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This article is part of the supplement: Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012)

Open Access Proceedings

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

Trupti Joshi1234, Kapil Patil12, Michael R Fitzpatrick12, Levi D Franklin12, Qiuming Yao12, Jeffrey R Cook12, Zheng Wang1, Marc Libault235, Laurent Brechenmacher235, Babu Valliyodan35, Xiaolei Wu35, Jianlin Cheng1234, Gary Stacey235, Henry T Nguyen235 and Dong Xu1234*

Author Affiliations

1 Department of Computer Science, University of Missouri, Columbia, MO 65211, USA

2 Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA

3 National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA

4 Informatics Institute, University of Missouri, Columbia, MO 65211, USA

5 Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA

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BMC Genomics 2012, 13(Suppl 1):S15  doi:10.1186/1471-2164-13-S1-S15

Published: 17 January 2012

Abstract

Background

Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs).

Methods

SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers of registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers.

Conclusions

SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/ webcite.