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| Sasaki, Y., Thompson, P., Cotter, P., McNaught, J. and Ananiadou, S., Event Frame Extraction Based on a Gene Regulation Corpus, in: Proceedings of the 22nd International Conference on Computational Linguistics (Coling 2008), pages 761--768, Coling 2008 Organizing Committee, 2008
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| Thew, S., Sutcliffe, A., de Bruijn, O., McNaught, J., Procter, R., Venters, C.C. and Buchan, I., Experience in e-Science Requirements Engineering, pages 277-282, 2008
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| Kano, Y., Nguyen, N. T. H., Sætre, R., Yoshida, K., Miyao, Y., Tsuruoka, Y., Matsubayashi, Y., Ananiadou, S. and Tsujii, J., Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example., in: Proceedings of the Pacific Symposium on Biocomputing 2008 (PSB 2008), pages 616--627, 2008
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| 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
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| Sasaki, Y., Tsuruoka, Y., McNaught, J. and Ananiadou, S., How to Make the Most of NE Dictionaries in Statistical NER, in: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008), pages 63--70, Association for Computational Linguistics, 2008
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| Hirohata, K., Okazaki, N., Ananiadou, S. and Ishizuka, M., Identifying Sections in Scientific Abstracts using Conditional Random Fields, in: Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008), pages 381-388, 2008
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| Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Kleio: a knowledge-enriched information retrieval system for biology, in: Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval, Singapore, Singapore, pages 787--788, ACM, 2008
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| 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)
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| Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., PathText: Text Mining Tools Integrated with Biological Pathway, in: Genomes to Systems Conference 2008 Handbook, pages 65, The Consortium for Post-Genome Science, 2008
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| Kano, Y., Nguyen, N. T. H., Sætre, R., Fukamachi, K., Yoshida, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., Sharable type system design for tool inter-operability and combinatorial comparison, in: Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL), pages 122--129, 2008
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| Miyao, Y., Sætre, R., Sagae, K., Matsuzaki, T. and Tsujii, J., Task-Oriented Evaluation of Syntactic Parsers and Their Representations, in: Proceedings of ACL-08:HLT, pages 46-54, 2008
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| Kano, Y., Nguyen, N. T. H., Sætre, R., Yoshida, K., Fukamachi, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., Towards Data And Goal Oriented Analysis: Tool Inter-Operability And Combinatorial Comparison, in: Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP-2008), pages 859-864, 2008
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| Pyysalo, S., Sætre, R., Tsujii, J. and Salakoski, T., Why Biomedical Relation Extraction Results are Incomparable and What to do about it, in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pages 149--152, 2008
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| Ninomiya, T., Matsuzaki, T., Miyao, Y. and Tsujii, J., A log-linear model with an n-gram reference distribution for accurate HPSG parsing, in: Proceedings of the Tenth International Conference on Parsing Technologies (IWPT), Prague, Czech Republic, pages 60--68, 2007
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| Yoshida, K., Tsuruoka, Y., Miyao, Y. and Tsujii, J., Ambiguous Part-of-Speech Tagging for Improving Accuracy and Domain Portability of Syntactic Parsers, in: Proceedings of the Twentieth International Joint Conference on Artificial Intelligence (IJCAI-07), pages 1783-1788, 2007
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| Hahn, U., Buyko, E., Tomanek, K., Piao, S., McNaught, J., Tsuruoka, Y. and Ananiadou, S., An Annotation Type System for a Data-Driven NLP Pipeline, in: Proceedings of the Linguistic Annotation Workshop, pages 33--40, Association for Computational Linguistics, 2007
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