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. 2006 Feb 7:7:55.
doi: 10.1186/1471-2105-7-55.

PathSys: integrating molecular interaction graphs for systems biology

Michael Baitaluk  1 , Xufei Qian, Shubhada Godbole, Alpan Raval, Animesh Ray, Amarnath Gupta
Affiliations

PathSys: integrating molecular interaction graphs for systems biology

Michael Baitaluk et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
PathSys System architecture.
Figure 2
Figure 2
The UML diagram of the internal data model.
Figure 3
Figure 3
Representation of a simplified model of mating pheromone activated signal transduction pathway.
Figure 4
Figure 4
MAPK signaling pathways produced by PathSys in comparison with the canonical KEGG MAPK signaling pathways. a). MAPK signaling pathways in Yeast reproduced by KEGG.b). Pathways generated by PathSys for (b1) Pheromone response, (b2) Cell Wall modeling and (b3) Filamentation of MAPK signaling pathways, with the proteins as red ovals, complexes as blue ovals; processes (binary and multiple) and interaction types as small colored circles, squares, diamonds, etc.; pathways (Cell Cycle pathway) as yellow triangles, compartments as grey boxes. Network graphs are produced by BiologicalNetworks client software.
Figure 5
Figure 5
A functional module (largest connected component) for cytoskeletal organization and coordination. Edge line types represent interaction types and node colors represent GO annotation.
See this image and copyright information in PMC

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