Reactome Graph Database

Reactome Graph Database provides graph-based storage and efficient querying of curated biomolecular pathway data to enable pathway analysis and exploration of complex biological interactions.

Key Features:

• Graph Database Technology: Uses Neo4j to represent Reactome's complex data model as a graph, reducing average query times by 93% compared with the previous relational approach.
• Cypher Query Language: Supports traversal and pattern-matching queries via Cypher for object-oriented and graph-structured analyses of pathway data.
• ContentService (REST API): Exposes programmatic access to Reactome data through a RESTful ContentService for automated queries and data retrieval.

Scientific Applications:

• Pathway analysis: Enables high-performance retrieval and interrogation of curated pathway information for pathway-centric studies.
• Network-based knowledge discovery: Facilitates graph traversal and relationship discovery to study molecular interactions and complex biological pathways.

Methodology:

Reactome migrated its data model to a Neo4j graph database, executes queries using the Cypher language, and exposes data programmatically via the ContentService REST API.