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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: MaizeGDB: enabling access to basic, translational, and applied research information

Authors
item Lawrence, Carolyn
item Andorf, Carson
item Birkett, Scott -
item Braun, Bremen
item Campbell, Darwin
item Cannon, Ethalinda -
item Gardiner, Jack -
item Harper, Elisabeth
item Portwood, John -
item Richter, Jacqueline -
item Schaeffer, Mary
item Sen, Taner
item Wimalanathan, Kokulapalan -

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: August 1, 2012
Publication Date: August 19, 2012
Citation: Lawrence, C.J., Andorf, C.M., Birkett, S., Braun, B.L., Campbell, D.A., Cannon, E., Gardiner, J., Harper, E.C., Portwood, J., Richter, J., Schaeffer, M.L., Sen, T.Z., Wimalanathan, K. 2012. MaizeGDB: enabling access to basic, translational, and applied research information. Meeting Proceedings. P. 233.

Interpretive Summary: MaizeGDB is the online database where information about corn genetics and genomics are housed. Alongside the information we provide tools for analyzing information. This seminar describes the current status of the project as well as both short and long-term plans for its continued development. By providing the information that plant biologists use for improving corn, MaizeGDB represents an invaluable tool that allows researchers access to the data and information they need.

Technical Abstract: MaizeGDB is the Maize Genetics and Genomics Database (available online at http://www.maizegdb.org). The MaizeGDB project is not simply an online database and website but rather an information service to maize researchers that supports customized data access and analysis needs to individual researchers upon request. By adapting workflows requested by individual researchers for unique projects to more mainstream uses, the personnel working at MaizeGDB create custom data access and analysis tools where gaps in technology exist. This has resulted in a presentation of traditional genetics data alongside genomics information within MaizeGDB that presents a holistic view of maize genome architecture and dynamics. Examples of tools developed include the Morgan2McClintock Translator, the Locus Lookup Tool, a B73 Assembly Incongruency Tool, and a GBrowse add-on that reports genetic coordinates alongside base-pair distances from within the MaizeGDB Genome Browser. Another area of strength for MaizeGDB is the development and incorporation large-scale gene expression data views into the website. In collaboration with developers of MapMan (Germany) and the Electronic Fluorescent Pictograph (eFP) browser (Canada) developers at MaizeGDB have deployed services that display expression data served off-site from within the MaizeGDB website. This includes plant-level expression data by tissue type as well as subcellular expression and biochemical pathway assignments for the Sekhon et al. 2011 Genome-wide Expression Atlas. For the same dataset, a histogram view of expression across 60 tissues and developmental stages that is accessible from within the GBrowse-based MaizeGDB Genome Browser was created in-house and was subsequently adapted for other expression datasets. MaizeGDB seeks to meet the information analysis and access needs of maize researchers worldwide and will only remain relevant by continuing to solve data analysis and access problems that are not addressed elsewhere. To prepare for both current and future needs of the maize research community, the MaizeGDB website is currently being redesigned with estimated release of the new site scheduled for March of 2013. The redesign is both cosmetic and functional. The overall goal is to create a clean modern interface with improved user interaction while expanding the overall functionality of MaizeGDB. Cosmetically, the appearance has been modernized and page organization and navigation have been simplified. A key component to the redesign is community involvement. To ensure that the new interface is useful, guidance and beta testing groups will be created and consulted. To get immediate feedback, an alpha version has been made accessible online at http://alpha.maizegdb.org. Redesign efforts currently are focused on functionality. Areas of emphasis include developing ways to view and compare multiple maize genomes, enabling access to billions of SNPs, and deploying novel search and browse methods for phenotypes, gel images, QTLs, and other data types. In the next five years focus areas for project development include coordinating the B73 reference genome sequence’s assembly and annotation projects, offering access to genome sequences for diverse maize lines, enhancing access to expanded datasets that reveal gene function and datasets for genetic and breeding analyses, and deploying tools to increase user-specified flexible queries. We welcome your input and look forward to continuing to collaborate.

Last Modified: 10/24/2014