Extracting drug-drug interactions from biomedical text using a feature-based kernel approach

Journal of Theoretical and Applied Information Technology

Volumn 92, Issue 1, 2016, Pages 109-120

  Raihani, Anass ^a   Laachfoubi, Nabil ^a  

^a HASSAN 1ST UNIVERSITY   (Morocco)

Author keywords

Biomedical informatics; Biomedical literature; Drug drug interaction; Feature based kernel approach; Natural language processing

Indexed keywords

EID: 84991633844     PISSN: 19928645     EISSN: 18173195     Source Type: Journal    
DOI: None     Document Type: Article

References (20)

1. Drug-Drug interaction. (n.d.) Mosby's Medical Dictionary, 8th edition. (2009). Retrieved April 13 2016 from http://medical-dictionary.thefreedictionary.com/drug-drug+interaction.
2. JW Payne.2007. A Dangerous Mix [Published in The Washington Feb 27 2007] washingtonpost.com/wp-dyn/content/article/2007/02/23/AR20070223017 80.html.
3. http://umm.edu/health/medical/drug-interaction-tool [accessed June 20 2016 ].
4. MEDLINE, https://www.nlm.nih.gov/bsd/pmresources.html [accessed June 20 2016].
5. I. Segura-Bedmar, P. Mart �nez, and C. de Pablo-S �nchez, “A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents,” BMC Bioinformatics, vol. 12,supplement 2, no. 1, 2011.
6. I. Segura-Bedmar, P. Mart �nez, and D. S �nchez-Cisneros, “The1st DDIExtraction-2011 challenge task: extraction of drug-drug interactions from biomedical texts,” in Proceedings of the 1st Challenge Task on Drug-Drug Interaction Extraction (DDIExtraction ’11), pp. 1–9, Huelva, Spain, September 2011.
7. I. Segura-Bedmar, P. Mart �nez, and M. Herrero-Zazo,“SemEval-2013 task 9: extraction of drug-drug interactions from biomedical texts (DDIExtraction 2013),” in Proceedings of the 7th International Workshop on Semantic Evaluation (SemEval ’13), pp. 341–350, Atlanta, Ga, USA, June 2013.
8. M. Herrero-Zazo, I. Segura-Bedmar, P. Martnez, T. Declerck, The DDI corpus: an annotated corpus with pharmacological substances and drugdrug interactions,J. Biomed. Inform. 46 (5) (2013) 914–920. http://dx.doi.org/10.1016/j.jbi.2013.07.011.
9. Shengyu Liu, Buzhou Tang, Qingcai Chen, and Xiaolong Wang, “Drug-Drug Interaction Extraction via Convolutional Neural Networks,” Computational and Mathematical Methods in Medicine, vol. 2016, Article ID 6918381, 8 pages, 2016. doi:10.1155/2016/6918381.
10. W. Zheng,H. Lin, Z. Zhao, B. Xu, Y. Zhang, Z. Yang, J. Wang, "A Graph Kernel Based on Context Vectors for Extracting Drug-Drug Interactions," Journal of Biomedical Informatics, Volume 61, June 2016, Pages 34-43.
11. S. Kim, H. Liu, L. Yeganova, and W. J. Wilbur, “Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach,” Journal of Biomedical Informatics, vol.55, pp. 23–30, 2015.
12. Q. Bui, P. M. Sloot, E. M. van Mulligen, and J. A. Kors, “A novel feature-based approach to extract drug-drug interactions from biomedical text,” Bioinformatics, vol. 30, no. 23, pp. 3365–3371, 2014.
13. V. Law, C. Knox, Y. Djoumbou et al., “DrugBank 4.0: shedding new light on drug metabolism,” Nucleic Acids Research, vol. 42,no. 1, pp. D1091–D1097, 2014.
14. alias-i: LingPipe, a tool kit for processing text using computational linguistics. http://alias-i.com/lingpipe/ [accessed June 20 2016].
15. apache: OpenNLP,a machine learning based toolkit for the processing of natural language text. https://opennlp.apache.org/ [accessed June 20 2016].
16. Chih-Chung Chang and Chih-Jen Lin, LIBSVM: a library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2:27:1--27:27, 2011. Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm [accessed June 20 2016].
17. Richard Socher, John Bauer, Christopher D. Manning and Andrew Y. Ng. 2013. Parsing With Compositional Vector Grammars. Proceedings of ACL 2013.
18. Danqi Chen and Christopher D Manning. 2014. A Fast and Accurate Dependency Parser using Neural Networks. Proceedings of EMNLP 2014.
19. L. He, Z. Yang, Z. Zhao, H. Lin, Y. Li, Extracting drug–drug interaction from the biomedical literature using a stacked generalization-based approach, PLoS One 8 (6) (2013) e65814.
20. A. Bokharaeian, B. D ́ıaz. 2013. NIL UCM: Extracting Drug-Drug interactions from text through combination of sequence and tree kernels. In Proceedings of the 7th International Workshop on Semantic Evaluation (SemEval 2013).