databases > DOI:10.25504/FAIRsharing.cr410r

ready Soybean Knowledge Base (SoyKB)

Abbreviation:SoyKB

General Information
Soybean Knowledge Base (SoyKB), is a comprehensive all-inclusive web resource developed for soybean translational genomics and molecular breeding. SoyKB stores information about genes/proteins, miRNAs/sRNAs, metabolites, SNPs, plant introduction (PI lines) and traits. It handles the management and integration of soybean genomics and multi-omics data along with gene function annotations, biological pathway and trait information. It has many useful tools including gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and data download and upload capacity. It has a user-friendly web interface together with genome browser and pathway viewer, which displays data in an intuitive manner to the soybean researchers, breeders and consumers. The QTLs, SNP, GWAS and traits information is seamlessly integrated in our newly developed suite of tools for the In Silico Breeding Program. It allows integration and extraction of the data in a tabular format as well as graphical visualization in our in-house Chromosome Visualizer. It also supports integration and visualization of Genotype by Sequencing (GBS) data for molecular breeding and phenotypic inferences. In addition, SoyKB now has capacity for incorporation of DNA methylation data and fast neutron mutation datasets. It is also linked seamlessly with P3DB for phosphorylation data. We have also incorporated suite of tools for differential expression analysis for microarray, transcriptomics RNA-seq, proteomics and metabolomics datasets. It includes access to gene lists, Venn diagrams, Volcano plots, functional annotations and pathway analysis. SoyKB is now powered by the iPlant Cyber-Infrastructure. The website is hosted on the iPlant’s advanced computing infrastructure established to leverage the data analysis capabilities.




How to cite this record FAIRsharing.org: SoyKB; Soybean Knowledge Base (SoyKB); DOI: https://doi.org/10.25504/FAIRsharing.cr410r; Last edited: Feb. 22, 2018, 2:57 p.m.; Last accessed: Nov 21 2018 3:32 a.m.


This record is maintained by joshitr

Record updated: Feb. 22, 2018, 2:57 p.m. by The FAIRsharing Team.



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

Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D.
BMC Genomics 2012

View Paper (PubMed) View Publication

Soybean Knowledge Base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding

Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D
Nucleic Acids Research 2013

View Publication

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