BioNLP Shared Task 2011: Supporting resources

Proceedings of BioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL HLT 2011

Volumn , Issue , 2011, Pages 112-120

  Stenetorp, Pontus ^a   Topić, Goran ^a   Pyysalo, Sampo ^a   Ohta, Tomoko ^a   Kim, Jin Dong ^b   Tsujii, Jun'ichi ^c  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c MICROSOFT RESEARCH ASIA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

NATURAL LANGUAGE PROCESSING SYSTEMS; VISUALIZATION;

DEVELOPMENT STAGES; EVALUATION SOFTWARE; EVENTS EXTRACTIONS; EXTRACTION SYSTEMS; PERFORMANCE; RESEARCH EFFORTS; SPECIFIC TOOL; SUPPORTING RESOURCES; SYSTEM DEVELOPMENT; VISUALIZATION TOOLS;

EXTRACTION;

EID: 84863715052     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (38)

1. Daniel M. Bikel. 2004. Intricacies of Collins’ Parsing Model. Computational Linguistics, 30(4):479–511.
2. J. Björne, F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski. 2010. Complex event extraction at PubMed scale. Bioinformatics, 26(12):i382.
3. Robert Bossy, Julien Jourde, Philippe Bessières, Marteen van de Guchte, and Claire Nédellec. 2011. BioNLP Shared Task 2011 - Bacteria Biotope. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
4. S. Buchholz and E. Marsi. 2006. CoNLL-X shared task on multilingual dependency parsing. In Proceedings of the Tenth Conference on Computational Natural Language Learning, pages 149–164. Association for Computational Linguistics.
5. E. Buyko and U. Hahn. 2010. Evaluating the impact of alternative dependency graph encodings on solving event extraction tasks. In Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, pages 982–992. Association for Computational Linguistics.
6. Eugene Charniak and Mark Johnson. 2005. Coarse-to-Fine n-Best Parsing and MaxEnt Discriminative Reranking. In Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL’05), pages 173–180.
7. Pallavi Choudhury, Michael Gamon, Chris Quirk, and Lucy Vanderwende. 2011. MSR-NLP entry in BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
8. S. Clark and J.R. Curran. 2004. Parsing the WSJ using CCG and log-linear models. In Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, page 103. Association for Computational Linguistics.
9. Michael John Collins. 1996. A new statistical parser based on bigram lexical dependencies. In Proceedings of the 34th Annual Meeting of the Association for Computational Linguistics, pages 184–191, Santa Cruz, California, USA, June. Association for Computational Linguistics.
10. Marie-Catherine de Marneffe, Bill MacCartney, and Christopher D. Manning. 2006. Generating Typed Dependency Parses from Phrase Structure Parses. In Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC’06), pages 449–454.
11. H.L. Dickensheets, C. Venkataraman, U. Schindler, and R.P. Donnelly. 1999. Interferons inhibit activation of STAT6 by interleukin 4 in human monocytes by inducing SOCS-1 gene expression. Proceedings of the National Academy of Sciences of the United States of America, 96(19):10800.
12. Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. A generalizable and efficient machine learning approach for biological event extraction from text. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
13. Charles J. Fillmore. 1976. Frame semantics and the nature of language. Annals of the New York Academy of Sciences, 280(1):20–32.
14. R. Johansson and P. Nugues. 2007. Extended constituent-to-dependency conversion for English. In Proc. of the 16th Nordic Conference on Computational Linguistics (NODALIDA).
15. Julien Jourde, Alain-Pierre Manine, Philippe Veber, Karën Fort, Robert Bossy, Erick Alphonse, and Philippe Bessières. 2011. BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
16. Yoshinobu Kano, William Baumgartner, Luke McCrohon, Sophia Ananiadou, Kevin Cohen, Larry Hunter, and Jun’ichi Tsujii. 2009. U-Compare: share and compare text mining tools with UIMA. Bioinformatics, 25(15):1997–1998, May.
17. Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun’ichi Tsujii. 2009. Overview of BioNLP’09 Shared Task on Event Extraction. In Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pages 1–9.
18. Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, and Jun’ichi Tsujii. 2011a. Overview of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
19. Jin-Dong Kim, Yue Wang, Toshihisa Takagi, and Akinori Yonezawa. 2011b. Overview of the Genia Event task in BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
20. D. Klein and C.D. Manning. 2003. Fast exact inference with a factored model for natural language parsing. Advances in neural information processing systems, pages 3–10.
21. M.P Marcus, B. Santorini, and M.A Marcinkiewicz. 1993. Building a large annotated corpus of English: The Penn Tree Bank. Computational Linguistics, pages 313–318.
22. D. McClosky. 2009. Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing. Ph.D. thesis, Ph. D. thesis, Department of Computer Science, Brown University.
23. M. Miwa, S. Pyysalo, T. Hara, and J. Tsujii. 2010. Evaluating Dependency Representation for Event Extraction. In In the 23rd International Conference on Computational Linguistics (COLING 2010), pages 779–787.
24. Y. Miyao and J. Tsujii. 2008. Feature forest models for probabilistic HPSG parsing. Computational Linguistics, 34(1):35–80.
25. Yusuke Miyao, Rune Sætre, Kenji Sagae, Takuya Matsuzaki, and Jun’ichi Tsujii. 2008. Task-oriented evaluation of syntactic parsers and their representations. In Proceedings of ACL-08: HLT, pages 46–54, Columbus, Ohio, June. Association for Computational Linguistics.
26. R. Morante, V. Van Asch, and W. Daelemans. 2010. Memory-based resolution of in-sentence scopes of hedge cues. CoNLL-2010: Shared Task, page 40.
27. Ngan Nguyen, Jin-Dong Kim, and Jun’ichi Tsujii. 2011. Overview of the Protein Coreference task in BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
28. Tomoko Ohta, Sampo Pyysalo, and Jun’ichi Tsujii. 2011. Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
29. S. Petrov, L. Barrett, R. Thibaux, and D. Klein. 2006. Learning accurate, compact, and interpretable tree annotation. In Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics, pages 433–440. Association for Computational Linguistics.
30. H. Poon and L. Vanderwende. 2010. Joint inference for knowledge extraction from biomedical literature. In Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, pages 813–821. Association for Computational Linguistics.
31. Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun’ichi Tsujii, and Sophia Ananiadou. 2011a. Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
32. Sampo Pyysalo, Tomoko Ohta, and Jun’ichi Tsujii. 2011b. Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
33. Laura Rimell and Stephen Clark. 2009. Porting a lexicalized-grammar parser to the biomedical domain. Journal of Biomedical Informatics, 42(5):852 – 865. Biomedical Natural Language Processing.
34. R. Sætre, K. Yoshida, A. Yakushiji, Y. Miyao, Y. Matsubyashi, and T. Ohta. 2007. AKANE system: protein-protein interaction pairs in BioCreAtIvE2 challenge, PPI-IPS subtask. In Proceedings of the Second BioCreative Challenge Workshop, pages 209–212.
35. Kenji Sagae and Jun’ichi Tsujii. 2007. Dependency parsing and domain adaptation with LR models and parser ensembles. In Proceedings of the CoNLL 2007 Shared Task.
36. G. Schneider, M. Hess, and P. Merlo. 2007. Hybrid long-distance functional dependency parsing. Unpublished PhD thesis, Institute of Computational Linguistics, University of Zurich.
37. G. Szarvas, V. Vincze, R. Farkas, and J. Csirik. 2008. The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, pages 38–45. Association for Computational Linguistics.
38. Y. Tateisi, A. Yakushiji, T. Ohta, and J. Tsujii. 2005. Syntax Annotation for the GENIA corpus. In Proceedings of the IJCNLP, pages 222–227.