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Bioinformatics Advance Access published online on April 15, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp245
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Bayesian Inference of Protein-protein Interactions from Biological Literature

Rajesh Chowdhary 1,2,{dagger}, Jinfeng Zhang 3,{dagger} and Jun S. Liu 1,*

1Department of Statistics, Harvard University, Cambridge, MA 02138, USA. Email: {chowdhary{at}stat.harvard.edu, jliu{at}stat.harvard.edu}
2Marshfield Clinic-Marshfield Center, MCRF-BIRC, 1000 North Oak Avenue, Marshfield, WI 54449, USA. Email: chowdhary.rajesh{at}mcrf.mfldclin.edu
3Department of Statistics, Florida State University, Tallahassee, FL 32306, USA. Email: jinfeng{at}stat.fsu.edu

*To whom correspondence should be addressed. Jun S. Liu, E-mail: jliu{at}stat.harvard.edu


  Abstract

Motivation: Protein-protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite significant progress, mining PPIs from literatures still rely heavily on time and resource consuming manual annotations.

Results: In this study, we developed a novel methodology based on Bayesian networks (BNs) for extracting PPI triplets (a PPI triplet consists of two protein names and the corresponding interaction word) from unstructured text. The method achieved an overall accuracy of 87% on a cross-validation test using manually annotated data set. We also showed, through extracting PPI triplets from a large number of PubMed abstracts, that our method was able to complement human annotations to extract large number of new PPIs from literature.

Availability: Programs/scripts we developed/used in the study are available at: http://stat.fsu.edu/~jinfeng/datasets/Bio-SI-programs-Bayesian-chowdhary-zhang-liu.zip.

Contact: jliu{at}stat.harvard.edu.

Supplementary Material: Available at Bioinformatics online.

Associate Editor: Dr. Jonathan Wren

{dagger}Authors contributed equally

Received on December 24, 2008; revised on March 30, 2009; accepted on April 5, 2009

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