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Volumn 21, Issue 9, 2005, Pages 2059-2066

Concept-based annotation of enzyme classes

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ANALYTICAL ERROR; ARTICLE; AUTOMATION; BIBLIOGRAPHIC DATABASE; CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; DISEASE ASSOCIATION; ENZYME ANALYSIS; INFORMATION PROCESSING; LINGUISTICS; MEDICAL LITERATURE; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SCORING SYSTEM; SEMANTICS; VALIDATION PROCESS;

EID: 18744408163     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti284     Document Type: Article
Times cited : (9)

References (51)
  • 1
    • 0035752429 scopus 로고    scopus 로고
    • Effecfive mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program
    • Aronson,A. (2001) Effecfive mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc. AMIA Symp., 17-21.
    • (2001) Proc. AMIA Symp. , pp. 17-21
    • Aronson, A.1
  • 2
    • 18744366252 scopus 로고    scopus 로고
    • Filtering the UMLS Metathesaurus forMetaMap
    • Technical Report, Semantic Knowledge Representation Group
    • Aronson,A.R. (2002) Filtering the UMLS Metathesaurus forMetaMap. Technical report, Semantic Knowledge Representation Group.
    • (2002)
    • Aronson, A.R.1
  • 5
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman,H. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.1
  • 6
    • 0033292011 scopus 로고    scopus 로고
    • Automatic extraction of biological information from scienfific text: Protein-protein interactions
    • Blaschke,C. et al. (1999) Automatic extraction of biological information from scienfific text: protein-protein interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol., 60-67.
    • (1999) Proc. Int. Conf. Intell. Syst. Mol. Biol. , pp. 60-67
    • Blaschke, C.1
  • 7
    • 0345863927 scopus 로고    scopus 로고
    • The Unified Medical Language System (UMLS): Integrating biomedical terminology
    • (Database issue)
    • Bodenreider,O. (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res., 32 (Database issue), D267-D270.
    • (2004) Nucleic Acids Res. , vol.32
    • Bodenreider, O.1
  • 10
    • 9144252016 scopus 로고    scopus 로고
    • The Gene ontology annotation (GOA) database: Sharing knowledge in Uniprot with gene ontology
    • (Database issue)
    • Camon,E. et al. (2004) The Gene ontology annotation (GOA) database: sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res., 32 (Database issue), D262-D266.
    • (2004) Nucleic Acids Res. , vol.32
    • Camon, E.1
  • 11
    • 0035222129 scopus 로고    scopus 로고
    • Including biological literature improvesl, homology search
    • Chang,J. et al. (2001) Including biological literature improvesl, homology search. Pac. Symp. Biocomput., 374-383.
    • (2001) Pac. Symp. Biocomput. , pp. 374-383
    • Chang, J.1
  • 13
    • 13844283290 scopus 로고    scopus 로고
    • Orange: From experimental machine learning to interactive data mining
    • White paper, Faculty of Computer and Information Science University of Ljubljana
    • Demsar,J. and Zupan,B. (2004) Orange: from experimental machine learning to interactive data mining. White paper, Faculty of Computer and Information Science, University of Ljubljana.
    • (2004)
    • Demsar, J.1    Zupan, B.2
  • 14
    • 0036371537 scopus 로고    scopus 로고
    • Mining MedLine: Abstracts, sentences, or phrases?
    • Ding,J. et al. (2002) Mining MedLine: abstracts, sentences, or phrases? Pac. Symp. Biocomput., 326-337.
    • (2002) Pac. Symp. Biocomput. , pp. 326-337
    • Ding, J.1
  • 15
    • 4944257920 scopus 로고    scopus 로고
    • Combining NLP and probabilistic categorisation for document and term selection for Swiss-Prot medical annotation
    • Dobrokhotov,P.B. et al. (2003) Combining NLP and probabilistic categorisation for document and term selection for Swiss-Prot medical annotation. Bioinformatics, 19 (Suppl 1), i91-i94.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Dobrokhotov, P.B.1
  • 16
    • 2942549190 scopus 로고    scopus 로고
    • PreBIND and Textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine
    • Donaldson,I. et al. (2003) PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics, 4, 11.
    • (2003) BMC Bioinformatics , vol.4 , pp. 11
    • Donaldson, I.1
  • 17
    • 15944417104 scopus 로고    scopus 로고
    • Mining the biomedical literature using semantic analysis of natural language processing techniques
    • Feldman,R. et al. (2003) Mining the biomedical literature using semantic analysis of natural language processing techniques. Biosilico, 1, 69-80.
    • (2003) Biosilico , vol.1 , pp. 69-80
    • Feldman, R.1
  • 18
    • 0033764169 scopus 로고    scopus 로고
    • The small world of metabolism
    • Fell,D.A. and Wagner,A. (2000) The small world of metabolism. Nat. Biotechnol., 18, 1121-1122.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1121-1122
    • Fell, D.A.1    Wagner, A.2
  • 19
    • 0347756650 scopus 로고    scopus 로고
    • The molecular biology database collection: 2004 update
    • (Database issue)
    • Galperin,M.Y. (2004) The molecular biology database collection: 2004 update. Nucleic Acids Res., 32 (Database issue), D3-D22.
    • (2004) Nucleic Acids Res. , vol.32
    • Galperin, M.Y.1
  • 20
    • 3943106585 scopus 로고    scopus 로고
    • Accomplishments and challenges in literature data mining for biology
    • Hirschman,L. et al. (2002) Accomplishments and challenges in literature data mining for biology. Bioinformatics, 18, 1553-1561.
    • (2002) Bioinformatics , vol.18 , pp. 1553-1561
    • Hirschman, L.1
  • 21
    • 0033643234 scopus 로고    scopus 로고
    • Two applications of information extraction to biological science journal articles: Enzyme interactions and protein structures
    • Humphreys,K. et al. (2000) Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures. Pac. Symp. Biocomput., 505-516.
    • (2000) Pac. Symp. Biocomput. , pp. 505-516
    • Humphreys, K.1
  • 22
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen,T. 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.1
  • 23
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong,H. et al. (2001) Lethality and centrality in protein networks. Nature, 411, 41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1
  • 24
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong,H. et al. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1
  • 25
    • 0036081062 scopus 로고    scopus 로고
    • The KEGG databases at GenomeNet
    • Kanehisa,M. et al. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res., 30, 42-46.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 42-46
    • Kanehisa, M.1
  • 27
    • 0346463223 scopus 로고    scopus 로고
    • Essentiality and damage in metabolic networks
    • Lemke,N. et al. (2004) Essentiality and damage in metabolic networks. Bioinformatics, 20, 115-119.
    • (2004) Bioinformatics , vol.20 , pp. 115-119
    • Lemke, N.1
  • 28
    • 0036828375 scopus 로고    scopus 로고
    • Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS
    • Liu,H. et al. (2002) Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS. J. Am. Med. Inform. Assoc., 9, 621-636.
    • (2002) J. Am. Med. Inform. Assoc. , vol.9 , pp. 621-636
    • Liu, H.1
  • 29
    • 0035002541 scopus 로고    scopus 로고
    • Mining literature for protein-protein interactions
    • Marcotte,E.M. et al. (2001) Mining literature for protein-protein interactions. Bioinformatics, 17, 359-363.
    • (2001) Bioinformatics , vol.17 , pp. 359-363
    • Marcotte, E.M.1
  • 30
    • 0040920369 scopus 로고    scopus 로고
    • Online mendelian inheritance in man OMIM (TM)
    • Technical report, McKusick-Nathans Institute for Genetic Medicine Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD)
    • McKusick,V (2000) Online mendelian inheritance in man OMIM (TM). Technical report, McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD).
    • (2000)
    • McKusick, V.1
  • 31
    • 0035180309 scopus 로고    scopus 로고
    • Use of general-purpose negation detection to augment concept indexing of medical documents: A quantitative study using the UMLS
    • Mutalik,P. et al. (2001) Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS. J. Am. Med. Inform. Assoc., 8, 598-609.
    • (2001) J. Am. Med. Inform. Assoc. , vol.8 , pp. 598-609
    • Mutalik, P.1
  • 32
    • 0035895239 scopus 로고    scopus 로고
    • The structure of scientific collaboration networks
    • Newman,M.E. (2001) The structure of scientific collaboration networks. Proc. Natl Acad. Sci. USA, 98, 404-409.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 404-409
    • Newman, M.E.1
  • 33
    • 0035104866 scopus 로고    scopus 로고
    • Automated extraction of information on protein-protein interactions from the biological literature
    • Ono,T. et al. (2001) Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics, 17, 155-161.
    • (2001) Bioinformatics , vol.17 , pp. 155-161
    • Ono, T.1
  • 34
    • 0032233649 scopus 로고    scopus 로고
    • An ontological analysis of the UMLS Methathesaurus
    • Pisanelli,D.M. et al. (1998) An ontological analysis of the UMLS Methathesaurus. Proc. AMIA Symp., 810-814.
    • (1998) Proc. AMIA Symp. , pp. 810-814
    • Pisanelli, D.M.1
  • 36
    • 0036366650 scopus 로고    scopus 로고
    • Robust relational parsing over biomedical literature: Extracting inhibit relations
    • Pustejovsky,J. et al. (2002) Robust relational parsing over biomedical literature: extracting inhibit relations. Pac. Symp. Biocomput., 362-373.
    • (2002) Pac. Symp. Biocomput. , pp. 362-373
    • Pustejovsky, J.1
  • 38
    • 0033657546 scopus 로고    scopus 로고
    • EDGAR: Extraction of drugs, genes and relations from the biomedical literature
    • Rindflesch,T.C. et al. (2000b) EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac. Symp. Biocomput., 517-528.
    • (2000) Pac. Symp. Biocomput. , pp. 517-528
    • Rindflesch, T.C.1
  • 39
    • 0345863907 scopus 로고    scopus 로고
    • BRENDA, the enzyme database: Updates and major new developments
    • (Database issue)
    • Schomburg,I. et al. (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res., 32 (Database issue), D431-D433.
    • (2004) Nucleic Acids Res. , vol.32
    • Schomburg, I.1
  • 40
    • 0033655017 scopus 로고    scopus 로고
    • Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in MedLine abstracts
    • Stapley,B. and Benoit,G. (2000) Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in MedLine abstracts. Pac. Symp. Biocomput., 529-540.
    • (2000) Pac. Symp. Biocomput. , pp. 529-540
    • Stapley, B.1    Benoit, G.2
  • 41
    • 14044268098 scopus 로고    scopus 로고
    • The large-scale structure of semantic networks: Statistical analysis and a model of semantic growth
    • Steyvers,M. and Tenenbaum,J.B. (2005) The large-scale structure of semantic networks: Statistical analysis and a model of semantic growth. Cognitive Science, 29.
    • (2005) Cognitive Science , vol.29
    • Steyvers, M.1    Tenenbaum, J.B.2
  • 42
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • Strogatz,S.H. (2001) Exploring complex networks. Nature, 410, 268-276.
    • (2001) Nature , vol.410 , pp. 268-276
    • Strogatz, S.H.1
  • 43
    • 0642311815 scopus 로고    scopus 로고
    • Identifying functional relationships among human genes by systematic analysis of biological literature
    • Tao,Y.-C. and Leibel,R. (2002) Identifying functional relationships among human genes by systematic analysis of biological literature. BMC Bioinformatics, 3, 16.
    • (2002) BMC Bioinformatics , vol.3 , pp. 16
    • Tao, Y.-C.1    Leibel, R.2
  • 44
    • 0242559066 scopus 로고    scopus 로고
    • Extraction of protein interaction information from unstructured text using a context-free grammar
    • Temkin,J.M. and Gilder,M.R. (2003) Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics, 19, 2046-2053.
    • (2003) Bioinformatics , vol.19 , pp. 2046-2053
    • Temkin, J.M.1    Gilder, M.R.2
  • 45
    • 18744414399 scopus 로고    scopus 로고
    • TouchGraph LLC
    • TouchGraph Technical report, Open Source
    • TouchGraph (2002) TouchGraph LLC. Technical report, Open Source.
    • (2002)
  • 46
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts,D.J. and Strogatz,S.H. (1998) Collective dynamics of 'small-world' networks. Nature, 393, 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 47
    • 0035337361 scopus 로고    scopus 로고
    • Using concepts in literature-based discovery: Simulating Swanson's Raynaud-fish oil and migraine-magnesium discoveries
    • Weeber,M. et al. (2001) Using concepts in literature-based discovery: Simulating Swanson's Raynaud-fish oil and migraine-magnesium discoveries. JASIST, 52, 548-577.
    • (2001) JASIST , vol.52 , pp. 548-577
    • Weeber, M.1
  • 48
    • 1042269463 scopus 로고    scopus 로고
    • Shared relationship analysis: Ranking set cohesion and commonalities within a literature-derived relationship network
    • Wren,J.D. and Garner,H.R. (2004) Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics, 20, 191-198.
    • (2004) Bioinformatics , vol.20 , pp. 191-198
    • Wren, J.D.1    Garner, H.R.2
  • 49
    • 1342330525 scopus 로고    scopus 로고
    • Knowledge discovery by automated identification and ranking of implicit relationships
    • Wren,J.D. et al. (2004) Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics, 20, 389-398.
    • (2004) Bioinformatics , vol.20 , pp. 389-398
    • Wren, J.D.1
  • 50
    • 27144441097 scopus 로고    scopus 로고
    • An evaluation of statistical approaches to text categorization
    • Yang,Y. (1999) An evaluation of statistical approaches to text categorization. Information Retrieval, 1, 69-90.
    • (1999) Information Retrieval , vol.1 , pp. 69-90
    • Yang, Y.1
  • 51
    • 4944235422 scopus 로고    scopus 로고
    • Evaluation of text data mining for database curation: Lessons learned from the KDD Challenge Cup
    • Yeh,A.S. et al. (2003) Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup. Bioinformatics, 19 (Suppl 1), 1331-1339.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1 , pp. 1331-1339
    • Yeh, A.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.