메뉴 건너뛰기




Volumn 2014, Issue , 2014, Pages

BC4GO: A full-text corpus for the BioCreative IV GO task

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; COMPUTER PROGRAM; CONTROLLED VOCABULARY; DATA MINING; GENETIC DATABASE; HUMAN; MOLECULAR GENETICS; PROCEDURES;

EID: 84943157830     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau074     Document Type: Article
Times cited : (35)

References (49)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 2
    • 84892683484 scopus 로고    scopus 로고
    • A guide to best practices for gene ontology (GO) manual annotation
    • Balakrishnan, R., Harris, M.A., Huntley, R. et al. (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database, 2013, bat054.
    • (2013) Database , vol.2013
    • Balakrishnan, R.1    Harris, M.A.2    Huntley, R.3
  • 3
    • 77950550898 scopus 로고    scopus 로고
    • Representing ontogeny through ontology: A developmental biologist's guide to the gene ontology
    • Hill, D.P., Berardini, T.Z., Howe, D.G. et al. (2010) Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. Mol. Reprod. Dev., 77, 314-329.
    • (2010) Mol. Reprod. Dev. , vol.77 , pp. 314-329
    • Hill, D.P.1    Berardini, T.Z.2    Howe, D.G.3
  • 4
    • 84879394069 scopus 로고    scopus 로고
    • Use of gene ontology annotation to understand the peroxisome proteome in humans
    • Mutowo-Meullenet, P., Huntley, R.P., Dimmer, E.C. et al. (2013) Use of gene ontology annotation to understand the peroxisome proteome in humans. Database, 2013, bas062.
    • (2013) Database , vol.2013
    • Mutowo-Meullenet, P.1    Huntley, R.P.2    Dimmer, E.C.3
  • 5
    • 34547693374 scopus 로고    scopus 로고
    • Incorporation of gene ontology annotations to enhance micro-array data analysis
    • Ochs, M.F., Peterson, A.J., Kossenkov, A. et al. (2007) Incorporation of gene ontology annotations to enhance micro-array data analysis. Methods Mol. Biol., 377, 243-254.
    • (2007) Methods Mol. Biol. , vol.377 , pp. 243-254
    • Ochs, M.F.1    Peterson, A.J.2    Kossenkov, A.3
  • 6
    • 15944386344 scopus 로고    scopus 로고
    • GO molecular function terms are predictive of subcellular localization
    • Lu, Z. and Hunter, L. (2005) GO molecular function terms are predictive of subcellular localization. Pac. Symp. Biocomput., 151-161.
    • (2005) Pac. Symp. Biocomput. , pp. 151-161
    • Lu, Z.1    Hunter, L.2
  • 7
    • 84860848426 scopus 로고    scopus 로고
    • Manual GO annotation of predictive protein signatures: The InterPro approach to GO curation
    • Burge, S., Kelly, E., Lonsdale, D. et al. (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database, 2012, bar068.
    • (2012) Database , vol.2012
    • Burge, S.1    Kelly, E.2    Lonsdale, D.3
  • 8
    • 58149187893 scopus 로고    scopus 로고
    • The GOA database in 2009 - An integrated gene ontology annotation resource
    • Barrell, D., Dimmer, E., Huntley, R.P. et al. (2009) The GOA database in 2009 - an integrated gene ontology annotation resource. Nucleic Acids Res., 37, D396-D403.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D396-D403
    • Barrell, D.1    Dimmer, E.2    Huntley, R.P.3
  • 9
    • 84876480423 scopus 로고    scopus 로고
    • Building an efficient curation workflow for the arabidopsis literature corpus
    • Li, D., Berardini, T.Z., Muller, R.J. et al. (2012) Building an efficient curation workflow for the Arabidopsis literature corpus. Database, 2012, bas047.
    • (2012) Database , vol.2012
    • Li, D.1    Berardini, T.Z.2    Muller, R.J.3
  • 10
    • 43549101608 scopus 로고    scopus 로고
    • Text-mining assisted regulatory annotation
    • Aerts, S., Haeussler, M., van Vooren, S. et al. (2008) Text-mining assisted regulatory annotation. Genome Biol., 9, R31.
    • (2008) Genome Biol. , vol.9 , pp. R31
    • Aerts, S.1    Haeussler, M.2    Van Vooren, S.3
  • 11
    • 84879330505 scopus 로고    scopus 로고
    • An overview of the BioCreative 2012 workshop track III: Interactive text mining task
    • Arighi, C.N., Carterette, B., Cohen, K.B. et al. (2013) An overview of the BioCreative 2012 workshop track III: interactive text mining task. Database, 2013, bas056.
    • (2013) Database , vol.2013
    • Arighi, C.N.1    Carterette, B.2    Cohen, K.B.3
  • 12
    • 80053414432 scopus 로고    scopus 로고
    • Overview of the BioCreative III workshop
    • Arighi, C.N., Lu, Z., Krallinger, M. et al. (2011) Overview of the BioCreative III Workshop. BMC Bioinformatics, 12(Suppl. 8), S1.
    • (2011) BMC Bioinformatics , vol.12 , pp. S1
    • Arighi, C.N.1    Lu, Z.2    Krallinger, M.3
  • 13
    • 84864051137 scopus 로고    scopus 로고
    • Improving links between literature and biological data with text mining: A case study with GEO, PDB and MEDLINE
    • Neveol, A., Wilbur, W.J., Lu, Z. (2012) Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database, 2012, bas026.
    • (2012) Database , vol.2012
    • Neveol, A.1    Wilbur, W.J.2    Lu, Z.3
  • 14
    • 70350455266 scopus 로고    scopus 로고
    • Semi-automated curation of protein subcellular localization: A text mining-based approach to gene ontology (GO) cellular component curation
    • van Auken, K., Jaffery, J., Chan, J. et al. (2009) Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics, 10, 228.
    • (2009) BMC Bioinformatics , vol.10 , pp. 228
    • Van Auken, K.1    Jaffery, J.2    Chan, J.3
  • 15
    • 84876501269 scopus 로고    scopus 로고
    • BioCreative-2012 virtual issue
    • Wu, C.H., Arighi, C.N., Cohen, K.B. et al. (2012) BioCreative-2012 virtual issue. Database, 2012, bas049.
    • (2012) Database , vol.2012
    • Wu, C.H.1    Arighi, C.N.2    Cohen, K.B.3
  • 16
    • 84876499465 scopus 로고    scopus 로고
    • Accelerating literature curation with text-mining tools: A case study of using PubTator to curate genes in PubMed abstracts
    • Wei, C.-H., Harris, B.R., Li, D. et al. (2012) Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database, 2012, bas041.
    • (2012) Database , vol.2012
    • Wei, C.-H.1    Harris, B.R.2    Li, D.3
  • 17
    • 84861878785 scopus 로고    scopus 로고
    • PubTator: A PubMed-like interactive curation system for document triage and literature curation
    • Washington, D.C.
    • Wei, C.-H., Kao, H.-Y., Lu, Z. (2012) PubTator: a PubMed-like interactive curation system for document triage and literature curation. Proceedings of the BioCreative 2012 Workshop, Washington, D.C., pp. 20-24.
    • (2012) Proceedings of the BioCreative 2012 Workshop , pp. 20-24
    • Wei, C.-H.1    Kao, H.-Y.2    Lu, Z.3
  • 18
    • 84883572716 scopus 로고    scopus 로고
    • PubTator: A web-based text mining tool for assisting biocuration
    • Wei, C.-H., Kao, H.-Y., Lu, Z. (2013) PubTator: a Web-based text mining tool for assisting biocuration. Nucleic Acids Res., 41, W518-W522.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W518-W522
    • Wei, C.-H.1    Kao, H.-Y.2    Lu, Z.3
  • 19
    • 82255163997 scopus 로고    scopus 로고
    • Extraction of data deposition statements from the literature: A method for automatically tracking research results
    • Neveol, A., Wilbur, W.J. and Lu, Z. (2011) Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinformatics, 27, 3306-3312.
    • (2011) Bioinformatics , vol.27 , pp. 3306-3312
    • Neveol, A.1    Wilbur, W.J.2    Lu, Z.3
  • 20
    • 0036144742 scopus 로고    scopus 로고
    • Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
    • Raychaudhuri, S., Chang, J.T., Sutphin, P.D. et al. (2002) Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res., 12, 203-214.
    • (2002) Genome Res. , vol.12 , pp. 203-214
    • Raychaudhuri, S.1    Chang, J.T.2    Sutphin, P.D.3
  • 21
    • 34547771661 scopus 로고    scopus 로고
    • Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
    • Daraselia, N., Yuryev, A., Egorov, S. et al. (2007) Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics, 8, 243.
    • (2007) BMC Bioinformatics , vol.8 , pp. 243
    • Daraselia, N.1    Yuryev, A.2    Egorov, S.3
  • 22
    • 70350455266 scopus 로고    scopus 로고
    • Semi-automated curation of protein subcellular localization: A text mining-based approach to gene ontology (GO) cellular component curation
    • Auken, K.V., Jaffery, J., Chan, J. et al. (2009) Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) cellular component curation. BMC Bioinformatics, 10, 228.
    • (2009) BMC Bioinformatics , vol.10 , pp. 228
    • Auken, K.V.1    Jaffery, J.2    Chan, J.3
  • 23
    • 79960622303 scopus 로고    scopus 로고
    • Using computational predictions to improve literature-based gene ontology annotations: A feasibility study
    • Costanzo, M.C., Park, J., Balakrishnan, R. et al. (2011) Using computational predictions to improve literature-based gene ontology annotations: a feasibility study. Database, 2011, bar004.
    • (2011) Database , vol.2011
    • Costanzo, M.C.1    Park, J.2    Balakrishnan, R.3
  • 24
    • 84862256421 scopus 로고    scopus 로고
    • CvManGO, a method for leveraging computational predictions to improve literature-based gene ontology annotations
    • Park, J., Costanzo, M.C., Balakrishnan, R. et al. (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database, 2012, bas001.
    • (2012) Database , vol.2012
    • Park, J.1    Costanzo, M.C.2    Balakrishnan, R.3
  • 25
    • 84862267399 scopus 로고    scopus 로고
    • Argo: An integrative, interactive, text mining-based workbench supporting curation
    • Rak, R., Rowley, A., Black, W. et al. (2012) Argo: an integrative, interactive, text mining-based workbench supporting curation. Database, 2012, bas010.
    • (2012) Database , vol.2012
    • Rak, R.1    Rowley, A.2    Black, W.3
  • 26
    • 84885895986 scopus 로고    scopus 로고
    • Managing the data deluge: Data-driven GO category assignment improves while complexity of functional annotation increases
    • Gobeill, J., Pasche, E., Vishnyakova, D. et al. (2013) Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database, 2013, bat041.
    • (2013) Database , vol.2013
    • Gobeill, J.1    Pasche, E.2    Vishnyakova, D.3
  • 27
    • 19944390518 scopus 로고    scopus 로고
    • Automatic extraction of gene/protein biological functions from biomedical text
    • Koike, A., Niwa, Y. and Takagi, T. (2004) Automatic extraction of gene/protein biological functions from biomedical text. Bioinformatics, 2005, 7.
    • (2004) Bioinformatics , vol.2005 , pp. 7
    • Koike, A.1    Niwa, Y.2    Takagi, T.3
  • 28
    • 42549119088 scopus 로고    scopus 로고
    • Discovering gene annotations in biomedical text databases
    • Cakmak, A. and Ozsoyoglu, G. (2008) Discovering gene annotations in biomedical text databases. BMC Bioinformatics, 9, 143.
    • (2008) BMC Bioinformatics , vol.9 , pp. 143
    • Cakmak, A.1    Ozsoyoglu, G.2
  • 29
  • 30
    • 84876462011 scopus 로고    scopus 로고
    • Biocuration workflows and text mining: Overview of the BioCreative 2012 workshop track II
    • Lu, Z. and Hirschman, L. (2012) Biocuration workflows and text mining: overview of the BioCreative 2012 workshop track II. Database, 2012, bas043.
    • (2012) Database , vol.2012
    • Lu, Z.1    Hirschman, L.2
  • 31
    • 33947311528 scopus 로고    scopus 로고
    • An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
    • Camon, E.B., Barrell, D.G., Dimmer, E.C. et al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics, 6(Suppl. 1), S17.
    • (2005) BMC Bioinformatics , vol.6 , pp. S17
    • Camon, E.B.1    Barrell, D.G.2    Dimmer, E.C.3
  • 32
    • 51049090818 scopus 로고    scopus 로고
    • Concept recognition for extracting protein interaction relations from biomedical text
    • Baumgartner, W.A. Jr, Lu, Z., Johnson, H.L. et al. (2008) Concept recognition for extracting protein interaction relations from biomedical text. Genome Biol., 9, S9.
    • (2008) Genome Biol. , vol.9 , pp. S9
    • Baumgartner, W.A.1    Lu, Z.2    Johnson, H.L.3
  • 33
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of BioCreative II
    • Krallinger, M., Leitner, F., Rodriguez-Penagos, C. et al. (2008) Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol., 9, S4.
    • (2008) Genome Biol. , vol.9 , pp. S4
    • Krallinger, M.1    Leitner, F.2    Rodriguez-Penagos, C.3
  • 34
    • 84863516719 scopus 로고    scopus 로고
    • Concept annotation in the CRAFT corpus
    • Bada, M., Eckert, M., Evans, D. et al. (2012) Concept annotation in the CRAFT corpus. BMC Bioinformatics, 13, 161.
    • (2012) BMC Bioinformatics , vol.13 , pp. 161
    • Bada, M.1    Eckert, M.2    Evans, D.3
  • 35
    • 4944229711 scopus 로고    scopus 로고
    • GENIA corpus - Semantically annotated corpus for bio-textmining
    • Kim, J.D., Ohta, T., Tateisi, Y. et al. (2003) GENIA corpus - semantically annotated corpus for bio-textmining. Bioinformatics, 19(Suppl. 1), i180-i182.
    • (2003) Bioinformatics , vol.19 , pp. i180-i182
    • Kim, J.D.1    Ohta, T.2    Tateisi, Y.3
  • 36
    • 84875575941 scopus 로고    scopus 로고
    • An improved corpus of disease mentions in PubMed citations
    • Association for Computational Linguistics, Montreal, Canada
    • Dogan, R.I. and Lu, Z. (2012) An improved corpus of disease mentions in PubMed citations. Proceedings of the 2012 Workshop on Biomedical Natural Language Processing. Association for Computational Linguistics, Montreal, Canada, pp. 91-99.
    • (2012) Proceedings of the 2012 Workshop on Biomedical Natural Language Processing , pp. 91-99
    • Dogan, R.I.1    Lu, Z.2
  • 37
    • 51049088874 scopus 로고    scopus 로고
    • Overview of BioCreative II gene mention recognition
    • Smith, L., Tanabe, L.K., Ando, R.J. et al. (2008) Overview of BioCreative II gene mention recognition. Genome Biol., 9(Suppl. 2), S2.
    • (2008) Genome Biol. , vol.9 , pp. S2
    • Smith, L.1    Tanabe, L.K.2    Ando, R.J.3
  • 38
    • 84895437465 scopus 로고    scopus 로고
    • NCBI disease corpus: A resource for disease name recognition and concept normalization
    • Doǧan, R.I., Leaman, R. and Lu, Z. (2014) NCBI disease corpus: a resource for disease name recognition and concept normalization. J. Biomed. Inform., 47, 1-10
    • (2014) J. Biomed. Inform. , vol.47 , pp. 1-10
    • Doǧan, R.I.1    Leaman, R.2    Lu, Z.3
  • 39
    • 84892683484 scopus 로고    scopus 로고
    • A guide to best practices for gene ontology (GO) manual annotation
    • Balakrishnan, R., Harris, M.A., Huntley, R. et al. (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database, 2013, bat054.
    • (2013) Database , vol.2013
    • Balakrishnan, R.1    Harris, M.A.2    Huntley, R.3
  • 41
    • 79952765434 scopus 로고    scopus 로고
    • Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction
    • Névéol, A., Islamaj Doǧan, R. and Lu, Z. (2011) Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. J. Biomed. Inform., 44, 310-318.
    • (2011) J. Biomed. Inform. , vol.44 , pp. 310-318
    • Névéol, A.1    Islamaj Doǧan, R.2    Lu, Z.3
  • 44
    • 84892753494 scopus 로고    scopus 로고
    • BioC: A minimalist approach to interoperability for biomedical text processing
    • Comeau, D.C., Islamaj Dogan, R., Ciccarese, P. et al. (2013) BioC: a minimalist approach to interoperability for biomedical text processing. Database, 2013, bat064.
    • (2013) Database , vol.2013
    • Comeau, D.C.1    Islamaj Dogan, R.2    Ciccarese, P.3
  • 45
    • 33947311528 scopus 로고    scopus 로고
    • An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
    • Camon, E.B., Barrell, D.G., Dimmer, E.C. et al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics, 6, S17.
    • (2005) BMC Bioinformatics , vol.6 , pp. S17
    • Camon, E.B.1    Barrell, D.G.2    Dimmer, E.C.3
  • 47
    • 80053244362 scopus 로고    scopus 로고
    • Recommending MeSH terms for annotating biomedical articles
    • Huang, M., Névéol, A. and Lu, Z. (2011) Recommending MeSH terms for annotating biomedical articles. J. Am. Med. Inform. Assoc., 18, 660-667.
    • (2011) J. Am. Med. Inform. Assoc. , vol.18 , pp. 660-667
    • Huang, M.1    Névéol, A.2    Lu, Z.3
  • 48
    • 84987617568 scopus 로고    scopus 로고
    • BioCreative-IV virtual issue
    • Arighi, C.N., Wu, C.H., Cohen, K.B. et al. (2014) BioCreative-IV virtual issue. Database, 2014, bau039.
    • (2014) Database , vol.2014
    • Arighi, C.N.1    Wu, C.H.2    Cohen, K.B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.