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Volumn 13, Issue 5, 2006, Pages 497-507

Quantitative Assessment of Dictionary-based Protein Named Entity Tagging

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PROTEIN;

EID: 33747894083     PISSN: 10675027     EISSN: None     Source Type: Journal    
DOI: 10.1197/jamia.M2085     Document Type: Article
Times cited : (32)

References (57)
  • 1
    • 0033643234 scopus 로고    scopus 로고
    • Two applications of information extraction to biological science journal articles. enzyme interactions and protein structures
    • Humphreys K., Demetriou G., and Gaizauskas R. Two applications of information extraction to biological science journal articles. enzyme interactions and protein structures. Pac Symp Biocomput (2000) 505-516
    • (2000) Pac Symp Biocomput , pp. 505-516
    • Humphreys, K.1    Demetriou, G.2    Gaizauskas, R.3
  • 2
    • 0033657546 scopus 로고    scopus 로고
    • EDGAR. extraction of drugs, genes and relations from the biomedical literature
    • Rindflesch T.C., Tanabe L., Weinstein J.N., and Hunter L. EDGAR. extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput (2000) 517-528
    • (2000) Pac Symp Biocomput , pp. 517-528
    • Rindflesch, T.C.1    Tanabe, L.2    Weinstein, J.N.3    Hunter, L.4
  • 4
    • 0031690080 scopus 로고    scopus 로고
    • Automatic extraction of keywords from scientific text. application to the knowledge domain of protein families
    • Andrade M.A., and Valencia A. Automatic extraction of keywords from scientific text. application to the knowledge domain of protein families. Bioinformatics 14 7 (1998) 600-607
    • (1998) Bioinformatics , vol.14 , Issue.7 , pp. 600-607
    • Andrade, M.A.1    Valencia, A.2
  • 5
    • 0033290514 scopus 로고    scopus 로고
    • Constructing biological knowledge bases by extracting information from text sources
    • Craven M., and Kumlien J. Constructing biological knowledge bases by extracting information from text sources. Proc Int Conf Intell Syst Mol Biol (1999) 77-86
    • (1999) Proc Int Conf Intell Syst Mol Biol , pp. 77-86
    • Craven, M.1    Kumlien, J.2
  • 6
    • 0041592528 scopus 로고    scopus 로고
    • MeKE. discovering the functions of gene products from biomedical literature via sentence alignment
    • Chiang J.H., and Yu H.C. MeKE. discovering the functions of gene products from biomedical literature via sentence alignment. Bioinformatics 19 (2003) 1417-1422
    • (2003) Bioinformatics , vol.19 , pp. 1417-1422
    • Chiang, J.H.1    Yu, H.C.2
  • 7
    • 0347724100 scopus 로고    scopus 로고
    • GIS. a biomedical text-mining system for gene information discovery
    • Chiang J.H., Yu H.C., and Hsu H.J. GIS. a biomedical text-mining system for gene information discovery. Bioinformatics 20 1 (2004) 120-121
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 120-121
    • Chiang, J.H.1    Yu, H.C.2    Hsu, H.J.3
  • 8
    • 12144290446 scopus 로고    scopus 로고
    • GeneWays. a system for extracting, analyzing, visualizing, and integrating molecular pathway data
    • Rzhetsky A., Iossifov I., Koike T., et al. GeneWays. a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform 37 1 (2004) 43-53
    • (2004) J Biomed Inform , vol.37 , Issue.1 , pp. 43-53
    • Rzhetsky, A.1    Iossifov, I.2    Koike, T.3
  • 9
    • 1842559914 scopus 로고    scopus 로고
    • Extracting human protein interactions from MEDLINE using a full-sentence parser
    • Daraselia N., Yuryev A., Egorov S., Novichkova S., Nikitin A., and Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 20 5 (2004) 604-611
    • (2004) Bioinformatics , vol.20 , Issue.5 , pp. 604-611
    • Daraselia, N.1    Yuryev, A.2    Egorov, S.3    Novichkova, S.4    Nikitin, A.5    Mazo, I.6
  • 10
    • 33645831306 scopus 로고    scopus 로고
    • Automatic pathway building in biological association networks
    • Yuryev A., Mulyukov Z., Kotelnikova E., et al. Automatic pathway building in biological association networks. BMC Bioinformatics 7 (2006) 171
    • (2006) BMC Bioinformatics , vol.7 , pp. 171
    • Yuryev, A.1    Mulyukov, Z.2    Kotelnikova, E.3
  • 11
    • 0035230208 scopus 로고    scopus 로고
    • Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar
    • Park J.C., Kim H.S., and Kim J.J. Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar. Pac Symp Biocomput (2001) 396-407
    • (2001) Pac Symp Biocomput , pp. 396-407
    • Park, J.C.1    Kim, H.S.2    Kim, J.J.3
  • 12
    • 33947321307 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE task 1B. normalized gene lists
    • Hirschman L., Colosimo M., Morgan A., and Yeh A. Overview of BioCreAtIvE task 1B. normalized gene lists. BMC Bioinformatics 6 Suppl 1 (2005) S11
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hirschman, L.1    Colosimo, M.2    Morgan, A.3    Yeh, A.4
  • 13
    • 3943106585 scopus 로고    scopus 로고
    • Accomplishments and challenges in literature data mining for biology
    • Hirschman L., Park J.C., Tsujii J., Wong L., and Wu C.H. Accomplishments and challenges in literature data mining for biology. Bioinformatics 18 12 (2002) 1553-1561
    • (2002) Bioinformatics , vol.18 , Issue.12 , pp. 1553-1561
    • Hirschman, L.1    Park, J.C.2    Tsujii, J.3    Wong, L.4    Wu, C.H.5
  • 14
    • 33947304181 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE. critical assessment of information extraction for biology
    • Hirschman L., Yeh A., Blaschke C., and Valencia A. Overview of BioCreAtIvE. critical assessment of information extraction for biology. BMC Bioinformatics 6 Suppl 1 (2005) S1
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hirschman, L.1    Yeh, A.2    Blaschke, C.3    Valencia, A.4
  • 15
    • 0742321913 scopus 로고    scopus 로고
    • Mining the biomedical literature in the genomic era. an overview
    • Shatkay H., and Feldman R. Mining the biomedical literature in the genomic era. an overview. J Comput Biol 10 6 (2003) 821-855
    • (2003) J Comput Biol , vol.10 , Issue.6 , pp. 821-855
    • Shatkay, H.1    Feldman, R.2
  • 16
    • 8444226720 scopus 로고    scopus 로고
    • Term identification in the biomedical literature
    • Krauthammer M., and Nenadic G. Term identification in the biomedical literature. J Biomed Inform 37 6 (2004) 512-526
    • (2004) J Biomed Inform , vol.37 , Issue.6 , pp. 512-526
    • Krauthammer, M.1    Nenadic, G.2
  • 17
    • 33947359082 scopus 로고    scopus 로고
    • BioCreAtIvE task 1A. gene mention finding evaluation
    • Yeh A., Morgan A., Colosimo M., and Hirschman L. BioCreAtIvE task 1A. gene mention finding evaluation. BMC Bioinformatics 6 Suppl 1 (2005) S2
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Yeh, A.1    Morgan, A.2    Colosimo, M.3    Hirschman, L.4
  • 18
    • 0043130572 scopus 로고    scopus 로고
    • Playing biology's name game. identifying protein names in scientific text
    • Hanisch D., Fluck J., Mevissen H.T., and Zimmer R. Playing biology's name game. identifying protein names in scientific text. Pac Symp Biocomput (2003) 403-414
    • (2003) Pac Symp Biocomput , pp. 403-414
    • Hanisch, D.1    Fluck, J.2    Mevissen, H.T.3    Zimmer, R.4
  • 20
    • 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., and Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28 1 (2001) 21-28
    • (2001) Nat Genet , vol.28 , Issue.1 , pp. 21-28
    • Jenssen, T.K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 21
    • 0031633368 scopus 로고    scopus 로고
    • Toward information extraction. identifying protein names from biological papers
    • Fukuda K., Tamura A., Tsunoda T., and Takagi T. Toward information extraction. identifying protein names from biological papers. Pac Symp Biocomput (1998) 707-718
    • (1998) Pac Symp Biocomput , pp. 707-718
    • Fukuda, K.1    Tamura, A.2    Tsunoda, T.3    Takagi, T.4
  • 22
    • 0036678776 scopus 로고    scopus 로고
    • Tagging gene and protein names in biomedical text
    • Tanabe L., and Wilbur W.J. Tagging gene and protein names in biomedical text. Bioinformatics 18 8 (2002) 1124-1132
    • (2002) Bioinformatics , vol.18 , Issue.8 , pp. 1124-1132
    • Tanabe, L.1    Wilbur, W.J.2
  • 23
    • 0002284942 scopus 로고    scopus 로고
    • Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts
    • Sekimizu T., Park H.S., and Tsujii J. Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts. Genome Inform Ser Workshop Genome Inform 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
  • 24
    • 33947250174 scopus 로고    scopus 로고
    • GENETAG. a tagged corpus for gene/protein named entity recognition
    • Tanabe L., Xie N., Thom L.H., Matten W., and Wilbur W.J. GENETAG. a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics 6 Suppl 1 (2005) S3
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Tanabe, L.1    Xie, N.2    Thom, L.H.3    Matten, W.4    Wilbur, W.J.5
  • 26
    • 33947305118 scopus 로고    scopus 로고
    • Identifying gene and protein mentions in text using conditional random fields
    • McDonald R., and Pereira F. Identifying gene and protein mentions in text using conditional random fields. BMC Bioinformatics 6 Suppl 1 (2005) S6
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • McDonald, R.1    Pereira, F.2
  • 27
    • 33947307025 scopus 로고    scopus 로고
    • Recognition of protein/gene names from text using an ensemble of classifiers
    • Zhou G., Shen D., Zhang J., Su J., and Tan S. Recognition of protein/gene names from text using an ensemble of classifiers. BMC Bioinformatics 6 Suppl 1 (2005) S7
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Zhou, G.1    Shen, D.2    Zhang, J.3    Su, J.4    Tan, S.5
  • 28
    • 33947304479 scopus 로고    scopus 로고
    • Systematic feature evaluation for gene name recognition
    • Hakenberg J., Bickel S., Plake C., et al. Systematic feature evaluation for gene name recognition. BMC Bioinformatics 6 Suppl 1 (2005) S9
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hakenberg, J.1    Bickel, S.2    Plake, C.3
  • 29
    • 30744457935 scopus 로고    scopus 로고
    • Gene/protein name recognition based on support vector machine using dictionary as features
    • Mitsumori T., Fation S., Murata M., Doi K., and Doi H. Gene/protein name recognition based on support vector machine using dictionary as features. BMC Bioinformatics 6 Suppl 1 (2005) S8
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Mitsumori, T.1    Fation, S.2    Murata, M.3    Doi, K.4    Doi, H.5
  • 30
    • 33947312171 scopus 로고    scopus 로고
    • Text detective. a rule-based system for gene annotation in biomedical texts
    • Tamames J. Text detective. a rule-based system for gene annotation in biomedical texts. BMC Bioinformatics 6 Suppl 1 (2005) S10
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Tamames, J.1
  • 32
    • 13444249991 scopus 로고    scopus 로고
    • Fungal BLAST and Model Organism BLASTP Best Hits. new comparison resources at the Saccharomyces Genome Database (SGD)
    • Balakrishnan R., Christie K.R., Costanzo M.C., et al. Fungal BLAST and Model Organism BLASTP Best Hits. new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res 33 Database issue (2005) D374-D377
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database issue
    • Balakrishnan, R.1    Christie, K.R.2    Costanzo, M.C.3
  • 34
    • 13444301461 scopus 로고    scopus 로고
    • FlyBase. genes and gene models
    • Drysdale R.A., and Crosby M.A. FlyBase. genes and gene models. Nucleic Acids Res 33 Database issue (2005) D390-D395
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database issue
    • Drysdale, R.A.1    Crosby, M.A.2
  • 35
    • 33947373992 scopus 로고    scopus 로고
    • A simple approach for protein name identification. prospects and limits
    • Fundel K., Guttler D., Zimmer R., and Apostolakis J. A simple approach for protein name identification. prospects and limits. BMC Bioinformatics 6 Suppl 1 (2005) S15
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Fundel, K.1    Guttler, D.2    Zimmer, R.3    Apostolakis, J.4
  • 36
    • 33947315795 scopus 로고    scopus 로고
    • Automatically annotating documents with normalized gene lists
    • Crim J., McDonald R., and Pereira F. Automatically annotating documents with normalized gene lists. BMC Bioinformatics 6 Suppl 1 (2005) S13
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Crim, J.1    McDonald, R.2    Pereira, F.3
  • 37
    • 33747889336 scopus 로고    scopus 로고
    • Liu H, Wu C, Friedman C. BioTagger: a biological entity tagging system. Paper presented at: BioCreAtive Workshop, 2004; Spain.
  • 38
    • 30344472426 scopus 로고    scopus 로고
    • BioThesaurus. a web-based thesaurus of protein and gene names
    • Liu H., Hu Z.Z., Zhang J., and Wu C. BioThesaurus. a web-based thesaurus of protein and gene names. Bioinformatics 22 1 (2006) 103-105
    • (2006) Bioinformatics , vol.22 , Issue.1 , pp. 103-105
    • Liu, H.1    Hu, Z.Z.2    Zhang, J.3    Wu, C.4
  • 39
    • 33644873213 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt). an expanding universe of protein information
    • Wu C.H., Apweiler R., Bairoch A., et al. The Universal Protein Resource (UniProt). an expanding universe of protein information. Nucleic Acids Res 34 Database issue (2006) D187-D191
    • (2006) Nucleic Acids Res , vol.34 , Issue.Database issue
    • Wu, C.H.1    Apweiler, R.2    Bairoch, A.3
  • 40
    • 0842330093 scopus 로고    scopus 로고
    • The iProClass integrated database for protein functional analysis
    • Wu C.H., Huang H., Nikolskaya A., Hu Z., and Barker W.C. The iProClass integrated database for protein functional analysis. Comput Biol Chem Feb 28 1 (2004) 87-96
    • (2004) Comput Biol Chem Feb , vol.28 , Issue.1 , pp. 87-96
    • Wu, C.H.1    Huang, H.2    Nikolskaya, A.3    Hu, Z.4    Barker, W.C.5
  • 41
    • 0345863927 scopus 로고    scopus 로고
    • The Unified Medical Language System (UMLS). integrating biomedical terminology
    • Bodenreider O. The Unified Medical Language System (UMLS). integrating biomedical terminology. Nucleic Acids Res 32 Database issue (2004) D267-D270
    • (2004) Nucleic Acids Res , vol.32 , Issue.Database issue
    • Bodenreider, O.1
  • 43
    • 1242349373 scopus 로고    scopus 로고
    • Extracting synonymous gene and protein terms from biological literature
    • Yu H., and Agichtein E. Extracting synonymous gene and protein terms from biological literature. Bioinformatics 19 Suppl 1 (2003) i340-i349
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Yu, H.1    Agichtein, E.2
  • 44
    • 0035224502 scopus 로고    scopus 로고
    • Disambiguating proteins, genes, and RNA in text. a machine learning approach
    • Hatzivassiloglou V., Duboue P.A., and Rzhetsky A. Disambiguating proteins, genes, and RNA in text. a machine learning approach. Bioinformatics 17 Suppl 1 (2001) S97-S106
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Hatzivassiloglou, V.1    Duboue, P.A.2    Rzhetsky, A.3
  • 45
    • 0035564886 scopus 로고    scopus 로고
    • Disambiguating ambiguous biomedical terms in biomedical narrative text. an unsupervised method
    • Liu H., Lussier Y.A., and Friedman C. Disambiguating ambiguous biomedical terms in biomedical narrative text. an unsupervised method. J Biomed Inform 34 4 (2001) 249-261
    • (2001) J Biomed Inform , vol.34 , Issue.4 , pp. 249-261
    • Liu, H.1    Lussier, Y.A.2    Friedman, C.3
  • 46
    • 3042723139 scopus 로고    scopus 로고
    • A multi-aspect comparison study of supervised word sense disambiguation
    • Liu H., Teller V., and Friedman C. A multi-aspect comparison study of supervised word sense disambiguation. J Am Med Inform Assoc 11 4 (2004) 320-331
    • (2004) J Am Med Inform Assoc , vol.11 , Issue.4 , pp. 320-331
    • Liu, H.1    Teller, V.2    Friedman, C.3
  • 47
    • 0036828375 scopus 로고    scopus 로고
    • Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS
    • Liu H., Johnson S.B., and Friedman C. Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS. J Am Med Inform Assoc 9 6 (2002) 621-636
    • (2002) J Am Med Inform Assoc , vol.9 , Issue.6 , pp. 621-636
    • Liu, H.1    Johnson, S.B.2    Friedman, C.3
  • 48
    • 24644505245 scopus 로고    scopus 로고
    • Resolving abbreviations to their senses in Medline
    • Gaudan S., Kirsch H., and Rebholz-Schuhmann D. Resolving abbreviations to their senses in Medline. Bioinformatics 21 18 (2005) 3658-3664
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3658-3664
    • Gaudan, S.1    Kirsch, H.2    Rebholz-Schuhmann, D.3
  • 50
    • 1042269470 scopus 로고    scopus 로고
    • GAPSCORE. finding gene and protein names one word at a time
    • Chang J.T., Schutze H., and Altman R.B. GAPSCORE. finding gene and protein names one word at a time. Bioinformatics 22 20 2 (2004) 216-225
    • (2004) Bioinformatics 22 , vol.20 , Issue.2 , pp. 216-225
    • Chang, J.T.1    Schutze, H.2    Altman, R.B.3
  • 52
    • 0035072551 scopus 로고    scopus 로고
    • Clustering of highly homologous sequences to reduce the size of large protein databases
    • Li W., Jaroszewski L., and Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17 3 (2001) 282-283
    • (2001) Bioinformatics , vol.17 , Issue.3 , pp. 282-283
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 54
    • 0033045704 scopus 로고    scopus 로고
    • Isolation and chromosomal assignment of human genes encoding cofactor of LIM homeodomain proteins, CLIM1 and CLIM2
    • Ueki N., Seki N., Yano K., Ohira M., Saito T., Masuho Y., and Muramatsu M. Isolation and chromosomal assignment of human genes encoding cofactor of LIM homeodomain proteins, CLIM1 and CLIM2. J Hum Genet 44 2 (1999) 112-115
    • (1999) J Hum Genet , vol.44 , Issue.2 , pp. 112-115
    • Ueki, N.1    Seki, N.2    Yano, K.3    Ohira, M.4    Saito, T.5    Masuho, Y.6    Muramatsu, M.7
  • 55
    • 13444250867 scopus 로고    scopus 로고
    • Gene name ambiguity of eukaryotic nomenclatures
    • Aug 27
    • Chen L., Liu H., and Friedman C. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics (2004) Aug 27
    • (2004) Bioinformatics
    • Chen, L.1    Liu, H.2    Friedman, C.3
  • 56
    • 9144231826 scopus 로고    scopus 로고
    • PIRSF. family classification system at the Protein Information Resource
    • Wu C.H., Nikolskaya A., Huang H., et al. PIRSF. family classification system at the Protein Information Resource. Nucleic Acids Res 32 Database issue (2004) D112-D114
    • (2004) Nucleic Acids Res , vol.32 , Issue.Database issue
    • Wu, C.H.1    Nikolskaya, A.2    Huang, H.3
  • 57
    • 33745611541 scopus 로고    scopus 로고
    • An online literature mining tool for protein phosphorylation
    • Apr 27
    • Yuan X., Hu Z.Z., Wu H.T., et al. An online literature mining tool for protein phosphorylation. Bioinformatics (2006) Apr 27
    • (2006) Bioinformatics
    • Yuan, X.1    Hu, Z.Z.2    Wu, H.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.