Soybean Knowledge Base
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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.
大豆知识库（Soybean Knowledge Base，SoyKB）是专为大豆转化基因组学与分子育种开发的综合性、全覆盖网络资源。该库存储了基因/蛋白质、microRNA（miRNA）/小RNA（sRNA）、代谢物、单核苷酸多态性（SNP）、植物引种系（PI系）以及各类性状相关信息。它可对大豆基因组学与多组学数据进行管理与整合，同时涵盖基因功能注释、生物通路及性状相关信息。平台内置多款实用工具，包括基因家族搜索、多基因/代谢物分析、基序分析工具、蛋白质三维结构查看器，同时支持数据上传与下载功能。其配备用户友好的网页界面，集成基因组浏览器与通路查看器，能够以直观易懂的方式向大豆研究人员、育种者及相关从业者展示数据。定量性状位点（QTL）、单核苷酸多态性、全基因组关联分析（GWAS）及各类性状信息已无缝集成至全新开发的虚拟育种程序工具套件中。该工具支持数据以表格形式进行整合与提取，同时可通过自研的染色体可视化工具实现图形化展示。此外，它还支持测序分型（GBS）数据的整合与可视化，以支撑分子育种与表型推断工作。除此之外，SoyKB现已支持纳入DNA甲基化数据与快中子诱变数据集。它还与磷酸化数据平台P3DB实现了无缝对接。团队还开发了针对微阵列、转录组RNA测序、蛋白质组学与代谢组学数据集的差异表达分析工具套件，可提供基因列表、韦恩图、火山图、功能注释及通路分析等服务。当前，SoyKB依托iPlant网络基础设施（iPlant Cyber-Infrastructure）运行，其网站部署于iPlant搭建的先进计算架构之上，以充分发挥数据分析能力。
