A novel feature-based approach to extract drug-drug interactions from biomedical text

Bioinformatics

Volumn 30, Issue 23, 2014, Pages 3365-3371

  Bui, Quoc Chinh ^a   Sloot, Peter M A ^b,c,d   Van Mulligen, Erik M ^a   Kors, Jan A ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^d ITMO UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DATA MINING; DRUG INTERACTION; HUMAN; PROCEDURES; SUPPORT VECTOR MACHINE;

DATA MINING; DRUG INTERACTIONS; HUMANS; SUPPORT VECTOR MACHINES;

EID: 84925553600     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu557     Document Type: Article

References (25)

1. Airola, A. et al. (2008) All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatics, 9 (Suppl. 11), S2.
2. Bui, Q.-C. et al. (2011) A hybrid approach to extract protein-protein interactions. Bioinformatics, 27, 259-265.
3. Bui, Q.-C. and Sloot, P.M.A. (2012) A robust approach to extract biomedical events from literature. Bioinformatics, 28, 2654-2661.
4. Chowdhury, M. and Lavelli, A. (2013a) Exploiting the scope of negations and heterogeneous features for relation extraction: a case study for drug-drug interaction extraction. In: Proceedings of NAACL-HLT. Atlanta, GA, USA, pp. 765-771.
5. Chowdhury, M. and Lavelli, A. (2013b) FBK-irst: a multi-phase kernel based approach for drug-drug interaction detection and classification that exploits linguistic information. In: Proceedings of the 7th International Workshop on Semantic Evaluation (SemEval 2013). Atlanta, GA, USA, pp. 351-355.
6. Cohen, K.B. et al. (2010) The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics, 11, 492.
7. Dechanont, S. et al. (2014) Hospital admissions/visits associated with drug-drug interactions: a systematic review and meta-analysis. Pharmacoepidemiol. Drug Saf., 23, 489-497.
8. Giuliano, C. et al. (2006) Exploiting shallow linguistic information for relation extraction from biomedical literature. In: Proceedings of ACL 2006. Trento, Italy, pp. 401-408.
9. Hahn, U. et al. (2012) Mining the pharmacogenomics literature-a survey of the state of the art. Brief. Bioinform., 13, 460-494.
10. He, L. et al. (2013) Extracting drug-drug interaction from the biomedical literature using a stacked generalization-based approach. PLoS One, 8, e65814.
11. Herrero-Zazo, M. et al. (2013) The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. J. Biomed. Inform., 46, 914-920.
12. Miwa, M. et al. (2009) A rich feature vector for protein-protein interaction extraction from multiple corpora. In: Proceedings of the 2009 Conference on Empirical Methods in NLP. ACL, Singapore, pp. 121-130.
13. Moschitti, A. (2004) A study on convolution kernels for shallow semantic parsing. In: Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics - ACL'04. ACL, Morristown, NJ, USA, pp. 335-342.
14. Nédellec, C. et al. (2013) Overview of BioNLP shared task 2013. In: Proceedings of the BioNLP Shared Task 2013 Workshop. Sophia, Bulgaria, pp. 1-7.
15. Rebholz-Schuhmann, D. et al. (2012) Text-mining solutions for biomedical research: enabling integrative biology. Nat. Rev. Genet., 13, 829-839.
16. Segura-Bedmar, I. et al. (2013) Semeval-2013 task 9: extraction of drug-drug interactions from biomedical texts. In: Proceedings of the 7th International Workshop on Semantic Evaluation (SemEval 2013). Atlanta, GA, USA, pp. 341-350.
17. Segura-Bedmar, I. et al. (2011a) The 1st DDIExtraction-2011 challenge task: extraction of drug-drug interactions from biomedical texts. In: Proceedings of the First Challenge task on Drug-Drug Interaction Extraction (DDI Extraction 2011). Huelva, Spain.
18. Segura-Bedmar, I. et al. (2011b) Using a shallow linguistic kernel for drug-drug interaction extraction. J. Biomed. Inform., 44, 789-804.
19. Tari, L. et al. (2010) Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism. Bioinformatics, 26, i547-i553.
20. Thomas, P. et al. (2011) Relation extraction for drug-drug interactions using ensemble learning. In: Proceedings of the First Challenge task on Drug-Drug Interaction Extraction (DDI Extraction 2011). Huelva, Spain.
21. Thomas, P. et al. (2013) WBI-DDI: drug-drug interaction extraction using majority voting. In: Proceedings of the 7th International Workshop on Semantic Evaluation (SemEval 2013). Atlanta, GA, USA, pp. 628-635.
22. Tikk, D. et al. (2013) A detailed error analysis of 13 kernel methods for protein-protein interaction extraction. BMC Bioinformatics, 14, 12.
23. Van Hulse, J. et al. (2007) Experimental Perspectives on Learning from Imbalanced Data. In: Proceedings of the 24th International Conference on Machine Learning, ICML'07. ACM, New York, NY, USA, pp. 935-942.
24. Van Roon, E.N. et al. (2009) An evidence-based assessment of the clinical significance of drug-drug interactions between disease-modifying antirheumatic drugs and non-antirheumatic drugs according to rheumatologists and pharmacists. Clin. Ther., 31, 1737-1746.
25. Wong, C.-M. et al. (2008) Clinically significant drug-drug interactions between oral anticancer agents and nonanticancer agents: profiling and comparison of two drug compendia. Ann. Pharmacother., 42, 1737-1748.