BioGateway

BioGateway provides access to the BioGateway RDF triple store, integrating protein functional and interaction data from multiple curated databases and text mining for SPARQL-based queries and Cytoscape (version 3) network analysis of protein interactions and regulatory relationships.

Key Features:

• BioGateway RDF triple store: Centralized RDF triple store that aggregates protein-related functional and interaction information.
• SPARQL Query Access: Enables complex SPARQL queries over integrated RDF data to retrieve protein functions, interactions, and regulatory links.
• Cytoscape (version 3) plugin compatibility: Provides integration as a Cytoscape plugin for constructing and analyzing molecular networks within Cytoscape.
• Regulatory network dataset: Includes a dataset of regulatory relationships between mammalian DNA-binding transcription factors and their target genes compiled from curated resources and text mining.
• Data aggregation from curated databases: Integrates protein functional and interaction data sourced from multiple curated databases into the triple store.
• Visualization and verification: Supports visualization of query-derived networks in Cytoscape and verification of network links against curated databases or original publications.

Scientific Applications:

• Systems biology: Reconstruction and analysis of protein interaction and regulatory networks for systems-level investigations.
• Genomics: Mapping and exploration of transcription factor–target gene relationships in mammalian genomes.
• Proteomics: Integration and querying of protein functional and interaction data to support proteomic studies.
• Network exploration and hypothesis generation: Explorative network building and querying to identify candidate interactions and regulatory mechanisms.
• Regulatory network validation: Cross-referencing and validation of inferred network links against curated databases and primary publications.

Methodology:

Functional and interaction data from multiple curated databases and text mining are aggregated into the BioGateway RDF triple store and exposed for SPARQL queries, with integration provided as a Cytoscape (version 3) plugin for network visualization and verification.