BioPAX-Parser

BioPAX-Parser parses BioPAX-formatted pathway data to extract structured pathway entities and interactions for pathway enrichment analysis and downstream tabulation in systems biology and biomedical research.

Key Features:

• BioPAX parsing: Parses BioPAX-format pathway files to extract pathway entities, interactions, and annotations.
• Pathway Enrichment Analysis (PEA): Performs pathway enrichment analysis using information derived from BioPAX-encoded pathways.
• Data extraction and tabulation: Extracts pathway elements and exports them in tabular formats for downstream computational analyses.

Scientific Applications:

• Systems biology: Provides standardized extraction of BioPAX-encoded pathways to support network modeling and systems-level interpretation.
• Biomedical research: Enables identification of enriched pathways in studies of normal physiology and pathological conditions.
• Bioinformatics integration: Produces structured pathway tables for integration with other datasets and computational pipelines.

Methodology:

Parses BioPAX-format files to extract pathway entities and interactions, conducts pathway enrichment analysis on the extracted information, and exports pathway data into tabular files.