A multi-level text mining method to extract biological relationships

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002

Volumn , Issue , 2002, Pages 97-108

  Palakal, M ^a   Stephens, M ^a   Mukhopadhyay, S ^a   Raje, R ^a   Rhodes, S ^b  

^a IN 46202 USA   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; BIOINFORMATICS; DATA MINING; MARKOV PROCESSES; SEMANTICS; SPEECH PROCESSING; TEXT PROCESSING;

BIOLOGICAL OBJECTS; BIOLOGICAL RELATIONSHIPS; COMPUTATIONALLY EFFICIENT; HIDDEN MARKOV MODELS (HMMS); INTERMEDIATE RESULTS; OBJECT IDENTIFICATION; REFERENCE RESOLUTION; RELATIONSHIP EXTRACTION;

HIDDEN MARKOV MODELS;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; DATA BASE; DOCUMENTATION; EVALUATION; GENE EXPRESSION PROFILING; INFORMATION RETRIEVAL; LINGUISTICS; MEDLINE; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PUBLICATION; SYSTEMS BIOLOGY;

ABSTRACTING AND INDEXING; ALGORITHMS; ARTIFICIAL INTELLIGENCE; DATABASE MANAGEMENT SYSTEMS; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; MEDLINE; NATURAL LANGUAGE PROCESSING; PERIODICALS; SYSTEMS BIOLOGY; VOCABULARY, CONTROLLED;

EID: 18244362340     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2002.1039333     Document Type: Conference Paper

References (15)

1. Ventor, C. et al. (2001) "The Human Genome.", Science 291, 1304-1351
2. Friedman, C., Kra, P., Yu, H., Krauthamrner, M., Rzhetsky, A. (2001) "Genies: A Natural-Language Processing System for the Extraction of Molecular Pathways From Journal Articles.", Bioinformatics 17 Suppl. 1, S74-S82.
3. Blaschke, C., Andrade, M., Ouzounis, C., Valencia, A. (1999) "Automatic Extraction of Biological Information From Scientific Text: Protein-Protein Interactions.", ISMB: 8-16.
4. Stephens, M., Palakal, M., Mukhopadhyay, S., Raje, R., Mostafa, J. (2001) "Detecting Gene Relations From Medline Abstracts.", PSB 2001: 483-495.
5. Yakushiji, A., Tateisi, Y., Tsujii, J., Miyao, Y. (2000) "Use of a Full Parser for Information Extraction in Molecular Biology Domain.", Genome Informatics II: 446-447.
6. Nobata, C., Collier, N., and Tsujii, J. (2000) "Automatic Term Identification and Classification in Biology Texts.", in Proceedings of the Natural Language Pacific Rim Symposium (NLPRS '2000), 369-375.
7. Fukuda, K., Tsunoda, T., Tamura, A., and Takagi, T. (1998) "Torward Information Extraction: Identifying Protein Names From Biological Papers.", PSB 1998,705-716.
8. Collier, N., Nobata, C., and Tsujii, J. (2000a) "Extracting the Names of Genes and Gene Products with a Hidden Markov Model.", Coling2000, 201-207.
9. Chinchor, N. (1995) "MUC-5 Evaluation Metrices.", In Proceedings of the Fifth Message Understanding Conference (MUC-5), Baltimore, Maryland, USA. 69-78.
10. Hatzivassiloglou, V., Duboue, P., Rzhetsky, A. (2001) "Disambiguating Proteins, Genes, and RNA in Text: A Machine Learning Approach." Bioinformatics, 17 Suppl. 1, S97-S106.
11. Fellbaum C. (1998). WordNet: An Electronic Lexical Database. MIT Press, Cambridge, MA.
12. Jurafsky, D., and Martin, J. (2000) Speech and Language Processing. Prentice-Hall, Inc. Upper Saddle River, New Jersey.
13. Durbin, R., Eddy S., Krogh A., Mitchison G. (1998) Biological Sequence Analysis. Cambridge University Press. New York, NY.
14. Yoshida, M., Fukuda, K., and Takagi, T. (2000) "PNAD-CSS: A Workbench for Constructing a Protein Name Abbreviation Dictionary.", Bioinformatics, 16, 169-175.
15. Atschul, S.F., Gish, W., Miller, W., Myers, E., Lipman, D. (1990) "Basic Local Alignment Search Tool.", J. Mol Biol. 215, 403-410.