Sentence identification of biological interactions using PATRICIA tree generated patterns and genetic algorithm optimized parameters

Data and Knowledge Engineering

Volumn 69, Issue 1, 2010, Pages 137-152

  Liu, Haibin ^a   Blouin, Christian ^a   Kešelj, Vlado ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Biological interactions patterns; Genetic algorithm; Interaction sentences; PATRICIA tree; Pattern matching

Indexed keywords

BIOLOGICAL INTERACTIONS; BIOLOGICAL INTERACTIONS PATTERNS; CLASSIFICATION PERFORMANCE; CLASSIFICATION TASKS; F-SCORE; INNOVATIVE COMPONENT; OPTIMIZED PARAMETER; PAIRWISE ALIGNMENT; PART-OF-SPEECH TAGS; PATRICIA TREE; POS TAGGING; PRE-PROCESSING STEP; SCIENTIFIC LITERATURE; SCORING SCHEMES;

ALIGNMENT; BIOCHEMISTRY; INFORMATION SERVICES; MOLECULAR BIOLOGY; PATTERN MATCHING;

GENETIC ALGORITHMS;

EID: 71649086890     PISSN: 0169023X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.datak.2009.09.002     Document Type: Article

References (42)

1. Blaschke C., Andrade M.A., Ouzounis C., and Valencia A. Automatic extraction of biological information from scientific text: protein-protein interactions. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (1999), AAAI Press 60-67
2. Ono T., Hishigaki H., Tanigami A., and Takagi T. Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17 2 (2001) 155-161
3. Jang H., Lim J., Lim J.-H., Park S.-J., Lee K.-C., and Park S.-H. Finding the evidence for protein-protein interactions from pubmed abstracts. Bioinformatics 22 14 (2006) e220-e226
4. Skusa A., Ruegg A., and Kohler J. Extraction of biological interaction networks from scientific literature. Brief Bioinformatics 6 3 (2005) 263-276
5. J. Li, X. Zhang, Y. Hao, M. Huang, X. Zhu, Learning domain-specific knowledge from context-THUIR at TREC2005 Genomics Track, in: Proceedings of 14th Text Retrireval Conference (TREC2005), Gaithersburg, USA, 2005.
6. Raychaudhuri S. Computational Text Analysis: For Functional Genomics and Bioinformatics (2006), Oxford University Press
7. J. Pustejovsky, J.M. Castano, J. Zhang, M. Kotecki, B. Cochran, Robust relational parsing over biomedical literature: extracting inhibit relations, in: Proceedings of the seventh Pacific Symposium on Biocomputing, 2002, pp. 362-373.
8. C. Friedman, P. Kra, H. Yu, M. Krauthammer, A. Rzhetsky, Genies: a natural-language processing system for the extraction of molecular pathways from journal articles, Bioinformatics 17 (Suppl 1) (2001).
9. K. Humphreys, G. Demetriou, R. Gaizauskas, Two applications of information extraction to biological science: enzyme interactions and protein structures, in: Proceedings of the Pacific symposium on Biocomputing, Hawaii, USA, 2000, pp. 502-513.
10. Abulaish M., and Dey L. Biological relation extraction and query answering from medline abstracts using ontology-based text mining. Data & Knowledge Engineering 61 2 (2007) 228-262
11. Chiang J.-H., and Yu H.-C. Literature extraction of protein functions using sentence pattern mining. IEEE Transactions on Knowledge and Data Engineering 17 8 (2005) 1088-1098
12. Califf M.E., and Mooney R.J. Bottom-up relational learning of pattern matching rules for information extraction. Journal of Machine Learning Research 4 (2003) 177-210
13. Huang M., Zhu X., Hao Y., Payan D.G., Qu K., and Li M. Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics 20 (2004) 3604-3612
14. C. Nédellec, Machine learning applied to information extraction in specific domains - an example gene interaction extraction from bibliography in genomics, 2002.
15. A. Ramani, R. Bunescu, R. Mooney, E. Marcotte, Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome, Genome Biology 6 (5) (2005).
16. Yeh A.S., Hirschman L., and Morgan A.A. Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup. Bioinformatics 19 Suppl. 1 (2003) 331-339
17. Divoli A., and Attwood T.K. BioIE: extracting informative sentences from the biomedical literature. Bioinformatics 21 9 (2005) 2138-2139
18. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. Journal of Molecular Biology 147 1 (1981) 195-197
19. V. Keselj, H. Liu, N. Zeh, C. Blouin, C. Widden, Finding optimal parameters for edit distance based sequence classification is NP-hard, in: Proceedings of KDD-09 Workshop on Statistical Relational Mining and Learning in Bioinformatics (StReBio'09), Paris, France, 2009.
20. H. Liu, C. Blouin, V. Kešelj, Identifying interaction sentences from biological literature using automatically extracted patterns, in: Proceedings of BioNLP 2009, NAACL/HLT 2009 Workshop, Boulder, CO, USA, 2009.
21. Koza J.R. Genetic Programming (1992), The MIT Press
22. C. Plake, J. Hakenberg, U. Leser, Learning patterns for information extraction from free text, in: Proceedings of AKKD 2005, Karlsruhe, Germany, 2005.
23. Bunescu R., Ge R., Kate R.J., Marcotte E.M., Mooney R.J., Ramani A.K., and Wong Y.W. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine 33 2 (2005) 139-155
24. R. Bunescu, R. Ge, R.J. Kate, R.J. Mooney, Y.W. Wong, E.M. Marcotte, A. Ramani, Learning to extract proteins and their interactions from medline abstracts, in: Proceedings of ICML-2003 Workshop on Machine Learning in Bioinformatics (2003), 2002, pp. 46-53.
25. J. Hakenberg, C. Plake, U. Leser, H. Kirsch, D. Rebholz-Schuhmann, Lll'05 challenge: genic interaction extraction with alignments and finite state automata, in: Proceedings of Learning Language in Logic Workshop (LLL'05) at ICML, Bonn, Germany, 2005, p. 38C45.
26. Mikheev A. Periods, capitalized words, etc. Computational Linguistics 28 3 (2002) 289-318
27. S. Jiampojamarn, N. Cercone, V. Kešelj, Biological Named Entity Recognition using N-grams and Classification Methods, in: Proceedings of the Conference Pacific Association for Computational Linguistics, PACLING'05, Tokyo, Japan, 2005.
28. H. Liu, C. Blouin, V. Kešelj, An unsupervised method for extracting domain-specific affixes in biological literature, in: Proceedings of BioNLP 2007, Association for Computational Linguistics, Prague, Czech Republic, 2007.
29. L. Ramshaw, M. Marcus, Text chunking using transformation-based learning, in: Proceedings of the Third Workshop on Very Large Corpora, Somerset, NJ, 1995, pp. 82-94.
30. MEDLINE, National Library of Medicine (accessed in August 2009).
31. Cimino J.J., and Barnett G.O. Automatic knowledge acquisition from medline. Methods of Information in Medicine 32 2 (1993) 120-130
32. Hatzivassiloglou V., and Weng W. Learning anchor verbs for biological interaction patterns from published text articles. International Journal of Medical Informatics 67 1 (2002) 19-32
33. F. Rinaldi, G. Schneider, K. Kaljurand, J. Dowdall, C. Andronis, A. Persidis, O. Konstanti, Mining relations in the GENIA corpus, in: Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics, Pisa, Italy, 2004.
34. Morrison D.R. Patricia - practical algorithm to retrieve information coded in alphanumeric. Journal of the ACM 15 4 (1968) 514-534
35. Chien L.-F. Pat-tree-based keyword extraction for chinese information retrieval. SIGIR Forum 31 SI (1997) 50-58
36. K.-J. Chen, W. Tsuei, L.-F. Chien, Pat-trees with the deletion function as the learning device for linguistic patterns, in: Proceedings of the 17th international conference on Computational linguistics, Association for Computational Linguistics, Morristown, NJ, USA, 1998, pp. 244-250.
37. Needleman S., and Wunsch C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48 3 (1970) 443-453
38. Dan G. Algorithms on Strings, Trees, and Sequences (1997), Cambridge University Press
39. S.S. Shapiro, M.B. Wilk, An analysis of variance test for normality (complete samples), Biometrika 3 (52).
40. SAS Institute Inc., SAS Procedure Guide, Version 8, SAS Institute Inc., Cary, NC, 1999.
41. Mccray A.T., and Bodenreider O. A Conceptual Framework for the Biomedical Domain. Semantics of Relationships (2002), Kluwer Academic Publishers 181-198
42. Gene Ontology Consortium, Creating the gene ontology resource: design and implementation, Genome Research 11 (8) (2001) 1425-1433.