SBGNview

SBGNview enables pathway-based data visualization, integration, and analysis using the Systems Biology Graphical Notation (SBGN) standard.

Key Features:

• SBGN Pathway Definition: Pathways are defined using the widely adopted Systems Biology Graphical Notation (SBGN) standard.
• Multiple Database Support: Supports major pathway databases beyond KEGG, including Reactome, MetaCyc, SMPDB, PANTHER, and METACROP, as well as user-defined pathways.
• Extensive Pathway Coverage: Covers 5,200 reference pathways and over 3,000 species by default.
• Graphics Controls: Provides extensive controls for glyph and edge attributes, graph layout, and sub-pathway highlight.
• Pathway Data Manipulation: Supports SBGN pathway data manipulation, processing, extraction, and analysis.

Scientific Applications:

• Pathway Visualization: Visualizes omics and other data on SBGN-defined pathways from multiple databases.
• Data Integration: Integrates diverse data types onto unified pathway representations for comparative analysis.
• Pathway Analysis: Performs extraction and analysis of sub-pathways and pathway components from SBGN maps.

Methodology:

SBGNview processes data for visualization and analysis on pathways defined in the Systems Biology Graphical Notation format, with support for multiple pathway database formats and user-defined pathway inputs.