A hybrid approach to extract protein-protein interactions

Bioinformatics

Volumn 27, Issue 2, 2011, Pages 259-265

  Bui, Quoc Chinh ^a   Katrenko, Sophia ^a   Sloot, Peter M A ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; DATA MINING; EVALUATION; METHODOLOGY; PROTEIN ANALYSIS;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; DATA MINING; PROTEIN INTERACTION MAPPING;

EID: 78651423600     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq620     Document Type: Article

References (27)

1. Airola,A. et al. (2008) All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatics, 9, S11.
2. Ananiadou,S. et al. (2006) Text mining and its potential applications in systems biology. Trends Biotechnol., 24, 571-579.
3. Björne,J. et al. (2010) Complex event extraction at PubMed scale. Bioinformatics, 26, i382-i390.
4. Bui,Q.C. et al. (2010) Extracting causal relations on HIV drug resistance from literature. BMC Bioinformatics, 11, 101.
5. Bunescu,R. and Mooney,R. (2005) Subsequence kernels for relation extraction. In Proceedings of the 19th conference on Neural Information Processing Systems. Vancouver, Canada.
6. Chowdhary,R. et al. (2009) Bayesian inference of protein-protein interactions from biological literature. Bioinformatics, 25, 1536-1542.
7. Cusick,M.E. et al. (2009) Literature-curated protein interaction datasets. Nat. Methods, 6, 39-46.
8. Fayruzov,T. et al. (2009) Linguistic feature analysis for protein interaction extraction. BMC Bioinformatics, 10, 374.
9. Fundel,K. et al. (2007) RelEx - Relation extraction using dependency parse trees. Bioinformatics, 23, 365-371.
10. Giles,C. and Wren,J. (2008) Large-scale directional relationship extraction and resolution. BMC Bioinformatics, 9, S11.
11. Giuliano,C. et al. (2006) Exploiting shallow linguistic information for relation extraction from biomedical literature. In Proceedings of the 11th Conference of the European Chapter of the Association for Computational Linguistics, Trento.
12. Kabiljo,R. et al. (2009) A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics, 10, 233.
13. Katrenko,S. and Adriaans,P. (2007) Learning Relations from Biomedical Corpora Using Dependency Trees. Knowl. Discov. Emerg. Compl. Bioinformatics, 4366, 61-80.
14. Kim,S. et al. (2008) Kernel approaches for genic interaction extraction. Bioinformatics, 24, 118-126.
15. Kim,S. et al. (2010)Walk-weighted subsequence kernels for protein-protein interaction extraction. BMC Bioinformatics, 11, 107.
16. Klein,D. and Manning,C.D. (2003) Fast Exact Inference with a Factored Model for Natural Language Parsing. In Advances in Neural Information Processing Systems 15 (NIPS 2002). MIT Press, Cambridge, MA, pp. 3-10.
17. Miwa,M. et al. (2009a) Protein-protein interaction extraction by leveraging multiple kernels and parsers. Int. J. Med. Inform., 78, e39-e46.
18. Miwa,M. et al. (2009b)Arich feature vector for protein-protein extraction from multiple corpora. In Proceedings of EMNLP, Singapore, pp. 121-130.
19. Miwa,M. et al. (2010) Event extraction with complex event classification using rich features. J. Bioinform. Comput. Biol., 8, 131-146.
20. Miyao,Y. et al. (2009) Evaluating contributions of natural language parsers to proteinprotein interaction extraction. Bioinformatics, 25, 394-400.
21. Niu,Y. et al. (2009) Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics, 26, 111-119.
22. Pyysalo,S. et al. (2008) Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics, 9, S6.
23. Rinaldi,F. et al. (2010) OntoGene in BioCreative II.5. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 7, 472-480.
24. Sætre,R. et al. (2007) Syntactic features for protein-protein interaction extraction. In Proceedings of the 2nd International Symposium on Languages in Biology and Medicine, Singapore.
25. Sætre,R. et al. (2010) Extracting Protein-Interactions from Text with the Unified AkaneRE Event Extraction System. IEEE/ACM Trans. Comput. Biol. Bioinform., 99, 442-453.
26. Van Landeghem,S. et al. (2008) Extracting protein-protein interactions from text using rich feature vectors and feature selection. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, pp. 77-84.
27. Witten,I.H. and Frank,E. (2005) Data Mining: Practical Machine Learning Tools and Techniques, 2nd edn. Morgan Kaufmann, San Francisco, CA. 265.