BioPAX-pattern

BioPAX-pattern identifies and searches user-defined graph patterns within BioPAX models to detect specific molecular interactions and signaling relations.

Key Features:

• Graph pattern definition and search: Allows definition and systematic searching of graph patterns that capture complex relationships within BioPAX models.
• Directed signaling detection: Detects directed signaling relations between proteins and other molecular entities represented in BioPAX.
• BioPAX and database compatibility: Operates directly on BioPAX-formatted models and can query databases such as Pathway Commons.
• Extensible framework: Provides an extensible architecture for adding new pattern types and search criteria.
• Java-based implementation: Implemented in Java for execution of pattern definition and search algorithms.

Scientific Applications:

• Discovery of undocumented signaling relations: Identifies signaling relations that are not present in signaling databases such as SPIKE and SignaLink.
• Mining Pathway Commons: Enables application of sample patterns to Pathway Commons to uncover previously undocumented interactions and cellular processes.
• Subnetwork analysis: Facilitates detection of subnetworks within metabolic networks, signal transduction, and gene regulation represented in BioPAX.

Methodology:

Define specific graph patterns that represent biological interactions or pathways and use those patterns to query BioPAX models stored in databases like Pathway Commons, returning matched subgraphs corresponding to candidate signaling relations.