PAX2GRAPHML

PAX2GRAPHML converts BioPAX source files into regulated reaction graphs in .graphml format to enable large-scale analysis of regulatory, signaling, and metabolic networks.

Key Features:

• BioPAX input support: Generates regulated reaction graphs directly from BioPAX source files.
• Regulated reaction representation: Models substrates, products, activators, and inhibitors as components of regulated reactions.
• Integration across biological levels: Integrates regulatory, signaling, and metabolic levels through the regulated-reaction concept.
• Multi-source combination and filtering: Combines and filters multiple BioPAX sources to produce cohesive large-scale networks.
• GraphML export: Produces graphs in .graphml format for graph exchange and downstream analysis.
• Compatibility with graph libraries: .graphml outputs are compatible with standard Python and R graph libraries for further analysis.

Scientific Applications:

• Regulation network analysis: Construction and analysis of large-scale regulatory interaction networks from BioPAX data.
• Signaling and metabolic network integration: Unified analysis of signaling pathways and metabolic reactions within the same regulated-reaction framework.
• Biochemical interaction modeling: Study of reaction-level mechanisms by representing substrates, products, activators, and inhibitors explicitly.
• Dataset integration for systems biology: Integration of diverse BioPAX datasets into cohesive networks for systems-level studies.

Methodology:

Generates regulated reaction graphs from BioPAX source files, represents substrates, products, activators, and inhibitors within regulated reactions, supports combination and filtering of multiple BioPAX sources, and outputs networks in .graphml format.