A Single Kernel-Based Approach to Extract Drug-Drug Interactions from Biomedical Literature

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Zhang, Yijia ^a   Lin, Hongfei ^a   Yang, Zhihao ^a   Wang, Jian ^a   Li, Yanpeng ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACARBOSE; ACETAZOLAMIDE; ALCOHOL; AMIKACIN; AZLOCILLIN; BUSPIRONE; CASPOFUNGIN; CIMETIDINE; CIPROFLOXACIN; CYCLOSPORIN; ERTAPENEM; GENTAMICIN; INSULIN ASPART; INSULIN ZINC SUSPENSION; METHENAMINE; NETILMICIN; PROBENECID; TOBRAMYCIN; VALPROIC ACID; WARFARIN;

ACCURACY; AREA UNDER THE CURVE; ARTICLE; CALCULATION; DRUG ALCOHOL INTERACTION; DRUG ANTAGONISM; DRUG BIOAVAILABILITY; DRUG BLOOD LEVEL; DRUG CLEARANCE; DRUG EFFECT; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; HUMAN; KERNEL METHOD; MATHEMATICAL COMPUTING; PROTHROMBIN TIME; STATISTICAL MODEL;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DATABASES, FACTUAL; DATABASES, PROTEIN; DRUG INTERACTIONS; HUMANS; MODELS, STATISTICAL; NATURAL LANGUAGE PROCESSING; PREDICTIVE VALUE OF TESTS; PROTEIN INTERACTION MAPPING; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84868334650     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048901     Document Type: Article

References (38)

1. Segura-Bedma I, Martínez P, Pablo-Sánchez C, (2011) Using a shallow linguistic kernel for drug-drug interaction extraction. Journal of Biomedical Informatics 44: 789-804.
2. Segura-Bedmar I, Martínez P, Pablo-Sánchez C, (2011) A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents in biomedical texts. BMC Bioinformatics 12: S1.
3. Rodríguez-Terol A, Camacho C, (2009) Others, calidad estructural de las bases de datos de interacciones. Farmacia Hospitalaria 33: 134.
4. Segura-Bedmar I, Martínez P, Segura-Bedmar M, (2008) Drug name recognition and classification in biomedical texts: a case study outlining approaches underpinning automated systems. Drug Discov Today 13: 816-823.
5. Zweigenbaum P, Demner-Fushman D, Yu H, Cohen K, (2007) Frontiers of biomedical text mining: current progress. Briefings in Bioinformatics 8: 358-375.
6. Pyysalo S, Ginter F, Heimonen J, Björne J, Boberg J, et al. (2007) BioInfer: A Corpus for Information Extraction in the Biomedical Domain. BMC Bioinformatics 8: 50.
7. Kim D, Ohta T, Tsujii J, (2008) Corpus Annotation for Mining Biomedical Events from Literature. BMC Bioinformatics 9: 10.
8. Segura-Bedmar I, Martínez P, Sanchez-Cisneros D (2011) The 1st DDIExtraction-2011 challenge task: Extraction of Drug-Drug Interactions from biomedical texts. Proc of DDIExtraction-2011 challenge task Spain. 1-9.
9. Bunescu R, Ge R, Kate R, Marcotte E, Mooney R, et al. (2005) Comparative Experiments on Learning Information Extractors for Proteins and their Interactions. Artificial Intelligence in Medicine 33: 139-155.
10. Blaschke C, Valencia A, (2002) The frame-based module of the suiseki information extraction system. IEEE Intelligent Systems 17: 14-20.
11. Corney D, Buxton B, Langdon, Jones D, (2004) BioRAT: extracting biological information from full-length papers. Bioinformatics 20: 3206-3213.
12. Blaschke C, Andrade M, Ouzounis C, Valencia A (1999) Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int. Conf. Intell. Syst. Mol. Biol. 60-67.
13. Ono T, Hishigaki H, Tanigam A, Takagi T, (2001) Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17: 156-161.
14. Fundel K, Kuffner R, Zimmer R, (2007) RelEx-Relation extraction using dependency parse trees. Bioinformatics 23: 365-371.
15. Airola A, Pyysalo S, Björne J, Pahikkala T, Ginter T, et al. (2008) All-Paths graph kernel for protein-Protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatic 9: S2.
16. Bunescu R, Mooney R (2006) Subsequence kernels for relation extraction. Proc 18th Advances in Neural Information Processing Systems.: 171-178.
17. Kim S, Yoon J, Yang J, Park S, (2010) Walk-Weighted subsequence kernels for protein-protein interaction extraction. BMC Bioinformatics 11: 107.
18. Zelenko D, Aone C, Richardella A, (2003) Kernel methods for relation extraction. Journal of Machine Learning Research 4: 1083-1106.
19. Bunescu R, Mooney R (2005) A shortest path dependency kernel for relation extraction. Proc Human Language Technology Conf. and Conf. Empirical Methods in Natural Language Processing Association for Computational Linguistics. 724-731.
20. Gärtner T, Lach P, Wrobel S (2003) On graph kernels: hardness results and efficient alternatives. Proc 16th Learning Theory Conf. 129-143.
21. Zhang Y, Lin H, Yang Z, Li Y, (2011) Neighborhood hash graph kernel for protein-protein interaction extraction. Journal of biomedical informatics 44: 1086-1092.
22. Miwa M, Soetre R, Miyao Y, Tsujii J, (2009) Protein-protein interaction extraction by leveraging multiple kernels and parsers. Journal of Medical Informatics 78: 39-46.
23. Yang Z, Tang N, Zhang X, Lin H, Li Y, et al. (2011) Multiple kernel learning in protein-protein interaction extraction from biomedical literature. Artificial Intelligence in Medicine 51: 163-17.
24. Lease M, Charniak E (2005) Parsing biomedical literature. Proc 2nd Int. Joint Conf. Natural Language Processing Korea: 58-69.
25. Pyysalo S, Airola A, Heimonen J, Björne J, Ginter F, et al. (2008) Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 9: S6.
26. Shohei H, Hisashi K (2009) A linear-time graph kernel. Proc IEEE international conference on data mining Florida: 179-88.
27. Zhang M, Zhang J, Su J, Zhou G (2006) A composite kernel to extract relations between entities with both flat and structured features. Proc International Conference on Computational Linguistics and Annual Meeting of the ACL: 825-832.
28. Zhang M, Dong G, Aiti A, (2008) Exploring syntactic structured features over parse trees for relation extraction using kernel methods. Information Processing and Management 44: 687-701.
29. Zhou G, Zhang M, Ji D, Zhu Q (2007) Tree kernel-based relation extraction with context-sensitive structured pares tree information. Proc EMNLP and CNLL Prague Czech Republic 728-736.
30. Hanley J, McNeil B, (1982) The meaning and use of the area under a receiver operating characteristic (ROC) rurve. Radiology 143: 29-36.
31. Thomas P, Neves M, Solt I, Tikk D, Leser U (2011) Relation extraction for drug-drug interactions using ensemble learning. Proc DDIExtraction-2011 challenge task Spain: 11-18.
32. Chowdhury M, Abacha A, Lavelli A, Zweigenbaum P (2011) Two diferent machine learning techniques for drug-drug interaction extraction. Proc DDIExtraction-2011 challenge task Spain: 19-26.
33. Chowdhury M, Lavelli A (2011) Drug-drug interaction extraction using composite kernels. Proc DDIExtraction-2011 challenge task Spain: 27-33.
34. Björne J, Airola A, Pahikkala T, Salakoski T (2011) Drug-drug interaction extraction with rls and svm classiffers. Proc DDIExtraction-2011 challenge task Spain: 35-42.
35. Wishart D, Knox C, Guo A, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research 36: D901-D906.
36. Garcia-Blasco S, Mola-Velasco S, Danger R, Rosso P (2011) Automatic drug-drug ineraction detection: a machine learning approach with maximal frequent sequence extraction. Proc DDIExtraction-2011 challenge task Spain: 51-58.
37. Baldi P, Brunak S, Chauvin Y, Andersen C A, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
38. Carugo O, (2007) Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots. BMC Bioinformatics 8: 380.