Knowledgebase · FAIRsharing

Soybean Knowledge Base (SoyKB)

Bioassays and chemical biology

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.

What is known per question

The questions of the decision tree, with what FAIRsharing says about this repository. ✓ supported, ✗ excluded, ? not known.

What kind of data do you want to archive?

Subjects: Bioinformatics; Computational Biology; Life Science; Metabolomics; Proteomics; Transcriptomics

Domains: ChIP-seq assay; DNA methylation; RNA-seq assay; SNP; genome; genome-wide association study; germ plasm; miRNA; phenotype

Does the journal or publisher you publish with require or recommend a repository?

FAIRsharing has no information on this.

Which discipline does your data belong to?

FAIRsharing has no information on this.

Which publisher?

FAIRsharing has no information on this.

Does your funder have requirements for where data is archived?

FAIRsharing has no information on this.

Which funder?

FAIRsharing has no information on this.

Does your institution offer a data repository?

FAIRsharing has no information on this.

Which institution?

FAIRsharing has no information on this.

Can your data be shared openly?

Data access: open

Data deposition: open

How large is your dataset?

FAIRsharing has no information on this.

Why can the data not be open?

FAIRsharing has no information on this.

Under which license do you want to share the data?

FAIRsharing has no information on this.

Do you need a persistent identifier, such as a DOI, for citing the data?

FAIRsharing has no information on this.

Must the data be stored in a specific region?

Country: United States

Must archiving be free of charge?

FAIRsharing has no information on this.

Which country?

✓ 1 of 15 in the list ✗ excludes 14

Country: United States