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

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...

• Type: Conference
• Year: 2006
• Where: IEEECGIV
• Authors: Joshua Wing Kei Ho, Tristan Manwaring, Seok-Hee Hong, Uwe Röhm, David Cho Yau Fung, Kai Xu 0003, Tim Kraska, David Hart
• Keywords: Biological Pathways, Computer Graphics, IEEECGIV 2006, Integrated Pathway Database, Webbased Database Query