Semantic annotation of biomedical literature using google

Lecture Notes in Computer Science

Volumn 3482, Issue III, 2005, Pages 327-337

  Sætre, Rune ^a   Tveit, Amund ^a   Steigedal, Tonje S ^a   Lægreid, Astrid ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

Biomedical Literature Data Mining; Semantic Annotation

Indexed keywords

AUTOMATION; COMPUTER SCIENCE; DATA PROCESSING; DATABASE SYSTEMS; GLOSSARIES; LEARNING SYSTEMS; WEBSITES;

BIOMEDICAL LITERATURE DATA MINING; COMPUTATIONAL SCIENCE; CONTEXTUAL RULES; SEMANTIC ANNOTATION;

SEMANTICS;

EID: 24944531415     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/11424857_36     Document Type: Conference Paper

References (36)

1. Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jrg Hakenberg, Ulf Leser, Condrad Plake, , and Tobias Scheffer. A Support Vector Machine classifier for gene name recognition. In Proceedings of the EMBO Workshop: A Critical Assessment of Text Mining Methods in Molecular Biology, March 2004.
2. C. Blaschke, MA. Andrade, C. Ouzounis, and A. Valencia. Automatic Extraction of biological information from scientific text: Protein-protein interactions. In Proceedings of International Conference on Intelligent Systems for Molecular Biology, pages 60-67. AAAI, 1999.
3. B. Boeckmann, A. Bairoch, R. Apweiler, MC. Blatter, A. Estreicher, E. Gasteiger, MJ Martin, K Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research, 31(1):365-370, January 2003.
4. Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun Kumar Ramani, and Yuk Wah Wong. Comparative Experiments on Learning Information Extractors for Proteins and their Interactions. Journal Artificial Intelligence in Medicine: Special Issue on Summarization and Information Extraction from Medical Documents (Forthcoming), 2004.
5. Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Raymond J. Mooney, Yuk Wah Wong, Edward M. Marcotte, and Arun Kumar Ramani. Learning to Extract Proteins and their Interactions from Medline Abstracts. In Proceedings of the ICML-2003 Workshop on Machine Learning in Bioinformatics, pages 46-53, August 2003.
6. Razvan Bunescu, Ruifang Ge, Raymond J. Mooney, Edward Marcotte, and Arun Kumar Ramani. Extracting Gene and Protein Names from Biomedical Abstracts. Unpublished Technical Note, Machine Learning Research Group, University of Texas at Austin, USA, March 2002.
7. Philipp Cimiano and Steffen Staab. Learning by Googling. SIGKDD Explorations Newsletter, 6(2):24-34, December 2004.
8. J. Cowie and W. Lehnert. Information Extraction. Communications of the ACM, 39(1):80-91, January 1996.
9. Stephen Dill, Nadav Eiron, David Gibson, Daniel Gruhl, R. Guha, Anant Jhingran, Tapas Kanungo, Sridhar Rajagopalan, Andrew Tomkins, John A. Tomlin, and Jason Y. Zien. SemTag and seeker: bootstrapping the semantic web via automated semantic annotation. In Proceedings of the Twelfth International World Wide Web Conference, WWW2003, pages 178-186. ACM, 2003.
10. Shipra Dingare, Jenny Finkel, Christopher Manning, Malvina Nissim, and Beatrice Alex. Exploring the Boundaries: Gene and Protein Identification in Biomedical Text. In Proceedings of the BioCreative Workshop, March 2004.
11. Shipra Dingare, Jenny Finkel, Christopher Manning, Malvina Nissim, Beatrice Alex, and Claire Grover. Exploring the Boundaries: Gene and Protein Identification in Biomedical Text. Submitted to BMC Bioinformatics, 2004.
12. Oren Etzioni, Michael Cafarella, Doug Downey, Ana-Maria Popescu, Tal Shaked, Stephen Soderland, Daniel S. Weld, and Alexander Yates. Unsupervised Named-Entity Extraction from the Web: An Experimental Study. Submitted to Artificial Intelligence, 2004.
13. K. Fukuda, A. Tamura, T. Tsunoda, and T. Takagi. Toward information extraction: identifying protein names from biological papers. In Proceedings of Pacific Symposium on Biocomputing, pages 707-718, 1998.
14. Filip Ginter, Jorma Boberg, Jouni Jarvinen, and Tapio Salakoski. New Techniques for Disambiguation in Natural Language and Their Application to Biological Texts. Journal of Machine Learning Research, 5:605-621, June 2004.
15. Jun ichi Tsuji and Limsoon Wong. Natural Language Processing and Information Extraction in Biology. In Proceedings of the Pacific Symposium on Biocomputing 2001, pages 372-373, 2001.
16. Tor-Kristian Jenssen, Astrid Lægreid, Jan Komorowski, and Eivind Hovig. A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics, 28(1):21-28, May 2001.
17. Sittichai Jiampojamarn. Biological term extraction using classification methods. Presentation at Dalhousie Natural Language Processing Meeting, June 2004.
18. Vinay Kakade and Madhura Sharangpani. Improving the Precision of Web Search for Medical Domain using Automatic Query Expansion. Online, 2004.
19. Udo Kruschwitz. Automatically Acquired Domain Knowledge for ad hoc Search: Evaluation Results. In Proceedings of the 2003 Intl. Conf. on Natural Language Processing and Knowledge Engineering (NLP-KE'03). IEEE, 2003.
20. Sougata Mukherjea, L. Venkata Subramaniam, Gaurav Chanda, Sriram Sankararaman, Ravi Kothari, Vishal Batra, Deo Bhardwaj, and Biplav Srivastava. Enhancing a biomedical information extraction system with dictionary mining and context disambiguation. IBM Journal of Research and Development, 48(5/6):693-701, September/November 2004.
21. M. Narayanaswamy, KE Ravikumar, and K Vijay-Shanker. A biological named entity recognizer. In Proceedings of the Pacific Symposium on Biocomputing 2003, pages 427-438, 2003.
22. David Parry. A fuzzy ontology for medical document retrieval. In Proceedings of the second workshop on Australasian information security, Data Mining and Web Intelligence, and Software Internationalisation - Volume 32, pages 121-126. ACM Press, 2004.
23. JU. Pontius, L. Wagner, and GD. Schuler. The NCBI Handbook, chapter UniGene: a unified view of the transcriptome. National Center for Biotechnology Information, 2003.
24. KD Pruitt and DR Maglott. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Research, 29(1):137-140, January 2001.
25. Rune Sætre. GeneTUC, A Biolinguistic Project. (Master Project) Norwegian University of Science and Technology, Norway, June 2002.
26. Rune Sætre. Natural Language Processing of Gene Information. Master's thesis, Norwegian University of Science and Technology, Norway and CIS/LMU Munchen, Germany, April 2003.
27. Urvi Shah, Tim Finin, and Anupam Joshi. Information Retrieval on the Semantic Web. In Proceedings of CIKM 2002, pages 461-468. ACM Press, 2002.
28. Hagit Shatkay and Ronen Feldman. Mining the Biomedical Literature in the Genomic Era: An Overview. Journal of Computational Biology, 10(6):821-855, 2003.
29. Lorraine Tanabe and W. John Wilbur. Tagging gene and protein names in biomedical text. Bioinformatics, 18(8):1124-1132, 2002.
30. Manabu Torii and K. Vijay-Shanker. Using Unlabeled MEDLINE Abstracts for Biological Named Entity Classification. In Proceedings of the 13th Conference on Genome Informatics, pages 567-568, 2002.
31. Yoshimasa Tsuruoka and Jun'ichi Tsuji. Probabilistic Term Variant Generator for Biomedical Terms. In Proceedings of the 26th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, pages 167-173. ACM, July/August 2003.
32. Amund Tveit, Rune Sætre, Tonje S. Steigedal, and Astrid Lægreid. ProtChew: Automatic Extraction of Protein Names from. In Proceedings of the International Workshop on Biomedical Data Engineering (BMDE 2005, in conjunction with ICDE 2005), Tokyo, Japan, April 2005. IEEE Press (Forthcoming).
33. Limsoon Wong. A Protein Interaction Extraction System. In Proceedings of the Pacific Symposium on Biocomputing 2001, pages 520-530, 2001.
34. Limsoon Wong. Gaps in Text-based Knowledge Discovery for Biology. Drug Discovery Today, 7(17):897-898, September 2002.
35. Hong Yu, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky, and W. John Wilbur. Automatic Extraction of Gene and Protein Synonyms from MEDLINE and Journal Articles. In Proceedings of the AMIA Symposium 2002, pages 919-923, 2002.
36. Hong Yu, Vasileios Hatzivassiloglou, Andrey Rzhetsky, and W. John Wilbur. Automatically identifying gene/protein terms in MEDLINE abstracts. Journal of Biomedical Informatics, 35(5/6):322-330, October 2002.