U-Compare: A modular NLP workflow construction and evaluation system

IBM Journal of Research and Development

Volumn 55, Issue 3, 2011, Pages

  Kano, Y ^a   Miwa, M ^a   Cohen, K B ^b   Hunter, L E ^b   Ananiadou, S ^c   Tsujii, J ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPONENT REUSE; CUSTOMIZABLE; ENGINEERING PERSPECTIVE; EVALUATION SYSTEM; MANAGEMENT ARCHITECTURES; NATURAL LANGUAGE PROCESSING; SUBTASKS;

COMPUTATIONAL LINGUISTICS; COMPUTER ARCHITECTURE; INTEROPERABILITY; NATURAL LANGUAGE PROCESSING SYSTEMS; VISUALIZATION;

INFORMATION MANAGEMENT;

EID: 81255191685     PISSN: 00188646     EISSN: 21518556     Source Type: Journal    
DOI: 10.1147/JRD.2011.2105691     Document Type: Article

References (18)

1. D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. R. Pocock, P. Li, and T. Oinn, " Taverna: A tool for building and running workflows of services," Nucleic Acids Res., vol. 34, no. Suppl 2, pp. W729-W732, Jul. 1, 2006. (Pubitemid 44529867)
2. D. Blankenberg, G. Von Kuster, N. Coraor, G. Ananda, R. Lazarus, M. Mangan, A. Nekrutenko, and J. Taylor, " Galaxy: A web-based genome analysis tool for experimentalists," Curr. Protocols Mol. Biol., vol. Chapter 19, pp. 19.10-1-19.10-21, Jan. 2010.
3. I. Altintas, C. Berkley, E. Jaeger, M. Jones, B. Ludascher, and S. Mock, " Kepler: An extensible system for design and execution of scientific workflows," in Proc. 16th Int. Conf. Sci. Stat. Database Manage., 2004, pp. 423-424.
4. H. Cunningham, D. Maynard, K. Bontcheva, and V. Tablan, " GATE: A framework and graphical development environment for robust NLP tools and applications," in Proc. 40th Anniv. Meeting Assoc. Comput. Linguistics, 2002, pp. 168-175.
5. D. Ferrucci, A. Lally, D. Gruhl, E. Epstein, M. Schor, J. W. Murdock, A. Frenkiel, E. W. Brown, T. Hampp, Y. Doganata, C. Welty, L. Amini, G. Kofman, L. Kozakov, and Y. Mass, " Towards an interoperability standard for text and multi-modal analytics," IBM, Yorktown Heights, NY, Res. Rep. RC24122, 2006.
6. Apache UIMA. [Online]. Available: http://uima.apache.org/
7. OASIS UIMA TC. [Online]. Available: http://www.oasis-open. org/committees/uima/
8. W. A. Baumgartner, Jr., K. B. Cohen, and L. Hunter, " An open-source framework for large-scale, flexible evaluation of biomedical text mining systems," J. Biomed. Discov. Collab., vol. 3, no. 1, p. 1, Jan. 2008, DOI: 10.1186/1747-5333-3-1.
9. U. Hahn, E. Buyko, R. Landefeld, M. Mühlhausen, M. Poprat, K. Tomanek, and J. Wermter, " An overview of JCoRe, the JULIE Lab UIMA component repository," in Proc. LREC Workshop, Towards Enhanc. Interoperability Large HLT Syst.: UIMA NLP, Marrakech, Morocco, 2008, pp. 1-8.
10. Open Health Natural Language Processing (OHNLP) Consortium. [Online]. Available: http://cabig-kc.nci.nih.gov/Vocab/KC/index. php/OHNLP
11. N. Hernandez, F. Poulard, M. Vernier, and J. Rocheteau, " Building a French-speaking community around UIMA, gathering research, education and industrial partners, mainly in Natural Language Processing and Speech Recognizing domains," in Proc. LREC Workshop New Challenges NLP Frameworks, Valletta, Malta, 2010. [Online]. Available: http://hal.archives-ouvertes.fr/ hal-00481459/en/.
12. U-Compare: Share and Compare Tools With UIMA. [Online]. Available: http://u-compare.org/
13. Y. Kano, L. McCrohon, S. Ananiadou, and J. Tsujii, " Integrated NLP evaluation system for pluggable evaluation metrics with extensive interoperable toolkit," in Proc. SETQA-NLP Workshop, NAACL-HLT, Boulder, CO, 2009, pp. 22-30.
14. Y. Kano, P. Dobson, M. Nakanishi, J. Tsujii, and S. Ananiadou, " Text mining meets workflow: Linking U-Compare with Taverna," Bioinformatics, vol. 26, no. 19, pp. 2486-2487, Oct. 2010.
15. J. D. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, " Overview of BioNLP'09 shared task on event extraction," in Proc. BioNLP Workshop Companion Volume Shared Task, Boulder, CO, 2009, pp. 1-9.
16. R. Farkas, V. Vincze, G. Móra, J. Csirik, and G. Szarvas, " The CoNLL 2010 shared task: Learning to detect hedges and their scope in natural language text," in Proc. 14th Conf. CoNLL: Shared Task, Uppsala, Sweden, 2010, pp. 1-12.
17. R. Sætre, K. Yoshida, M. Miwa, T. Matsuzaki, Y. Kano, and J. Tsujii, " AkaneRE relation extraction: Protein interaction and normalization in the BioCreAtIvE II.5 challenge," in Proc. BioCreative II.5 Workshop Special Sessionj Digit. Annotations, Madrid, Spain, 2009, p. 33.
18. CheTA: Chemistry Using Text Annotations. [Online]. Available: http://nactem.ac.uk/cheta/