Design and prototype of a system to integrate and visualize biological interaction data : International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria: (July 21-25, 2007) : Poster

Abstract

Biomolecular interaction data is an increasingly important bioinformatics dataset used to examine biological systems. However, these data are spread across multiple databases and expressed in disparate data structures and formats. A prerequisite for working with these data would be consolidation into a single non-redundant updated repository. An initial design and prototype for consolidating and visualizing interaction data will be presented in this poster with an especial emphasis on providing scalable and reliable web-services as part of the solution. The central point of operation is a data warehouse with numerous parsers retrieving updated information from existing data sources. We have designed parsers for PSI-MI 1.0, PSI-MI 2.5 XML files and tab delimited text files. The parsers for XML files are built using an event-driven pull-parsing API which gives them the ability to handle very large files. A local application interface provides access to this data warehouse for local programmers, java servlets and web services. The usage of various operating systems and programming languages by the intended clients were considered when designing the system. Therefore, platform independent protocols were used. Moreover, multiple implementations of hosting the services were considered with respect to their ability to handle large data sets reliably in a stateful manner. Using these web-services, a tool was developed to retrieve and present interaction data visually. The approach taken was to construct modules as plugins to existing molecular visualization software.