grain_icon  Agenda  | Exercises and tutorials  | Survey  | Participants  | Funding 
grain_icon  Ontologies @ Gramene  | Gene Ontology (GO)  | Plant Ontology (PO)  | Open Biological Ontologies (OBO) 

RCN Workshop: Development and Implemention of Ontologies in the Database

Plant and Animal Genome XIII Conference
Royal Palm Salon 1, 2 & 3, 
Town & Country Convention Center, San Diego, California
Monday, 17 January 2005
12:50 pm - 3:00 pm
Who can attend
You are most welcome to attend it. The workshop is free and open for everyobody.

This training workshop will emphasize the use of controlled vocabularies (ontologies) to help build queries on data sets currently available in any model organism database. These include molecular functions of gene products, biological processes and cellular locations in which gene products may act, expression patterns of gene(s), and phenotype(s). The presentations at the workshop will include an overview of how ontologies can be used to represent biological concepts. They will also show how genes, gene products and phenotypes can be categorized using the ontologies and what curation standards and protocols are used. The community-developed ontologies, namely the gene and plant ontologies will be the focus of the discussion.

The goal of the workshop is to demonstrate how the GO and PO can be useful for bench scientists and to enable database groups and bench scientists to contribute annotations from species not currently represented.


Exercises and Tutorials

Workshop Survey

Everyone atending the workshop or the website visitors that have browsed the tutorials and exercises are encouraged to send us the feedback using the survey form.
Download survey form (PDF format | MS-Word format)

List of Participants

The workshop is open for anyone participating at the Plant and Animal Genome confrerence (PAG-XIII) and has an interest in the ontologies. However, the following list of participants have confirmed their participation. Some of the participants are funded by the NSF funded RCN grant to Gramene.

Project PIs
E mail
Clare Nelson Suzhi Wang Germplasm Challenge Program
Robin Buell Willem Rensink na
Michael Scanlon Diane Janick-Buckner NSF Award #0321595
Functional analyses of genes involved in meristem organization and leaf initiation
Steve Gantt Sergey Ivashuta Cool season legume root nodules and roots description
Doug Cook Seth Debolt Grape and legume genomes
Peggy Lemaux Jaswinder Singh Transposon-mediated functional genomics in barley
Tim Nelson Neeru Gandotra Virtual center for analysis of rice cellular expression
Karen Moldenhauer Virginia Boyett CAPS project at University of Arkansas
Vicki Chandler Li Zheng Maize oligo expression
Anna McClung Self Whole genome oligo arrays
Jim Oard Self
QTL and molecular breeding in rice
John Quackenbush Self
TIGR gene expression database
Lucas Mueller Self
Solanceae genome project
Nevin Young Self
Sequecning gene space of Medicago. Medicago genome sequencing project.
Lee Pratt Chun Liang Sorghum ESTs
Volker Brendel Carolyn Lawrence Maizegdb
Guo Liang Wang Mohan Raghupathy Disease and LongSAGE in rice and maize
William Thompson Dorrie Main Rosacae database
Georgia Eizenga Self
Rice breeding (USDA-Dale Bumpers, Stutgart)
Niel Rutger Self
Rice breeding (USDA-Dale Bumpers, Stutgart)
Scot Hulbert Self
Rice CAPS project with Anna McClung and Clare Nelson
Peggy Ozias Self
Apoximis in cereals and expressed genes in gynoecium
Gary Stacey Self
Functional genomics of Soybean root hair infection

Funding support

The workshop is supported by the RCN grants funded by NSF to the Gramene database (Award# 0234147 )and the Deep Gene (Award# 0090227 ) projects.