Use of morphological analysis in protein name recognition

Journal of Biomedical Informatics

Volumn 37, Issue 6, 2004, Pages 471-482

  Yamamoto, Kaoru ^a   Kudo, Taku ^b   Konagaya, Akihiko ^c   Matsumoto, Yuji ^d  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b NTT Corporation   (Japan)

^c INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^d NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Changing nomenclature in biomedicine; Morphological analysis; Named entity recognition; Protein name recognition; SVMs (kernel method) and feature engineering; Tokenization and part of speech ambiguity

Indexed keywords

EXECUTION TIME; NAME RECOGNITION;

MORPHOLOGY; PROTEINS; TEXT PROCESSING;

PATTERN RECOGNITION;

PROTEIN;

ARTICLE; FUNCTIONAL MORPHOLOGY; INFORMATION PROCESSING; JAPAN; MEDICAL INFORMATICS; MEDICAL LITERATURE; MEDICAL RESEARCH; PERFORMANCE; PRIORITY JOURNAL; PROTEIN DETERMINATION; PUBLISHING; TECHNIQUE;

ABSTRACTING AND INDEXING; ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DATABASES, BIBLIOGRAPHIC; DATABASES, GENETIC; DATABASES, PROTEIN; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MARKOV CHAINS; MODELS, STATISTICAL; NAMES; NATURAL LANGUAGE PROCESSING; PROTEINS; SOFTWARE;

EID: 8444223103     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2004.08.001     Document Type: Article

References (23)

1. J. Aoe An efficient digital search algorithm by using a double-array structure IEEE Trans Software Eng 15 9 1989 1066 1077
2. E. Brill Transformation-based error-driven learning and natural language processing: a case study in part-of-speech tagging Comput Linguist 21 4 1995 543 565
3. Critical Assessment of Information Extraction systems in Biology. Available from: http://www.pdg.cnb.uam.es/BioLink/BioCreative.eval.html
4. M. Collins, and Y. Singer Unsupervised models for named entity classification Emp Methods NLP Very Large Corpora 1999 100 110
5. Fukuda K, Tsunoda T, Tamura A, Takai T. Toward information extraction: identifying protein names from biological papers. In: Proceedings of the Pacific Symposium Biocomputing '98, World Scientific, 1998, p. 705-16
6. Florian R, Ngai G. fnTBL. Available from: http://nlp.cs.jhu.edu/rflorian/ fntbl/
7. GOA. Available from: http://www.ebi.ac.uk/GOA/index.html
8. T.K. Jenssen, A. Lgreid, J. Komorowski, and E. Hovig A literature network of human genes for high-throughput analysis of gene expression Nat Genet 28 2001 21 28
9. M. Krauthammer, A. Rzhetsky, P. Morozov, and C. Friedman Using BLAST for identifying gene and protein names in journal articles Gene 259 2000 244 252
10. Kudo T, Matsumoto Y. Chunking with support vector machines. In: Proceedings of the 2nd Meeting of North American Chapter of Association for Computational Linguistics 2001, p. 192-9
11. Kudo T, Matsumoto Y. Fast methods for Kernel-based text analysis. In: Proceedings of 41st Annual Meeting of the Association for Computational Linguistics 2003, p. 24-31
12. Kudo T. YamCha. Available from: http://chasen.org/taku/software/yamcha/
13. C. Manning, and H. Schütze Foundation of Statistical Natural Language Processing 1999 MIT Press
14. M. Narayanaswamy, K.E. Ravikumar, and K. Vijay-shanker A biological named entity recognizer Pac Symp Biocomput 2003
15. T. Nobata, N. Collier, and J. Tsujii Automatic term identification and classification in biology texts Nat Lang Process Pacific Rim Symp 1999 369 374
16. Ohta T, Tateisi Y, Mima H, Tsujii J. GENIA corpus: an annotated research abstract corpus in molecular biology domain. In: Proceedings of the Human Language Technology 2002, 2002
17. Santorini B. Part-of-speech tagging guidelines for the penn treebank project. In: Linguistic Data Consortium, Penn Treebank II CD-ROM 1991
18. Shen D, Zhang J, Zhou G, Su J, Tan CL. Effective adaptation of hidden markov model-based named entity recognizer for biomedical domain. In: ACL-03 Workshop on Natural Language Processing in Biomedicine, 2003. p. 49-56
19. Takeuchi T, Collier N. Bio-Medical entity extraction using support vector machines. In: ACL-03 Workshop on Natural Language Processing in Biomedicine, 2003. p. 57-64
20. L. Tanabe, and W.J. Wilbur Tagging gene and protein names in biomedical text J Bioinformatics 18 8 2002 1124 1132
21. Tsuruoka Y, Tsujii J. Boosting Precision and recall of dictionary-based protein name recognition. In: ACL-03 Workshop on Natural Language Processing in Biomedicine, 2003. p. 41-8
22. E.F. Tjong Kim Sang, and J. Veenstra Representing text chunks Eur Chap ACL 1999 173 179
23. Yamashita T, Matsumoto Y. Language independent morphological analysis. In: 6th Applied Natural Language Processing Conference, 2000. p. 232-8