메뉴 건너뛰기




Volumn 46, Issue 4, 2013, Pages 585-593

A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine

Author keywords

Information extraction; Personalized medicine; Pharmacogenomics; Text mining

Indexed keywords

BIOMEDICAL LITERATURE; EXTRACTION ALGORITHMS; INTEGRATIVE ANALYSIS; PERSONALIZED MEDICINES; PHARMACOGENOMICS; RELATIONSHIP KNOWLEDGE; SEMI-SUPERVISED LEARNING; TEXT MINING;

EID: 84880331830     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2013.04.001     Document Type: Article
Times cited : (17)

References (38)
  • 2
    • 0037421590 scopus 로고    scopus 로고
    • Pharmacogenomics: drug disposition, drug targets, and side effects
    • Evans W.E., McLeod H.L. Pharmacogenomics: drug disposition, drug targets, and side effects. N Engl J Med 2003, 348:538-549.
    • (2003) N Engl J Med , vol.348 , pp. 538-549
    • Evans, W.E.1    McLeod, H.L.2
  • 3
    • 33750332747 scopus 로고    scopus 로고
    • Pharmacogenetics and pharmacogenomics: development, science, and translation
    • Weinshilboum R.M., Wang L. Pharmacogenetics and pharmacogenomics: development, science, and translation. Annu Rev Genom Hum Genet 2006, 7:223-245.
    • (2006) Annu Rev Genom Hum Genet , vol.7 , pp. 223-245
    • Weinshilboum, R.M.1    Wang, L.2
  • 4
    • 79951782033 scopus 로고    scopus 로고
    • Pharmacogenomics at the tipping point: challenges and opportunities
    • Roden D.M., Tyndale R.F. Pharmacogenomics at the tipping point: challenges and opportunities. Clin Pharmacol Ther 2011, 89:323-327.
    • (2011) Clin Pharmacol Ther , vol.89 , pp. 323-327
    • Roden, D.M.1    Tyndale, R.F.2
  • 5
    • 48249123433 scopus 로고    scopus 로고
    • Pharmacogenomic biomarker information in drug labels approved by the United States Food and Drug Administration: prevalence of related drug use
    • Frueh F.W., Amur S., Mummaneni P., Epstein R.S., Aubert R.E., DeLuca T.M., et al. Pharmacogenomic biomarker information in drug labels approved by the United States Food and Drug Administration: prevalence of related drug use. Pharmacotherapy 2008, 28:992-998.
    • (2008) Pharmacotherapy , vol.28 , pp. 992-998
    • Frueh, F.W.1    Amur, S.2    Mummaneni, P.3    Epstein, R.S.4    Aubert, R.E.5    DeLuca, T.M.6
  • 6
    • 77950348508 scopus 로고    scopus 로고
    • DNA, drugs and chariots: on a decade of pharmacogenomics at the US FDA
    • Lesko L.J., Zineh I. DNA, drugs and chariots: on a decade of pharmacogenomics at the US FDA. Pharmacogenomics 2010, 11:507-512.
    • (2010) Pharmacogenomics , vol.11 , pp. 507-512
    • Lesko, L.J.1    Zineh, I.2
  • 7
    • 46449123868 scopus 로고    scopus 로고
    • Creating and evaluating genetic tests predictive of drug response
    • Weiss S.T. Creating and evaluating genetic tests predictive of drug response. Nat Rev Drug Discov 2008, 7:568-574.
    • (2008) Nat Rev Drug Discov , vol.7 , pp. 568-574
    • Weiss, S.T.1
  • 8
    • 82955233708 scopus 로고    scopus 로고
    • Personalizing medicine with clinical pharmacogenetics
    • Scott S.A. Personalizing medicine with clinical pharmacogenetics. Genet Med 2011 Dec, 13(12):987-995.
    • (2011) Genet Med , vol.13 , Issue.12 , pp. 987-995
    • Scott, S.A.1
  • 9
    • 0035755351 scopus 로고    scopus 로고
    • Integrating genotype and phenotype information: an overview of the PharmGKB project: pharmacogenetics research network and knowledge base
    • Klein T.E., Chang J.T., Cho M.K., Easton K.L., Fergerson R., Hewett M., et al. Integrating genotype and phenotype information: an overview of the PharmGKB project: pharmacogenetics research network and knowledge base. Pharmacogenomics J 2001, 1:167-170.
    • (2001) Pharmacogenomics J , vol.1 , pp. 167-170
    • Klein, T.E.1    Chang, J.T.2    Cho, M.K.3    Easton, K.L.4    Fergerson, R.5    Hewett, M.6
  • 10
    • 78149321695 scopus 로고    scopus 로고
    • Recent progress in automatically extracting information from the pharmacogenomic literature
    • Garten Y., Coulet A., Altman R.B. Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics 2010, 11:1467-1489.
    • (2010) Pharmacogenomics , vol.11 , pp. 1467-1489
    • Garten, Y.1    Coulet, A.2    Altman, R.B.3
  • 11
    • 4644252679 scopus 로고    scopus 로고
    • Extracting and characterizing gene-drug relationships from the literature
    • Chang J.T., Altman R.B. Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics 2004, 14:577-586.
    • (2004) Pharmacogenetics , vol.14 , pp. 577-586
    • Chang, J.T.1    Altman, R.B.2
  • 12
    • 63049114009 scopus 로고    scopus 로고
    • Pharmspresso: a text-mining tool for extraction of pharmacogenomic concepts and relationships from full text
    • Garten Y., Altman R.B. Pharmspresso: a text-mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics 2009, 10:S6.
    • (2009) BMC Bioinformatics , vol.10
    • Garten, Y.1    Altman, R.B.2
  • 13
    • 84865957041 scopus 로고    scopus 로고
    • Extraction of conditional probabilities of the relationships between drugs, diseases, and genes from PubMed guided by relationships in PharmGKB
    • Theobald M, Shah N, Shrager J. Extraction of conditional probabilities of the relationships between drugs, diseases, and genes from PubMed guided by relationships in PharmGKB. AMIA summit on translational, bioinformatics; 2009. p. 124-8.
    • (2009) AMIA summit on translational, bioinformatics , pp. 124-8
    • Theobald, M.1    Shah, N.2    Shrager, J.3
  • 14
    • 67651166638 scopus 로고    scopus 로고
    • Generating genome-scale candidate gene lists for pharmacoge-nomics
    • Hansen N.I., Brunak S., Altman R.B. Generating genome-scale candidate gene lists for pharmacoge-nomics. Clin Pharmacol Ther 2009, 86:183-189.
    • (2009) Clin Pharmacol Ther , vol.86 , pp. 183-189
    • Hansen, N.I.1    Brunak, S.2    Altman, R.B.3
  • 15
    • 84891455493 scopus 로고    scopus 로고
    • Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation
    • Wu Y, Liu M, Zheng W, Zhao Z, Xu H. Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation. Pacific symposium on biocomputing; 2012.
    • (2012) Pacific symposium on biocomputing
    • Wu, Y.1    Liu, M.2    Zheng, W.3    Zhao, Z.4    Xu, H.5
  • 18
    • 84865989623 scopus 로고    scopus 로고
    • A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text
    • Xu R., Wang Q. A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text. J Biomed Inform 2012, 45:827-834.
    • (2012) J Biomed Inform , vol.45 , pp. 827-834
    • Xu, R.1    Wang, Q.2
  • 19
    • 84874413599 scopus 로고    scopus 로고
    • An iterative searching and ranking algorithm for prioritizing pharmacogenomics genes
    • Xu R., Wang Q. An iterative searching and ranking algorithm for prioritizing pharmacogenomics genes. Int J Comput Biol Drug Des 2013, 6(1-2):18-31.
    • (2013) Int J Comput Biol Drug Des , vol.6 , Issue.1-2 , pp. 18-31
    • Xu, R.1    Wang, Q.2
  • 21
    • 33746075572 scopus 로고    scopus 로고
    • Unsupervised named entity recognition: generating gazetteers and resolving ambiguity
    • Nadeau D., Turney P., Matwin S. Unsupervised named entity recognition: generating gazetteers and resolving ambiguity. Adv Artif Intell 2006, 266-277.
    • (2006) Adv Artif Intell , pp. 266-277
    • Nadeau, D.1    Turney, P.2    Matwin, S.3
  • 23
    • 84956968949 scopus 로고    scopus 로고
    • Extracting patterns and relations from the World Wide Web
    • Brin S. Extracting patterns and relations from the World Wide Web. World Wide Web Databases 1999, 172-183.
    • (1999) World Wide Web Databases , pp. 172-183
    • Brin, S.1
  • 31
    • 83455188192 scopus 로고    scopus 로고
    • Investigation of unsupervised pattern learning techniques for bootstrap construction of a medical treatment lexicon
    • Xu R, Morgan A, Das A, Garber AM. Investigation of unsupervised pattern learning techniques for bootstrap construction of a medical treatment lexicon. Association for Computational Linguistics BioNLP Workshop; 2009. p. 63-70.
    • (2009) Association for Computational Linguistics BioNLP Workshop , pp. 63-70
    • Xu, R.1    Morgan, A.2    Das, A.3    Garber, A.M.4
  • 32
    • 79953783049 scopus 로고    scopus 로고
    • Unsupervised method for extracting machine understandable medical knowledge from a large free text collection
    • Xu R, Das A, Garber AM. Unsupervised method for extracting machine understandable medical knowledge from a large free text collection. Annual American Medical Informatics Association Symposium; 2009. p. 709-13.
    • (2009) Annual American Medical Informatics Association Symposium , pp. 709-13
    • Xu, R.1    Das, A.2    Garber, A.M.3
  • 35
    • 84880327785 scopus 로고    scopus 로고
    • PageRank: bringing order to the web. Stanford Digital Library Project, talk; August 18, [archived 2002].
    • Page L. PageRank: bringing order to the web. Stanford Digital Library Project, talk; August 18, 1997 [archived 2002].
    • (1997)
    • Page, L.1
  • 36
    • 60349110472 scopus 로고    scopus 로고
    • Data-driven methods to discover molecular determinants of serious adverse drug events
    • Chiang A.P., Butte A.J. Data-driven methods to discover molecular determinants of serious adverse drug events. Clin Pharmacol Ther 2009, 85:259-268.
    • (2009) Clin Pharmacol Ther , vol.85 , pp. 259-268
    • Chiang, A.P.1    Butte, A.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.