메뉴 건너뛰기




Volumn 1158, Issue , 2009, Pages 14-28

Creating reference datasets for systems biology applications using text mining

Author keywords

High throughput evaluation; Systems biology; Text categorization; Text mining

Indexed keywords

ACCURACY; ARTICLE; BIBLIOMETRICS; EXPERIMENTAL STUDY; FACTUAL DATABASE; INFORMATION PROCESSING; MEDICAL LITERATURE; REFERENCE DATABASE; SYSTEMS BIOLOGY;

EID: 63849195206     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.2008.03750.x     Document Type: Article
Times cited : (11)

References (59)
  • 1
    • 38549097071 scopus 로고    scopus 로고
    • The universal protein resource (UniProt)
    • UniProt Consortium.
    • UniProt Consortium. 2008. The universal protein resource (UniProt). Nucleic Acids Res. 36 : D190 D195.
    • (2008) Nucleic Acids Res. , vol.36
  • 2
    • 34547844156 scopus 로고    scopus 로고
    • Manual curation is not sufficient for annotation of genomic databases
    • Baumgartner, W.A., Jr. et al. 2007. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 23 : i41 48.
    • (2007) Bioinformatics , vol.23 , pp. 41-48
    • Baumgartner, W.A.1    Jr.et, Al.2
  • 3
    • 41249090605 scopus 로고    scopus 로고
    • Linking entries in protein interaction database to structured text: The FEBS Letters experiment
    • Ceol, A. et al. 2008. Linking entries in protein interaction database to structured text: The FEBS Letters experiment. FEBS Lett. 582 : 1171 1177.
    • (2008) FEBS Lett. , vol.582 , pp. 1171-1177
    • Ceol, A.1
  • 4
    • 41149178971 scopus 로고    scopus 로고
    • A text-mining perspective on the requirements for electronically annotated abstracts
    • Leitner, F. A. Valencia. 2008. A text-mining perspective on the requirements for electronically annotated abstracts. FEBS Lett. 582 : 1178 1181.
    • (2008) FEBS Lett. , vol.582 , pp. 1178-1181
    • Leitner, F.1    Valencia, A.2
  • 5
    • 14044254746 scopus 로고    scopus 로고
    • Textpresso: An ontology-based information retrieval and extraction system for biological literature
    • Muller, H.M. et al. 2004. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2 : e309.
    • (2004) PLoS Biol. , vol.2 , pp. 309
    • Muller, H.M.1
  • 6
    • 2642576816 scopus 로고    scopus 로고
    • A protocol for the update of references to scientific literature in biological databases
    • Perez-Iratxeta, C. et al. 2003. A protocol for the update of references to scientific literature in biological databases. Appl. Bioinformatics 2 : 189 191.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 189-191
    • Perez-Iratxeta, C.1
  • 7
    • 3342901682 scopus 로고    scopus 로고
    • Finding kinetic parameters using text mining
    • Hakenberg, J. et al. 2004. Finding kinetic parameters using text mining. Omics 8 : 131 152.
    • (2004) Omics , vol.8 , pp. 131-152
    • Hakenberg, J.1
  • 8
    • 33747859675 scopus 로고    scopus 로고
    • BABELOMICS: A systems biology perspective in the functional annotation of genome-scale experiments
    • Al-Shahrour, F. et al. 2006. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 34 : W472 W476.
    • (2006) Nucleic Acids Res. , vol.34
    • Al-Shahrour, F.1
  • 9
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen, T.K. et al. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet. 28 : 21 28.
    • (2001) Nat. Genet. , vol.28 , pp. 21-28
    • Jenssen, T.K.1
  • 10
    • 33845450589 scopus 로고    scopus 로고
    • Mining literature for systems biology
    • Roberts, P.M. 2006. Mining literature for systems biology. Brief Bioinform. 7 : 399 406.
    • (2006) Brief Bioinform. , vol.7 , pp. 399-406
    • Roberts, P.M.1
  • 11
    • 0034766349 scopus 로고    scopus 로고
    • Mining functional information associated with expression arrays
    • Blaschke, C. et al. 2001. Mining functional information associated with expression arrays. Funct. Integr. Genomics 1 : 256 268.
    • (2001) Funct. Integr. Genomics , vol.1 , pp. 256-268
    • Blaschke, C.1
  • 12
    • 34547561588 scopus 로고    scopus 로고
    • FatiGO +: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
    • Al-Shahrour, F. et al. 2007. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 35 : W91 W96.
    • (2007) Nucleic Acids Res. , vol.35
    • Al-Shahrour, F.1
  • 13
    • 34447304880 scopus 로고    scopus 로고
    • SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
    • Shatkay, H. et al. 2007. SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 23 : 1410 1417.
    • (2007) Bioinformatics , vol.23 , pp. 1410-1417
    • Shatkay, H.1
  • 14
    • 14844329372 scopus 로고    scopus 로고
    • Ranking the whole MEDLINE database according to a large training set using text indexing
    • Suomela, B.P. M.A. Andrade. 2005. Ranking the whole MEDLINE database according to a large training set using text indexing. BMC Bioinformatics 6 : 75.
    • (2005) BMC Bioinformatics , vol.6 , pp. 75
    • Suomela, B.P.1    Andrade, M.A.2
  • 15
    • 40549145521 scopus 로고    scopus 로고
    • MScanner: A classifier for retrieving Medline citations
    • Poulter, G.L. et al. 2008. MScanner: a classifier for retrieving Medline citations. BMC Bioinformatics 9 : 108.
    • (2008) BMC Bioinformatics , vol.9 , pp. 108
    • Poulter, G.L.1
  • 16
    • 34548493473 scopus 로고    scopus 로고
    • Automating document classification for the Immune Epitope Database
    • Wang, P. et al. 2007. Automating document classification for the Immune Epitope Database. BMC Bioinformatics 8 : 269.
    • (2007) BMC Bioinformatics , vol.8 , pp. 269
    • Wang, P.1
  • 17
    • 33845703344 scopus 로고    scopus 로고
    • What is a support vector machine?
    • Noble, W.S. 2006. What is a support vector machine? Nat. Biotechnol. 24 : 1565 1567.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1565-1567
    • Noble, W.S.1
  • 18
    • 33645344339 scopus 로고    scopus 로고
    • LSAT: Learning about alternative transcripts in MEDLINE
    • Shah, P.K. P. Bork. 2006. LSAT: learning about alternative transcripts in MEDLINE. Bioinformatics 22 : 857 865.
    • (2006) Bioinformatics , vol.22 , pp. 857-865
    • Shah, P.K.1    Bork, P.2
  • 19
    • 33745497535 scopus 로고    scopus 로고
    • Investigation into biomedical literature classification using support vector machines
    • Polavarapu, N. et al. 2005. Investigation into biomedical literature classification using support vector machines. Proc. IEEE Comput. Syst. Bioinform. Conf. 2005 : 366 374.
    • (2005) Proc. IEEE Comput. Syst. Bioinform. Conf. , vol.2005 , pp. 366-374
    • Polavarapu, N.1
  • 20
    • 34748876540 scopus 로고    scopus 로고
    • An effective general purpose approach for automated biomedical document classification
    • Cohen, A.M. 2006. An effective general purpose approach for automated biomedical document classification. AMIA Annu. Symp. Proc. 2006 : 161 165.
    • (2006) AMIA Annu. Symp. Proc. , vol.2006 , pp. 161-165
    • Cohen, A.M.1
  • 21
    • 33751111173 scopus 로고    scopus 로고
    • Text mining and its potential applications in systems biology
    • Ananiadou, S. et al. 2006. Text mining and its potential applications in systems biology. Trends Biotechnol. 24 : 571 579.
    • (2006) Trends Biotechnol. , vol.24 , pp. 571-579
    • Ananiadou, S.1
  • 22
    • 13444256580 scopus 로고    scopus 로고
    • Gene name ambiguity of eukaryotic nomenclatures
    • Chen, L. et al. 2005. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 21 : 248 256.
    • (2005) Bioinformatics , vol.21 , pp. 248-256
    • Chen, L.1
  • 23
    • 33947321307 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE task 1B: Normalized gene lists
    • Hirschman, L. et al. 2005. Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 6 (Suppl 1 S11.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1 , pp. 11
    • Hirschman, L.1
  • 24
    • 33644877427 scopus 로고    scopus 로고
    • The University of Minnesota biocatalysis/biodegradation database: The first decade
    • Ellis, L.B. et al. 2006. The University of Minnesota biocatalysis/ biodegradation database: the first decade. Nucleic Acids Res. 34 : D517 D521.
    • (2006) Nucleic Acids Res. , vol.34
    • Ellis, L.B.1
  • 25
    • 25144520247 scopus 로고    scopus 로고
    • ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text
    • Settles, B. 2005. ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 21 : 3191 3192.
    • (2005) Bioinformatics , vol.21 , pp. 3191-3192
    • Settles, B.1
  • 26
    • 43549101608 scopus 로고    scopus 로고
    • Text-mining assisted regulatory annotation
    • Aerts, S. et al. 2008. Text-mining assisted regulatory annotation. Genome Biol. 9 : R31.
    • (2008) Genome Biol. , vol.9 , pp. 31
    • Aerts, S.1
  • 27
    • 40549106856 scopus 로고    scopus 로고
    • Assisted curation: Does text mining really help?
    • Alex, B. et al. 2008. Assisted curation: does text mining really help? Pac. Symp. Biocomput. 2008 : 556 567.
    • (2008) Pac. Symp. Biocomput. , vol.2008 , pp. 556-567
    • Alex, B.1
  • 28
    • 0027306070 scopus 로고
    • Ecology and evolution of microbial populations for bioremediation
    • Liu, S. J.M. Suflita. 1993. Ecology and evolution of microbial populations for bioremediation. Trends Biotechnol. 11 : 344 352.
    • (1993) Trends Biotechnol. , vol.11 , pp. 344-352
    • Liu, S.1    Suflita, J.M.2
  • 29
    • 13444262329 scopus 로고    scopus 로고
    • MetaRouter: Bioinformatics for bioremediation
    • Pazos, F. et al. 2005. MetaRouter: bioinformatics for bioremediation. Nucleic Acids Res. 33 : D588 D592.
    • (2005) Nucleic Acids Res. , vol.33
    • Pazos, F.1
  • 30
    • 0242522894 scopus 로고    scopus 로고
    • The organization of the microbial biodegradation network from a systems-biology perspective
    • Pazos, F. et al. 2003. The organization of the microbial biodegradation network from a systems-biology perspective. EMBO Rep. 4 : 994 999.
    • (2003) EMBO Rep. , vol.4 , pp. 994-999
    • Pazos, F.1
  • 31
    • 34249940105 scopus 로고    scopus 로고
    • The environmental fate of organic pollutants through the global microbial metabolism
    • Gomez, M.J. et al. 2007. The environmental fate of organic pollutants through the global microbial metabolism. Mol. Syst. Biol. 3 : 114.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 114
    • Gomez, M.J.1
  • 32
    • 63849270528 scopus 로고    scopus 로고
    • Systemic approaches to biodegradation
    • In Press
    • Trigo, A. et al. 2009. Systemic approaches to biodegradation. FEMS Microbiol. Rev. (In Press 2005. Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet. 39 : 69 94.
    • (2009) FEMS Microbiol. Rev. , vol.39 , pp. 69-94
    • Trigo, A.1
  • 33
    • 33747874092 scopus 로고    scopus 로고
    • Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
    • Faure, A. et al. 2006. Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22 : e124 e131.
    • (2006) Bioinformatics , vol.22
    • Faure, A.1
  • 34
    • 33645743420 scopus 로고    scopus 로고
    • The more the merrier: Comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast
    • Marguerat, S. et al. 2006. The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast 23 : 261 277.
    • (2006) Yeast , vol.23 , pp. 261-277
    • Marguerat, S.1
  • 35
    • 33749535603 scopus 로고    scopus 로고
    • Co-evolution of transcriptional and post-translational cell-cycle regulation
    • Jensen, L.J. et al. 2006. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443 : 594 597.
    • (2006) Nature , vol.443 , pp. 594-597
    • Jensen, L.J.1
  • 36
    • 28844455307 scopus 로고    scopus 로고
    • New weakly expressed cell cycle-regulated genes in yeast
    • de Lichtenberg, U. et al. 2005. New weakly expressed cell cycle-regulated genes in yeast. Yeast 22 : 1191 1201.
    • (2005) Yeast , vol.22 , pp. 1191-1201
    • De Lichtenberg, U.1
  • 37
    • 14844285655 scopus 로고    scopus 로고
    • Comparison of computational methods for the identification of cell cycle-regulated genes
    • de Lichtenberg, U. et al. 2005. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21 : 1164 1171.
    • (2005) Bioinformatics , vol.21 , pp. 1164-1171
    • De Lichtenberg, U.1
  • 38
    • 33751331633 scopus 로고    scopus 로고
    • Morphogenesis and cell cycle progression in Candida albicans
    • Berman, J. 2006. Morphogenesis and cell cycle progression in Candida albicans. Curr. Opin. Microbiol. 9 : 595 601.
    • (2006) Curr. Opin. Microbiol. , vol.9 , pp. 595-601
    • Berman, J.1
  • 39
    • 33751292143 scopus 로고    scopus 로고
    • Cytoplasmic microtubule organization in fission yeast
    • Sawin, K.E. P.T. Tran. 2006. Cytoplasmic microtubule organization in fission yeast. Yeast 23 : 1001 1014.
    • (2006) Yeast , vol.23 , pp. 1001-1014
    • Sawin, K.E.1    Tran, P.T.2
  • 40
    • 33751238139 scopus 로고    scopus 로고
    • Eavesdropping on the cytoskeleton: Progress and controversy in the yeast morphogenesis checkpoint
    • Keaton, M.A. D.J. Lew. 2006. Eavesdropping on the cytoskeleton: progress and controversy in the yeast morphogenesis checkpoint. Curr. Opin. Microbiol. 9 : 540 546.
    • (2006) Curr. Opin. Microbiol. , vol.9 , pp. 540-546
    • Keaton, M.A.1    Lew, D.J.2
  • 41
    • 33947099463 scopus 로고    scopus 로고
    • Connecting cell-cycle activation to neurodegeneration in Drosophila
    • Khurana, V. M.B. Feany. 2007. Connecting cell-cycle activation to neurodegeneration in Drosophila. Biochim. Biophys. Acta 1772 : 446 456.
    • (2007) Biochim. Biophys. Acta , vol.1772 , pp. 446-456
    • Khurana, V.1    Feany, M.B.2
  • 42
    • 33748419116 scopus 로고    scopus 로고
    • Signaling meets chromatin during tissue regeneration in Drosophila
    • Maurange, C. et al. 2006. Signaling meets chromatin during tissue regeneration in Drosophila. Curr. Opin. Genet. Dev. 16 : 485 489.
    • (2006) Curr. Opin. Genet. Dev. , vol.16 , pp. 485-489
    • Maurange, C.1
  • 43
    • 33747818012 scopus 로고    scopus 로고
    • RNA interference pinpoints regulators of cell size and the cell cycle
    • Cully, M.J. S.J. Leevers. 2006. RNA interference pinpoints regulators of cell size and the cell cycle. Genome Biol. 7 : 219.
    • (2006) Genome Biol. , vol.7 , pp. 219
    • Cully, M.J.1    Leevers, S.J.2
  • 44
    • 33745679153 scopus 로고    scopus 로고
    • RNA interference takes flight: A new RNAi screen reveals cell cycle regulators in Drosophila cells
    • Lents, N.H. J.J. Baldassare. 2006. RNA interference takes flight: a new RNAi screen reveals cell cycle regulators in Drosophila cells. Trends Endocrinol. Metab. 17 : 173 174.
    • (2006) Trends Endocrinol. Metab. , vol.17 , pp. 173-174
    • Lents, N.H.1    Baldassare, J.J.2
  • 45
    • 33744905801 scopus 로고    scopus 로고
    • The role of polycomb group proteins in cell cycle regulation during development
    • Martinez, A.M. G. Cavalli. 2006. The role of polycomb group proteins in cell cycle regulation during development. Cell Cycle 5 : 1189 1197.
    • (2006) Cell Cycle , vol.5 , pp. 1189-1197
    • Martinez, A.M.1    Cavalli, G.2
  • 46
    • 33747496717 scopus 로고    scopus 로고
    • Cyclin-dependent kinase inhibitors in yeast, animals, and plants: A functional comparison
    • De Clercq, A. D. Inze. 2006. Cyclin-dependent kinase inhibitors in yeast, animals, and plants: a functional comparison. Crit. Rev. Biochem. Mol. Biol. 41 : 293 313.
    • (2006) Crit. Rev. Biochem. Mol. Biol. , vol.41 , pp. 293-313
    • De Clercq, A.1    Inze, D.2
  • 47
    • 33746079244 scopus 로고    scopus 로고
    • Control and regulation of the cellular responses to cold shock: The responses in yeast and mammalian systems
    • Al-Fageeh, M.B. C.M. Smales. 2006. Control and regulation of the cellular responses to cold shock: the responses in yeast and mammalian systems. Biochem. J. 397 : 247 259.
    • (2006) Biochem. J. , vol.397 , pp. 247-259
    • Al-Fageeh, M.B.1    Smales, C.M.2
  • 48
    • 0036789555 scopus 로고    scopus 로고
    • The spindle checkpoint: Structural insights into dynamic signalling
    • Musacchio, A. K.G. Hardwick. 2002. The spindle checkpoint: structural insights into dynamic signalling. Nat. Rev. Mol. Cell Biol. 3 : 731 741.
    • (2002) Nat. Rev. Mol. Cell Biol. , vol.3 , pp. 731-741
    • Musacchio, A.1    Hardwick, K.G.2
  • 49
    • 0033792092 scopus 로고    scopus 로고
    • Control of microtubule dynamics by the antagonistic activities of XMAP215 and XKCM1 in Xenopus egg extracts
    • Tournebize, R. et al. 2000. Control of microtubule dynamics by the antagonistic activities of XMAP215 and XKCM1 in Xenopus egg extracts. Nat. Cell Biol. 2 : 13 19.
    • (2000) Nat. Cell Biol. , vol.2 , pp. 13-19
    • Tournebize, R.1
  • 51
    • 0030785518 scopus 로고    scopus 로고
    • A method that allows the assembly of kinetochore components onto chromosomes condensed in clarified Xenopus egg extracts
    • Desai, A. et al. 1997. A method that allows the assembly of kinetochore components onto chromosomes condensed in clarified Xenopus egg extracts. Proc. Natl. Acad. Sci. USA 94 : 12378 12383.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 12378-12383
    • Desai, A.1
  • 52
    • 0034618565 scopus 로고    scopus 로고
    • Microtubule motors in mitosis
    • Sharp, D.J. et al. 2000. Microtubule motors in mitosis. Nature 407 : 41 47.
    • (2000) Nature , vol.407 , pp. 41-47
    • Sharp, D.J.1
  • 53
    • 0035146128 scopus 로고    scopus 로고
    • The spindle: A dynamic assembly of microtubules and motors
    • Wittmann, T. et al. 2001. The spindle: a dynamic assembly of microtubules and motors. Nat. Cell Biol. 3 : E28 E34.
    • (2001) Nat. Cell Biol. , vol.3
    • Wittmann, T.1
  • 54
    • 36249013650 scopus 로고    scopus 로고
    • ENFIN a network to enhance integrative systems biology
    • Kahlem, P. E. Birney. 2007. ENFIN a network to enhance integrative systems biology. Ann. N. Y. Acad. Sci. 1115 : 23 31.
    • (2007) Ann. N. Y. Acad. Sci. , vol.1115 , pp. 23-31
    • Kahlem, P.1    Birney, E.2
  • 55
    • 33646061361 scopus 로고    scopus 로고
    • HURP is a Ran-importin beta-regulated protein that stabilizes kinetochore microtubules in the vicinity of chromosomes
    • Sillje, H.H. et al. 2006. HURP is a Ran-importin beta-regulated protein that stabilizes kinetochore microtubules in the vicinity of chromosomes. Curr. Biol. 16 : 731 742.
    • (2006) Curr. Biol. , vol.16 , pp. 731-742
    • Sillje, H.H.1
  • 56
    • 33751569886 scopus 로고    scopus 로고
    • Timely anaphase onset requires a novel spindle and kinetochore complex comprising Ska1 and Ska2
    • Hanisch, A. et al. 2006. Timely anaphase onset requires a novel spindle and kinetochore complex comprising Ska1 and Ska2. Embo J. 25 : 5504 5515.
    • (2006) Embo J. , vol.25 , pp. 5504-5515
    • Hanisch, A.1
  • 57
    • 3042786293 scopus 로고    scopus 로고
    • A gene network for navigating the literature
    • Hoffmann, R. A. Valencia. 2004. A gene network for navigating the literature. Nat. Genet. 36 : 664.
    • (2004) Nat. Genet. , vol.36 , pp. 664
    • Hoffmann, R.1    Valencia, A.2
  • 58
    • 14644419063 scopus 로고    scopus 로고
    • Proteome analysis of the human mitotic spindle
    • Sauer, G. et al. 2005. Proteome analysis of the human mitotic spindle. Mol Cell Proteomics 4 : 35 43.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 35-43
    • Sauer, G.1
  • 59
    • 36749016685 scopus 로고    scopus 로고
    • Genome-scale RNAi profiling of cell division in human tissue culture cells
    • Kittler, R. et al. 2007. Genome-scale RNAi profiling of cell division in human tissue culture cells. Nat Cell Biol. 9 : 1401 1412.
    • (2007) Nat Cell Biol. , vol.9 , pp. 1401-1412
    • Kittler, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.