PyBEL

PyBEL parses, validates, converts, stores, queries, and visualizes knowledge networks encoded in the Biological Expression Language (BEL) to assemble and analyze biological relations across multiple domains and scales.

Key Features:

• Parsing and Validation: Parses BEL scripts and enforces BEL syntactic and semantic rules to maintain the integrity of encoded biological relations.
• Conversion and Storage: Converts BEL-encoded data into multiple formats and stores networks in structured representations to enable interoperability with other bioinformatics tools and databases.
• Querying: Extracts specific information from large BEL knowledge networks for targeted analysis and hypothesis testing.
• Visualization: Produces graphical representations of complex BEL-encoded relationships to facilitate interpretation of network structure and interactions.

Scientific Applications:

• Pathway Analysis: Visualizes and queries biological pathways represented in BEL to support investigation of cellular processes and mechanisms.
• Network Medicine: Identifies key nodes and interactions within BEL knowledge networks relevant to understanding complex disease mechanisms.
• Data Integration: Integrates heterogeneous biological relations encoded in BEL to enable multi-scale analyses across domains.

Methodology:

Implemented in platform-independent Python.