Soybean knowledge base (SoyKB): A web resource for soybean translational genomics

Trupti Joshi, Kapil Patil, Michael R. Fitzpatrick, Levi D. Franklin, Qiuming Yao, Jeffrey R. Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T. Nguyen, Dong Xu

Research output: Contribution to journalConference articlepeer-review

45 Scopus citations

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/.

Original languageEnglish (US)
Article numberS15
JournalSeries on Advances in Bioinformatics and Computational Biology
Volume13
DOIs
StatePublished - 2012
Event10th Asia Pacific Bioinformatics Conference, APBC 2012 - Melbourne, Australia
Duration: Jan 17 2012Jan 19 2012

ASJC Scopus subject areas

  • Bioengineering
  • Information Systems
  • Biotechnology
  • Genetics

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