1. Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries
- Author
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Shuai Zeng, Dong Xu, Siva Ratna Kumari Narisetti, Zhen Lyu, and Trupti Joshi
- Subjects
Knowledge Base ,lcsh:QH426-470 ,lcsh:Biotechnology ,Knowledge Bases ,Data management ,Information Storage and Retrieval ,Visualization and analysis ,Biology ,computer.software_genre ,Workflow ,03 medical and health sciences ,Data visualization ,Data retrieval ,lcsh:TP248.13-248.65 ,Databases, Genetic ,Genetics ,Animals ,Humans ,030304 developmental biology ,Multi-omics data ,Internet ,0303 health sciences ,Genome ,business.industry ,Research ,030302 biochemistry & molecular biology ,Computational Biology ,Organism-specific database ,Genomics ,Data science ,lcsh:Genetics ,Knowledge base ,Data analysis ,Database Management Systems ,Web resource ,business ,computer ,Biotechnology ,Data integration - Abstract
Background Knowledge Base Commons (KBCommons) v1.1 is a universal and all-inclusive web-based framework providing generic functionalities for storing, sharing, analyzing, exploring, integrating and visualizing multiple organisms’ genomics and integrative omics data. KBCommons is designed and developed to integrate diverse multi-level omics data and to support biological discoveries for all species via a common platform. Methods KBCommons has four modules including data storage, data processing, data accessing, and web interface for data management and retrieval. It provides a comprehensive framework for new plant-specific, animal-specific, virus-specific, bacteria-specific or human disease-specific knowledge base (KB) creation, for adding new genome versions and additional multi-omics data to existing KBs, and for exploring existing datasets within current KBs. Results KBCommons has an array of tools for data visualization and data analytics such as multiple gene/metabolite search, gene family/Pfam/Panther function annotation search, miRNA/metabolite/trait/SNP search, differential gene expression analysis, and bulk data download capacity. It contains a highly reliable data privilege management system to make users’ data publicly available easily and to share private or pre-publication data with members in their collaborative groups safely and securely. It allows users to conduct data analysis using our in-house developed workflow functionalities that are linked to XSEDE high performance computing resources. Using KBCommons’ intuitive web interface, users can easily retrieve genomic data, multi-omics data and analysis results from workflow according to their requirements and interests. Conclusions KBCommons addresses the needs of many diverse research communities to have a comprehensive multi-level OMICS web resource for data retrieval, sharing, analysis and visualization. KBCommons can be publicly accessed through a dedicated link for all organisms at http://kbcommons.org/.
- Published
- 2019