Bilkent University
Department of Computer Engineering

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CS 590/690 SEMINAR

 

Using a Graph Database for Querying and Integrating Pathways in SBGN Process Description Language

 

Noor Muhammad
Master Student
(Supervisor: Prof.Dr.Uğur Doğrusöz)

Computer Engineering Department
Bilkent University

Abstract: System Biological Graphical Notation (SBGN) Process Description (PD) is widely used to visually represent complex biological pathways in a standardized and intuitive graphical form. It promotes clarity and interoperability among researchers by ensuring consistent and understandable pathway representations. However, managing and integrating multiple SBGN pathway maps from diverse sources is a challenging task, primarily due to the existence of overlapping nodes and interactions across pathways. To address these challenges, we propose leveraging a graph database, specifically a Neo4j graph database to efficiently store, query, and integrate biological pathways represented in SBGN PD format. Our method involves representing SBGN components as graph entities and their interactions as graph relationships, allowing precise queries using Cypher. We introduce algorithms to accurately integrate and merge overlapping nodes and interactions in biological pathway representations, preserving the pathway integrity and avoiding redundancy. This approach enhances scalability, data consistency, and collaborative pathway manipulation.

 

DATE: April 07, Monday @ 13:20 Place: EA 409