New Data and Functionality in NRSP10 Databases

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Presentation transcript:

New Data and Functionality in NRSP10 Databases Sook Jung, Taein Lee, Chun-Huai Cheng, Jodi Humann, Jing Yu, Ping Zheng, Katheryn Bubble, Morgan Frank, Kristin Scott, Deah McGaughey, Heidi Hough, Ksenija Gasic, Todd Campbell, Don Jones, James Crabb, Kate Evans, Lisa DeVetter, Jim McFerson, Cameron Peace, Mike Khan, Meg Staton, Jill Wegrzyn, Stephen Ficklin, Albert Abbott, Dorrie Main

Databases for crop research Outline Databases for crop research GDR, CottonGEN, CSFL, Citrus genome DB, Vaccinium genome DB Demo of new functionality using GDR Resources for database construction MCL (Mainlab Chado Loader) TripalMap BIMS (Breeding Information Management System)

Databases for crop scientists GDR, CottonGEN, CSFL, Citrus genome DB, Vaccinium genome DB Host publicly available genomic, genetic and breeding data for 25 crops

www.rosaceae.org

citrusgenomedb.org

cottongen.org

coolseasonfoodlegume.org

vaccinium.org

Databases for crop scientists New functionalities of GDR Synteny viewer New functionalities in search pages Map viewer BIMS (Breeding Information Management System)

New Synteny Viewer

GDR Search Interfaces

Search and Download

Customizing output in Gene Search

SNP Genotype Search Download only polymorphic results

Map Viewer

Map Viewer (zoom and link to marker page)

Map Viewer Control Pannel: choose maps for comparison Change display settings

Map Viewer (compare maps)

BIMS (Breeding Information Management System) To provide individual breeders with a secure and comprehensive online breeding management system Details will be presented in the next presentation by Ksenija Gasic!

Resources for database construction Tripal Extension modules from NRSP10 to share TripalMap (Map Viewer): to be released soon BIMS (Breeding Information Management System): to be released soon Mainlab Tripal: customized display of data (gene, QTL, marker, etc) Mainlab Chado Search: customized search pages Mainlab Chado Loader: provide data templates and web interface for data loading

MCL User Interface: templates

MCL User Interface: upload data

Future Development Continue to integrate genomic/genetic/breeding data Site-wide search Bio-Mart type search/download tools Further development of BIMS and TripalMap All these are being developed as Tripal Modules

The Team Finally, I’d like to thank the organizations listed here for providing funding to support CottonGen. If you have any questions or suggestions, please don’t hesitate to use the contact form on the website to contact us or catch us in person during the conference Any Questions?

Funding and Acknowledgement

Thank you!