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Volumn 4, Issue 1, 2008, Pages 64-80

Extracting protein-protein interactions from MEDLINE using the hidden vector state model

Author keywords

Bioinformatics; Hidden vector state model; Information extraction; PPIs; Protein protein interactions

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; MEDICAL INFORMATION SYSTEM; MEDLINE; MODEL; PROTEIN PROTEIN INTERACTION; STATISTICAL ANALYSIS;

EID: 39449096977     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2008.017164     Document Type: Article
Times cited : (8)

References (29)
  • 1
    • 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. (1998) 'Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families', Bioinformatic, Vol. 14, No. 7, pp.600-607.
    • (1998) Bioinformatic , vol.14 , Issue.7 , pp. 600-607
    • Andrade, M.A.1    Valencia, A.2
  • 2
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The biomolecular interaction network database
    • Bader, G.D., Betel, D. and Hogue, C.W. (2003) 'BIND: the biomolecular interaction network database', Nucleic Acids Research, Vol. 31, No. 1, pp.248-250.
    • (2003) Nucleic Acids Research , vol.31 , Issue.1 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 3
    • 1642405506 scopus 로고    scopus 로고
    • Achieving high-accuracy text-to-speech with machine learning
    • Damper, B, Ed, Chapman and Hall
    • Bakiri, G. and Dietterich, T.G. (2002) 'Achieving high-accuracy text-to-speech with machine learning', in Damper, B. (Ed.): Data Mining in Speech Synthesis, Chapman and Hall.
    • (2002) Data Mining in Speech Synthesis
    • Bakiri, G.1    Dietterich, T.G.2
  • 4
    • 0036522638 scopus 로고    scopus 로고
    • The frame-based module of the SUISEKI information extraction system
    • Blaschke, C. and Valencia, A. (2002) 'The frame-based module of the SUISEKI information extraction system', IEEE Intelligent Systems, Vol. 17, No. 2, pp.14-20.
    • (2002) IEEE Intelligent Systems , vol.17 , Issue.2 , pp. 14-20
    • Blaschke, C.1    Valencia, A.2
  • 6
    • 2942549190 scopus 로고    scopus 로고
    • PreBIND and textomy-mining the biomedical literature for protein-protein interactions using a support vector machine
    • Donaldson, I., Martin, J., de Bruijn, B. and Wolting, C. (2003) 'PreBIND and textomy-mining the biomedical literature for protein-protein interactions using a support vector machine', BMC Bioinformatics, Vol. 4, No. 11.
    • (2003) BMC Bioinformatics , vol.4 , Issue.11
    • Donaldson, I.1    Martin, J.2    de Bruijn, B.3    Wolting, C.4
  • 7
    • 9644303420 scopus 로고    scopus 로고
    • Semantic processing using the hidden vector state model
    • He, Y. and Young, S. (2005) 'Semantic processing using the hidden vector state model', Computer Speech and Language, Vol. 19, No. 1, pp.85-106.
    • (2005) Computer Speech and Language , vol.19 , Issue.1 , pp. 85-106
    • He, Y.1    Young, S.2
  • 8
    • 9144248312 scopus 로고    scopus 로고
    • Hermjakob, H., Montecchi-Palazzi, L. and Lewington, C. (2004) 'IntAct: an open source molecular interaction database', Nucleic Acids Research, 1, No. 32, Database Issue, pp.452-455.
    • Hermjakob, H., Montecchi-Palazzi, L. and Lewington, C. (2004) 'IntAct: an open source molecular interaction database', Nucleic Acids Research, Vol. 1, No. 32, Database Issue, pp.452-455.
  • 9
    • 33947304181 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE: Critical assessment of information extraction for biology
    • Hirschman, L., Yeh, A., Blaschke, C. and Valencia, A. (2004) 'Overview of BioCreAtIvE: critical assessment of information extraction for biology', BMC Bioinformatics, Vol. 6, Suppl. 1, p.S1.
    • (2004) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hirschman, L.1    Yeh, A.2    Blaschke, C.3    Valencia, A.4
  • 10
    • 12344282809 scopus 로고    scopus 로고
    • Discovering patterns to extract protein-protein interactions from full text
    • Huang, M., Zhu, X. and Hao, Y. (2004) 'Discovering patterns to extract protein-protein interactions from full text', Bioinformatics, Vol. 20, No. 18, pp.3604-3612.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3604-3612
    • Huang, M.1    Zhu, X.2    Hao, Y.3
  • 11
    • 0031209168 scopus 로고    scopus 로고
    • Using out-of-domain data to improve in-domain language models
    • Iyer, R., Ostendorf, M. and Gish, H. (1997) 'Using out-of-domain data to improve in-domain language models', IEEE Signal Processing Letters, Vol. 4, No. 9, pp.221-223.
    • (1997) IEEE Signal Processing Letters , vol.4 , Issue.9 , pp. 221-223
    • Iyer, R.1    Ostendorf, M.2    Gish, H.3
  • 12
    • 4944229711 scopus 로고    scopus 로고
    • Kim, J.D., Ohta, T., Tateisi, Y. and Tsujii, J. (2003) 'GENIA corpus-semantically annotated corpus for bio-textmining', Bioinformatics, 19, Suppl. 1, pp.i180-182.
    • Kim, J.D., Ohta, T., Tateisi, Y. and Tsujii, J. (2003) 'GENIA corpus-semantically annotated corpus for bio-textmining', Bioinformatics, Vol. 19, Suppl. 1, pp.i180-182.
  • 13
    • 85128385376 scopus 로고    scopus 로고
    • Log-linear interpolation of language models
    • Sydney, Australia, November, pp
    • Klakow, D. (1998) 'Log-linear interpolation of language models', Proc. Intl. Conf. on Spoken Language Processing, Sydney, Australia, November, pp.1695-1698.
    • (1998) Proc. Intl. Conf. on Spoken Language Processing , pp. 1695-1698
    • Klakow, D.1
  • 14
    • 0142192295 scopus 로고    scopus 로고
    • Conditional random fields: Probabilistic models for segmenting and labeling sequence data
    • Morgan Kaufmann, San Francisco, CA. pp
    • Lafferty, J., McCallum, A. and Pereira, F. (2001) 'Conditional random fields: probabilistic models for segmenting and labeling sequence data', International Conference Machine Learning, Morgan Kaufmann, San Francisco, CA. pp.282-289.
    • (2001) International Conference Machine Learning , pp. 282-289
    • Lafferty, J.1    McCallum, A.2    Pereira, F.3
  • 15
    • 0032203257 scopus 로고    scopus 로고
    • Gradient-based learning applied to document recognition
    • LeCun, Y., Bottou, L., Bengio, Y. and Haffner, P. (1998) 'Gradient-based learning applied to document recognition', Proceedings of the IEEE, Vol. 86, No. 11, pp.2278-2324.
    • (1998) Proceedings of the IEEE , vol.86 , Issue.11 , pp. 2278-2324
    • LeCun, Y.1    Bottou, L.2    Bengio, Y.3    Haffner, P.4
  • 16
    • 0035002541 scopus 로고    scopus 로고
    • Mining literature for protein-protein interactions
    • Marcotte, E.M., Xenarios, I. and Eisenberg, D. (2001) 'Mining literature for protein-protein interactions', Bioinformatics, Vol. 17, No. 4, pp.359-363.
    • (2001) Bioinformatics , vol.17 , Issue.4 , pp. 359-363
    • Marcotte, E.M.1    Xenarios, I.2    Eisenberg, D.3
  • 18
    • 85009145359 scopus 로고    scopus 로고
    • Interpolation of stochastic grammar and word bigram models in natural language understanding
    • Beijing, China, October
    • Martin, S., Kellner, A. and Portele, T. (2000) 'Interpolation of stochastic grammar and word bigram models in natural language understanding', Proc. Intl. Conf. on Spoken Language Processing, Beijing, China, October, Vol. 1, pp.234-237.
    • (2000) Proc. Intl. Conf. on Spoken Language Processing , vol.1 , pp. 234-237
    • Martin, S.1    Kellner, A.2    Portele, T.3
  • 19
    • 0000747663 scopus 로고    scopus 로고
    • Maximum entropy Markov models for information extraction and segmentation
    • Morgan Kaufmann, San Francisco, CA, pp
    • McCallum, A., Freitag, D. and Pereira, F. (2000) 'Maximum entropy Markov models for information extraction and segmentation', Proc. 17th International Conf. on Machine Learning, Morgan Kaufmann, San Francisco, CA, pp.591-598.
    • (2000) Proc. 17th International Conf. on Machine Learning , pp. 591-598
    • McCallum, A.1    Freitag, D.2    Pereira, F.3
  • 20
    • 0035104866 scopus 로고    scopus 로고
    • Automated extraction of information on protein-protein interactions from the biological literature
    • Ono, T., Hishigaki, H., Tanigam, A. and Takagi, T. (2001) 'Automated extraction of information on protein-protein interactions from the biological literature', Bioinformatics, Vol. 17, No. 2, pp.155-161.
    • (2001) Bioinformatics , vol.17 , Issue.2 , pp. 155-161
    • Ono, T.1    Hishigaki, H.2    Tanigam, A.3    Takagi, T.4
  • 22
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner, L.R. (1989) 'A tutorial on hidden Markov models and selected applications in speech recognition', Proceedings of the IEEE, Vol. 77, No. 2, pp.257-286.
    • (1989) Proceedings of the IEEE , vol.77 , Issue.2 , pp. 257-286
    • Rabiner, L.R.1
  • 24
    • 4544269058 scopus 로고    scopus 로고
    • Corrective language modeling for large vocabulary asr with the perceptron algorithm
    • Montreal, Quebec, Canada, pp
    • Roark, B., Saraclar, M. and Collins, M. (2004) 'Corrective language modeling for large vocabulary asr with the perceptron algorithm', Proceedings of ICASSP, Montreal, Quebec, Canada, pp.749-752.
    • (2004) Proceedings of ICASSP , pp. 749-752
    • Roark, B.1    Saraclar, M.2    Collins, M.3
  • 25
    • 0033655017 scopus 로고    scopus 로고
    • Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts
    • Hawaii, USA, pp
    • Stapley, B. and Benoit, G. (2000) 'Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts', Proceedings of the Pacific Symposium on Biocomputing, Hawaii, USA, pp.529-540.
    • (2000) Proceedings of the Pacific Symposium on Biocomputing , pp. 529-540
    • Stapley, B.1    Benoit, G.2
  • 26
    • 0242559066 scopus 로고    scopus 로고
    • Extraction of protein interaction information from unstructured text using a context-free grammar
    • Temkin, J.M. and Gilder, M.R. (2003) 'Extraction of protein interaction information from unstructured text using a context-free grammar', Bioinformatics, Vol. 19, No. 16, pp.2046-2053.
    • (2003) Bioinformatics , vol.19 , Issue.16 , pp. 2046-2053
    • Temkin, J.M.1    Gilder, M.R.2
  • 27
    • 13444249988 scopus 로고    scopus 로고
    • von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D. and Krupp, M. (2005) 'STRING: known and predicted protein-protein associations, integrated and transferred across organisms', Nucleic Acids Research, 33, Database Issue, pp.433-437.
    • von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D. and Krupp, M. (2005) 'STRING: known and predicted protein-protein associations, integrated and transferred across organisms', Nucleic Acids Research, Vol. 33, Database Issue, pp.433-437.
  • 29
    • 33746654139 scopus 로고    scopus 로고
    • Extracting protein-protein interactions from the literature using the hidden vector state model
    • Reading, UK, pp
    • Zhou, D., He, Y. and Kwoh, C.K. (2006) 'Extracting protein-protein interactions from the literature using the hidden vector state model', International Workshop on Bioinformatics Research and Applications, Reading, UK, pp.718-725.
    • (2006) International Workshop on Bioinformatics Research and Applications , pp. 718-725
    • Zhou, D.1    He, Y.2    Kwoh, C.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.