PathBank: Web-Based Querying and Visualziation of an Integrated Biological Pathway Database

  • Authors:

  • Joshua Wing Kei Ho;Tristan Manwaring;Seok-Hee Hong;Uwe Roehm;David Cho Yau Fung;Kai Xu;Tim Kraska;David Hart

  • Affiliations:

  • University of Sydney, Australia;University of Sydney, Australia;University of Sydney, Australia;University of Sydney, Australia;University of Sydney, Australia;NICTA (National ICT Australia), Australia;University of Munster, Germany;Axogenic Pty Ltd, Australia

  • Venue:
  • CGIV '06 Proceedings of the International Conference on Computer Graphics, Imaging and Visualisation
  • Year:
  • 2006

Quantified Score

Hi-index 0.00

Visualization

Abstract

PathBank is a web-based query and visualization system for biological pathways using an integrated pathway database. To address the needs for biologists to visualize and analyze biological pathways, PathBank is designed to be user-friendly, flexible and extensible. It is, to the best of our knowledge, the first web-based system that allows biological pathways to be visualized in three dimensions. PathBank demonstrates the ability to automatically generate and layout biological pathways in response to webbased database query about proteins, genes, gene ontology and small molecules. Using a novel OWL-to-relational database schema generation approach, it can automatically integrate biological data from different sources that support the BioPAX exchange format (e.g. KEGG, Bio- Cyc). The systems web interface allows both simple keyword and complex query-based searches in the database. The pathway visualization component provides fast and interactive data access by using asynchronous data retrieval. Due to its modular implementation, it can be easily extended with new visualization algorithms.