Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis

BMC Bioinformatics

Volumn 16, Issue 16, 2015, Pages

  Hakala, Kai ^a   Van Landeghem, Sofie ^c,d   Salakoski, Tapio ^a,b   Van de Peer, Yves ^c,d,e   Ginter, Filip ^a,b  

^a UNIVERSITY OF TURKU   (Finland)

^b TURKU CENTRE FOR COMPUTER SCIENCE   (Finland)

^c DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^d GHENT UNIVERSITY   (Belgium)

^e UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

Distributed vector representations of words; Event extraction; Large scale data; Network construction; Text mining

Indexed keywords

ARTIFICIAL INTELLIGENCE; DATA REDUCTION; EXTRACTION; GENES; INFORMATION ANALYSIS; LEARNING SYSTEMS;

EVENT EXTRACTION; LARGE SCALE DATA; NETWORK CONSTRUCTION; TEXT MINING; VECTOR REPRESENTATIONS;

DATA MINING;

BIOLOGY; EXTRACTION; GENE CONTROL; GENE REGULATORY NETWORK; MACHINE LEARNING; MINING; MOTIVATION; RECALL; DATA MINING; MOLECULAR GENETICS; NATURAL LANGUAGE PROCESSING;

DATA MINING; GENE REGULATORY NETWORKS; MOLECULAR SEQUENCE ANNOTATION; NATURAL LANGUAGE PROCESSING;

EID: 84961641630     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-16-S16-S3     Document Type: Article

References (25)

1. Van Landeghem S, Björne J, Wei CH, Hakala K, Pyysalo S, Ananiadou S, Kao HY, Lu Z, Salakoski T, Van de Peer Y, Ginter F: Large-scale event extraction from literature with multi-level gene normalization. PLoS ONE. 2013, 8 (4): 55814-
2. Kim JD, Nguyen N, Wang Y, Tsujii J, Takagi T, Yonezawa A: The Genia event and protein coreference tasks of the BioNLP Shared Task 2011. BMC Bioinformatics. 2012, 13 (Suppl 11): 1-
3. McClosky D, Riedel S, Surdeanu M, McCallum A, Manning C: Combining joint models for biomedical event extraction. BMC Bioinformatics. 2012, 13 (Suppl 11): 9-
4. Björne J, Ginter F, Salakoski T: University of Turku in the BioNLP'11 Shared Task. BMC Bioinformatics. 2012, 13 (Suppl 11): 4-
5. Vlachos A, Craven M: Biomedical event extraction from abstracts and full papers using search-based structured prediction. BMC Bioinformatics. 2012, 13 (Suppl 11): 5-
6. Yoshikawa K, Riedel S, Hirao T, Asahara M, Matsumoto Y: Coreference based event-argument relation extraction on biomedical text. Journal of Biomedical Semantics. 2011, 2 (Suppl 5): 6-
7. Miwa M, Thompson P, Ananiadou S: Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. Bioinformatics. 2012, 28 (13): 1759-1765.
8. Hakala K, Van Landeghem S, Salakoski T, Van de Peer Y, Ginter F: EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction. Proceedings of the BioNLP Shared Task 2013 Workshop. 2013, 26-34.
9. Leaman R, Gonzalez G: BANNER: an executable survey of advances in biomedical named entity recognition. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2008, 652-663.
10. Björne J, Ginter F, Salakoski T: Generalizing biomedical event extraction. BMC Bioinformatics. 2012, 13 (suppl. 8): 4-
11. Van Landeghem S, Ginter F, Van de Peer Y, Salakoski T: EVEX: a PubMed-scale resource for homology-based generalization of text mining predictions. Proceedings of the BioNLP 2011 Workshop. 2011, 28-37.
12. Wei CH, Kao HY: Cross-species gene normalization by species inference. BMC Bioinformatics. 2011, 12 (Suppl 8): 5-
13. Kaewphan S, Kreula S, Van Landeghem S, Van de Peer Y, Jones P, Ginter F: Integrating large-scale text mining and co-expression networks: Targeting NADP(H) metabolism in E. coli with event extraction. Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012). 2012
14. Van Landeghem S, De Bodt S, Drebert ZJ, Van de Peer Y: The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis. The Plant Cell. 2013, 25 (3): 794-807.
15. Chang CC, Lin CJ: LIBSVM: A library for Support Vector Machines. ACM Trans Intell Syst Technol. 2011, 2 (3): 27-12727.
16. Björne J, Salakoski T: TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 Shared Task. Proceedings of BioNLP Shared Task 2013 Workshop. 2013
17. Joachims T: Training linear SVMs in linear time. Proceedings of the ACM Conference on Knowledge Discovery and Data Mining (KDD). 2006
18. Joachims T: Making large-scale SVM learning practical. Advances in Kernel Methods - Support Vector Learning. 1999
19. Van Landeghem S, Hakala K, Rönnqvist S, Salakoski T, Van de Peer Y, Ginter F: Exploring biomolecular literature with EVEX: Connecting genes through events, homology and indirect associations. Advances in Bioinformatics. 2012, 2012 (582765): 1-12.
20. Mikolov T, Chen K, Corrado G, Dean J: Efficient estimation of word representations in vector space. ICLR Workshop. 2013
21. Mikolov T, Yih Wt, Zweig G: Linguistic regularities in continuous space word representations. Proceedings of NAACL HLT. 2013, 746-751.
22. McClosky D, Surdeanu M, Manning C: Event extraction as dependency parsing for bionlp 2011. Proceedings of BioNLP Shared Task 2011 Workshop. 2011, Association for Computational Linguistics, Portland, Oregon, USA, 41-45. [ http://www.aclweb.org/anthology/W11-1806 ]
23. Zhou D, Zhong D, He Y: Event trigger identification for biomedical events extraction using domain knowledge. Bioinformatics. 2014, 30 (11): 1587-1594.
24. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Édouard Duchesnay: Scikit-learn: Machine learning in Python. Journal of Machine Learning Research. 2011, 12: 2825-2830.
25. Sculley D: Web-scale k-means clustering. Proceedings of the 19th International Conference on World Wide Web. 2010, 177-1178.