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Volumn 45, Issue 5, 2012, Pages 870-878

Systematic identification of pharmacogenomics information from clinical trials

Author keywords

Clinical outcome; Clinical trial; Pharmacogenomics; Text mining

Indexed keywords

CANDIDATE GENES; CLINICAL OUTCOME; CLINICAL TRIAL; CROSSLINKS; FACTUAL KNOWLEDGE; HIGH-THROUGHPUT; KNOWLEDGE BASIS; MUTANT ALLELES; PHARMACOGENOMICS; RECENT PROGRESS; SYSTEMATIC IDENTIFICATION; TEXT MINING;

EID: 84865961913     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2012.04.005     Document Type: Article
Times cited : (21)

References (45)
  • 1
    • 0033569516 scopus 로고    scopus 로고
    • Pharmacogenomics: translating functional genomics into rational therapeutics
    • Evans W.E., Relling M.V. Pharmacogenomics: translating functional genomics into rational therapeutics. Science 1999, 286(5439):487-491.
    • (1999) Science , vol.286 , Issue.5439 , pp. 487-491
    • Evans, W.E.1    Relling, M.V.2
  • 2
    • 18744369628 scopus 로고    scopus 로고
    • Pharmacogenomics and the drug discovery pipeline: when should it be implemented?
    • Penny M.A., McHale D. Pharmacogenomics and the drug discovery pipeline: when should it be implemented?. Am J Pharmacogenomics 2005, 5(1):53-62.
    • (2005) Am J Pharmacogenomics , vol.5 , Issue.1 , pp. 53-62
    • Penny, M.A.1    McHale, D.2
  • 3
    • 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(3):167-170.
    • (2001) Pharmacogenomics J , vol.1 , Issue.3 , 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
  • 4
    • 77950352522 scopus 로고    scopus 로고
    • Pharmacogenomics and bioinformatics: PharmGKB
    • Thorn C.F., Klein T.E., Altman R.B. Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics 2010, 11(4):501-505.
    • (2010) Pharmacogenomics , vol.11 , Issue.4 , pp. 501-505
    • Thorn, C.F.1    Klein, T.E.2    Altman, R.B.3
  • 6
    • 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(10):1467-1489.
    • (2010) Pharmacogenomics , vol.11 , Issue.10 , pp. 1467-1489
    • Garten, Y.1    Coulet, A.2    Altman, R.B.3
  • 7
    • 2442692780 scopus 로고    scopus 로고
    • Empirical evidence for selective reporting of outcomes in randomized trials: comparison of protocols to published articles
    • Chan A.W., Hrobjartsson A., Haahr M.T., Gotzsche P.C., Altman D.G. Empirical evidence for selective reporting of outcomes in randomized trials: comparison of protocols to published articles. JAMA 2004, 291(20):2457-2465.
    • (2004) JAMA , vol.291 , Issue.20 , pp. 2457-2465
    • Chan, A.W.1    Hrobjartsson, A.2    Haahr, M.T.3    Gotzsche, P.C.4    Altman, D.G.5
  • 8
    • 40449088049 scopus 로고    scopus 로고
    • Medicine. Moving toward transparency of clinical trials
    • Zarin D.A., Tse T. Medicine. Moving toward transparency of clinical trials. Science 2008, 319(5868):1340-1342.
    • (2008) Science , vol.319 , Issue.5868 , pp. 1340-1342
    • Zarin, D.A.1    Tse, T.2
  • 9
    • 0013557454 scopus 로고    scopus 로고
    • The Food and Drug Administration Modernization Act of 1997. Pub. L. No
    • The Food and Drug Administration Modernization Act of 1997. Pub. L. No. 105-115, 113; 1997.
    • (1997) , vol.113 , pp. 105-115
  • 10
    • 84875803720 scopus 로고    scopus 로고
    • ClinicalTrials.gov. <>
    • ClinicalTrials.gov. http://clinicaltrials.gov/.
  • 11
    • 56149107209 scopus 로고    scopus 로고
    • Leveraging semantic knowledge in IRB databases to improve translation science
    • Hurdle JF, Botkin J, Rindflesch TC. Leveraging semantic knowledge in IRB databases to improve translation science. AMIA Annu Symp Proc; 2007. p. 349-53.
    • (2007) AMIA Annu Symp Proc; , pp. 349-53
    • Hurdle, J.F.1    Botkin, J.2    Rindflesch, T.C.3
  • 12
    • 4544370265 scopus 로고    scopus 로고
    • Trial registration: a great idea switches from ignored to irresistible
    • Rennie D. Trial registration: a great idea switches from ignored to irresistible. JAMA 2004, 292(11):1359-1362.
    • (2004) JAMA , vol.292 , Issue.11 , pp. 1359-1362
    • Rennie, D.1
  • 13
    • 67650269170 scopus 로고    scopus 로고
    • Extracting subject demographic information from abstracts of randomized clinical trial reports
    • Xu R., Garten Y., Supekar K.S., Das A.K., Altman R.B., Garber A.M. Extracting subject demographic information from abstracts of randomized clinical trial reports. Stud Health Technol Inform 2007, 129(Pt 1):550-554.
    • (2007) Stud Health Technol Inform , vol.129 , Issue.PART 1 , pp. 550-554
    • Xu, R.1    Garten, Y.2    Supekar, K.S.3    Das, A.K.4    Altman, R.B.5    Garber, A.M.6
  • 14
    • 34748896536 scopus 로고    scopus 로고
    • Combining text classification and Hidden Markov Modeling techniques for categorizing sentences in randomized clinical trial abstracts
    • Xu R, Supekar K, Huang Y, Das A, Garber A. Combining text classification and Hidden Markov Modeling techniques for categorizing sentences in randomized clinical trial abstracts. AMIA Annu Symp Proc; 2006. p. 824-8.
    • (2006) AMIA Annu Symp Proc , pp. 824-8
    • Xu, R.1    Supekar, K.2    Huang, Y.3    Das, A.4    Garber, A.5
  • 16
    • 34547656228 scopus 로고    scopus 로고
    • The application of discovery toxicology and pathology towards the design of safer pharmaceutical lead candidates
    • Kramer J.A., Sagartz J.E., Morris D.L. The application of discovery toxicology and pathology towards the design of safer pharmaceutical lead candidates. Nat Rev Drug Discov 2007, 6(8):636-649.
    • (2007) Nat Rev Drug Discov , vol.6 , Issue.8 , pp. 636-649
    • Kramer, J.A.1    Sagartz, J.E.2    Morris, D.L.3
  • 17
    • 28044466277 scopus 로고    scopus 로고
    • Introduction to drug utilization research
    • Oslo, Norway: World Health Organization
    • Introduction to drug utilization research. Oslo, Norway: World Health Organization; 2003. p. 8.
    • (2003) , pp. 8
  • 18
    • 84875814346 scopus 로고    scopus 로고
    • ClinicalTrials.gov identifier to be added to MEDLINE®/PubMed® data
    • ClinicalTrials.gov identifier to be added to MEDLINE®/PubMed® data. http://www.nlm.nih.gov/pubs/techbull/mj05/mj05_ct.html.
  • 19
    • 77950350248 scopus 로고    scopus 로고
    • Genetic polymorphisms of cytochrome P450 enzymes influence metabolism of the antidepressant escitalopram and treatment response
    • Tsai M.H., Lin K.M., Hsiao M.C., Shen W.W., Lu M.L., Tang H.S., et al. Genetic polymorphisms of cytochrome P450 enzymes influence metabolism of the antidepressant escitalopram and treatment response. Pharmacogenomics 2010, 11(4):537-546.
    • (2010) Pharmacogenomics , vol.11 , Issue.4 , pp. 537-546
    • Tsai, M.H.1    Lin, K.M.2    Hsiao, M.C.3    Shen, W.W.4    Lu, M.L.5    Tang, H.S.6
  • 20
    • 0037161062 scopus 로고    scopus 로고
    • Polymorphism of the thymidylate synthase gene and outcome of acute lymphoblastic leukaemia
    • Krajinovic M., Costea I., Chiasson S. Polymorphism of the thymidylate synthase gene and outcome of acute lymphoblastic leukaemia. Lancet 2002, 359(9311):1033-1034.
    • (2002) Lancet , vol.359 , Issue.9311 , pp. 1033-1034
    • Krajinovic, M.1    Costea, I.2    Chiasson, S.3
  • 21
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: from information retrieval to biological discovery
    • Jensen L.J., Saric J., Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 2006, 7(2):119-129.
    • (2006) Nat Rev Genet , vol.7 , Issue.2 , pp. 119-129
    • Jensen, L.J.1    Saric, J.2    Bork, P.3
  • 22
    • 1042269470 scopus 로고    scopus 로고
    • GAPSCORE: finding gene and protein names one word at a time
    • Chang J.T., Schutze H., Altman R.B. GAPSCORE: finding gene and protein names one word at a time. Bioinformatics 2004, 20(2):216-225.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 216-225
    • Chang, J.T.1    Schutze, H.2    Altman, R.B.3
  • 23
    • 34547879631 scopus 로고    scopus 로고
    • MutationFinder: a high-performance system for extracting point mutation mentions from text
    • Caporaso J.G., Baumgartner W.A., Randolph D.A., Cohen K.B., Hunter L. MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics 2007, 23(14):1862-1865.
    • (2007) Bioinformatics , vol.23 , Issue.14 , pp. 1862-1865
    • Caporaso, J.G.1    Baumgartner, W.A.2    Randolph, D.A.3    Cohen, K.B.4    Hunter, L.5
  • 24
    • 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(Suppl. 2(S6)).
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 2 S6
    • Garten, Y.1    Altman, R.B.2
  • 26
    • 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. Summit on Translat Bioinforma; 2009. p. 124-8.
    • (2009) Summit on Translat Bioinforma , pp. 124-8
    • Theobald, M.1    Shah, N.2    Shrager, J.3
  • 27
    • 78149308924 scopus 로고    scopus 로고
    • Using text to build semantic networks for pharmacogenomics
    • Coulet A., Shah N.H., Garten Y., Musen M., Altman R.B. Using text to build semantic networks for pharmacogenomics. J Biomed Inform 2010, 43(6):1009-1019.
    • (2010) J Biomed Inform , vol.43 , Issue.6 , pp. 1009-1019
    • Coulet, A.1    Shah, N.H.2    Garten, Y.3    Musen, M.4    Altman, R.B.5
  • 28
    • 84873032104 scopus 로고    scopus 로고
    • Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application
    • Coulet A, Shah N, Hunter L, Barral C, Altman RB. Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application. Pac Symp Biocomput, 2010. p. 485-7.
    • (2010) Pac Symp Biocomput , pp. 485-7
    • Coulet, A.1    Shah, N.2    Hunter, L.3    Barral, C.4    Altman, R.B.5
  • 29
    • 84865964232 scopus 로고    scopus 로고
    • Mining the pharmacogenomics literature - workshop introduction
    • Cohen KB, Garten Y, Hahn U, Shah NH. Mining the pharmacogenomics literature - workshop introduction. Pac Symp Biocomput; 2011. p. 362-3.
    • (2011) Pac Symp Biocomput , pp. 362-3
    • Cohen, K.B.1    Garten, Y.2    Hahn, U.3    Shah, N.H.4
  • 30
    • 79952761747 scopus 로고    scopus 로고
    • A practical method for transforming free-text eligibility criteria into computable criteria
    • Tu S.W., Peleg M., Carini S., Bobak M., Ross J., Rubin D., et al. A practical method for transforming free-text eligibility criteria into computable criteria. J Biomed Inform 2011, 44(2):239-250.
    • (2011) J Biomed Inform , vol.44 , Issue.2 , pp. 239-250
    • Tu, S.W.1    Peleg, M.2    Carini, S.3    Bobak, M.4    Ross, J.5    Rubin, D.6
  • 34
    • 34247370651 scopus 로고    scopus 로고
    • Essie: a concept-based search engine for structured biomedical text
    • Ide N.C., Loane R.F., Demner-Fushman D. Essie: a concept-based search engine for structured biomedical text. J Am Med Inform Assoc 2007, 14(3):253-263.
    • (2007) J Am Med Inform Assoc , vol.14 , Issue.3 , pp. 253-263
    • Ide, N.C.1    Loane, R.F.2    Demner-Fushman, D.3
  • 36
    • 84964928019 scopus 로고    scopus 로고
    • Semi-automatically inducing semantic classes of clinical research eligibility criteria using UMLS and hierarchical clustering
    • Luo Z, Johnson SB, Weng C. Semi-automatically inducing semantic classes of clinical research eligibility criteria using UMLS and hierarchical clustering. In: AMIA annual symposium proceedings. Washington, DC, USA; 2010. p. 487-91.
    • (2010) AMIA annual symposium proceedings. Washington, DC, USA , pp. 487-91
    • Luo, Z.1    Johnson, S.B.2    Weng, C.3
  • 37
    • 84875814326 scopus 로고    scopus 로고
    • Well known PGx gene-drug relationships
    • Well known PGx gene-drug relationships. http://www.pharmgkb.org/resources/forScientificUsers/well_known_pairs_of_gene-drug_pgx_relationships.jsp.
  • 38
    • 84875805422 scopus 로고    scopus 로고
    • PubMed®. <>
    • PubMed®. http://www.ncbi.nlm.nih.gov/pubmed/.
  • 39
    • 84875810797 scopus 로고    scopus 로고
    • Medical Subject Headings (MeSH®). <>
    • Medical Subject Headings (MeSH®). http://www.nlm.nih.gov/mesh/.
  • 40
    • 84875806382 scopus 로고    scopus 로고
    • How are pharmacogenomics articles annotated in PharmGKB? <>
    • How are pharmacogenomics articles annotated in PharmGKB? http://www.pharmgkb.org/resources/faqs.jsp#FAQs-annotatedPKPD.
  • 41
    • 6344276917 scopus 로고    scopus 로고
    • Mining MEDLINE for implicit links between dietary substances and diseases
    • Srinivasan P., Libbus B. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 2004, 20(Suppl. 1):i290-i296.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Srinivasan, P.1    Libbus, B.2
  • 42
    • 13444278595 scopus 로고    scopus 로고
    • Using literature-based discovery to identify disease candidate genes
    • Hristovski D., Peterlin B., Mitchell J.A., Humphrey S.M. Using literature-based discovery to identify disease candidate genes. Int J Med Inform 2005, 74(2-4):289-298.
    • (2005) Int J Med Inform , vol.74 , Issue.2-4 , pp. 289-298
    • Hristovski, D.1    Peterlin, B.2    Mitchell, J.A.3    Humphrey, S.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.