A Comparative Mapping Resource for Grains

Gramene Outreach Summary 2005

Claire HebbardPresented to the Gramene SAB

January 13, 2006

Outreach

• Gramene’s outreach programbridges the interface between program staff and a diverse audience that includes researchers, agriculturalists, and students of all ages.

• Gramene aims to improve research through the dissemination of information. This dissemination of information is the definition of outreach.

Outreach Components

1. Database development and maintenance.

2. Database promotion, education and support.

3. Community Collaboration.

4. Education.

1. Database development and maintenance.

Provide Resources = Education = Outreach

Add data

Simplify web design and graphical displays

Tailor the website to meet users’ needs

Develop tools / GrameneMart

2. Database promotion, education and support.

Promotion is essential for letting users know about the availability of data (information) and updates to that data.

• Announcements list-serve– Reviewed and expanded in 2005

• Brochures• Articles and press releases • Participation on other projects • Posters and abstracts (12) (also serve as

education)

2. Database promotion, education and support

Plant and Animal Genome XIII, January 2005, CA, USA

Computer Demo •Ontology Workshop

Poster & Demo •Gramene: A Comparative Mapping Resource For The Grasses

Workshop •Intl. Grass Genome Initiative - Genomes And Phenomes, What Do Rice, Maize, Millet And Wheat Have In Common?

Poster & Abstract. •An Update On Gramene QTL Data Module Poster & Abstract

•Gramene Comparative Genome Views: How Can Gramene Leverage Rice For The Other Grasses?

•Gramene Diversity Module: Sharing The Data Behind Germplasm, QTL, And Breeding Studies

•Gramene: A Comparative Mapping Resource For The Grasses

•GDPC: The Genomic Diversity And Phenotype Connection: Open-Source Platform For Accessing Public Data Via XML Web Services

2. Database promotion, education and support

47th Annual Maize Genetics Conference, March 13-15, 2005,

Poster •Gramene Diversity Module: Sharing the Data Behind Germplasm, QTL, and Breeding Studies•An Update on Gramene QTL Data Module•The Gramene Database

Plant Biology, 2005, July 16-20.

Poster •Comparative Genome Analysis in Gramene

Cereal Genomic Workshop, September 2005

Workshop

Poster

•Gramene Overview and Database Exercises, •The Gramene Database

2. Database promotion, education and support

American Society of Plant Biology Plant Genetics; October 2005,

Poster The Gramene Database: A Comparative Genomics Resource for Grasses.

Graduate Plant Breeding Lab, Oct 18, 2005

Workshop Computer Demo and Lab exercises

1st International Biocurator Meeting,, December 8-11, 2005,

Access resources on cereal genetics,

including Gramene’s Species pages.

Use the “Feedback”

button for questions or

suggestions. We would like to hear

from you.

Access help documents, FAQ’s tutorials, glossary

and mail archives.About Gramene and its personnel

Search database

Web site www.gramene.org

For more detail on Gramene datasets see brochure back

cover.

Search all or a single Gramene database from the top of any

page.Gramene software and data

installation information.

Browse Rice, Maize or Arabidopsis genomes

Click logo to return to Home Page

Brochure

2. Database promotion, education and support.

Education - The outreach program assists individuals in using the Gramene database

• 6 workshops and computer demonstrations • 12 Tutorials• 2 new exercises

Tutorials

Tutorials

• Develop 6 new tutorials• Update 6 other tutorials

• Versions to allow for different browser preferences,

Tutorials

• Notes pages with detailed explanations of the material.

Exercises

• Questions and answers that are explained

Support - User assistance

Email gramene@gramene.org

Feedback buttons On every web page

Listserves •Archived Online

•Gramene listserve•Announce listserve

2. Database promotion, education and support

2. Database promotion, education and support

Help Files

Documentation

FAQsGlossary

2. Database promotion, education and support

3. Community Collaboration

Diverse Gramene TeamSAB Project Participation

OMAP Plant ontology project VPIN projectGramene Diversity Database Integration Project Maize genomic sequencing (pending)

Networking at Conferences Work with Contributors

PersonnelPI Team Lincoln Stein, Ph.D PI, Database design and software

development

Susan R. McCouch , Ph.D. Co-PI, rice data curation

Doreen Ware, Ph.D. Co-PI, Comparative genome analysis

Pankaj Jaiswal, Ph.D Co-PI; Proteins, Ontologies, QTL

Ed Buckler, Ph.D Co-PI, Diversity, Maize

Biological Curation Junjian Ni, Ph.D. Genes, QTL

Immanuel Yap, Ph.D. Maps, Markers, QTL

Isaak Yosief Tecle, Ph.D. Germplasm, Genetic Diversity

Dean Ravenscroft, Ph.D. Pathways

Bioinformatics Developers

Steven Schmidt Gramene Genome Database & Browser

Ken Youens-Clark Comparative Maps, QTL, Markers, Diversity

Shulamit Avraham (Shuly)

Database Management

Liya Ren Proteins, Literature, Ontologies, Genes

William Spooner, Ph.D. Genome Browser, Gramene Blast & Mart

Payan Canaran Protein Annotation Pipeline

Sharon Wei Gramene Pipeline and Genome Browser

Terry Casstevens Diversity

Coordinators Chengzhi Liang, Ph.D Project Management, Gene Build

Claire Hebbard Outreach Coordinator

Other Collaborators

• Ben Faga – CMap• Bonnie Hurwitz – OMap

• Scientific Advisory Board– Anna M McClung– Georgia Davis– James H. Oard– David Marshall– Patricia Klein

ContributorsControlled Vocabulary• TAIR• IRRI• MaizeGDB• Gene Ontology Consortium • ICIS• INGER• CIMMYT • Oryzabase• Scottish Crop Research Institute • Plant Ontology Consortium  • Monsanto• Pioneer

Maps• Cari Soderland, University of Arizona• Rod Wing, University of Arizona• John Mullet, Texas A & M• Patricia Klein, Texas A & M• Robert Klein, USDA-ARS • Andrew Paterson, Univ of GA• Dave Matthews, USDA-ARS• Mary Polacco, USDA-ARS• Maize GDB

Sequences and Proteins• National Center for Gene

Research Chinese Academy of Sciences

• NCBI• TIGR• Uniprot/SPTremble• LGB• BGI• Interpro• MaizeGDB• BarleyBase• Orion Genomics• NASC for the arabidopsis

genome view in Ensembl. • Cari Soderland SAGE• GuoLiang Wang SAGE• Blake Meyers MPSS

QTL• MaizeGDB• GrainGenes

Genes

• Oryzabase

• MaizeGDB

Reference Databases•Albert Mann Library, Cornell University•TEEAL

Software Development•Ensembl•Gene Ontology Consortium•GMOD•Pioneer

Germplasm•NPGS/GRIN

4. EducationHigh Schools

Science Career Development 8th graders– web resources for science careers under development

Dolan Learning Center • Creating Internet Site using rice gene annotation to help students

learn concepts of structure and function, and participate in research. This will be pilot tested in February.

– History of gene concept– Methods of identifying genes– Building gene models– Tutorials and tools for gene annotation

4. EducationGeneral Education

• Species Pages• Glossary – Updated• Resources page –

updated

Outreach

Contact with me feedback on Gramene’s tutorials, workshops, and other outreach.

• cer17@cornell.edu

• 607-255-4199