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| Wang, Y., Kim, J.-D., Sætre, 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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| Miyao, Y., Sagae, K., Sætre, R., Matsuzaki, T. and Tsujii, J., Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction (2009), in: Bioinformatics, 25:3(394-400)
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| Sætre, R., Miwa, M., Yoshida, K. and Tsujii, J., From Protein-Protein Interaction to Molecular Event Extraction, in: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 103--106, 2009
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| Tekiner, F., Ananiadou, S., Tsuruoka, Y. and Tsujii, J., Highly Scalable Text Mining Parallel Tagging Application, in: Proceedings of ICSSCW2009, Famgusta, Cyprus, 2009
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| Piao, S., Rea, B., McNaught, J. and Ananiadou, S., Improving Full Text Search With Text Mining Tools, in: Proceedings of the 14th International Conference on Applications of Natural Language to Information Systems, pages 301-302, 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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| Kano, Y., McCrochon, L., Ananiadou, S. and Tsujii, J., Integrated NLP Evaluation System for Pluggable Evaluation Metrics with Extensive Interoperable Toolkit, in: Proceedings of the NAACL HLT Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing, pages 22--30, 2009
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| Wang, Y., Kim, J.-D., Sætre, R., Pyysalo, S. and Tsujii, J., Investigating heterogeneous protein annotations toward cross-corpora utilization (2009), in: BMC Bioinformatics, 10(403)
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| Sun, X., Matsuzaki, T., Okanohara, D. and Tsujii, J., Latent Variable Perceptron Algorithm for Structured Classification, in: Proceedings of International Joint Conferences on Artificial Intelligence (IJCAI), pages 1236--1242, 2009
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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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| Thew, S., Sutcliffe, A., Procter, R., de Bruijn, O., McNaught, J., Venters, C.C. and Buchan, I., Requirements Engineering for E-science: Experiences in Epidemiology (2009), in: IEEE Software, 26:1(80-87)
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| Nobata, C., Sasaki, Y., Okazaki, N., Rupp, C. J., Tsujii, J. and Ananiadou, S., Semantic Search on Digital Document Repositories based on Text Mining Results, in: International Conferences on Digital Libraries and the Semantic Web 2009 (ICSD2009), pages 34--48, 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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