MaizeGDB's new data types, resources and activities

MaizeGDB is the Maize Genetics and Genomics Database. Available at MaizeGDB are diverse data that support maize research including maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers worldwide. Also available through MaizeGDB are various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize Genetics Conference and the Jobs board where employment opportunities are posted. Reported here are data updates, improvements to interfaces and changes to standard operating procedures that have been made during the past 2 years. MaizeGDB is freely available and can be accessed online at

Choosing a genome browser for a Model Organism Database: surveying the Maize community

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly

The Maize Genetics and Genomics Database. The Community Resource for Access to Diverse Maize Data

The Maize Genetics and Genomics Database (MaizeGDB) serves the maize (Zea mays) research community by making a wealth of genetics and genomics data available through an intuitive Web-based interface. The goals of the MaizeGDB project are 3-fold: to provide a central repository for public maize information; to present the data through the MaizeGDB Web site in a way that recapitulates biological relationships; and to provide an array of computational tools that address biological questions in an easy-to-use manner at the site. In addition to these primary tasks, MaizeGDB team members also serve the community of maize geneticists by lending technical support for community activities, including the annual Maize Genetics Conference and various workshops, teaching researchers to use both the MaizeGDB Web site and Community Curation Tools, and engaging in collaboration with individual research groups to make their unique data types available through MaizeGDB

Predicting Chromosomal Locations of Genetically Mapped Loci in Maize Using the Morgan2McClintock Translator

The Morgan2McClintock Translator permits prediction of meiotic pachytene chromosome map positions from recombination-based linkage data using recombination nodule frequency distributions. Its outputs permit estimation of DNA content between mapped loci and help to create an integrated overview of the maize nuclear genome structure

MaizeGDB, the community database for maize genetics and genomics

The Maize Genetics and Genomics Database (MaizeGDB) is a central repository for maize sequence, stock, phenotype, genotypic and karyotypic variation, and chromosomal mapping data. In addition, MaizeGDB provides contact information for over 2400 maize cooperative researchers, facilitating interactions between members of the rapidly expanding maize community. MaizeGDB represents the synthesis of all data available previously from ZmDB and from MaizeDB—databases that have been superseded by MaizeGDB. MaizeGDB provides web-based tools for ordering maize stocks from several organizations including the Maize Genetics Cooperation Stock Center and the North Central Regional Plant Introduction Station (NCRPIS). Sequence searches yield records displayed with embedded links to facilitate ordering cloned sequences from various groups including the Maize Gene Discovery Project and the Clemson University Genomics Institute. An intuitive web interface is implemented to facilitate navigation between related data, and analytical tools are embedded within data displays. Web-based curation tools for both designated experts and general researchers are currently under development. MaizeGDB can be accessed at http://www.maizegdb.org/

Important information, data centers, tools and news items are accessible from the MaizeGDB home page

<p><b>Copyright information:</b></p><p>Taken from "MaizeGDB's new data types, resources and activities"</p><p>Nucleic Acids Research 2007;35(Database issue):D895-D900.</p><p>Published online Jan 2007</p><p>PMCID:PMC1899092.</p><p>© 2006 The Author(s)</p> Data and bulletin boards as well as links to noteworthy or high profile projects are accessible directly on the front page. All MaizeGDB pages have the same header, which is loaded with functionality enabling, e.g. searches of all data from any page () and access to tools including the Community Curation Tools. The ‘Maps’ Data Center () can limit results by contained loci, chromosome, source or mapping panel and also allows direct access to unique map types including the Recombination Nodule maps through its ‘Map Reports and Tools’ section. Likewise, the ‘Stocks’ Data Center () enables queries by focus linkage group, genotypic variation, karyotypic variation and other limitors. Bulletin boards that keep researchers connected with the community include the Editorial Board (), the Maize Genetics Executive Committee pages (), and the Annual Maize Genetics Conference, (which is referred to simply as ‘The Maize Meeting’) site (). Dates of database updates are available directly on the front page (), as are important major efforts of interest to all maize researchers like the Maize Genome Sequencing project

The Gene Ontology project in 2008

The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of \u2018reference\u2019 genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface