Bio-Broker: a tool for integration of biological data sources and data analysis tools

In this work we present an architecture for XML-based mediator systems and a framework for helping systems developers in the construction of mediator-services for the integration of heterogeneous data sources. A unique feature of our architecture is its capability to manage (proprietary) user’s software tools and algorithms, modelled as Extended Value Added Services (EVASs), and integrated in the data flow. The mediator offers a view of the system as a single data source where EVASs are readily available for enhancing query processing. A Web-based graphic interface has been developed to allow dynamic and flexible EVASs inter-connection, thus creating complex distributed bioinformatics machines. The feasibility and usefulness of our ideas has been validated by the development of a mediator system (Bio-Broker) and by a diverse set of applications aimed at combining gene expression data with genomic, sequence-based and structural information, so as to provide a general, transparent and powerful solution that integrates data analysis tools and algorithms. Copyright c © 2006 John Wiley & Sons, Ltd.