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Volumn 61, Issue 2, 2007, Pages 228-262

Biological relation extraction and query answering from MEDLINE abstracts using ontology-based text mining

Author keywords

Biological query processing; Biological relation extraction; Ontology; Text mining

Indexed keywords

ABSTRACTING; DATA MINING; DATA STRUCTURES; FEATURE EXTRACTION; INFORMATION ANALYSIS; ONTOLOGY;

EID: 33947136723     PISSN: 0169023X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.datak.2006.06.007     Document Type: Article
Times cited : (39)

References (36)
  • 1
    • 33646409836 scopus 로고    scopus 로고
    • A. Schutz, P. Buitelaar, RelExt: a tool for relation extraction from text in ontology extension, in: International Semantic Web Conference 2005, pp. 593-606.
  • 2
    • 0035236527 scopus 로고    scopus 로고
    • A. Yakushiji, Y. Teteisi, Y. Miyao, J. Tsujii, Event extraction from biomedical papers using a full parser, in: Pac Symp Biocomput, 2001, pp. 408-419.
  • 3
    • 0033655017 scopus 로고    scopus 로고
    • B.J. Stapley, G. Benoit, Bibliometrics: Information retrieval and visualization from co-occurrence of gene names in MEDLINE abstracts, in: Proceedings of the Pacific Symposium on Biocomputing, Oahu, Hawaii, 2000, pp. 529-540.
  • 4
    • 0035236048 scopus 로고    scopus 로고
    • GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
    • Friedman C., Kra P., Yu H., Krauthammer M., and Rzhetsky A. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17 Suppl. 1 (2001) s74-s82
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Friedman, C.1    Kra, P.2    Yu, H.3    Krauthammer, M.4    Rzhetsky, A.5
  • 5
    • 33947124228 scopus 로고    scopus 로고
    • C. Nobata, N. Collier, J. Tsujii, Automatic term identification and classification in biology texts, in: Proceedings of the Natural language Pacific Rim Symposium, 1999, pp. 369-375.
  • 6
    • 33947136487 scopus 로고    scopus 로고
    • D. Gavrilis, E. Dermatas, Automatic Extraction of Information from Molecular Biology Scientific, Abstracts, Specom, 2003.
  • 8
    • 33947181114 scopus 로고    scopus 로고
    • D. Proux, F. Rechenmann, L. Julliard, V. Pillet, B. Jacq, Detecting gene symbols and names in biological texts: a first step toward pertinent information extraction, in: Genome Inform Ser Workshop Genome Inform 9, 1998, pp. 72-80.
  • 9
    • 0016942292 scopus 로고
    • A space-economical suffix tree construction algorithm
    • McCreight E. A space-economical suffix tree construction algorithm. Journal of the ACM 23 1 (1976) 262-272
    • (1976) Journal of the ACM , vol.23 , Issue.1 , pp. 262-272
    • McCreight, E.1
  • 10
    • 33947141108 scopus 로고    scopus 로고
    • F. Rinaldi, G. Scheider, C. Andronis, A. Persidis, O. Konstani, Mining relations in the GENIA corpus, in: Proceedings of the 2nd European Workshop on Data Mining and Text Mining for Bioinformatics, Pisa, Italy, 24 September 2004.
  • 11
    • 14044254746 scopus 로고    scopus 로고
    • Textpresso: an ontology-based information retrieval and extraction system for biological literature
    • Muller H.M., Kenny E.E., and Strenber P.W. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PloS Biology 2 11 (2004) e309. Available from:
    • (2004) PloS Biology , vol.2 , Issue.11
    • Muller, H.M.1    Kenny, E.E.2    Strenber, P.W.3
  • 13
    • 4944229711 scopus 로고    scopus 로고
    • GENIA corpus - a semantically annotated corpus for bio-textmining
    • Kim J.-D., Ohta T., Tateisi Y., and Tsujii J. GENIA corpus - a semantically annotated corpus for bio-textmining. Bioinformatics 19 suppl. 1 (2003) i180-i182
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Kim, J.-D.1    Ohta, T.2    Tateisi, Y.3    Tsujii, J.4
  • 14
    • 33947146779 scopus 로고    scopus 로고
    • J. Kazama, T. Makino, Y. Ohta, J. Tsujii, Tuning support vector machines for biomedical named entity recognition, in: Proceedings of the ACL Workshop of the Natural Language Processing in the Biomedical Domain, Philadelphia, PA, USA, July 2002, pp. 1-8.
  • 15
    • 33947134554 scopus 로고    scopus 로고
    • J. Thomas, D. Milward, C. Ouzounis, S. Pulman, M. Carroll, Automatic extraction of protein interactions from scientific abstracts, in: Pacific Symposium on Biocomputing, 2000, pp. 538-549.
  • 16
    • 0031633368 scopus 로고    scopus 로고
    • K. Fukuda, T. Tsunoda, A. Tamura, T. Takagi, Toward information extraction: identifying protein names from biological papers, in: Proceedings of the Pacific Symposium on Biocomputing, Hawaii, 1998, pp. 707-718.
  • 17
    • 33947155484 scopus 로고    scopus 로고
    • K. Su, M. Wu, J. Chang, A corpus-based approach to automatic compound extraction, in: Proceedings of the 32nd Annual Meeting of the Association for Computational Linguistics (ACL'94).
  • 18
    • 0032776303 scopus 로고    scopus 로고
    • Molecular interaction map of the mammalian cell cycle control and DNA repair systems
    • Kohn K.W. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Molecular Biology of the Cell 10 (1999) 2703-2734
    • (1999) Molecular Biology of the Cell , vol.10 , pp. 2703-2734
    • Kohn, K.W.1
  • 19
    • 0031690080 scopus 로고    scopus 로고
    • Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families
    • Andrade M.A., and Valencia A. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 14 7 (1998) 600-607
    • (1998) Bioinformatics , vol.14 , Issue.7 , pp. 600-607
    • Andrade, M.A.1    Valencia, A.2
  • 20
    • 33645984852 scopus 로고    scopus 로고
    • An ontology-based pattern mining system for extracting information from biological texts
    • Proceedings of the 10th International Conference on Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing (RSFDGrC'05), Canada, Springer
    • Abulaish M., and Dey L. An ontology-based pattern mining system for extracting information from biological texts. Proceedings of the 10th International Conference on Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing (RSFDGrC'05), Canada. Lecture Notes in Artificial Intelligence vol. 3642, Part II (2005), Springer 420-429
    • (2005) Lecture Notes in Artificial Intelligence , vol.3642 PART II , pp. 420-429
    • Abulaish, M.1    Dey, L.2
  • 21
    • 33748850207 scopus 로고    scopus 로고
    • M. Abulaish, L. Dey, Biological ontology enhancements: a text mining framework, in: Proceedings of the 2005 IEEE/WIC/ACM Int'l Conference on Web Intelligence, France, 2005, pp. 379-385.
  • 23
    • 84880761875 scopus 로고    scopus 로고
    • M. Ciaramita, A. Gangemi, E. Ratsch, J. Saric, I. Rojas, Unsupervised learning of semantic relations between concepts of a molecular biology ontology, in: Proceedings of the 19th International Joint Conference on Artificial Intelligence (IJCAI'05), pp. 659-664.
  • 24
    • 0033290514 scopus 로고    scopus 로고
    • M. Craven, J. Kumlien, Constructing biological knowledge bases by extracting information from text sources, in: Proceedings of the 8th Int'l Conference on Intelligent Systems for Molecular Biology (ISMB'99), 1999, pp. 77-86.
  • 25
    • 33947120858 scopus 로고    scopus 로고
    • N. Collier, C. Nobata, J. Tsujii, Extracting the names of genes and gene products with a hidden Markov model, in: Proceedings of the 18th Int'l Conference on Computational Linguistics (COLING'2000), 2000, pp. 201-207.
  • 28
    • 0037250015 scopus 로고    scopus 로고
    • Protein structures and information extraction from biological texts: the PASTA system
    • Gaizauskas R., Demetriou G., Artymiuk P.J., and Willett P. Protein structures and information extraction from biological texts: the PASTA system. Bioinformatics 19 1 (2003) 135-143
    • (2003) Bioinformatics , vol.19 , Issue.1 , pp. 135-143
    • Gaizauskas, R.1    Demetriou, G.2    Artymiuk, P.J.3    Willett, P.4
  • 30
    • 33947137358 scopus 로고    scopus 로고
    • T. Berners-Lee, Semantic Web Road Map, W3C Design Issues, 1998. Available from: .
  • 31
    • 0033257971 scopus 로고    scopus 로고
    • T.C. Rindflesch, L. Hunter, A.R. Aronson, Mining molecular binding terminology from biomedical text, in: Proceedings of the AMIA Symposium, 1999, pp. 127-131.
  • 32
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen T.-K., Laegreid A., Komorowski J., and Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics 28 (2001) 21-28
    • (2001) Nature Genetics , vol.28 , pp. 21-28
    • Jenssen, T.-K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 33
    • 0035104866 scopus 로고    scopus 로고
    • Automated extraction of information on protein-protein interactions from the biological literature
    • Ono T., Hishigaki H., Tanigami A., and Takagi T. Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17 2 (2001) 155-161
    • (2001) Bioinformatics , vol.17 , Issue.2 , pp. 155-161
    • Ono, T.1    Hishigaki, H.2    Tanigami, A.3    Takagi, T.4
  • 34
    • 0002284942 scopus 로고    scopus 로고
    • Identifying the interactions between genes and genes products based on frequently seen verbs in MEDLINE abstract
    • Sekimizu T., Park H.S., and Tsujii J. Identifying the interactions between genes and genes products based on frequently seen verbs in MEDLINE abstract. Genome Informatics 9 (1998) 62-71
    • (1998) Genome Informatics , vol.9 , pp. 62-71
    • Sekimizu, T.1    Park, H.S.2    Tsujii, J.3
  • 35
    • 33947095671 scopus 로고    scopus 로고
    • T.T. Quan, S.C. Hui, T.H. Cao, FOGA: a fuzzy ontology generation framework for scholarly semantic Web, in: Proceedings of the 2004 Knowledge Discovery and Ontologies Workshop (KDO'04), Pisa, Italy, 24 September 2004.
  • 36
    • 33947139867 scopus 로고    scopus 로고
    • Y. Tateisi, T. Ohta, N. Collier, C. Nobata, J. Tsujii, Building annotated corpus in the molecular-biology domain, in: Proceedings of the COLING 2000 Workshop on Semantic Annotation and Intelligent Content, 2000, pp. 28-34.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.