Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Mixture of logistic models and an ensemble approach for protein-protein interaction extraction
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
Learning bayesian network using parse trees for extraction of protein-protein interaction
CICLing'13 Proceedings of the 14th international conference on Computational Linguistics and Intelligent Text Processing - Volume 2
PIMiner: a web tool for extraction of protein interactions from biomedical literature
International Journal of Data Mining and Bioinformatics
| Hi-index | 3.84 |
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 Contact: jliu@stat.harvard.edu Supplementary information:Supplementary data are available at Bioinformatics online.