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. 2009 Jun 15;25(12):1536-42.
doi: 10.1093/bioinformatics/btp245. Epub 2009 Apr 15.

Bayesian inference of protein-protein interactions from biological literature

Rajesh Chowdhary  1 , Jinfeng Zhang, Jun S Liu
Affiliations

Bayesian inference of protein-protein interactions from biological literature

Rajesh Chowdhary et al. Bioinformatics. .

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 dataset. 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.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Bayesian network structure learned from the cross-validation dataset.
Fig. 2.
Fig. 2.
ROC curve for cross-validation done on cross-validation dataset.
See this image and copyright information in PMC

References

    1. Alfarano C, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 2005;33:D418–D424. - PMC - PubMed
    1. Baumgartner WA, Jr, et al. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics. 2007;23:i41–i48. - PMC - PubMed
    1. Beuming T, et al. PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics. 2005;21:827–828. - PubMed
    1. Blaschke C, et al. Automatic extraction of biological information from scientific text: protein-protein interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1999:60–67. - PubMed
    1. Ceol A, et al. Linking entries in protein interaction database to structured text: the FEBS Letters experiment. FEBS Lett. 2008;582:1171–1177. - PubMed

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