KBCommons

KBCommons integrates multi-level omics data to store, analyze, and visualize genomics and integrative omics datasets across diverse organisms to support biological discovery.

Key Features:

• Modular Architecture: Modular architecture comprising Data Storage Module, Data Processing Module, and Data Accessing Module to manage, integrate, and retrieve multi-level omics datasets.
• Comprehensive Framework: Supports creation of species-specific knowledge bases (plant, animal, virus, bacteria, human disease), addition of new genome versions, incorporation of multi-omics datasets, and exploration of existing datasets.
• Data Visualization and Analytics Tools: Provides multiple gene and metabolite searches, function annotation searches (gene family/Pfam/Panther), miRNA/metabolite/trait/SNP searches, differential gene expression analysis, and bulk data download.
• Data Privilege Management System: Implements privilege management for secure sharing of private or pre-publication data within collaborative groups and controls for making data public.
• In-House Workflow Functionalities: Integrates with XSEDE high-performance computing resources to support in-house workflows and tailored analyses.

Scientific Applications:

• Genomics and Integrative Omics: Supports retrieval, integration, and analysis of genomics and multi-omics datasets for biological discovery across species.
• Plant Biology: Enables creation and analysis of plant-specific knowledge bases and multi-omics datasets.
• Animal Science: Enables creation and analysis of animal-specific knowledge bases and multi-omics datasets.
• Virology: Supports virus-focused knowledge bases and analyses of viral omics data.
• Bacteriology: Supports bacteria-focused knowledge bases and analyses of bacterial omics data.
• Human Disease Research: Supports human disease-focused knowledge bases and integration of genomic and multi-omics data for disease studies.

Methodology:

Computational methods explicitly include data storage, integration, analysis, and visualization via modular Data Storage/Processing/Accessing modules; function annotation using gene family/Pfam/Panther searches; multiple gene/metabolite and miRNA/metabolite/trait/SNP searches; differential gene expression analysis; bulk data export; data privilege management; and integration with XSEDE high-performance computing resources.