RCN Workshop: Development and Implemention of Ontologies in the Database

Venue	Plant and Animal Genome XIII Conference
Place	Royal Palm Salon 1, 2 & 3, Town & Country Convention Center, San Diego, California
Time	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 Gene Ontology (GO) (www.geneontology.org) is a controlled vocabulary used to describe the molecular function of a gene product, its role in biological processes and localization in a cellular component. The use of GO is not limited to any single taxonomic kingdom.
The Plant Ontology (PO) (www.plantontology.org) is a controlled vocabulary used to describe patterns of gene(s) and phenotypes expressed in the plant structure(s) (anatomy) and at various growth stages. As of now their use is limited to the information on flowering plant species.

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.

Agenda:

12.50 pm Introduction
Overview talks:

1.00 pm-- Jennifer Clark, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SD, UK
Does Your Gene Product Show On GO? (ABSTRACT)
1.15 pm-- Katica Ilic Carnegie Institution of Washington, Department of Plant Biology, 260 Panama St, Stanford, CA, 94305, USA
Controlled Vocabularies For Describing And Comparing Phenotypes And Gene Expression In Angiosperms (ABSTRACT)

Hands on training modules:

1.35 pm-- Harold Drabkin Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609
Functional Genome Annotations Using the GO (ABSTRACT)
2.10 pm-- Leonore Reiser Carnegie Institution Department of Plant Biology, 260 Panama St, Stanford, CA, 94305,USA
Using The Plant Ontologies: Searching/Browsing Terms And Annotations And Methods For Annotation Of Gene Expression And Phenotypes (ABSTRACT)

2.45 pm-- Open Discussion and followup with the invited participants.

Exercises and Tutorials

Gramene's ontology tutorial (Download in PDF format | MS-Powerpoint format)
Gramene's ontology exercise (Download in PDF format | MS-Word format)
Gene Ontology AmiGO Browser Users Guide
Gene Ontology Annotation Guide
Plant Ontology AmiGO Browser Users Guide
Plant Ontology Tutorials
MaizeGDB curation manual (Download in PDF format)

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	Participant	Interest	E mail
Clare Nelson	Suzhi Wang	Germplasm Challenge Program	swa5777@ksu.edu
Robin Buell	Willem Rensink	na	rbuell@tigr.org
Michael Scanlon	Diane Janick-Buckner	NSF Award #0321595 Functional analyses of genes involved in meristem organization and leaf initiation	mjscanlo@plantbio.uga.edu
Steve Gantt	Sergey Ivashuta	Cool season legume root nodules and roots description	gantt001@tc.umn.edu
Doug Cook	Seth Debolt	Grape and legume genomes	drcook@ucdavis.edu
Peggy Lemaux	Jaswinder Singh	Transposon-mediated functional genomics in barley	lemauxpg@nature.berkeley.edu
Tim Nelson	Neeru Gandotra	Virtual center for analysis of rice cellular expression	timothy.nelson@yale.edu
Karen Moldenhauer	Virginia Boyett	CAPS project at University of Arkansas	kmolden@uark.edu
Vicki Chandler	Li Zheng	Maize oligo expression	chandler@Ag.arizona.edu
Anna McClung	Self	Whole genome oligo arrays	AMCCLUNG@ag.tamu.edu
Jim Oard	Self	QTL and molecular breeding in rice	joard@agctr.lsu.edu
John Quackenbush	Self	TIGR gene expression database	johnq@tigr.org
Lucas Mueller	Self	Solanceae genome project	lam87@cornell.edu
Nevin Young	Self	Sequecning gene space of Medicago. Medicago genome sequencing project.	neviny@tc.umn.edu
Lee Pratt	Chun Liang	Sorghum ESTs	leepratt@uga.edu
Volker Brendel	Carolyn Lawrence	Maizegdb	triffid@iastate.edu
Guo Liang Wang	Mohan Raghupathy	Disease and LongSAGE in rice and maize	mohanbabu_r@yahoo.com
William Thompson	Dorrie Main	Rosacae database	wftb@ncsu.edu
Georgia Eizenga	Self	Rice breeding (USDA-Dale Bumpers, Stutgart)	geizenga@spa.ars.usda.gov
Niel Rutger	Self	Rice breeding (USDA-Dale Bumpers, Stutgart)	jnrutger@spa.ars.usda.gov
Scot Hulbert	Self	Rice CAPS project with Anna McClung and Clare Nelson	shulbrt@plantpath.ksu.edu
Peggy Ozias	Self	Apoximis in cereals and expressed genes in gynoecium	ozias@tifton.uga.edu
Gary Stacey	Self	Functional genomics of Soybean root hair infection	staceyg@missouri.edu

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.