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Volumn 2013, Issue , 2013, Pages

BioC: A minimalist approach to interoperability for biomedical text processing

Author keywords

[No Author keywords available]

Indexed keywords

DATA MINING; HUMAN; MEDICAL RESEARCH; NATURAL LANGUAGE PROCESSING; SOFTWARE; ARTICLE; COMPUTER PROGRAM;

EID: 84892753494     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat064     Document Type: Article
Times cited : (130)

References (67)
  • 1
    • 0003717511 scopus 로고
    • Cambridge University Press, Cambridge, UK
    • Devlin,K. (1991) Logic and Information. Cambridge University Press, Cambridge, UK.
    • (1991) Logic and Information
    • Devlin, K.1
  • 2
    • 84888336648 scopus 로고    scopus 로고
    • January 2013, date last accessed
    • TEI: Text Encoding Initiative. http://www.tei-c.org/index.xml (January 2013, date last accessed).
    • Text Encoding Initiative
  • 4
    • 84942922199 scopus 로고    scopus 로고
    • ATLAS: A flexible and extensible architecture for linguistic annotation
    • cs.CL/0007022
    • Bird,S., Day,D., Garofolo,J.S. et al. (2000) ATLAS: a flexible and extensible architecture for linguistic annotation. CoRR, cs.CL/0007022, 1-8.
    • (2000) CoRR , pp. 1-8
    • Bird, S.1    Day, D.2    Garofolo, J.S.3
  • 6
    • 7444236194 scopus 로고    scopus 로고
    • UIMA: An architectural approach to unstructured information processing in the corporate research environment
    • Ferrucci,D. and Lally,A. (2004) UIMA: an architectural approach to unstructured information processing in the corporate research environment. Nat. Lang. Eng., 10, 327-348.
    • (2004) Nat. Lang. Eng. , vol.10 , pp. 327-348
    • Ferrucci, D.1    Lally, A.2
  • 8
    • 0038569942 scopus 로고
    • Encoding the British National Corpus
    • Aarts,J., de Haan,P. and Oostdijk,N. (eds), Rodopi, Amsterdam
    • Burnage,G. and Dunlop,D. (1993) Encoding the British National Corpus. In: Aarts,J., de Haan,P. and Oostdijk,N. (eds), English Language Corpora: Design, Analysis and Exploitation. Rodopi, Amsterdam, pp. 79-95.
    • (1993) English Language Corpora: Design, Analysis and Exploitation , pp. 79-95
    • Burnage, G.1    Dunlop, D.2
  • 9
    • 84976721124 scopus 로고
    • The DARPA TIPSTER project
    • Harman,D. (1992) The DARPA TIPSTER project. SIGIR Forum, 26, 26-28.
    • (1992) SIGIR Forum , vol.26 , pp. 26-28
    • Harman, D.1
  • 10
    • 0035152118 scopus 로고    scopus 로고
    • A formal framework for linguistic annotation
    • Bird,S. and Liberman,M. (2000) A formal framework for linguistic annotation. Speech Commun., 33, 23-60.
    • (2000) Speech Commun. , vol.33 , pp. 23-60
    • Bird, S.1    Liberman, M.2
  • 14
    • 79953685181 scopus 로고    scopus 로고
    • Building Watson: An overview of the DeepQA project
    • Ferrucci,D., Brown,E., Chu-Carroll,J. et al. (2010) Building Watson: an overview of the DeepQA project. AI MAGAZINE, 31, 59-79.
    • (2010) AI MAGAZINE , vol.31 , pp. 59-79
    • Ferrucci, D.1    Brown, E.2    Chu-Carroll, J.3
  • 15
    • 40549100761 scopus 로고    scopus 로고
    • Filling the gaps between tools and users: A tool comparator, using protein-protein interaction as an example
    • Kano,Y., Nguyen,N., Saetre,R. et al. (2008) Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example. Pac. Symp. Biocomp., 13, 616-627.
    • (2008) Pac. Symp. Biocomp. , vol.13 , pp. 616-627
    • Kano, Y.1    Nguyen, N.2    Saetre, R.3
  • 16
    • 84892741747 scopus 로고    scopus 로고
    • The JULIE Lab (the Jena University Language & Information Engineering Lab). http://www.julielab.de/.
  • 18
    • 67650714409 scopus 로고    scopus 로고
    • U-Compare: Share and compare text mining tools with UIMA
    • Kano,Y., Baumgartner,W.A. Jr, McCrohon,L. et al. (2009) U-Compare: share and compare text mining tools with UIMA. Bioinformatics, 25, 1997-1998.
    • (2009) Bioinformatics , vol.25 , pp. 1997-1998
    • Kano, Y.1    Baumgartner Jr., W.A.2    McCrohon, L.3
  • 19
    • 84892749313 scopus 로고    scopus 로고
    • The National Centre for text mining: A vision for the future
    • October 2007
    • Ananiadou,S. (2007) The National Centre for text mining: a vision for the future. Ariadne, October 2007, Ariadne Issue 53 http://www.ariadne.ac.uk/ issue53/ananiadou/.
    • (2007) Ariadne , Issue.53
    • Ananiadou, S.1
  • 22
    • 84880315865 scopus 로고    scopus 로고
    • GrAF: A graph-based format for linguistic annotations
    • Association for Computational Linguistics, Prague, Czech Republic
    • Ide,N. and Suderman,K. (2007) GrAF: a graph-based format for linguistic annotations. In: Proceedings of the Linguistic Annotation Workshop. Association for Computational Linguistics, Prague, Czech Republic, pp. 1-8.
    • (2007) Proceedings of the Linguistic Annotation Workshop , pp. 1-8
    • Ide, N.1    Suderman, K.2
  • 23
    • 84859942549 scopus 로고    scopus 로고
    • The manually annotated sub-corpus: A community resource for and by the people
    • Association for Computational Linguistics, Uppsala, Sweden
    • Ide,N., Fellbaum,C., Baker,C. et al. (2010) The manually annotated sub-corpus: a community resource for and by the people. In: Proceedings of the ACL 2010 Conference Short Papers. Association for Computational Linguistics, Uppsala, Sweden, pp. 68-73.
    • (2010) Proceedings of the ACL 2010 Conference Short Papers , pp. 68-73
    • Ide, N.1    Fellbaum, C.2    Baker, C.3
  • 24
    • 84958058705 scopus 로고    scopus 로고
    • A registry of standard data categories for linguistic annotation
    • European Language Resources Association
    • Ide,N. and Romary,L. (2004) A registry of standard data categories for linguistic annotation. In: Fourth Language Resources and Evaluation Conference (LREC). European Language Resources Association, pp. 135-139.
    • (2004) Fourth Language Resources and Evaluation Conference (LREC) , pp. 135-139
    • Ide, N.1    Romary, L.2
  • 25
    • 84863875817 scopus 로고    scopus 로고
    • Towards international standards for language resources
    • Dybkjaer,L., Hemsen,H. and Minker,W. (eds), Springer, Netherlands
    • Ide,N. and Romary,L. (2007) Towards international standards for language resources. In: Dybkjaer,L., Hemsen,H. and Minker,W. (eds), Evaluation of Text and Speech Systems. Springer, Netherlands, pp. 263-284.
    • (2007) Evaluation of Text and Speech Systems , pp. 263-284
    • Ide, N.1    Romary, L.2
  • 26
    • 33947304181 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE: Critical assessment of information extraction for biology
    • Hirschman,L., Yeh,A., Blaschke,C. et al. (2005) Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics, 6 (Suppl. 1), S1.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hirschman, L.1    Yeh, A.2    Blaschke, C.3
  • 27
    • 51049084462 scopus 로고    scopus 로고
    • Evaluation of text-mining systems for biology: Overview of the Second BioCreative community challenge
    • Krallinger,M., Morgan,A., Smith,L. et al. (2008) Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol., 9 (Suppl. 2), S1.
    • (2008) Genome Biol. , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1    Morgan, A.2    Smith, L.3
  • 28
    • 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 , Issue.SUPPL. 8
    • Arighi, C.N.1    Lu, Z.2    Krallinger, M.3
  • 29
    • 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
  • 31
    • 84873426487 scopus 로고    scopus 로고
    • Learning Language in Logic - Genic Interaction Extraction Challenge
    • Nedellec,C. (2005) Learning Language in Logic - Genic Interaction Extraction Challenge. In: International Conference on Machine Learning, http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.96.5066.
    • (2005) International Conference on Machine Learning
    • Nedellec, C.1
  • 32
    • 75149158079 scopus 로고    scopus 로고
    • Investigating heterogeneous protein annotations toward cross-corpora utilization
    • Wang,Y., Kim,J.D., Saetre,R. et al. (2009) Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinformatics, 10, 403.
    • (2009) BMC Bioinformatics , vol.10 , pp. 403
    • Wang, Y.1    Kim, J.D.2    Saetre, R.3
  • 33
    • 84874280242 scopus 로고    scopus 로고
    • The genia event and protein coreference tasks of the BioNLP shared task 2011
    • Kim,J.D., Nguyen,N., Wang,Y. et al. (2012) The genia event and protein coreference tasks of the BioNLP shared task 2011. BMC Bioinformatics, 13 (Suppl. 11), S1.
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL. 11
    • Kim, J.D.1    Nguyen, N.2    Wang, Y.3
  • 35
    • 84949749640 scopus 로고    scopus 로고
    • Assessment of NER solutions against the first and second CALBC Silver Standard Corpus
    • Rebholz-Schuhmann,D., Yepes,A.J., Li,C. et al. (2011) Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. J. Biomed. Semantics, 2 (Suppl. 5), S11.
    • (2011) J. Biomed. Semantics , vol.2 , Issue.SUPPL. 5
    • Rebholz-Schuhmann, D.1    Yepes, A.J.2    Li, C.3
  • 36
    • 84874255818 scopus 로고    scopus 로고
    • IeXML: Towards a framework for interoperability of text processing modules to improve annotation of semantic types in biomedical text
    • Rebholz-Schuhmann,D., Kirsch,H. and Nenadic,G. (2006) IeXML: towards a framework for interoperability of text processing modules to improve annotation of semantic types in biomedical text. In: Proceedings of BioLINK, ISMB, http://www.ebi.ac.uk/Rebholz-srv/IeXML/.
    • (2006) Proceedings of BioLINK, ISMB
    • Rebholz-Schuhmann, D.1    Kirsch, H.2    Nenadic, G.3
  • 38
    • 44649108373 scopus 로고    scopus 로고
    • Comparative analysis of five protein-protein interaction corpora
    • Pyysalo,S., Airola,A., Heimonen,J. et al. (2008) Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics, 9 (Suppl. 3), S6.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 3
    • Pyysalo, S.1    Airola, A.2    Heimonen, J.3
  • 39
    • 84880316498 scopus 로고    scopus 로고
    • The SILT and FlaReNet international collaboration for interoperability
    • Association for Computational Linguistics, Suntec, Singapore
    • Ide,N., Pustejovsky,J., Calzolari,N. et al. (2009) The SILT and FlaReNet international collaboration for interoperability. In: Third Linguistic Annotation Workshop, held in conjunction with ACL. Association for Computational Linguistics, Suntec, Singapore, pp. 178-181.
    • (2009) Third Linguistic Annotation Workshop, Held in Conjunction with ACL. , pp. 178-181
    • Ide, N.1    Pustejovsky, J.2    Calzolari, N.3
  • 40
    • 84880295746 scopus 로고    scopus 로고
    • Bridging the gaps: Interoperability for GrAF, GATE, and UIMA
    • Association for Computational Linguistics, Suntec, Singapore
    • Ide,N. and Suderman,K. (2009) Bridging the gaps: interoperability for GrAF, GATE, and UIMA. In: Proceedings of the Third Linguistic Annotation Workshop. Association for Computational Linguistics, Suntec, Singapore, pp. 27-34.
    • (2009) Proceedings of the Third Linguistic Annotation Workshop , pp. 27-34
    • Ide, N.1    Suderman, K.2
  • 42
    • 5044241106 scopus 로고    scopus 로고
    • MedPost: A part-of-speech tagger for bioMedical text
    • Smith,L., Rindflesch,T. and Wilbur,W.J. (2004) MedPost: a part-of-speech tagger for bioMedical text. Bioinformatics, 20, 2320-2321.
    • (2004) Bioinformatics , vol.20 , pp. 2320-2321
    • Smith, L.1    Rindflesch, T.2    Wilbur, W.J.3
  • 43
    • 84871639988 scopus 로고    scopus 로고
    • BioLemmatizer: A lemmatization tool for morphological processing of biomedical text
    • Liu,H., Christiansen,T., Baumgartner,W.A. Jr et al. (2012) BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J. Biomed. Semantics, 3, 3.
    • (2012) J. Biomed. Semantics , vol.3 , pp. 3
    • Liu, H.1    Christiansen, T.2    Baumgartner Jr., W.A.3
  • 44
    • 55249111767 scopus 로고    scopus 로고
    • Abbreviation definition identification based on automatic precision estimates
    • Sohn,S., Comeau,D.C., Kim,W. et al. (2008) Abbreviation definition identification based on automatic precision estimates. BMC Bioinformatics, 9, 402.
    • (2008) BMC Bioinformatics , vol.9 , pp. 402
    • Sohn, S.1    Comeau, D.C.2    Kim, W.3
  • 45
    • 0041627757 scopus 로고    scopus 로고
    • A simple algorithm for identifying abbreviation definitions in biomedical text
    • Schwartz,A.S. and Hearst,M.A. (2003) A simple algorithm for identifying abbreviation definitions in biomedical text. Pac. Symp. Biocomput, 451-462.
    • (2003) Pac. Symp. Biocomput , pp. 451-462
    • Schwartz, A.S.1    Hearst, M.A.2
  • 46
    • 79958078390 scopus 로고    scopus 로고
    • Machine learning with naturally labeled data for identifying abbreviation definitions
    • Yeganova,L., Comeau,D.C. and Wilbur,W.J. (2011) Machine learning with naturally labeled data for identifying abbreviation definitions. BMC Bioinformatics, 12 (Suppl. 3), S6.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 3
    • Yeganova, L.1    Comeau, D.C.2    Wilbur, W.J.3
  • 47
    • 84865548093 scopus 로고    scopus 로고
    • Open semantic annotation of scientific publications using DOMEO
    • Ciccarese,P., Ocana,M. and Clark,T. (2012) Open semantic annotation of scientific publications using DOMEO. J. Biomed. Semantics, 3 (Suppl. 1), S1.
    • (2012) J. Biomed. Semantics , vol.3 , Issue.SUPPL. 1
    • Ciccarese, P.1    Ocana, M.2    Clark, T.3
  • 48
  • 49
    • 46249122042 scopus 로고    scopus 로고
    • Introducing meta-services for biomedical information extraction
    • Leitner,F., Krallinger,M., Rodriguez-Penagos,C. et al. (2008) Introducing meta-services for biomedical information extraction. Genome Biol., 9 (Suppl. 2), S6.
    • (2008) Genome Biol. , vol.9 , Issue.SUPPL. 2
    • Leitner, F.1    Krallinger, M.2    Rodriguez-Penagos, C.3
  • 52
    • 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
  • 53
    • 84861856856 scopus 로고    scopus 로고
    • SR4GN: A species recognition software tool for gene normalization
    • Wei,C.H., Kao,H.Y. and Lu,Z. (2012) SR4GN: a species recognition software tool for gene normalization. PloS One, 7, e38460.
    • (2012) PloS One , vol.7
    • Wei, C.H.1    Kao, H.Y.2    Lu, Z.3
  • 54
    • 40549140499 scopus 로고    scopus 로고
    • BANNER: An executable survey of advances in biomedical named entity recognition
    • Leaman,R. and Gonzalez,G. (2008) BANNER: an executable survey of advances in biomedical named entity recognition. Pac. Symp. Biocomput, 652-663.
    • (2008) Pac. Symp. Biocomput , pp. 652-663
    • Leaman, R.1    Gonzalez, G.2
  • 55
    • 9544257285 scopus 로고    scopus 로고
    • iProLINK: An integrated protein resource for literature mining
    • Hu,Z.Z., Mani,I., Hermoso,V. et al. (2004) iProLINK: an integrated protein resource for literature mining. Comput. Biol. Chem., 28, 409-416.
    • (2004) Comput. Biol. Chem. , vol.28 , pp. 409-416
    • Hu, Z.Z.1    Mani, I.2    Hermoso, V.3
  • 56
    • 33745611541 scopus 로고    scopus 로고
    • An online literature mining tool for protein phosphorylation
    • Yuan,X., Hu,Z.Z., Wu,H.T. et al. (2006) An online literature mining tool for protein phosphorylation. Bioinformatics, 22, 1668-1669.
    • (2006) Bioinformatics , vol.22 , pp. 1668-1669
    • Yuan, X.1    Hu, Z.Z.2    Wu, H.T.3
  • 57
    • 84876494115 scopus 로고    scopus 로고
    • The eFIP system for text mining of protein interaction networks of phosphorylated proteins
    • Tudor,C.O., Arighi,C.N., Wang,Q. et al. (2012) The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database, 2012, bas044.
    • (2012) Database , vol.2012
    • Tudor, C.O.1    Arighi, C.N.2    Wang, Q.3
  • 60
    • 84879382162 scopus 로고    scopus 로고
    • Using the OntoGene pipeline for the triage task of BioCreative 2012
    • Rinaldi,F., Clematide,S., Hafner,S. et al. (2013) Using the OntoGene pipeline for the triage task of BioCreative 2012. Database, 2013, bas053.
    • (2013) Database , vol.2013
    • Rinaldi, F.1    Clematide, S.2    Hafner, S.3
  • 61
    • 84862250892 scopus 로고    scopus 로고
    • Using ODIN for a PharmGKB revalidation experiment
    • Rinaldi,F., Clematide,S., Garten,Y. et al. (2012) Using ODIN for a PharmGKB revalidation experiment. Database, 2012, bas021.
    • (2012) Database , vol.2012
    • Rinaldi, F.1    Clematide, S.2    Garten, Y.3
  • 62
    • 84861735473 scopus 로고    scopus 로고
    • Interoperability of corpora and annotations
    • Chiarcos,C., Nordhoff,S. and Hellmann,S. (eds), Springer, Berlin, Heidelberg
    • Chiarcos,C. (2012) Interoperability of corpora and annotations. In: Chiarcos,C., Nordhoff,S. and Hellmann,S. (eds), Linked Data in Linguistics. Springer, Berlin, Heidelberg, pp. 161-179.
    • (2012) Linked Data in Linguistics , pp. 161-179
    • Chiarcos, C.1
  • 64
    • 33745795732 scopus 로고    scopus 로고
    • The comparative toxicogenomics database: A cross-species resource for building chemical-gene interaction networks
    • Mattingly,C.J., Rosenstein,M.C., Davis,A.P. et al. (2006) The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol. Sci., 92, 587-595.
    • (2006) Toxicol. Sci. , vol.92 , pp. 587-595
    • Mattingly, C.J.1    Rosenstein, M.C.2    Davis, A.P.3
  • 65
    • 84876467333 scopus 로고    scopus 로고
    • The Comparative Toxicogenomics Database: Update 2013
    • Davis,A.P., Murphy,C.G., Johnson,R. et al. (2013) The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res., 41, D1104-D1114.
    • (2013) Nucleic Acids Res. , vol.41
    • Davis, A.P.1    Murphy, C.G.2    Johnson, R.3
  • 66
    • 84855743190 scopus 로고    scopus 로고
    • The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database
    • Davis,A.P., Wiegers,T.C., Rosenstein,M.C. et al. (2011) The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database. Database, 2011, bar034.
    • (2011) Database , vol.2011
    • Davis, A.P.1    Wiegers, T.C.2    Rosenstein, M.C.3
  • 67
    • 84876219466 scopus 로고    scopus 로고
    • Collaborative biocuration - Text-mining development task for document prioritization for curation
    • Wiegers,T.C., Davis,A.P. and Mattingly,C.J. (2012) Collaborative biocuration - text-mining development task for document prioritization for curation. Database, 2012, bas037.
    • (2012) Database , vol.2012
    • Wiegers, T.C.1    Davis, A.P.2    Mattingly, C.J.3


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