A probabilistic model for identifying protein names and their name boundaries

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Volumn , Issue , 2003, Pages 251-258

  Seki, K ^a   Mostafa, J ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; SYNTACTICS;

BIOMEDICAL TEXT; NATURAL LANGUAGE PROCESSING TOOLS; PART-OF-SPEECH TAGGER; PROBABILISTIC MODELING; PROCESSING OVERHEAD; STATE OF THE ART; SYNTACTIC PARSERS; SYSTEM OUTPUT;

PROTEINS;

EID: 84960375509     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2003.1227325     Document Type: Conference Paper

References (24)

1. L. A. Adamic, D. Wilkinson, B. A. Huberman, and E. Adar. A literature based method for identifying gene-disease connections. In Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB 2002), pages 109-117, 2002.
2. S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17):3389-3402, 1997.
3. N. Collier, C. Nobata, and J. Tsujii. Extracting the names of genes and gene products with a hidden markov model. In Proceedings of the 18th International Conference on Computational Linguistics, pages 201-207, 2000.
4. B. de Bruijn and J. Martin. Literature mining in molecular biology. In Proceedings of the Workshop on Natural Language Processing in Biomedical Applications (NLPBA 2002), pages 7-18, 2002.
5. K. Franzén. Proteinhalt i text (protein concentration in text), 2003. Retrieved March 27, 2003, from http://www.sics.se/humle/projects/prothalt/.
6. K. Franzén, G. Eriksson, F. Olsson, L. Asker, and P. Lidén. Exploiting syntax when detecting protein names in text. In Workshop on Natural Language Processing in Biomedical Applications, 2002.
7. C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics, 17 Suppl. 1:S74-S82, 2001.
8. Y. Fu, J. Mostafa, and K. Seki. Protein association discovery in biomedical literature. In Proceedings of the Joint Conference on Digital Libraries (JCDL 2003), pages 113-115, 2003.
9. K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi. Toward information extraction: Identifying protein names from biological papers. In Proceedings of the Pacific Symposium on Biocomputing, volume 3, pages 705-716, 1998.
10. R. Grishman and B. Sundheim. Message Understanding Conference - 6: A brief history. In Proceedings of the 16th International Conference on Computational Linguistics, pages 466-471, 1996.
11. L. Hirschman, J. C. Park, J. Tsujii, L. Wong, and C. H. Wu. Accomplishments and challenges in literature data mining for biology. Bioinformatics, 18(12):1553-1561, 2002.
12. J. Kazama, T. Makino, Y. Ohta, and J. Tsujii. Tuning support vector machines for biomedical named entity recognition. In Proceedings of the Workshop on Natural Language Processing in the Biomedical Domain, pages 1-8, 2002.
13. M. Krauthammer, A. Rzhetsky, P. Morozov, and C. Friedman. Using BLAST for identifying gene and protein names in journal articles. GENE, (259):245-252, 2001.
14. M. Narayanaswamy, K. E. Ravikumar, and V. K. Shanker. A biological named entity recognizer. In Proceedings of the Pacific Symposium on Biocomputing, volume 8, 2003.
15. S. Ng and M. Wong. Toward routine automatic pathway discovery from on-line scientific text abstracts. In Proceedings of Genome Informatics, volume 10, pages 104-112, 1999.
16. C. Nobata, N. Collier, and J. Tsujii. Automatic term identification and classification in biology texts. In Proceedings of the 5th Natural Language Processing Pacific Rim Symposium, pages 369-374, 1999.
17. F. Olsson, G. Eriksson, K. Franzén, L. Asker, and P. Lidén. Notions of correctness when evaluating protein name taggers. In Proceedings of the 19th International Conference on Computational Linguistics, 2002.
18. M. Palakal, M. Stephens, S. Mukhopadhyay, R. Raje, and S. Rhodes. A multi-level text mining method to extract biological relationships. In Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB 2002), pages 97-108, 2002.
19. D. Proux, F. Rechenmann, and L. Julliard. Detecting gene symbols and names in biological texts: A first step toward pertinent information extraction. In Proceedings of Genome Informatics, volume 9, pages 72-80, 1998.
20. K. Seki and J. Mostafa. An approach to protein name extraction using heuristics and a dictionary. In Proceedings of the American Society for Information Science and Technology Annual Conference (ASIST 2003), October 2003. (To appear).
21. T. Sekimizu, H. S. Park, and J. Tsujii. Identifying the interaction between genes and gene products based on frequently seen verbs in MEDLINE abstracts. In Proceedings of Genome Informatics, volume 9, pages 62-71, 1998.
22. L. Tanabe and J. Wilbur. Tagging gene and protein names in full text article. In Proceedings of the Workshop on Natural Language Processing in the Biomedical Domain, pages 9-13, 2002.
23. J. Thomas, D. Milward, C. Ouzounis, S. Pulman, and M. Carroll. Automatic extraction of protein interactions from scientific abstracts. In Proceedings of the Pacific Symposium on Biocomputing, volume 5, pages 538-549, 2000.
24. I. H. Witten and T. C. Bell. The zero-frequency problem: Estimating the probabilities of novel events in adaptive text compression. IEEE Transactions on Information Theory, 37(4):1085-1094, 1991.