메뉴 건너뛰기




Volumn 30, Issue 3, 2013, Pages 278-285

The Functional Genomics Network in the evolution of biological text mining over the past decade

Author keywords

[No Author keywords available]

Indexed keywords

EVALUATION OF METHODS; EXPERIMENTAL DATUM; EXTRACTING INFORMATION; FUNCTIONAL GENOMICS; GENOME ANNOTATION; HIGH-THROUGHPUT GENOMICS; HISTORICAL DEVELOPMENT; TEXT MINING;

EID: 84878105593     PISSN: 18716784     EISSN: 18764347     Source Type: Journal    
DOI: 10.1016/j.nbt.2012.11.020     Document Type: Article
Times cited : (10)

References (86)
  • 1
    • 0022786956 scopus 로고
    • Fish oil, Raynaud's syndrome, and undiscovered public knowledge
    • Swanson D.R. Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspectives in Biology and Medicine 1986, 30(Autumn (1)):7-18.
    • (1986) Perspectives in Biology and Medicine , vol.30 , Issue.AUTUMN 1 , pp. 7-18
    • Swanson, D.R.1
  • 2
    • 0025265976 scopus 로고
    • Medical literature as a potential source of new knowledge
    • Swanson D.R. Medical literature as a potential source of new knowledge. Bulletin of the Medical Library Association 1990, 78(January (1)):29-37.
    • (1990) Bulletin of the Medical Library Association , vol.78 , Issue.JANUARY 1 , pp. 29-37
    • Swanson, D.R.1
  • 3
    • 0032211335 scopus 로고    scopus 로고
    • Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses
    • Smalheiser N.R., Swanson D.R. Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Computer Methods and Programs in Biomedicine 1998, 57(November (3)):149-153.
    • (1998) Computer Methods and Programs in Biomedicine , vol.57 , Issue.NOVEMBER 3 , pp. 149-153
    • Smalheiser, N.R.1    Swanson, D.R.2
  • 5
    • 0029989103 scopus 로고    scopus 로고
    • An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts
    • Wilbur W.J., Yang Y. An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Computers in Biology and Medicine 1996, 26(May (3)):209-222.
    • (1996) Computers in Biology and Medicine , vol.26 , Issue.MAY 3 , pp. 209-222
    • Wilbur, W.J.1    Yang, Y.2
  • 7
    • 0031690080 scopus 로고    scopus 로고
    • Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families
    • Andrade M.A., Valencia A. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 1998, 14(7):600-607.
    • (1998) Bioinformatics , vol.14 , Issue.7 , pp. 600-607
    • Andrade, M.A.1    Valencia, A.2
  • 10
  • 14
    • 0002284942 scopus 로고    scopus 로고
    • Identifying the interaction between genes and gene products based on frequently seen verbs in Medline abstract
    • Sekimizu T., Park H.S., Tsujii J. Identifying the interaction between genes and gene products based on frequently seen verbs in Medline abstract. Genome Inform Ser Workshop Genome Inform, vol. 9 1998, 62-71.
    • (1998) Genome Inform Ser Workshop Genome Inform, vol. 9 , pp. 62-71
    • Sekimizu, T.1    Park, H.S.2    Tsujii, J.3
  • 17
    • 16244403024 scopus 로고    scopus 로고
    • Text-mining approaches in molecular biology and biomedicine
    • Krallinger M., Erhardt R.A., Valencia A. Text-mining approaches in molecular biology and biomedicine. Drug Discovery Today 2005, 10(March (6)):439-445.
    • (2005) Drug Discovery Today , vol.10 , Issue.MARCH 6 , pp. 439-445
    • Krallinger, M.1    Erhardt, R.A.2    Valencia, A.3
  • 18
    • 51049110331 scopus 로고    scopus 로고
    • Linking genes to literature: text mining, information extraction, and retrieval applications for biology
    • Krallinger M., Valencia A., Hirschman L. Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biology 2008, 9(Suppl. 2):S8.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1    Valencia, A.2    Hirschman, L.3
  • 19
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 2000, 25(May (1)):25-29.
    • (2000) Nature Genetics , vol.25 , Issue.MAY 1 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5    Cherry, J.M.6
  • 20
    • 33947302428 scopus 로고    scopus 로고
    • A sentence sliding window approach to extract protein annotations from biomedical articles
    • Krallinger M., Padron M., Valencia A. A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics 2005, 6(Suppl. 1):S19.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Krallinger, M.1    Padron, M.2    Valencia, A.3
  • 23
    • 66549127733 scopus 로고    scopus 로고
    • Improving classification in protein structure databases using text mining
    • Koussounadis A., Redfern O.C., Jones D.T. Improving classification in protein structure databases using text mining. BMC Bioinformatics 2009, 10(May):129.
    • (2009) BMC Bioinformatics , vol.10 , Issue.MAY , pp. 129
    • Koussounadis, A.1    Redfern, O.C.2    Jones, D.T.3
  • 24
    • 84857664634 scopus 로고    scopus 로고
    • Text mining improves prediction of protein functional sites
    • Verspoor K.M., Cohn J.D., Ravikumar K.E., Wall M.E. Text mining improves prediction of protein functional sites. PLoS One 2012, 7(2):e32171.
    • (2012) PLoS One , vol.7 , Issue.2
    • Verspoor, K.M.1    Cohn, J.D.2    Ravikumar, K.E.3    Wall, M.E.4
  • 25
    • 33847119363 scopus 로고    scopus 로고
    • BBP: Brucella genome annotation with literature mining and curation
    • Xiang Z., Zheng W., He Y. BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics 2006, 7(July):347.
    • (2006) BMC Bioinformatics , vol.7 , Issue.JULY , pp. 347
    • Xiang, Z.1    Zheng, W.2    He, Y.3
  • 30
    • 70350455266 scopus 로고    scopus 로고
    • Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation
    • Van Auken K., Jaffery J., Chan J., Müller H.M., Sternberg P.W. Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics 2009, 10(July):228.
    • (2009) BMC Bioinformatics , vol.10 , Issue.JULY , pp. 228
    • Van Auken, K.1    Jaffery, J.2    Chan, J.3    Müller, H.M.4    Sternberg, P.W.5
  • 31
    • 70449720821 scopus 로고    scopus 로고
    • Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD)
    • Wiegers T.C., Davis A.P., Cohen K.B., Hirschman L., Mattingly C.J. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics 2009, 10(October):326.
    • (2009) BMC Bioinformatics , vol.10 , Issue.OCTOBER , pp. 326
    • Wiegers, T.C.1    Davis, A.P.2    Cohen, K.B.3    Hirschman, L.4    Mattingly, C.J.5
  • 33
    • 84862243600 scopus 로고    scopus 로고
    • Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database
    • bas023
    • Jamieson D.G., Gerner M., Sarafraz F., Nenadic G., Robertson DL Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. Database (Oxford) 2012, 23(April):bas023.
    • (2012) Database (Oxford) , vol.23 , Issue.APRIL
    • Jamieson, D.G.1    Gerner, M.2    Sarafraz, F.3    Nenadic, G.4    Robertson, D.L.5
  • 36
    • 84857966320 scopus 로고    scopus 로고
    • Automatic extraction of microorganisms and their habitats from free text using text mining workflows
    • Kolluru B., Nakjang S., Hirt R.P., Wipat A., Ananiadou S. Automatic extraction of microorganisms and their habitats from free text using text mining workflows. Journal of Integrative Bioinformatics 2011, 8(October (2)):184.
    • (2011) Journal of Integrative Bioinformatics , vol.8 , Issue.OCTOBER 2 , pp. 184
    • Kolluru, B.1    Nakjang, S.2    Hirt, R.P.3    Wipat, A.4    Ananiadou, S.5
  • 37
    • 79751531194 scopus 로고    scopus 로고
    • Mining metabolites: extracting the yeast metabolome from the literature
    • Nobata C., Dobson P.D., Iqbal S.A., Mendes P., Tsujii J., Kell D.B., et al. Mining metabolites: extracting the yeast metabolome from the literature. Metabolomics 2011, 7(March (1)):94-101.
    • (2011) Metabolomics , vol.7 , Issue.MARCH 1 , pp. 94-101
    • Nobata, C.1    Dobson, P.D.2    Iqbal, S.A.3    Mendes, P.4    Tsujii, J.5    Kell, D.B.6
  • 38
    • 84868014906 scopus 로고    scopus 로고
    • Automated extraction and semantic analysis of mutation impacts from the biomedical literature
    • Nona N., René W. Automated extraction and semantic analysis of mutation impacts from the biomedical literature. BMC Genomics 2012, 13(Suppl. 4):S10.
    • (2012) BMC Genomics , vol.13 , Issue.SUPPL. 4
    • Nona, N.1    René, W.2
  • 40
    • 84864051137 scopus 로고    scopus 로고
    • Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE
    • bas026
    • Névéol A., Wilbur W.J., Lu Z Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database (Oxford) 2012, 2012(June):bas026.
    • (2012) Database (Oxford) , vol.2012 , Issue.JUNE
    • Névéol, A.1    Wilbur, W.J.2    Lu, Z.3
  • 41
    • 0034766349 scopus 로고    scopus 로고
    • Mining functional information associated with expression arrays
    • Blaschke C., Oliveros J.C., Valencia A. Mining functional information associated with expression arrays. Functional & Integrative Genomics 2001, 1(March (4)):256-268.
    • (2001) Functional & Integrative Genomics , vol.1 , Issue.MARCH 4 , pp. 256-268
    • Blaschke, C.1    Oliveros, J.C.2    Valencia, A.3
  • 43
    • 0038017587 scopus 로고    scopus 로고
    • Mining microarray expression data by literature profiling
    • RESEARCH0055
    • Chaussabel D., Sher A. Mining microarray expression data by literature profiling. Genome Biology 2002, 3(September (10)). RESEARCH0055.
    • (2002) Genome Biology , vol.3 , Issue.SEPTEMBER 10
    • Chaussabel, D.1    Sher, A.2
  • 45
    • 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., Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics 2001, 28(May (1)):21-28.
    • (2001) Nature Genetics , vol.28 , Issue.MAY 1 , pp. 21-28
    • Jenssen, T.K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 47
    • 84859510774 scopus 로고    scopus 로고
    • Pathway-based evaluation in early onset colorectal cancer suggests focal adhesion and immunosuppression along with epithelial-mesenchymal transition
    • Nam S., Park T. Pathway-based evaluation in early onset colorectal cancer suggests focal adhesion and immunosuppression along with epithelial-mesenchymal transition. PLoS One 2012, 7(4):e31685.
    • (2012) PLoS One , vol.7 , Issue.4
    • Nam, S.1    Park, T.2
  • 48
    • 80052692064 scopus 로고    scopus 로고
    • Identification of hub genes related to the recovery phase of irradiation injury by microarray and integrated gene network analysis
    • Zhang J., Yang Y., Wang Y., Zhang J., Wang Z., Yin M., et al. Identification of hub genes related to the recovery phase of irradiation injury by microarray and integrated gene network analysis. PLoS One 2011, 6(9):e24680.
    • (2011) PLoS One , vol.6 , Issue.9
    • Zhang, J.1    Yang, Y.2    Wang, Y.3    Zhang, J.4    Wang, Z.5    Yin, M.6
  • 49
    • 78651299880 scopus 로고    scopus 로고
    • Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation
    • Pedicini M., Barrenäs F., Clancy T., Castiglione F., Hovig E., Kanduri K., et al. Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation. PLoS Computation Biology 2010, 6(December (12)):e1001032.
    • (2010) PLoS Computation Biology , vol.6 , Issue.DECEMBER 12
    • Pedicini, M.1    Barrenäs, F.2    Clancy, T.3    Castiglione, F.4    Hovig, E.5    Kanduri, K.6
  • 50
    • 80053219980 scopus 로고    scopus 로고
    • Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics
    • Yang X., Ye C.Y., Bisaria A., Tuskan G.A., Kalluri U.C. Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics. Plant Science 2011, 181(December (6)):675-687.
    • (2011) Plant Science , vol.181 , Issue.DECEMBER 6 , pp. 675-687
    • Yang, X.1    Ye, C.Y.2    Bisaria, A.3    Tuskan, G.A.4    Kalluri, U.C.5
  • 54
    • 63049090130 scopus 로고    scopus 로고
    • Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology
    • Tipney H.J., Leach S.M., Feng W., Spritz R., Williams T., Hunter L. Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. BMC Bioinformatics 2009, 10(February (Suppl. 2)):S12.
    • (2009) BMC Bioinformatics , vol.10 , Issue.FEBRUARY SUPPL. 2
    • Tipney, H.J.1    Leach, S.M.2    Feng, W.3    Spritz, R.4    Williams, T.5    Hunter, L.6
  • 56
    • 77953063043 scopus 로고    scopus 로고
    • Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor
    • Frijters R., Fleuren W., Toonen E.J., Tuckermann J.P., Reichardt H.M., van der Maaden H., et al. Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor. BMC Genomics 2010, 11(June):359.
    • (2010) BMC Genomics , vol.11 , Issue.JUNE , pp. 359
    • Frijters, R.1    Fleuren, W.2    Toonen, E.J.3    Tuckermann, J.P.4    Reichardt, H.M.5    Van Der Maaden, H.6
  • 57
    • 77957919799 scopus 로고    scopus 로고
    • Altered gene expression profiles in the brain, kidney, and lung of deceased neonatal cloned pigs
    • Park J., Marjani S.L., Lai L., Samuel M., Wax D., Davis S.R., et al. Altered gene expression profiles in the brain, kidney, and lung of deceased neonatal cloned pigs. Cellular Reprogramming 2010, 12(October (5)):589-597.
    • (2010) Cellular Reprogramming , vol.12 , Issue.OCTOBER 5 , pp. 589-597
    • Park, J.1    Marjani, S.L.2    Lai, L.3    Samuel, M.4    Wax, D.5    Davis, S.R.6
  • 58
    • 77949410508 scopus 로고    scopus 로고
    • Regulators of cyclin-dependent kinases are crucial for maintaining genome integrity in S phase
    • Beck H., Nähse V., Larsen M.S., Groth P., Clancy T., Lees M., et al. Regulators of cyclin-dependent kinases are crucial for maintaining genome integrity in S phase. Journal of Cell Biology 2010, 188(March (5)):629-638.
    • (2010) Journal of Cell Biology , vol.188 , Issue.MARCH 5 , pp. 629-638
    • Beck, H.1    Nähse, V.2    Larsen, M.S.3    Groth, P.4    Clancy, T.5    Lees, M.6
  • 59
    • 0036649742 scopus 로고    scopus 로고
    • Association of genes to genetically inherited diseases using data mining
    • Perez-Iratxeta C., Bork P., Andrade M.A. Association of genes to genetically inherited diseases using data mining. Nature Genetics 2002, 31(July (3)):316-319.
    • (2002) Nature Genetics , vol.31 , Issue.JULY 3 , pp. 316-319
    • Perez-Iratxeta, C.1    Bork, P.2    Andrade, M.A.3
  • 60
    • 26444581337 scopus 로고    scopus 로고
    • G2D: a tool for mining genes associated with disease
    • Perez-Iratxeta C., Wjst M., Bork P., Andrade M.A. G2D: a tool for mining genes associated with disease. BMC Genetics 2005, 6(August):45.
    • (2005) BMC Genetics , vol.6 , Issue.AUGUST , pp. 45
    • Perez-Iratxeta, C.1    Wjst, M.2    Bork, P.3    Andrade, M.A.4
  • 61
    • 15044341082 scopus 로고    scopus 로고
    • Integration of text- and data-mining using ontologies successfully selects disease gene candidates
    • Tiffin N., Kelso J.F., Powell A.R., Pan H., Bajic V.B., Hide W.A. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Research 2005, 33(March (5)):1544-1552.
    • (2005) Nucleic Acids Research , vol.33 , Issue.MARCH 5 , pp. 1544-1552
    • Tiffin, N.1    Kelso, J.F.2    Powell, A.R.3    Pan, H.4    Bajic, V.B.5    Hide, W.A.6
  • 63
    • 84863987708 scopus 로고    scopus 로고
    • Computational tools for prioritizing candidate genes: boosting disease gene discovery
    • Moreau Y., Tranchevent L.C. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nature Reviews Genetics 2012, (July).
    • (2012) Nature Reviews Genetics , Issue.JULY
    • Moreau, Y.1    Tranchevent, L.C.2
  • 64
    • 75649117442 scopus 로고    scopus 로고
    • Analysis of biological processes and diseases using text mining approaches
    • Krallinger M., Leitner F., Valencia A. Analysis of biological processes and diseases using text mining approaches. Methods in Molecular Biology 2010, 593:341-382.
    • (2010) Methods in Molecular Biology , vol.593 , pp. 341-382
    • Krallinger, M.1    Leitner, F.2    Valencia, A.3
  • 65
    • 69549108302 scopus 로고    scopus 로고
    • Extraction of human kinase mutations from literature, databases and genotyping studies
    • Krallinger M., Izarzugaza J.M., Rodriguez-Penagos C., Valencia A. Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinformatics 2009, 10(August (Suppl. 8)):S1.
    • (2009) BMC Bioinformatics , vol.10 , Issue.AUGUST SUPPL. 8
    • Krallinger, M.1    Izarzugaza, J.M.2    Rodriguez-Penagos, C.3    Valencia, A.4
  • 66
    • 4944235422 scopus 로고    scopus 로고
    • Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup
    • Yeh A.S., Hirschman L., Morgan A.A. Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup. Bioinformatics 2003, 19(Suppl. 1):i331-i339.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Yeh, A.S.1    Hirschman, L.2    Morgan, A.A.3
  • 68
    • 58149242540 scopus 로고    scopus 로고
    • Trec genomics special issue overview
    • Hersh W., Voorhees E. Trec genomics special issue overview. Information Retrieval 2009, 12(1):1-15.
    • (2009) Information Retrieval , vol.12 , Issue.1 , pp. 1-15
    • Hersh, W.1    Voorhees, E.2
  • 69
    • 0037396730 scopus 로고    scopus 로고
    • The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro
    • amon E., Magrane M., Barrell D., Binns D., Fleischmann W., Kersey P., et al. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Research 2003, 13(April (4)):662-672.
    • (2003) Genome Research , vol.13 , Issue.APRIL 4 , pp. 662-672
    • Amon, E.1    Magrane, M.2    Barrell, D.3    Binns, D.4    Fleischmann, W.5    Kersey, P.6
  • 71
    • 51049084462 scopus 로고    scopus 로고
    • Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
    • Krallinger M., Morgan A., Smith L., Leitner F., Tanabe L., Wilbur J., et al. Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biology 2008, 9(Suppl. 2):S1.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1    Morgan, A.2    Smith, L.3    Leitner, F.4    Tanabe, L.5    Wilbur, J.6
  • 72
    • 77956665000 scopus 로고    scopus 로고
    • The FEBS Letters/BioCreative II.5 experiment: making biological information accessible
    • Leitner F., Chatr-aryamontri A., Mardis S.A., Ceol A., Krallinger M., Licata L., et al. The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nature Biotechnology 2010, 28(September (9)):897-899.
    • (2010) Nature Biotechnology , vol.28 , Issue.SEPTEMBER 9 , pp. 897-899
    • Leitner, F.1    Chatr-aryamontri, A.2    Mardis, S.A.3    Ceol, A.4    Krallinger, M.5    Licata, L.6
  • 74
    • 12444250044 scopus 로고    scopus 로고
    • Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature
    • Kim J.J., Park J.C. Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature. Journal of Bioinformatics and Computational Biology 2004, 2(September (3)):551-568.
    • (2004) Journal of Bioinformatics and Computational Biology , vol.2 , Issue.SEPTEMBER 3 , pp. 551-568
    • Kim, J.J.1    Park, J.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.