants work
                - Case studies and discussion

12:30pm Lunch

Afternoon
1:30pm Open discussion
                - Ontology development
                - Informatics and database development
                - Future collaboration

6:00pm Dinner

Workshop materials

National Plant Germplasm System Descriptors

Bioversity International Germplasm Documentation Crop Descriptors

OBO Ontology Editor

Workshop Accommondations

Holiday Inn Plainview
215 Sunnyside Blvd.
Plainview, NY 11803, USA
Phone: 1-516-349-7400
Check-in time: 3pm
Check-out time: 12pm
http://www.hiplainviewny.com/

Workshop Participants

Adriana Alercia   All species    IPGRI-bioversity international, Rome, Italy
Elizabeth Arnaud    Banana/Coconut/Cacao    IPGRI-bioversity international, Montpellier, France
Malli Aradhya    Tropical fruits   National Clonal Germplasm Repository, USDA-ARS, USA
Harold E. Bockelman    Wheat/Barley/Oat/Rice    National Small Grains Collection, USDA-ARS, USA
Mark A. Bohning   All crops    National Germplasm Resources Laboratory, USDA-ARS, USA
Richard Bruskiewich   Rice/Maize and Wheat via CIMMYT    Crop Research Informatics Laboratory, International Rice Research Institute, Philippines
Roland Cottin   Citrus   CIRAD, Montpellier, France
Jeffrey Detras   Rice    Crop Research Informatics Laboratory, International Rice Research Institute, Philippines
John Erpelding   Sorghum    Tropical Agriculture Research Station, USDA-ARS, USA
Jean Gerrath   Vitis spp., Vitaceae    University of Northern Iowa, IA, USA
Candice Gardner   North Central Regional Plant Introduction Station, USDA-ARS, USA
Tom Hazekamp   IPGRI-bioversity international, Rome, Italy
Mark J. Millard   Maize/Oilseeds    North Central Regional Plant Introduction Station, USDA-ARS, USA
Lukas Mueller    Solanaceae    SGN, Cornell University, USA
Rex Nelson   Soybean/Legumes    CICGR, USDA-ARS, USA
Shuly Avraham   Gramene, POC, CSHL, USA
Chih-Wei Tung   Gramene, POC, Cornell University, USA
Doreen Ware   Gramene, POC, USDA-ARS, CSHL, USA
Pankaj Jaiswal   Gramene, POC, Cornell University, USA
Lincoln Stein   Gramene, POC, CSHL, USA

Funding Support

The workshop is supported by the RCN grants funded by NSF to the Gramene database (Award# 0234147).
Richard Bruskiewich and Tom Hazekemp are supported by Generation Challenge Programme and other resource for their travel expenses.