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Volumn 1159, Issue , 2014, Pages 95-108

Roles for text mining in protein function prediction

(1)  Verspoor, Karin M a  

a NONE

Author keywords

Biomedical natural language processing; Concept recognition in text; Gene ontology annotation; Protein function prediction; Text mining

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CELLULAR DISTRIBUTION; DATA MINING; GENE ONTOLOGY; MOLECULAR GENETICS; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; ANIMAL; GENETICS; HUMAN; INFORMATION RETRIEVAL; METABOLISM; PREDICTIVE VALUE; PROCEDURES;

EID: 84927734457     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0709-0_6     Document Type: Article
Times cited : (14)

References (36)
  • 3
    • 84878105593 scopus 로고    scopus 로고
    • The Functional Genomics Network in the evolution of biological text mining over the past decade
    • Blaschke C, Valencia A (2013) The Functional Genomics Network in the evolution of biological text mining over the past decade. N Biotechnol 30(3):278-285
    • (2013) N Biotechnol , vol.30 , Issue.3 , pp. 278-285
    • Blaschke, C.1    Valencia, A.2
  • 4
    • 20444456581 scopus 로고    scopus 로고
    • Automatic annotation of protein function
    • Valencia A (2005) Automatic annotation of protein function. Curr Opin Struct Biol 15(3):267-274
    • (2005) Curr Opin Struct Biol , vol.15 , Issue.3 , pp. 267-274
    • Valencia, A.1
  • 6
    • 33748776559 scopus 로고    scopus 로고
    • Automated protein function prediction-the genomic challenge
    • Friedberg I (2006) Automated protein function prediction-the genomic challenge. Brief Bioinform 7(3):225-242
    • (2006) Brief Bioinform , vol.7 , Issue.3 , pp. 225-242
    • Friedberg, I.1
  • 9
    • 34447304880 scopus 로고    scopus 로고
    • SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
    • Shatkay H, Hoglund A, Brady S, Blum T, Donnes P, Kohlbacher O (2007) SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 23(11): 1410-1417
    • (2007) Bioinformatics , vol.23 , Issue.11 , pp. 1410-1417
    • Shatkay, H.1    Hoglund, A.2    Brady, S.3    Blum, T.4    Donnes, P.5    Kohlbacher, O.6
  • 11
  • 12
    • 84876122166 scopus 로고    scopus 로고
    • Protein function prediction using text-based features extracted from the biomedical literature: The CAFA challenge
    • Wong A, Shatkay H (2013) Protein function prediction using text-based features extracted from the biomedical literature: the CAFA challenge. BMC Bioinformatics 14(Suppl 3):S14
    • (2013) BMC Bioinformatics , vol.14
    • Wong, A.1    Shatkay, H.2
  • 13
    • 33947302428 scopus 로고    scopus 로고
    • A sentence sliding window approach to extract protein annotations from biomedical articles
    • Krallinger M, Padron M, Valencia A (2005) A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics 6 Suppl 1
    • (2005) BMC Bioinformatics , vol.6
    • Krallinger, M.1    Padron, M.2    Valencia, A.3
  • 14
    • 33947308770 scopus 로고    scopus 로고
    • Finding genomic ontology terms in text using evidence content
    • Couto FM, Silva MJ, Coutinho PM (2005) Finding genomic ontology terms in text using evidence content. BMC Bioinformatics 6 Suppl 1
    • (2005) BMC Bioinformatics , vol.6
    • Couto, F.M.1    Silva, M.J.2    Coutinho, P.M.3
  • 15
    • 33947301798 scopus 로고    scopus 로고
    • Learning statistical models for annotating proteins with function information using biomedical text
    • Ray S, Craven M (2005) Learning statistical models for annotating proteins with function information using biomedical text. BMC Bioinformatics 6(Suppl 1):S18
    • (2005) BMC Bioinformatics , vol.6
    • Ray, S.1    Craven, M.2
  • 17
    • 13244268370 scopus 로고    scopus 로고
    • GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes
    • Martin D, Berriman M, Barton G (2004) GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 5:178
    • (2004) BMC Bioinformatics , vol.5 , pp. 178
    • Martin, D.1    Berriman, M.2    Barton, G.3
  • 18
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa A, Gotz S, Garcia-Gome J, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674-3676
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gome, J.3    Terol, J.4    Talon, M.5    Robles, M.6
  • 19
    • 84879298648 scopus 로고    scopus 로고
    • Combining heterogeneous data sources for accurate functional annotation of proteins
    • Sokolov A, Funk C, Graim K, Verspoor K, Ben-Hur A (2013) Combining heterogeneous data sources for accurate functional annotation of proteins. BMC Bioinformatics 14(Suppl 3):S10
    • (2013) BMC Bioinformatics , vol.14
    • Sokolov, A.1    Funk, C.2    Graim, K.3    Verspoor, K.4    Ben-Hur, A.5
  • 20
    • 77951518446 scopus 로고    scopus 로고
    • Hierarchical classifi cation of Gene Ontology terms using the GOstruct method
    • Sokolov A and Ben-Hur A (2010) Hierarchical classifi cation of Gene Ontology terms using the GOstruct method. Journal of Bioinformatics and Computational Biology 8(2):357-376
    • (2010) Journal of Bioinformatics and Computational Biology , vol.8 , Issue.2 , pp. 357-376
    • Sokolov, A.1    Ben-Hur, A.2
  • 22
    • 84857664634 scopus 로고    scopus 로고
    • Text mining improves prediction of protein functional sites
    • Verspoor KM, Cohn JD, Ravikumar KE, Wall ME (2012) Text mining improves prediction of protein functional sites. PLoS One 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
  • 23
    • 48249125808 scopus 로고    scopus 로고
    • Integrating proteinprotein interactions and text mining for protein function prediction
    • Jaeger S, Gaudan S, Leser U, Rebholz-Schuhmann D (2008) Integrating proteinprotein interactions and text mining for protein function prediction. BMC Bioinformatics 9(Suppl 8):S2
    • (2008) BMC Bioinformatics , vol.9
    • Jaeger, S.1    Gaudan, S.2    Leser, U.3    Rebholz-Schuhmann, D.4
  • 25
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identifi ed in enzymes using structural data
    • (Database issue)
    • Porter CT, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identifi ed in enzymes using structural data. Nucleic Acids Res 32(Database issue):D129-133
    • (2004) Nucleic Acids Res , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 27
    • 84891420537 scopus 로고    scopus 로고
    • Detection of protein catalytic sites in the biomedical literature
    • Verspoor K, MacKinlay A, Cohn JA, Wall ME (2013) Detection of protein catalytic sites in the biomedical literature. Pac Symp Biocomput 18:433-444
    • (2013) Pac Symp Biocomput , vol.18 , pp. 433-444
    • Verspoor, K.1    Mackinlay, A.2    Cohn, J.A.3    Wall, M.E.4
  • 28
    • 17144408302 scopus 로고    scopus 로고
    • The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis
    • Card GL, Peterson NA, Smith CA, Rupp B, Schick BM, Baker EN (2005) The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis. J Biol Chem 280(14): 13978-13986
    • (2005) J Biol Chem , vol.280 , Issue.14 , pp. 13978-13986
    • Card, G.L.1    Peterson, N.A.2    Smith, C.A.3    Rupp, B.4    Schick, B.M.5    Baker, E.N.6
  • 29
    • 33744499195 scopus 로고    scopus 로고
    • A categorization approach to automated ontological function annotation
    • Verspoor K, Cohn J, Mniszewski S, Joslyn C (2006) A categorization approach to automated ontological function annotation. Protein Sci 15(6):1544-1549
    • (2006) Protein Sci , vol.15 , Issue.6 , pp. 1544-1549
    • Verspoor, K.1    Cohn, J.2    Mniszewski, S.3    Joslyn, C.4
  • 32
    • 84927710624 scopus 로고    scopus 로고
    • Neji: A tool for heterogeneous biomedical concept identification
    • ISMB/ECCB 2013, Berlin, Germany
    • Campos D, Matos S, Oliveira JL (2013) Neji: a tool for heterogeneous biomedical concept identification. In: Proceedings of BioLINK SIG 2013; ISMB/ECCB 2013, Berlin, Germany, pp 28-31, See: http://biolinksig.org/past-meetings/biolink-2013/
    • (2013) Proceedings of Biolink SIG 2013 , pp. 28-31
    • Campos, D.1    Matos, S.2    Oliveira, J.L.3
  • 33
    • 84927760070 scopus 로고    scopus 로고
    • Comprehensive Benchmark of gene ontology concept recognition tools
    • ISMB/ECCB 2013, Berlin, Germany
    • Jacob C, Thomas P, Leser U (2013) Comprehensive Benchmark of gene ontology concept recognition tools. In: Proceedings of BioLINK SIG 2013; ISMB/ECCB 2013, Berlin, Germany, pp 20-26, See: http://biolinksig.org/past-meetings/biolink-2013/
    • (2013) Proceedings of Biolink SIG 2013 , pp. 20-26
    • Jacob, C.1    Thomas, P.2    Leser, U.3
  • 34
    • 84893598483 scopus 로고    scopus 로고
    • Effective topdown active learning for hierarchical text classification
    • In: Pei J, Tseng V, Cao L, Motoda H, Xu G, Springer, Berlin
    • Li X, Ling C, Wang H (2013) Effective topdown active learning for hierarchical text classification. In: Pei J, Tseng V, Cao L, Motoda H, Xu G (eds) Advances in knowledge discovery and data mining, vol 7819. Springer, Berlin, pp 233-244
    • (2013) Advances in Knowledge Discovery and Data Mining , vol.7819 , pp. 233-244
    • Li, X.1    Ling, C.2    Wang, H.3
  • 35
    • 78651375098 scopus 로고    scopus 로고
    • A survey of hierarchical classifi cation across different application domains
    • Silla CN, Freitas AA (2011) A survey of hierarchical classifi cation across different application domains. Data Min Knowl Discov 22(1):31-72
    • (2011) Data Min Knowl Discov , vol.22 , Issue.1 , pp. 31-72
    • Silla, C.N.1    Freitas, A.A.2
  • 36
    • 84879904959 scopus 로고    scopus 로고
    • Informationtheoretic evaluation of predicted ontological annotations
    • Clark WT, Radivojac P (2013) Informationtheoretic evaluation of predicted ontological annotations. Bioinformatics 29(13):i53-i61
    • (2013) Bioinformatics , vol.29 , Issue.13
    • Clark, W.T.1    Radivojac, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.