Communications of the Korean Institute of Information Scientists and Engineers (정보과학회지)

Korean Institute of Information Scientists and Engineers (한국정보과학회)
권호 표지

커널을 이용한 바이오 개체간 상호작용 추출을 위한 텍스트 마이닝 연구 동향

  • Published : 2011.02.28
⟨ Previous Next ⟩

Abstract

Keywords

Acknowledgement

Supported by : 한국연구재단

References

  1. Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii, Overview of BioNLP'09 Shared Task on Event Extraction, In Proceedings of the Workshop on BioNLP: Shared Task, 1-9, 2009.
  2. Hersh, W., Voorhees, E., TREC Genomics special issue overview, Information Retrieval, 12: 1-15, 2009. https://doi.org/10.1007/s10791-008-9076-6
  3. http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/home/wiki. cgi?page=GENIA+Project
  4. Claire Nédellec, Learning Language in Logic - Genic Interaction Extraction Challenge, In Proceedings of the 4th Learning Language in Logic Workshop (LLL05), 31-37, 2005.
  5. Martin Krallinger, Florian Leitner, Carlos Rodriguez- Penagos, Alfonso Valencia, Overview of the proteinprotein interaction annotation extraction task of Bio- Creative II, Genome Biology, 9(Suppl 2):S4, 2008. https://doi.org/10.1186/gb-2008-9-s2-s4
  6. Jin-Dong Kim, Tomoko Ohta, and Jun'ichi Tsujii, Corpus annotation for mining biomedical events from literature, BMC Bioinformatics, 9(1):10, 2008. https://doi.org/10.1186/1471-2105-9-10
  7. http://mint.bio.uniroma2.it/mint/Welcome.do
  8. Pyysalo S, Airola A, Heimonen, J, Bjrne J, Ginter F, Salakoski T: Comparative Analysis of Five Proteinprotein Interaction corpora. BMC Bioinformatics, 9 (Suppl 3):S6, 2008. https://doi.org/10.1186/1471-2105-9-S3-S6
  9. Gary D. Bader, Michael P. Cary, and Chris Sander, Pathguide: a Pathway Resource List. Nucleic Acids Research, 34(suppl 1):D504-506, 2006. https://doi.org/10.1093/nar/gkj126
  10. Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, and Rolf Apweiler, The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology, Nucleic Acids Research, 32(suppl 1):D262-266, 2004.
  11. Ono,T. et al., Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics, 17, 155-161, 2001. https://doi.org/10.1093/bioinformatics/17.2.155
  12. Fundel, K. et al., RelEx - relation extraction sing dependency parse trees, Bioinformatics, 23, 365-371, 2006.
  13. Sætre R, Sagae K, Tsujii J, Syntactic Features for Protein-Protein Interaction Extraction, In Proceedings of LBM, 2007.
  14. Makoto Miwa, Rune Sætre, Yusuke Miyao, Jun'ichi Tsujii, A Rich Feature Vector for Protein-Protein Interaction Extraction from Multiple Corpora, In Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing, 121-130, 2009.
  15. Antti Airola, Sampo Pyysalo, Jari Bjorne, Tapio Pahikkala, Filip Ginter, and Tapio Salakoski, All-paths graph kernel for protein-protein interaction extraction with evaluation of cross corpus learning, BMC Bioinformatics, 9(Suppl 11):S2, 2008. https://doi.org/10.1186/1471-2105-9-S11-S2
  16. Jari Bjorne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapi Salakoski, Extracting Complex Events with Rich Graph-Based Feature Sets, In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 10-18, 2009.
  17. Ekaterina Buyko, Erik Faessler, Joachim Wermter, Udo Hahn, Event Extraction from Trimmed Dependency Graphs, In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 19-27, 2009.
  18. Sebastian Riedel, Hong-Woo Chun, Toshihisa Takagi, Jun'ichi Tsujii, A Markov Logic Approach to Bio-Molecular Event Extraction, In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 41-49, 2009.
  19. Sleator, D. and Temperly, D., Parsing English with a Link Grammar, In Proceedings of IWPT 1993, Tilburg, 277-291, 1993.
  20. Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii, Evaluating Dependency Representation for Event Extraction, In Proceedings of COLING 2010, 779-787, 2010.
  21. Razvan C. Bunescu, Raymond J. Mooney, A Shortest Path Dependency Kernel for Relation Extraction, In Proceedings of HLT/EMNLP 2005, 724-731, 2005.
  22. Zhou G, Zhang M, Ji DH, Zhu Q: Tree Kernel-based Relation Extraction with Context-Sensitive Structured Parse Tree Information, In Proceedings of EMNLP and CNLL 2007, 728-736, 2007.
  23. Cristianini, N., Shawe-Taylor, J., An Introduction to Support Vector Machines and Other Kernel-based Learning Methods, Cambridge University Press, 2000.
  24. D. Zelenko, C. Aone, and A. Richardella, Kernel methods for relation extraction. Journal of Machine Learning Research, 3:1083-1106, 2003.
  25. Michael Collins and Nigel Duffy, Convolution kernels for natural language, In Proceedings of NIPS 14, 625-632, 2001.
  26. Seonho Kim, Juntae Yoon, Jihoon Yang, Kernel approaches for genic interaction extraction, Bioinformatics 24(1):118-126, 2008. https://doi.org/10.1093/bioinformatics/btm544
  27. Seonho Kim, Juntae Yoon, Jihoon Yang, Seog Park, Walk-weighted subsequence kernels for protein-protein interaction extraction, BMC Bioinformatics 11: 107, 2010. https://doi.org/10.1186/1471-2105-11-107