Bilkent University
Department of Computer Engineering


Efficiently Querying Graph Database and Integrating Graph Database with SBGN


Mustafa Enes Karaca
MS Student
Computer Engineering Department
Bilkent University

Graphs are an effective and natural way of representation of biological networks. As biological data is unpredictable, heterogeneous and highly connected, property graph model which comprises connected entities with any number of attributes is powerful for modeling biological data. Neo4j is a graph database that implements property graph for storing data. In this study, we use Neo4j graph database in order to model, store and manage biological data. We propose a framework for integration of Neo4j and Systems Biology Graphical Notation (SBGN). By using an existing SBGN library, Java and Cypher, which is declarative query language of Neo4j, we import data from SBGN maps to Neo4j and Neo4j to SBGN maps. We plan to provide Cypher statements for efficient graph based queries/algorithms to SBGN models stored in Neo4j.


DATE: 30 October, 2017, Monday @ 15:40