Event extraction for post-translational modifications

Proceedings of the Annual Meeting of the Association for Computational Linguistics

Volumn , Issue , 2010, Pages 19-27

  Ohta, Tomoko ^a   Pyysalo, Sampo ^a   Miwa, Makoto ^a   Kim, Jin Dong ^a   Tsujii, Jun'ichi ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL LINGUISTICS; EXTRACTION; NATURAL LANGUAGE PROCESSING SYSTEMS; TRANSLATION (LANGUAGES);

EVENT TYPES; EVENTS EXTRACTIONS; EXTRACTION SYSTEMS; F-SCORE; HOMEPAGE; MODIFIED PROTEINS; POST-TRANSLATIONAL MODIFICATIONS; SCIENTIFIC PUBLICATIONS; STATE OF THE ART;

PROTEINS;

EID: 84874231679     PISSN: 0736587X     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Sophia Ananiadou, Sampo Pyysalo, Junichi Tsujii, and Douglas B. Kell. 2010. Event extraction for systems biology by text mining the literature. Trends in Biotechnology. (to appear).
2. Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, and Tapio Salakoski. 2009. Extracting complex biological events with rich graph-based feature sets. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 10-18, Boulder, Colorado, June. Association for Computational Linguistics.
3. Ekaterina Buyko, Erik Faessler, Joachim Wermter, and Udo Hahn. 2009. Event extraction from trimmed dependency graphs. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 19-27, Boulder, Colorado, June. Association for Computational Linguistics.
4. Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, and Andrey Rzhetsky. 2001. GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics, 17(Suppl. 1):S74-S82.
5. Z. Z. Hu, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu. 2005. Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics, 21(11):2759-2765.
6. Rudolf Jaenisch and Adrian Bird. 2003. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genetics, 33:245-254.
7. Jin-Dong Kim, Tomoko Ohta, and Jun'ichi Tsujii. 2008. Corpus annotation for mining biomedical events from lterature. BMC Bioinformatics, 9(1):10.
8. Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun'ichi Tsujii. 2009a. Overview of bionlp'09 shared task on event extraction. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 1-9, Boulder, Colorado, June. Association for Computational Linguistics.
9. Youngrae Kim, Hodong Lee, and Gwan-Su Yi. 2009b. Literature mining for protein acetylation. In Proceedings of LBM'09.
10. Hodong Lee, Gwan-Su Yi, and Jong C. Park. 2008. E3Miner: a text mining tool for ubiquitin-protein ligases. Nucl. Acids Res., 36(suppl.2):W416-422.
11. Matthias Mann and Ole N. Jensen. 2003. Proteomic analysis of post-translational modifications. Nature Biotechnology, 21:255-261.
12. Makoto Miwa, Rune Sætre, Jin-Dong Kim, and Jun'ichi Tsujii. 2010. Event extraction with complex event classification using rich features. Journal of Bioinformatics and Computational Biology (JBCB), 8(1):131-146, February.
13. Yusuke Miyao, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya, and Jun'ichi Tsujii. 2006. Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. In Proceedings of COLING-ACL 2006, pages 1017-1024.
14. M. Narayanaswamy, K. E. Ravikumar, and K. Vijay-Shanker. 2005. Beyond the clause: extraction of phosphorylation information from medline abstracts. Bioinformatics, 21(suppl.1):i319-327.
15. Tomoko Ohta, Yusuke Miyao, Takashi Ninomiya, Yoshimasa Tsuruoka, Akane Yakushiji, Katsuya Masuda, Jumpei Takeuchi, Kazuhiro Yoshida, Tadayoshi Hara, Jin-Dong Kim, Yuka Tateisi, and Jun'ichi Tsujii. 2006. An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing. In Proceedings of the COLING/ACL 2006 Interactive Presentation Sessions, pages 17-20.
16. Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, and Jun'ichi Tsujii. 2009. Incorporating GENETAGstyle annotation to GENIA corpus. In Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pages 106-107, Boulder, Colorado. Association for Computational Linguistics.
17. Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, and Tapio Salakoski. 2007. BioInfer: A corpus for information extraction in the biomedical domain. BMC Bioinformatics, 8(50).
18. Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboué, Wubin Weng, W. John Wilbur, Vasileios Hatzivassiloglou, and Carol Friedman. 2004. GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. Journal of Biomedical Informatics, 37(1):43-53.
19. Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, and Peer Bork. 2006. Extraction of regulatory gene/protein networks from Medline. Bioinformatics, 22(6):645-650.
20. The Gene Ontology Consortium. 2000. Gene ontology: tool for the unification of biology. Nature Genetics, 25:25-29.
21. Eric S Witze, William M Old, Katheryn A Resing, and Natalie G Ahn. 2007. Mapping protein post-translational modifications with mass spectrometry. Nature Methods, 4:798-806.
22. Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhangzhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, C.R. Vinayaka, Jian Zhang, and Winona C. Barker. 2003. The Protein Information Resource. Nucl. Acids Res., 31(1):345-347.