WikiPathways App

WikiPathways App imports WikiPathways pathway data into Cytoscape for visualization and network-level analysis of biological pathways.

Key Features:

• Integration with Cytoscape: Imports WikiPathways pathways into Cytoscape for visualization and computational analysis.
• Annotated pathway view: Displays annotated pathway diagrams that preserve pathway elements and annotations for detailed visual examination.
• Simplified network view: Converts pathway diagrams into simplified network graphs suitable for network-based computational analyses.
• Collaborative WikiPathways database access: Accesses the open, community-curated WikiPathways database where pathways are curated and shared in a wiki-style format.
• SOAP web service integration: Uses the WikiPathways SOAP web service for programmatic retrieval of pathway data.

Scientific Applications:

• Data Visualization: Annotated pathway view enables detailed visualization of biological processes and molecular interactions.
• Network Analysis: Simplified network view enables computational analyses such as identifying key nodes or interactions relevant to disease mechanisms or drug targets.
• Network biology research: Facilitates incorporation of curated pathway content into network biology studies within Cytoscape.

Methodology:

Pathways are retrieved programmatically from the WikiPathways database via its SOAP web service and imported into Cytoscape, where they are rendered as annotated pathway diagrams or converted into simplified network graphs.