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This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences, 2008

Open Access Open Badges Research

Service-based analysis of biological pathways

George Zheng1* and Athman Bouguettaya2

Author Affiliations

1 Virginia Tech, Blacksburg, Virginia, USA

2 CSIRO ICT Centre, Canberra, ACT, Australia

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BMC Bioinformatics 2009, 10(Suppl 10):S6  doi:10.1186/1471-2105-10-S10-S6

Published: 1 October 2009



Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach.


Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses.


Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper.