RDFScape

RDFscape integrates Semantic Web reasoning into Cytoscape to query, visualize, and infer knowledge from OWL- and RDF-encoded biological ontologies for analysis of molecular biology and pathway data, including high-throughput datasets.

Key Features:

• Ontology Integration: Queries, visualizes, and reasons over ontologies encoded in OWL (Web Ontology Language) and RDF (Resource Description Framework) within Cytoscape.
• Inference Capabilities: Performs reasoning on ontological data to derive new information and support inference-based analyses.
• Visualization of Biological Pathways: Abstracts and visualizes biological pathways as interaction networks for representation of complex processes.
• Causal Dependency Reasoning: Implements reasoning on causal dependencies among pathway elements to analyze component interactions and influences.

Scientific Applications:

• High-throughput data interpretation: Leverages ontological knowledge to improve interpretation of large-scale molecular biology datasets.
• Ontology-based inference and discovery: Uses reasoning over OWL/RDF ontologies to derive new hypotheses and information from existing knowledge bases.
• Pathway interaction analysis: Represents pathways as interaction networks to analyze and explore complex biological processes.
• Causal analysis of pathway components: Applies causal dependency reasoning to investigate how pathway elements influence each other.

Methodology:

Queries and visualizes ontologies encoded in OWL and RDF; applies Semantic Web technologies to enable distributed reasoning across ontologies; performs inference on ontological data and on causal dependencies and abstracts pathways into interaction networks.