neo4jsbml

neo4jsbml imports Systems Biology Markup Language (SBML) models into Neo4j graph databases to represent biological entities and interactions as nodes and relationships for graph-based analysis.

Key Features:

• Integration with Neo4j: Maps SBML model components to Neo4j graph elements, representing biological entities as nodes and interactions as relationships.
• Graphical Data Representation: Translates hierarchical SBML organization into a graph format to reflect interdependencies within models.
• User-Defined Schema: Supports user-defined schemas to control which SBML elements are imported into the Neo4j database.
• Cypher Query Support: Enables traversal and analysis of imported models using Neo4j's Cypher query language.
• Selective Loading and Performance: Allows selective import of relevant data from SBML to optimize database content and performance.

Scientific Applications:

• Metabolic model analysis: Enables representation and analysis of metabolic models as graphs for exploration of reactions, metabolites, and their relationships.
• Model sharing and interoperability: Facilitates exchange of SBML-encoded models by converting them into Neo4j graph representations that preserve structure and relationships.
• Network visualization and traversal: Supports visualization-ready graph representations and graph traversal analyses of complex biological networks.

Methodology:

Imports SBML into Neo4j, maps SBML entities to nodes and interactions to relationships, translates SBML hierarchical structure into a graph format, supports user-defined schemas for selective loading, and enables traversal and analysis via Cypher.