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Open Access Highly Accessed Software

PPLook: an automated data mining tool for protein-protein interaction

Shao-Wu Zhang1*, Yao-Jun Li1, Li Xia2 and Quan Pan1

Author Affiliations

1 Institute of Control and Information, School of Automation, Northwestern Polytechnical University, Xi'an, China

2 Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, USA

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BMC Bioinformatics 2010, 11:326  doi:10.1186/1471-2105-11-326

Published: 16 June 2010

Abstract

Background

Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results.

Results

We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface.

Conclusions

PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at http://meta.usc.edu/softs/PPLook webcite.