PathSys: integrating molecular interaction graphs for systems biology

doi:10.1186/1471-2105-7-55

BMC Bioinformatics
Volume 7

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Godbole S
Raval A
Ray A
Gupta A

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Methodology article

PathSys: integrating molecular interaction graphs for systems biology

Michael Baitaluk¹ , Xufei Qian¹ , Shubhada Godbole² , Alpan Raval²^,3 , Animesh Ray² and Amarnath Gupta¹

¹San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA

²Keck Graduate Institute, 535 Watson Drive, Claremont, CA, 91711, USA

³School of Mathematical Sciences, Claremont Graduate University, 710 N. College Ave, Claremont, CA 91711, USA

author email corresponding author email

BMC Bioinformatics 2006, 7:55doi:10.1186/1471-2105-7-55


Published:	7 February 2006

Abstract

Background

The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately.

Results

Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping.

Conclusion

Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks webcite.