RCN Plant and Trait Ontology Workshop
June 10-11, 2007
Genome Research Center
CSHL Woodbury CampusWorkshop 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-9:30am
Group introduction
Workshop rationale/goals
9:30am - 10:40am
Presentations
- GRIN, Bioversity-International
- GCP
Questions/Discussion
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
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
Benchmarks for this session:
-know ontologies
-their applications
12:30pm -1:30pm
Lunch
Afternoon
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
Morning
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
Afternoon
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
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
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.