Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011

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 26-35

  Pyysalo, Sampo ^a   Ohta, Tomoko ^a   Rak, Rafal ^c   Sullivan, Dan ^b   Mao, Chunhong ^b   Wang, Chunxia ^b   Sobral, Bruno ^b   Tsujii, Jun'ichi ^d   Ananiadou, Sophia ^c  

^a UNIVERSITY OF TOKYO   (Japan)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d MICROSOFT RESEARCH ASIA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

NATURAL LANGUAGE PROCESSING SYSTEMS;

EVENTS EXTRACTIONS; EXTRACTION METHOD; F-SCORE; INFECTIOUS DISEASE; MAIN TASKS; MOLECULAR MECHANISM; STATE-OF-THE-ART PERFORMANCE;

DISEASES;

EID: 85119282761     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (33)

1. Sophia Ananiadou, Sampo Pyysalo, Jun’ichi Tsujii, and Douglas B. Kell. 2010. Event extraction for systems biology by text mining the literature. Trends in Biotechnology, 28(7):381–390.
2. Sophia Ananiadou, Dan Sullivan, William Black, Gina-Anne Levow, Joseph J. Gillespie, Chunhong Mao, Sampo Pyysalo, BalaKrishna Kolluru, Junichi Tsujii, and Bruno Sobral. 2011. Named entity recognition for bacterial type IV secretion systems. PLoS ONE, 6(3):e14780.
3. M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, and G Sherlock. 2000. Gene ontology: tool for the unification of biology. Nature genetics, 25:25–29.
4. Jari Björne and Tapio Salakoski. 2011. Generalizing biomedical event extraction. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
5. 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.
6. Peter Corbett and Peter Murray-Rust. 2006. High-throughput identification of chemistry in life science texts. Computational Life Sciences II, pages 107–118.
7. 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.
8. Martin Gerner, Goran Nenadic, and Casey M. Bergman. 2010. LINNAEUS: a species name identification system for biomedical literature. BMC bioinformatics, 11(1):85+, February.
9. Yasuhiro Gotoh, Yoko Eguchi, Takafumi Watanabe, Sho Okamoto, Akihiro Doi, and Ryutaro Utsumi. 2010. Two-component signal transduction as potential drug targets in pathogenic bacteria. Current Opinion in Microbiology, 13(2):232–239. Cell regulation.
10. Halil Kilicoglu and Sabine Bergler. 2011. Adapting a general semantic interpretation approach to biological event extraction. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
11. Jin-Dong Kim, Tomoko Ohta, Yoshimasa Tsuruoka, Yuka Tateisi, and Nigel Collier, editors. 2004. Introduction to the bio-entity recognition task at JNLPBA, Geneva, Switzerland.
12. Jin-Dong Kim, Tomoko Ohta, and Jun’ichi Tsujii. 2008. Corpus annotation for mining biomedical events from lterature. BMC Bioinformatics, 9(1):10.
13. 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.
14. 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.
15. 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.
16. M. Krallinger, A. Morgan, L. Smith, F. Leitner, L. Tanabe, J. Wilbur, L. Hirschman, and A. Valencia. 2008. Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome biology, 9(Suppl 2):S1.
17. Tino Krell, Jess Lacal, Andreas Busch, Hortencia Silva-Jimnez, Mara-Eugenia Guazzaroni, and Juan Luis Ramos. 2010. Bacterial sensor kinases: Diversity in the recognition of environmental signals. Annual Review of Microbiology, 64(1):539–559.
18. Thorsten Mascher, John D. Helmann, and Gottfried Unden. 2006. Stimulus perception in bacterial signaltransducing histidine kinases. Microbiol. Mol. Biol. Rev., 70(4):910–938.
19. David McClosky, Mihai Surdeanu, and Christopher Manning. 2011. Event extraction as dependency parsing for bionlp 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
20. David McClosky. 2009. Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing. Ph.D. thesis, Department of Computer Science, Brown University.
21. Liam McGrath, Kelly Domico, Courtney Corley, and Bobbie-Jo Webb-Robertson. 2011. Complex biological event extraction from full text using signatures of linguistic and semantic features. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
22. Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, and Jun’ichi Tsujii. 2010. Evaluating dependency representation for event extraction. In Proceedings of COL-ING’10, pages 779–787.
23. Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang, and Jun’ichi Tsujii. 2009. Incorporating GENETAG-style annotation to GENIA corpus. In Proceedings of BioNLP’09, pages 106–107.
24. 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.
25. Sampo Pyysalo, Tomoko Ohta, Han-Cheol Cho, Dan Sullivan, Chunhong Mao, Bruno Sobral, Jun’ichi Tsujii, and Sophia Ananiadou. 2010. Towards event extraction from full texts on infectious diseases. In Proceedings of BioNLP’10, pages 132–140.
26. Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun’ichi Tsujii, and Sophia Ananiadou. 2011. Annotation guidelines for infectious diseases event corpus. Technical report, Tsujii Laboratory, University of Tokyo. To appear.
27. Sebastian Riedel and Andrew McCallum. 2011. Robust biomedical event extraction with dual decomposition and minimal domain adaptation. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
28. Sebastian Riedel, David McClosky, Mihai Surdeanu, Andrew McCallum, and Chris Manning. 2011. Model combination for event extraction in bionlp 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
29. Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught, and Sophia Ananiadou. 2008. How to make the most of NE dictionaries in statistical NER. BMC bioinformatics, 9 Suppl 11.
30. Pontus Stenetorp, Goran Topić, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, and Jun’ichi Tsujii. 2011. BioNLP Shared Task 2011: Supporting Resources. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
31. Peter Thomason and Rob Kay. 2000. Eukaryotic signal transduction via histidine-aspartate phosphorelay. J Cell Sci, 113(18):3141–3150.
32. Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, and Jun’ichi Tsujii. 2009. Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinformatics, 10(403).
33. Chunxia Wang, Jocelyn Kemp, Isabel O. Da Fonseca, Raymie C. Equi, Xiaoyan Sheng, Trevor C. Charles, and Bruno W. S. Sobral. 2010. Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvi and its phenotypic characteristics. Molecular Plant-Microbe Interactions, 23(2):153–160.