SoyBase: A Comprehensive Database for Soybean Genetic and Genomic Data

SoyBase, the USDA-ARS soybean genetics and genomics database, provides a comprehensive collection of data, analysis tools and links to external resources of interest to soybean researchers. SoyBase is an actively curated database with new data regularly being incorporated, including additions to the controlled vocabularies (ontologies) for soybean traits, genes, QTL, and genome sequences and annotations. The data in SoyBase are provided through intuitive interfaces, and are linked together wherever possible to allow easy identification and browsing of related subjects. Searching at SoyBase uses a trait-based approach that returns all information that is related to the search term.

The SoyBase home page (http://soybase.org) contains the SoyBase Toolbox, which provides quick access to a search of the SoyBase database or the SoyCyc metabolic pathways database, access to the data download page, a genome sequence BLAST tool, and direct links to the genetic and sequence maps. An extensive navigation menu and site description provides facile access to all sections of SoyBase. Numerous data types are available including genetic maps, the soybean reference genome sequence with annotation tracks covering genetic markers, genome organization, gene annotation and expression, and gene knockout mutants. SoyBase includes an extensive RNA-Seq gene atlas and innovative tools for identifying fast neutron-induced mutants affecting genes or traits of interest. Several “omics” tools, for example a GO Term Enrichment tool, enable sophisticated queries on lists of genes.