메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

LINNAEUS: A species name identification system for biomedical literature

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATICALLY GENERATED; BIOMEDICAL LITERATURE; DOCUMENT RETRIEVAL; FINITE-STATE AUTOMATA; FULL-TEXT DOCUMENTS; SEMANTIC ENRICHMENT; SOFTWARE SYSTEMS; STAND-ALONE SOFTWARE;

EID: 77949431037     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-85     Document Type: Article
Times cited : (291)

References (68)
  • 1
    • 84888279431 scopus 로고    scopus 로고
    • MEDLINE
    • MEDLINE. , http://www.nlm.nih.gov/databases/databases_medline.html
  • 2
    • 84872275493 scopus 로고    scopus 로고
    • PubMed Central
    • PubMed Central. , http://www.ncbi.nlm.nih.gov/pmc/
  • 3
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: from information retrieval to biological discovery
    • 10.1038/nrg1768, 16418747
    • Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews Genetics 2006, 7(2):119-129. 10.1038/nrg1768, 16418747.
    • (2006) Nature Reviews Genetics , vol.7 , Issue.2 , pp. 119-129
    • Jensen, L.J.1    Saric, J.2    Bork, P.3
  • 4
    • 51049110331 scopus 로고    scopus 로고
    • Current use of text mining and literature search systems for genome sciences
    • 10.1186/gb-2008-9-s2-s8, 2559992, 18834499
    • Krallinger M, Hirschman L, Valencia A. Current use of text mining and literature search systems for genome sciences. Genome Biology 2008, 9(Suppl 2):S8. 10.1186/gb-2008-9-s2-s8, 2559992, 18834499.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1    Hirschman, L.2    Valencia, A.3
  • 5
    • 33947258447 scopus 로고    scopus 로고
    • ProMiner: rule-based protein and gene entity recognition
    • 10.1186/1471-2105-6-S1-S14, 1869006, 15960826
    • Hanisch D, Fundel K, Mevissen HT, Zimmer R, Fluck J. ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 2005, 6(Suppl 1):S14. 10.1186/1471-2105-6-S1-S14, 1869006, 15960826.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hanisch, D.1    Fundel, K.2    Mevissen, H.T.3    Zimmer, R.4    Fluck, J.5
  • 6
    • 49549120418 scopus 로고    scopus 로고
    • Inter-species normalization of gene mentions with GNAT
    • 10.1093/bioinformatics/btn299, 18689813
    • Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzales G. Inter-species normalization of gene mentions with GNAT. Bioinformatics 2008, 24(16):i126-i132. 10.1093/bioinformatics/btn299, 18689813.
    • (2008) Bioinformatics , vol.24 , Issue.16
    • Hakenberg, J.1    Plake, C.2    Leaman, R.3    Schroeder, M.4    Gonzales, G.5
  • 7
    • 56649083754 scopus 로고    scopus 로고
    • Distinguishing the species of biomedical named entities for term identification
    • 10.1186/1471-2105-9-S11-S6, 2586755, 19025692
    • Wang X, Matthews M. Distinguishing the species of biomedical named entities for term identification. BMC Bioinformatics 2008, 9(Suppl 11):S6. 10.1186/1471-2105-9-S11-S6, 2586755, 19025692.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 11
    • Wang, X.1    Matthews, M.2
  • 8
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of BioCreative II
    • 10.1186/gb-2008-9-s2-s4, 2559988, 18834495
    • Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A. Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biology 2008, 9(Suppl 2):S4. 10.1186/gb-2008-9-s2-s4, 2559988, 18834495.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1    Leitner, F.2    Rodriguez-Penagos, C.3    Valencia, A.4
  • 11
    • 34447311379 scopus 로고    scopus 로고
    • UBioRSS: tracking taxonomic literature using RSS
    • 10.1093/bioinformatics/btm109, 17392332
    • Leary PR, Remsen DP, Norton CN, Patterson DJ, Sarkar IN. uBioRSS: tracking taxonomic literature using RSS. Bioinformatics 2007, 23(11):1434-1436. 10.1093/bioinformatics/btm109, 17392332.
    • (2007) Bioinformatics , vol.23 , Issue.11 , pp. 1434-1436
    • Leary, P.R.1    Remsen, D.P.2    Norton, C.N.3    Patterson, D.J.4    Sarkar, I.N.5
  • 12
    • 34250866940 scopus 로고    scopus 로고
    • TBMap: a taxonomic perspective on the phylogenetic database TreeBASE
    • 10.1186/1471-2105-8-158, 1885449, 17511869
    • Page RD. TBMap: a taxonomic perspective on the phylogenetic database TreeBASE. BMC Bioinformatics 2007, 8:158. 10.1186/1471-2105-8-158, 1885449, 17511869.
    • (2007) BMC Bioinformatics , vol.8 , pp. 158
    • Page, R.D.1
  • 13
    • 36348982664 scopus 로고    scopus 로고
    • Biodiversity informatics: organizing and linking information across the spectrum of life
    • 10.1093/bib/bbm037, 17704120
    • Sarkar IN. Biodiversity informatics: organizing and linking information across the spectrum of life. Briefings in Bioinformatics 2007, 8(5):347-357. 10.1093/bib/bbm037, 17704120.
    • (2007) Briefings in Bioinformatics , vol.8 , Issue.5 , pp. 347-357
    • Sarkar, I.N.1
  • 15
    • 48449101724 scopus 로고    scopus 로고
    • BioLit: integrating biological literature with databases
    • Web Server, 10.1093/nar/gkn317, 2447735, 18515836
    • Fink JL, Kushch S, Williams PR, Bourne PE. BioLit: integrating biological literature with databases. Nucleic Acids Research 2008, (36 Web Server):W385-389. 10.1093/nar/gkn317, 2447735, 18515836.
    • (2008) Nucleic Acids Research , Issue.36
    • Fink, J.L.1    Kushch, S.2    Williams, P.R.3    Bourne, P.E.4
  • 16
    • 66249092827 scopus 로고    scopus 로고
    • Adventures in semantic publishing: Exemplar semantic enhancements of a research article
    • 10.1371/journal.pcbi.1000361, 2663789, 19381256
    • Shotton D, Portwin K, Klyne G, Miles A. Adventures in semantic publishing: Exemplar semantic enhancements of a research article. PLoS Computational Biology 2009, 5(4):e1000361. 10.1371/journal.pcbi.1000361, 2663789, 19381256.
    • (2009) PLoS Computational Biology , vol.5 , Issue.4
    • Shotton, D.1    Portwin, K.2    Klyne, G.3    Miles, A.4
  • 17
    • 0034730608 scopus 로고    scopus 로고
    • The quiet revolution: biodiversity informatics and the internet
    • 10.1126/science.289.5488.2309, 11009408
    • Bisby FA. The quiet revolution: biodiversity informatics and the internet. Science 2000, 289(5488):2309-2312. 10.1126/science.289.5488.2309, 11009408.
    • (2000) Science , vol.289 , Issue.5488 , pp. 2309-2312
    • Bisby, F.A.1
  • 18
    • 67651252664 scopus 로고    scopus 로고
    • Evolving e-taxonomy
    • 10.1186/1471-2148-9-141, 2714837, 19555493
    • Zauner H. Evolving e-taxonomy. BMC Evolutionary Biology 2009, 9:141. 10.1186/1471-2148-9-141, 2714837, 19555493.
    • (2009) BMC Evolutionary Biology , vol.9 , pp. 141
    • Zauner, H.1
  • 19
    • 33644900680 scopus 로고    scopus 로고
    • Taxonomic indexing - extending the role of taxonomy
    • 10.1080/10635150500541680, 16861205
    • Patterson DJ, Remsen D, Marino WA, Norton C. Taxonomic indexing - extending the role of taxonomy. Systematic Biology 2006, 55(3):367-373. 10.1080/10635150500541680, 16861205.
    • (2006) Systematic Biology , vol.55 , Issue.3 , pp. 367-373
    • Patterson, D.J.1    Remsen, D.2    Marino, W.A.3    Norton, C.4
  • 21
    • 84874654621 scopus 로고    scopus 로고
    • Biodiversity Heritage Library
    • Biodiversity Heritage Library. , http://www.biodiversitylibrary.org/
  • 22
    • 0003395883 scopus 로고    scopus 로고
    • Systema Naturae
    • Linnaeus C. Systema Naturae. 1767.
    • Linnaeus, C.1
  • 24
    • 84888280554 scopus 로고    scopus 로고
    • TaxonGrab
    • TaxonGrab. , http://sourceforge.net/projects/taxongrab/
  • 25
    • 36348988138 scopus 로고    scopus 로고
    • A combining approach to find all taxon names (FAT) in legacy biosystematic literature
    • Sautter G, Böhm K, Agosti D. A combining approach to find all taxon names (FAT) in legacy biosystematic literature. Biodiversity Informatics 2006, 3:41-53.
    • (2006) Biodiversity Informatics , vol.3 , pp. 41-53
    • Sautter, G.1    Böhm, K.2    Agosti, D.3
  • 26
    • 38449095011 scopus 로고    scopus 로고
    • Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor
    • full_text, 17992751
    • Sautter G, Bohm K, Agosti D. Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor. Pacific Symposium on Biocomputing 2007, 391-402. full_text, 17992751.
    • (2007) Pacific Symposium on Biocomputing , pp. 391-402
    • Sautter, G.1    Bohm, K.2    Agosti, D.3
  • 27
    • 84888281255 scopus 로고    scopus 로고
    • The GoldenGATE Document Editor
    • The GoldenGATE Document Editor. , http://plazi.org/?q=GoldenGATE
  • 28
    • 84888280250 scopus 로고    scopus 로고
    • The Universal Biological Indexer and Organizer Project
    • The Universal Biological Indexer and Organizer Project. , http://www.ubio.org/
  • 29
    • 84888283610 scopus 로고    scopus 로고
    • TaxonFinder Web Service
    • TaxonFinder Web Service. , http://www.ubio.org/index.php?pagename=soap_methods/taxonFinder
  • 30
    • 84888282696 scopus 로고    scopus 로고
    • TaxonFinder Source Code
    • TaxonFinder Source Code. , http://code.google.com/p/taxon-finder/
  • 31
    • 84888280349 scopus 로고    scopus 로고
    • The National Center for Biotechnology Information Taxonomy Homepage
    • The National Center for Biotechnology Information Taxonomy Homepage. , http://www.ncbi.nlm.nih.gov/Taxonomy/
  • 32
    • 33750006879 scopus 로고    scopus 로고
    • AliBaba: PubMed as a graph
    • 10.1093/bioinformatics/btl408, 16870931
    • Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U. AliBaba: PubMed as a graph. Bioinformatics 2006, 22(19):2444-2445. 10.1093/bioinformatics/btl408, 16870931.
    • (2006) Bioinformatics , vol.22 , Issue.19 , pp. 2444-2445
    • Plake, C.1    Schiemann, T.2    Pankalla, M.3    Hakenberg, J.4    Leser, U.5
  • 33
    • 33846664313 scopus 로고    scopus 로고
    • Text processing through Web services: Calling Whatizit
    • 10.1093/bioinformatics/btl302, 17237098
    • Rebholz-Schuhmann D, Arregui M, Gaudan M, Kirsch H, Jimeno A. Text processing through Web services: Calling Whatizit. Bioinformatics 2007, 23(2):e237-e244. 10.1093/bioinformatics/btl302, 17237098.
    • (2007) Bioinformatics , vol.23 , Issue.2
    • Rebholz-Schuhmann, D.1    Arregui, M.2    Gaudan, M.3    Kirsch, H.4    Jimeno, A.5
  • 35
    • 58149191270 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) 2009
    • Database, 10.1093/nar/gkn664, 2686606, 18836194, The Uniprot Consortium
    • The Uniprot Consortium The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009, (37 Database):D169-174. 10.1093/nar/gkn664, 2686606, 18836194, The Uniprot Consortium.
    • (2009) Nucleic Acids Res , Issue.37
  • 36
    • 51049117464 scopus 로고    scopus 로고
    • Rule-based protein term identification with help from automatic species tagging
    • Wang X. Rule-based protein term identification with help from automatic species tagging. Proceedings of CICLING 2007: 2007 2007,
    • (2007) Proceedings of CICLING 2007: 2007
    • Wang, X.1
  • 38
    • 77949622808 scopus 로고    scopus 로고
    • Disambiguating the species of biomedical named entities using natural language parsers
    • Wang X, Tsujii J, Ananiadou S. Disambiguating the species of biomedical named entities using natural language parsers. Bioinformatics 2010,
    • (2010) Bioinformatics
    • Wang, X.1    Tsujii, J.2    Ananiadou, S.3
  • 39
    • 84888281217 scopus 로고    scopus 로고
    • U-Compare Compatible UIMA Semantic Tool Components
    • U-Compare Compatible UIMA Semantic Tool Components. , http://u-compare.org/components/components-semantic_tools.html
  • 40
    • 84888280590 scopus 로고    scopus 로고
    • Disease Extraction with Concept Association Project
    • Disease Extraction with Concept Association Project. , http://www.nactem.ac.uk/deca_details/start.cgi
  • 43
    • 33845358346 scopus 로고    scopus 로고
    • Building an abbreviation dictionary using a term recognition approach
    • 10.1093/bioinformatics/btl534, 17050571
    • Okazaki N, Ananiadou S. Building an abbreviation dictionary using a term recognition approach. Bioinformatics 2006, 22(24):3089-3095. 10.1093/bioinformatics/btl534, 17050571.
    • (2006) Bioinformatics , vol.22 , Issue.24 , pp. 3089-3095
    • Okazaki, N.1    Ananiadou, S.2
  • 44
    • 84880744131 scopus 로고    scopus 로고
    • Dk.brics.automaton
    • dk.brics.automaton. , http://www.brics.dk/automaton/
  • 45
    • 0003620778 scopus 로고
    • Introduction to automata theory languages and computation
    • Addison Wesley
    • Hopcroft J, Ullman J. Introduction to automata theory languages and computation. 1979, Addison Wesley.
    • (1979)
    • Hopcroft, J.1    Ullman, J.2
  • 46
    • 84888279030 scopus 로고    scopus 로고
    • MEDLINE/PubMed XML Data Elements
    • MEDLINE/PubMed XML Data Elements. , http://www.nlm.nih.gov/bsd/licensee/data_elements_doc.html
  • 47
    • 84888284625 scopus 로고    scopus 로고
    • PubMed Central XML Tagging Guidelines
    • PubMed Central XML Tagging Guidelines. , http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/style.html
  • 48
    • 84888275485 scopus 로고    scopus 로고
    • BioMed Central XML DTD
    • BioMed Central XML DTD. , http://www.biomedcentral.com/xml/
  • 49
    • 84888277054 scopus 로고    scopus 로고
    • Open Text Mining Initiative Specification
    • Open Text Mining Initiative Specification. , http://opentextmining.org/wiki/OTMI_Specification
  • 50
  • 52
    • 77049109254 scopus 로고    scopus 로고
    • GenBank and PubMed: How connected are they?
    • 10.1186/1756-0500-2-101, 2704225, 19508734
    • Miller H, Norton CN, Sarkar IN. GenBank and PubMed: How connected are they?. BMC Research Notes 2009, 2:101. 10.1186/1756-0500-2-101, 2704225, 19508734.
    • (2009) BMC Research Notes , vol.2 , pp. 101
    • Miller, H.1    Norton, C.N.2    Sarkar, I.N.3
  • 54
    • 50549096372 scopus 로고    scopus 로고
    • Yale Image Finder (YIF): a new search engine for retrieving biomedical images
    • 10.1093/bioinformatics/btn340, 2732221, 18614584
    • Xu S, McCusker J, Krauthammer M. Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Bioinformatics 2008, 24(17):1968-1970. 10.1093/bioinformatics/btn340, 2732221, 18614584.
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1968-1970
    • Xu, S.1    McCusker, J.2    Krauthammer, M.3
  • 55
    • 68549122908 scopus 로고    scopus 로고
    • Figure mining for biomedical research
    • 10.1093/bioinformatics/btp318, 19439564
    • Rodriguez-Esteban R, Iossifov I. Figure mining for biomedical research. Bioinformatics 2009, 25(16):2082-2084. 10.1093/bioinformatics/btp318, 19439564.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2082-2084
    • Rodriguez-Esteban, R.1    Iossifov, I.2
  • 56
    • 13444256580 scopus 로고    scopus 로고
    • Gene name ambiguity of eukaryotic nomenclatures
    • 10.1093/bioinformatics/bth496, 15333458
    • Chen L, Liu H, Friedman C. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 2005, 21(2):248-256. 10.1093/bioinformatics/bth496, 15333458.
    • (2005) Bioinformatics , vol.21 , Issue.2 , pp. 248-256
    • Chen, L.1    Liu, H.2    Friedman, C.3
  • 57
    • 44649183957 scopus 로고    scopus 로고
    • Exploring historical trends using taxonomic name metadata
    • 10.1186/1471-2148-8-144, 2408592, 18477399
    • Sarkar IN, Schenk R, Norton CN. Exploring historical trends using taxonomic name metadata. BMC Evolutionary Biology 2008, 8:144. 10.1186/1471-2148-8-144, 2408592, 18477399.
    • (2008) BMC Evolutionary Biology , vol.8 , pp. 144
    • Sarkar, I.N.1    Schenk, R.2    Norton, C.N.3
  • 58
    • 0037303467 scopus 로고    scopus 로고
    • Life cycles of successful genes
    • 10.1016/S0168-9525(02)00014-8, 12547515
    • Hoffmann R, Valencia A. Life cycles of successful genes. Trends in Genetics 2003, 19(2):79-81. 10.1016/S0168-9525(02)00014-8, 12547515.
    • (2003) Trends in Genetics , vol.19 , Issue.2 , pp. 79-81
    • Hoffmann, R.1    Valencia, A.2
  • 61
    • 84888280250 scopus 로고    scopus 로고
    • The Universal Biological Indexer and Organizer Project
    • The Universal Biological Indexer and Organizer Project. , http://www.ubio.org/
  • 62
    • 0642368715 scopus 로고    scopus 로고
    • Information extraction from full text scientific articles: where are the keywords?
    • 10.1186/1471-2105-4-20, 166134, 12775220
    • Shah PK, Perez-Iratxeta C, Bork P, Andrade MA. Information extraction from full text scientific articles: where are the keywords?. BMC Bioinformatics 2003, 4:20. 10.1186/1471-2105-4-20, 166134, 12775220.
    • (2003) BMC Bioinformatics , vol.4 , pp. 20
    • Shah, P.K.1    Perez-Iratxeta, C.2    Bork, P.3    Andrade, M.A.4
  • 64
    • 10244245424 scopus 로고    scopus 로고
    • BioRAT: extracting biological information from full-length papers
    • 10.1093/bioinformatics/bth386, 15231534
    • Corney DP, Buxton BF, Langdon WB, Jones DT. BioRAT: extracting biological information from full-length papers. Bioinformatics 2004, 20(17):3206-3213. 10.1093/bioinformatics/bth386, 15231534.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3206-3213
    • Corney, D.P.1    Buxton, B.F.2    Langdon, W.B.3    Jones, D.T.4
  • 65
    • 52649177788 scopus 로고    scopus 로고
    • Methodology capture: discriminating between the "best" and the rest of community practice
    • 10.1186/1471-2105-9-359, 2553348, 18761740
    • Eales JM, Pinney JW, Stevens RD, Robertson DL. Methodology capture: discriminating between the "best" and the rest of community practice. BMC Bioinformatics 2008, 9:359. 10.1186/1471-2105-9-359, 2553348, 18761740.
    • (2008) BMC Bioinformatics , vol.9 , pp. 359
    • Eales, J.M.1    Pinney, J.W.2    Stevens, R.D.3    Robertson, D.L.4
  • 66
    • 63449142390 scopus 로고    scopus 로고
    • Is searching full text more effective than searching abstracts?
    • 10.1186/1471-2105-10-46, 2695361, 19192280
    • Lin J. Is searching full text more effective than searching abstracts?. BMC Bioinformatics 2009, 10:46. 10.1186/1471-2105-10-46, 2695361, 19192280.
    • (2009) BMC Bioinformatics , vol.10 , pp. 46
    • Lin, J.1
  • 67
    • 56649114560 scopus 로고    scopus 로고
    • A bioinformatics analysis of the cell line nomenclature
    • 10.1093/bioinformatics/btn502, 2639272, 18849319
    • Sarntivijai S, Ade AS, Athey BD, States DJ. A bioinformatics analysis of the cell line nomenclature. Bioinformatics 2008, 24(23):2760-2766. 10.1093/bioinformatics/btn502, 2639272, 18849319.
    • (2008) Bioinformatics , vol.24 , Issue.23 , pp. 2760-2766
    • Sarntivijai, S.1    Ade, A.S.2    Athey, B.D.3    States, D.J.4
  • 68
    • 84872796163 scopus 로고    scopus 로고
    • Catalogue of Life
    • Catalogue of Life. , http://www.catalogueoflife.org/search.php


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.