Kim, J.-D. - NaCTeM Publications

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First name(s):	J.-D.
Last name(s):	Kim

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NÃ©dellec, C., Bossy, R., Kim, J.-D., Kim, J-J., Ohta, T., Pyysalo, S. and Zweigenbaum, P., Overview of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, pages 1--7, Association for Computational Linguistics, 2013

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Pyysalo, S., Stenetorp, P., Ohta, T., Kim, J.-D. and Ananiadou, S., New Resources and Perspectives for Biomedical Event Extraction, in: Proceedings of BioNLP 2012, pages 100-108, 2012

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Selected articles from the BioNLP Shared Task 2011, 2012

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Kocbek, S., SÃ¦tre, R., Stiglic, G., Kim, J.-D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., AGRA: Analysis of Gene Ranking Algorithms (2011), in: Bioinformatics, 27:8(1185-1186)

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Kocbek, S., SÃ¦tre, R., Stiglic, G., Kim, J.-D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from Pubmed publications, in: Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011

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Stenetorp, P., TopiÄ‡, G., Pyysalo, S., Ohta, T., Kim, J.-D. and Tsujii, J., BioNLP Shared Task 2011: Supporting Resources, in: Proceedings of the BioNLP Shared Task 2011 Workshop, pages 112--120, Association for Computational Linguistics, 2011

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Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y. and Tsujii, J., Extracting Bio-Molecular Events From Literatureâ€”The BioNLPâ€™09 Shared Task (2011), in: Computational Intelligence, 27:4(513-540)

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Nguyen, N. T. H., Kim, J.-D. and Tsujii, J., Overview of BioNLP 2011 Protein Coreference Shared Task, in: Proceedings of the BioNLP Shared Task 2011 Workshop, pages 74--82, Association for Computational Linguistics, 2011

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Kim, J.-D., Pyysalo, S., Ohta, T., Bossy, R., Nguyen, N. T. H. and Tsujii, J., Overview of BioNLP Shared Task 2011, in: Proceedings of the BioNLP Shared Task 2011 Workshop, pages 1--6, Association for Computational Linguistics, 2011

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Kano, Y., BjÃ¶rne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L., Kilicoglu, H., Bergler, S., Van Landeghem, S., Van Parys, T., Van de Peer, Y., Miwa, M., Ananiadou, S., Neves, M., Pascual-Montano, A., Ozgur, A., Radev, D. R., Riedel, S., SÃ¦tre, R., Chun, H.-W., Kim, J.-D., Pyysalo, S., Ohta, T. and Tsujii, J., U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011), in: BMC Bioinformatics, 12(481)

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Ohta, T., Pyysalo, S., Kim, J.-D. and Tsujii, J., A re-evaluation of biomedical named entity-term relations (2010), in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(917--928)

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Ohta, T., Pyysalo, S., Miwa, M., Kim, J.-D. and Tsujii, J., Event Extraction for Post-Translational Modifications, in: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pages 19--27, Association for Computational Linguistics, 2010

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Miwa, M., SÃ¦tre, R., Kim, J.-D. and Tsujii, J., Event Extraction with Complex Event Classification Using Rich Features (2010), in: Journal of Bioinformatics and Computational Biology, 8:1(131--146)

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Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S., Ohta, T. and Tsujii, J., Improving the Inter-corpora Compatibility for Protein Annotations (2010), in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(901-916)

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Uematsu, S., Kim, J.-D. and Tsujii, J., Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics, in: Proceedings of BioNLP 2009 Workshop, pages 162--170, 2009

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Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S., Ohta, T. and Tsujii, J., Demystifying protein annotations: toward increasing the compatibility of different corpora, in: Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM 2009), pages 103--108, 2009

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Ohta, T., Kim, J.-D., Pyysalo, S., Wang, Y. and Tsujii, J., Incorporating GENETAG-style annotation to GENIA corpus, in: Proceedings of BioNLP 2009 Workshop, pages 106--107, 2009

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Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S. and Tsujii, J., Investigating heterogeneous protein annotations toward cross-corpora utilization (2009), in: BMC Bioinformatics, 10(403)

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Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y. and Tsujii, J., Overview of BioNLP'09 Shared Task on Event Extraction, in: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 1--9, 2009

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Pyysalo, S., Ohta, T., Kim, J.-D. and Tsujii, J., Static Relations: a Piece in the Biomedical Information Extraction Puzzle, in: Proceedings of BioNLP 2009 Workshop, pages 1--9, 2009

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Nguyen, N. T. H., Kim, J.-D. and Tsujii, J., Challenges in Pronoun Resolution System for Biomedical Text, in: Proceedings of the 6th International Conference on Language Resources and Evaluation (LREC 2008), pages 2408--2412, 2008

Kim, J.-D., Ohta, T. and Tsujii, J., Corpus annotation for mining biomedical events from literature (2008), in: BMC Bioinformatics, 9:1(10)

Kim, J.-D., Ohta, T., Oda, K. and Tsujii, J., From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature, in: Proceedings of the 6th Asia Pacific Bioinformatics Conference, pages 165-176, Imperial College Press, 2008

Oda, K., Kim, J.-D., Ohta, T., Okanohara, D., Matsuzaki, T., Tateisi, Y. and Tsujii, J., New challenges for text mining: Mapping between text and manually curated pathways (2008), in: BMC Bioinformatics, 9:Suppl 3(S5)

Piao, S., Buyko, E., Tsuruoka, Y., Tomanek, K., Kim, J.-D., McNaught, J., Hahn, U., Su, J. and Ananiadou, S., BOOTStrep Annotation Scheme: Encoding Information for Text Mining, in: Proceedings of the 4th Corpus Linguistics Conference (CL2007), 2007

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