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
                Group introduction
                Workshop rationale/goals
9:30am - 10:40am
                    - GRIN, Bioversity-International 
                    - GCP

10:45am - 11:00am
                 Coffee Break

11:00am -12:00pm
                Introduction to ontologies
                      - TO, PO, EO ontology
                      - PATO
                      - Ontology-to-ontology mappings
                      - Associations/annotation

12:00pm to 12:30pm
                      - 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

Benchmarks for this session:
            -know ontologies
            -their applications

12:30pm -1:30pm

1:30pm - 3:15pm
                 Hands-on session
                    - Demo and use OBO-Edit/DAG-Edit
                    - Work on species-specific ontology on DAG-edit
                    - Discussion

3:15pm -3:30pm
                Coffee Break

3:30pm - 6:00pm
                Hands-on session
                    - Demo and use COBrA ontology mapping tool
                    - Generate species-specific and TO ontology mappings
                    - Discussion
 If time permits
                    - Evaluating and validating the mapping files
                    - Missed mappings to be added to the TO, PO and EO terms and synonyms
                    - Modify species-specific TOs if required
                    - Discussion

Benchmarks for this session
        -learned ontology design, relationships, formal definitions
        -learned OBO-Edit/DAG-Edit functionality
        -learned ontology mappings

7:00pm -
                Dinner in Holiday Inn Plainview

June 11

9:00am -10:45am
                Hands-on session
                - Use COBrA to generate species-specific and PO ontology mappings

10:45am -11:00am
                Coffee Break

11:00am - 12:30am
                Case studies and discussion

12:30pm Lunch

1:30pm - 3:15pm
               Open discussion driven by participants
                - Strategies on implementing the ontology mapping and association in participants work
                - Ontology development
                - Informatics and database development
                - Future collaboration and commitment

3:15pm - 3:30pm
                Coffee Break

3:30pm - 5:00pm
                - Any outstanding issue
                - Work on written document from following groups on the outcomes of the workshop. With the emphasis on previous session
                   - GCP/CGIAR/Bioversity International
                   - USDA-GRIN and other colleagues from USA
                - Survey

6:00pm    Dinner in Holiday Inn Plainview

Workshop materials

National Plant Germplasm System Descriptors

Bioversity International Germplasm Documentation Crop Descriptors

The International Crop Information System (ICIS)

The International Rice Information System (IRIS)

Generation Challenge Programme

OBO Ontology Editor and DAG-Edit

COBrA- An Ontology Browser for Anatomy

OBO Foundry Ontologies

GRIN_USDA Descriptor obo file

GRIN_GCP Descriptor obo file

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

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
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
Quinn P Sinnott   National Germplasm Resource, 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.