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. 2008;2008:496957.
doi: 10.1155/2008/496957.

MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

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Free PMC article

MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

Carolyn J Lawrence et al. Int J Plant Genomics. .
Free PMC article

Abstract

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities.

Figures

Figure 1
Figure 1
The MaizeGDB home page. The most commonly utilized search functionality for MaizeGDB is the search bar (A), which is available within the header of any MaizeGDB page. To browse data and to search specific data types using specific limiters, the Data Centers (B) are also quite useful. Also available is a Bin Viewer (C), which allows for a view of lots of data types within the context of their chromosomal location. To enable access to the Data Centers and other displays of interest from any MaizeGDB page, a pull-down menu for “Useful pages” (D) is accessible on the header of any MaizeGDB page. The footer of all MaizeGDB pages contains a context-sensitive “feedback form” link (E). Researchers use the feedback form to report errors, ask questions, and to contact the MaizeGDB team directly. For newcomers to the site, the MaizeGDB Tutorial (F) can help them to get a jump start on how to use the site.
Figure 2
Figure 2
Simplified infrastructure of MaizeGDB. The community of maize researchers can add data to the database (downward-facing arrows from the uppermost yellow box) via direct data deposition (upper left) and via a set of Community Curation Tools that interacts with the Curation Database (upper center). Researchers are also allowed access to maize data (upward-facing arrows from the lower dashed box) via a web interface that can be accessed at http://www.maizegdb.org/ (upper right) and by way of SQL access to the Curation Database, which houses the most up-to-date data available (upper center). These functionalities are supported by two of the three environments: Production and Staging, respectively (upper dashed gold boxes). Available for use by MaizeGDB personnel to facilitate data modeling and trial programming manipulations is a third environment called Test (lower left dashed gold box), which is identical to the Staging Environment. To ensure that the most up-to-date copy of the database is backed up, a Disaster Recovery process has been instituted (lower center dashed gold box) whereby a compressed copy of the database is backed up to a separate machine in Ames, Iowa daily, and to a server in Columbia, Missouri weekly.
Figure 3
Figure 3
Three types of biological research. Research can be divided into three categories: basic, translational, and applied. Outcomes from basic research feed into translational predictions, and developed uses for these findings constitute the basis for developing real-world applications that benefit humanity and the world. Listed after the flow of research are definitions for each research type as well as medical and plant biological models for how the different divisions are interrelated. Also shown are overviews of the example usage cases presented in Section 3.

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