MaizeGDB update: new tools, data and interface for the maize model organism database

Abstract

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, the original maize genetics database MaizeDB was created. In 2003, the combined contents of MaizeDB and the sequence data from ZmDB were made accessible as a single resource named MaizeGDB. Over the next decade, MaizeGDB became more sequence driven while still maintaining traditional maize genetics datasets. This enabled the project to meet the continued growing and evolving needs of the maize research community, yet the interface and underlying infrastructure remained unchanged. In 2015, the MaizeGDB team completed a multi-year effort to update the MaizeGDB resource by reorganizing existing data, upgrading hardware and infrastructure, creating new tools, incorporating new data types (including diversity data, expression data, gene models, and metabolic pathways), and developing and deploying a modern interface. In addition to coordinating a data resource, the MaizeGDB team coordinates activities and provides technical support to the maize research community. MaizeGDB is accessible online at http://www.maizegdb.org.

Figure 1.

The MaizeGDB web interface before and after the interface redesign. Panel (A) shows the MaizeGDB look-and-feel from 2003 to 2014. The old interface is currently archived and accessible for a short-time via the MaizeGDB website. Panel (B) shows the current web interface (released in March 2015). Webpages, tools, and data centers are organized in a menu within the header of each page (panel C).

Figure 2.

The MaizeGDB gene center and gene / gene model record page. Panel (A) shows the simple search form for querying genes and gene models. Note examples of the various terms and identifiers to search from the liguleless1 gene. Panel (B) shows the overview section of the gene mode tab for the liguleless1 gene and associated GRMZM2G036297 gene model record page. This gene model tab provides information related to the predicted mRNA. This figure shows a few examples of available data including a snapshot of the genome browser and various types of annotations. The ‘Sequence’ tab (unselected) provides FASTA sequence. The ‘Genetic Information’ tab (unselected) shows information about the associated gene liguleless1.