Sig2BioPAX

Sig2BioPAX converts structured text and tabular descriptions of molecular interactions into BioPAX Level 3 OWL to enable semantic representation and integration of biochemical networks in systems biology.

Key Features:

• Conversion Capability: Transforms tabular data describing molecular biochemical interactions into BioPAX Level 3 OWL format.
• Input Formats: Accepts structured text and tabular inputs commonly stored as Excel, text, or PDF for conversion.
• Semantic Web Output: Produces RDF/OWL representations that encode objects, object properties, and relationships for machine-readable semantic integration.
• Network Types Supported: Converts protein interactions, signaling pathways, and transcriptional regulatory networks into BioPAX.
• PathwayCommons Integration: Converted networks have been deposited in the PathwayCommons repository for consolidated access.
• Adherence to BioPAX Semantics: Encodes formal descriptors of objects, object properties, and their relationships consistent with systems biology knowledge representation.

Scientific Applications:

• Data Integration: Enables integration of molecular interaction datasets into BioPAX-based repositories for cross-study and cross-platform analyses.
• Interoperability and Sharing: Facilitates sharing and reuse of biochemical network data by providing RDF/OWL-compliant representations.
• Support for Systems Biology Research: Supports experimental and computational systems biologists in contributing and combining pathway and network data for broader analyses.

Methodology:

Takes structured text or tabular input describing molecular interactions and converts the information into BioPAX Level 3 OWL, encoding objects, object properties, and relationships per BioPAX semantics.