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Volumn 28, Issue 16, 2012, Pages 2154-2161

BioContext: An integrated text mining system for large-scale extraction and contextualization of biomolecular events

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCHEMISTRY; BIOLOGY; COMPUTER PROGRAM; DATA MINING; MEDLINE; METHODOLOGY;

EID: 84865085964     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts332     Document Type: Article
Times cited : (41)

References (33)
  • 1
    • 80053320011 scopus 로고    scopus 로고
    • pubmed2ensembl: a resource for mining the biological literature on genes
    • Baran, J. et al. (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PLoS ONE, 6, e24716.
    • (2011) PLoS ONE , vol.6
    • Baran, J.1
  • 2
    • 85121797056 scopus 로고    scopus 로고
    • Extracting complex biological events with rich graph-based feature sets
    • Boulder, Colorado
    • Björne, J. et al. (2009) Extracting complex biological events with rich graph-based feature sets. In Proceedings of the Workshop on BioNLP: Shared Task. Boulder, Colorado, pp. 10-18.
    • (2009) Proceedings of the Workshop on BioNLP: Shared Task , pp. 10-18
    • Björne, J.1
  • 3
    • 77954190136 scopus 로고    scopus 로고
    • Complex event extraction at PubMed scale
    • Björne, J. et al. (2010a) Complex event extraction at PubMed scale, Bioinformatics, 26, i382-390.
    • (2010) Bioinformatics , vol.26
    • Björne, J.1
  • 4
    • 84857112501 scopus 로고    scopus 로고
    • Scaling up Biomedical Event Extraction to the Entire PubMed
    • Uppsala, Sweden
    • Björne, J. et al. (2010b) Scaling up Biomedical Event Extraction to the Entire PubMed. BioNLP 2010, Uppsala, Sweden, pp. 28-36.
    • (2010) BioNLP 2010A , pp. 28-36
    • Björne, J.1
  • 5
    • 77949265998 scopus 로고    scopus 로고
    • Beyond genes, proteins, and abstracts: identifying scientific claims from full-text biomedical articles
    • Blake, C. (2010) Beyond genes, proteins, and abstracts: identifying scientific claims from full-text biomedical articles. J. Biomed. Inform., 43, 173-189.
    • (2010) J. Biomed. Inform. , vol.43 , pp. 173-189
    • Blake, C.1
  • 6
    • 75549083295 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2009 update
    • Ceol, A. et al. (2009) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res., 38, D532-D539.
    • (2009) Nucleic Acids Res , vol.38
    • Ceol, A.1
  • 7
    • 84865092694 scopus 로고    scopus 로고
    • Department of Computer Science, University of Sheffield
    • Cunningham, H. et al. (2011) Processing with GATE. Department of Computer Science, University of Sheffield.
    • (2011) Processing with GATE
    • Cunningham, H.1
  • 8
    • 77949431037 scopus 로고    scopus 로고
    • LINNAEUS: a species name identification system for biomedical literature
    • Gerner, M. et al. (2010a) LINNAEUS: a species name identification system for biomedical literature. BMC Bioinformatics, 11, 85.
    • (2010) BMC Bioinformatics , vol.11 , pp. 85
    • Gerner, M.1
  • 9
    • 84908464360 scopus 로고    scopus 로고
    • An exploration of mining gene expression mentions and their anatomical locations from biomedical text
    • Uppsala, Sweden
    • Gerner, M. et al. (2010b) An exploration of mining gene expression mentions and their anatomical locations from biomedical text. In Proceedings of the BioNLP workshop. Uppsala, Sweden, pp. 72-80.
    • (2010) Proceedings of the BioNLP workshop , pp. 72-80
    • Gerner, M.1
  • 10
    • 49549120418 scopus 로고    scopus 로고
    • Inter-species normalization of gene mentions with GNAT
    • Hakenberg, J. et al. (2008) Inter-species normalization of gene mentions with GNAT. Bioinformatics, 24, i126-i132.
    • (2008) Bioinformatics , vol.24
    • Hakenberg, J.1
  • 11
    • 80053441509 scopus 로고    scopus 로고
    • The GNAT library for local and remote gene mention normalization
    • Hakenberg, J. et al. (2011) The GNAT library for local and remote gene mention normalization. Bioinformatics, 27, 2769-2771.
    • (2011) Bioinformatics , vol.27 , pp. 2769-2771
    • Hakenberg, J.1
  • 12
    • 79959381867 scopus 로고    scopus 로고
    • ChemicalTagger: a tool for semantic text-mining in chemistry
    • Hawizy, L. et al. (2011) ChemicalTagger: a tool for semantic text-mining in chemistry. J. Cheminform., 3, 17.
    • (2011) J. Cheminform. , vol.3 , pp. 17
    • Hawizy, L.1
  • 13
    • 79953325924 scopus 로고    scopus 로고
    • GeneTUKit: a software for document-level gene normalization
    • Huang, M. et al. (2011) GeneTUKit: a software for document-level gene normalization. Bioinformatics, 27, 1032-1033.
    • (2011) Bioinformatics , vol.27 , pp. 1032-1033
    • Huang, M.1
  • 14
    • 83455255105 scopus 로고    scopus 로고
    • U-Compare bio-event meta-service: compatible BioNLP event extraction services
    • Kano, Y. et al. (2011) U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics, 12, 481.
    • (2011) BMC Bioinformatics , vol.12 , pp. 481
    • Kano, Y.1
  • 15
    • 40749087717 scopus 로고    scopus 로고
    • Corpus annotation for mining biomedical events from literature
    • Kim, J.D. et al. (2008) Corpus annotation for mining biomedical events from literature. BMC Bioinformatics, 9, 10.
    • (2008) BMC Bioinformatics , vol.9 , pp. 10
    • Kim, J.D.1
  • 16
    • 85104042765 scopus 로고    scopus 로고
    • Overview of BioNLP'09 shared task on event extraction
    • ACL, Boulder, Colorado
    • Kim, J.D. et al. (2009) Overview of BioNLP'09 shared task on event extraction. In Proceedings of the Workshop on BioNLP: Shared Task. ACL, Boulder, Colorado, pp. 1-9.
    • (2009) Proceedings of the Workshop on BioNLP: Shared Task , pp. 1-9
    • Kim, J.D.1
  • 17
    • 84987798660 scopus 로고    scopus 로고
    • Overview of Genia event task in BioNLP Shared Task 2011
    • Portland, Oregon, USA
    • Kim, J.-D. et al. (2011) Overview of Genia event task in BioNLP Shared Task 2011. In BioNLP Shared Task 2011, Portland, Oregon, USA, pp. 1-6.
    • (2011) BioNLP Shared Task 2011 , pp. 1-6
    • Kim, J.-D.1
  • 18
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of BioCreative II
    • Krallinger, M. et al. (2008a) Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol., 9 (Suppl. 2), S4.
    • (2008) Genome Biol , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1
  • 19
    • 51049110331 scopus 로고    scopus 로고
    • Linking genes to literature: text mining, information extraction, and retrieval applications for biology
    • Krallinger, M. et al. (2008b) Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol., 9 (Suppl. 2), S8.
    • (2008) Genome Biol , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1
  • 20
    • 40549140499 scopus 로고    scopus 로고
    • BANNER: an executable survey of advances in biomedical named entity recognition
    • Hawaii
    • Leaman, R. and Gonzales, G. (2008) BANNER: an executable survey of advances in biomedical named entity recognition. In Pacific Symp. on Biocomputing. Hawaii, pp. 652-663.
    • (2008) Pacific Symp. on Biocomputing. , pp. 652-663
    • Leaman, R.1    Gonzales, G.2
  • 21
    • 79954533893 scopus 로고    scopus 로고
    • PubMed and beyond: a survey of web tools for searching biomedical literature
    • baq036
    • Lu, Z. (2011) PubMed and beyond: a survey of web tools for searching biomedical literature. Database, 2011, baq036.
    • (2011) Database, 2011
    • Lu, Z.1
  • 22
    • 84863411425 scopus 로고    scopus 로고
    • Effective self-training for parsing
    • Brooklyn, New York
    • McClosky, D. et al. (2006) Effective self-training for parsing. In HLT-NAACL, Brooklyn, New York, pp. 152-159.
    • (2006) HLT-NAACL , pp. 152-159
    • McClosky, D.1
  • 25
    • 77958616587 scopus 로고    scopus 로고
    • Incorporating GENETAG-style annotation to GENIA corpus
    • Boulder, Colorado
    • Ohta, T. et al. (2009) Incorporating GENETAG-style annotation to GENIA corpus. In BioNLP Workshop. Boulder, Colorado, pp. 106-107.
    • (2009) BioNLP Workshop , pp. 106-107
    • Ohta, T.1
  • 27
    • 80053413137 scopus 로고    scopus 로고
    • Comparative parser performance analysis across grammar frameworks through automatic tree conversion using synchronous grammars
    • Manchester, UK
    • Sagae, K. et al. (2008) Comparative parser performance analysis across grammar frameworks through automatic tree conversion using synchronous grammars. In COLING 2008, Manchester, UK, pp. 545-552.
    • (2008) COLING 2008 , pp. 545-552
    • Sagae, K.1
  • 28
    • 80054032619 scopus 로고    scopus 로고
    • Biomedical event detection using rules, conditional random fields and parse tree distances
    • Boulder, Colorado
    • Sarafraz, F. et al. (2009) Biomedical event detection using rules, conditional random fields and parse tree distances. In BioNLP Workshop. Boulder, Colorado, pp. 115-118.
    • (2009) BioNLP Workshop , pp. 115-118
    • Sarafraz, F.1
  • 30
    • 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
  • 31
    • 84864074911 scopus 로고    scopus 로고
    • Gene mention normalization in full texts using GNAT and LINNAEUS
    • Bethesda, USA
    • Solt, I. et al. (2010) Gene mention normalization in full texts using GNAT and LINNAEUS. In Proceedings of the BioCreative III Workshop. Bethesda, USA, pp. 137-142.
    • (2010) Proceedings of the BioCreative III Workshop , pp. 137-142
    • Solt, I.1
  • 32
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Szklarczyk, D. et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 39, D561-D568.
    • (2011) Nucleic Acids Res , vol.39
    • Szklarczyk, D.1
  • 33
    • 40049083982 scopus 로고    scopus 로고
    • Extracting interactions between proteins from the literature
    • Zhou, D. and He, Y. (2008) Extracting interactions between proteins from the literature. J. Biomed. Inform., 41, 393-407.
    • (2008) J. Biomed. Inform , vol.41 , pp. 393-407
    • Zhou, D.1    He, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.