• Ahmed Amrani, Yves Kodratoff, and Oriane Matte-Tailliez. A semi-automatic system for tagging specialized corpora. In Advances in Knowledge Discovery and Data Mining 8th Pacific-Asia Conference, PAKDD 2004, volume 3056 of Lecture Notes in Computer Science, pages 670-681. Springer, 2004.

• M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, and G. M. Rubin & G. Sherlock. Gene ontology: tool for the unification of biology. Nature Genetics, 25:25-29, May 2000.

• K. Baclawski, J. Cigna, M. M. Kokar, P. Mager, and B. Indurkhya. Knowledge representation and indexing using the unified medical language system. In Proceedings of the Pacific Symposium on Biocomputing, pages 493-504, 2000.

• C. Blaschke and A. Valencia. The frame-based module of the suiseki information extraction system. IEEE Intelligent Systems, (17):14-20, 2002. (PDF)

• Olivier Bodenreider and Serguei V. Pakhomov. Exploring adjectival modification in biomedical discourse across two genres. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 105-112, 2003. (PDF)

• B. Bruijn and J. Martin. Getting to the (c)ore of knowledge: mining biomedical literature. Int. Journal Medical Informatics, (67):7-18, 2002.

• R. Bunescu, R. Ge, R.J. Kate, E.M. Marcotte, R.J. Mooney, A.K. Ramani, and Y.W. Wong. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine (Special Issue on Summarization and Information Extraction from Medical Documents), 2004.

• K. Bretonnel Cohen and Lawrence Hunter. Natural language processing and systems biology. Technical report, University of Colorado School of Medicine Denver, CO, USA, 2004.

• N. Collier, C. Nobata, and J. Tsujii. Extracting the names of genes and gene products with a hidden markov model. In Proceedings of the 18th International Conference on Computational Linguistics (COLING'2000), Saarbrucken, Germany, July 2000.

• N. Collier, C. Nobata, and J. Tsujii. Automatic acquisition and classification of terminology using a tagged corpus in the molecular biology domain. Journal of Terminology, John Benjamins, 7(2):239-257, 2002.

• D. P. Corney, B. F. Buxton, W. B. Langdon, and D. T. Jones. BioRAT: Extracting biological information from full-length papers. Bioinformatics, July 2004.

• M. Craven and J. Kumlien. Constructing biological knowledge bases by extracting information from text sources. In Proceedings of International Conference on Intelligent Systems for Molecular Biology, pages 77-86, 1999.

• D. Cutting, J. Kupiec, J. Pedersen, and P. Sibun. A practical part-of-speech tagger. In Proceedings of the Third Conference on Applied Natural Language Processing, pages 133-140, 1992.

• S. Dickman. Tough mining. PLoS Biology, 1(2):144-147, 2003.

• Tomaz Erjavec, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, and Jun'ichi Tsujii. Encoding biomedical resources in TEI: The case of the GENIA corpus. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 97-104, 2003.

• K. Franzen, G. Eriksson, F. Olsson, L. Asker, P. Liden, and J. Coster. Protein names: how to find them. Int J Med Inf., 4(67):49-61, December 2002.

• C. Friedman, P. Kra M. Krauthammer, H. Yu, and A. Rzhetsky. GENIES: a natural-langauge processing system for the extraction of molecular pathways from journal articles. Bioinformatics, 17(1):74-82, 2001.

• K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi. Toward information extraction: Identifying protein names from biological papers. In Proc. of the Pacific Symposium on Biocomputing, 1998.

• H. Harkema, R. Gaizauskas, M. Hepple, A. Roberts, I. Roberts, N. Davis, and Y. Guo. A large-scale terminology resource for biomedical text processing. In BionLINK 2004: Linking Biological Literature, Ontologies, and Databases, ACL, pages 53-60, 2004.

• M. Hepple. Indepedence and commitment: Assumptions for rapid training and execution of rule-based POS taggers. In Proceedings of the 38th Annual Meeting of the Association for Computational Linguistics (ACL-2000), pages 278-285, 2000. (PDF)

• L. Hirschman, L. Wong J.C. Park, J. Tsujii, and C. H. Wu. Accomplishments and challenges in literature data mining for biology. Bioinformatics, 18(12):1553-1561, 2002.

• Jerry R. Hobbs. Information extraction from biomedical text. Journal of Biomedical Informatics, 2004.

• Wen-Juan Hou and Hsin-Hsi Chen. Enhancing performance of protein name recognizers using collocation. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 25-32, 2003. (PDF)

• Minlie Huang, Xiaoyan Zhu, Yu Hao, Donald G. Payan, Kunbin Qu, and Ming Li. Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics, 20(18):3604-3612, July 2004.

• B. L. Humphreys, D. A. Lindberg, H. M. Schoolman, and G. O. Barnett. The unified medical language system: an informatics research collaboration. Journal of the American Medical Informatics Assoc., 5(1):1-11, 1998.

• K. Humphreys, G. Demetriou, and R. Gaizauskas. Two applications of information extraction to biological science journal articles: Enzyme interactions and protein structures. In Proceedings of the Pacific Symposium on Biocomputing (PSB-2000), pages 505-516, January 2000.

• L. Hunter. Artificial Intelligence and Molecular Biology, chapter Molecular Biology for Computer Scientists. AAAI Press, 1993. (PDF)

• J. Kazama, Y. Miyao, and J. Tsujii. A maximum entropy tagger with unsupervised hidden markov models. In Proceedings of the Sixth Natural Language Processing Pacific Rim Symposium (NLPRS2001), pages 333-340, 2001.

• J. D. Kim, T. Ohta, Y. Tatisi, and J. Tsujii. GENIA corpus - a semantically annotated corups for bio-textmining. Bioinformatics, 19(1):180-182, 2003.

• S. Kulick, A. Bies, M. Liberman, M. Mandel, R. McDonald, M. Palmer, A. Schein, and L. Ungar. Integrated annotation for biomedical information extraction. In NAACL/HLT Workshop on Linking Biological Literature, Ontologies and Databases: Tools for Users, pages 61-68, 2004.

• Ki-Joong Lee, Young-Sook Hwang, and Hae-Chang Rim. Two-phase biomedical NE recognition based on SVMs. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 33-40, 2003. (PDF)

• G. Leroy, H. Chen, and J. D. Martinez. A shallow parser based on closed-class words to capture relations in biomedical text. Journal of Biomedical Informatics, 36:145-158, 2003.

• Bisharah Libbus, Halil Kilicoglu, Thomas C. Rindflesch, James G. Mork, and Alan R. Aronson. Using natural language processing, locuslink and the gene ontology to compare OMIM to MEDLINE. In NAACL/HLT Workshop on Linking Biological Literature, Ontologies and Databases: Tools for Users, pages 69-76, 2004.

• D. M. McDonald, H. Chen, H. Su, and B. B. Marshall. Extracting gene pathway relations using a hybrid grammar: the arizona relation parser. Bioinformatics, 20(18):3370-3378, July 2004.

• Alex Morgan, Lynette Hirschman, Alexander Yeh, and Marc Colosimo. Gene name extraction using FlyBase resources. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 1-8, 2003. (PDF)

• Hans-Michael Müller, Eimear E. Kenny, and Paul W. Sternberg. Textpresso: An ontology-based information retrieval and extraction system for biological literature. Plos Biology, 2(11), November 2004.

• G. Nenadic, I. Spasi, and S. Ananiadou. Terminology-driven mining of biomedical literature. In Proceedings of the 2003 ACM symposium on Applied computing table of contents Melbourne, Florida, pages 83-87. ACM Press New York, NY, USA, 2003.

• Goran Nenadic, Simon Rice, Irena Spasic, Sophia Ananiadou, and Benjamin Stapley. Selecting text features for gene name classification: from documents to terms. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 121-128, 2003. (PDF)

• J. Casta no, J. Zhang, and J. Pustejovsky. Anaphora resolution in biomedical literature. In International Symposium on Reference Resolution, 2002.

• T. Ohta, Y. Tatisi, and J. D. Kim. GENIA corpus: an annotated research abstract corpus in molecular biology domain. In Proceedings of he Human Language Technology Conference (HLT 2002), pages 73-77, 2002.

• H. Pearson. Biology's name game. Nature, (411):631-632, June 2001.

• D. Proux, F. Rechenmann, L. Julliard, V. Pillet, and B. Jacq. Detecting gene symbols and names in biological texts: A first step toward pertinent information extraction. Genome Inform Ser Workshop Genome Inform., 9:72-80, 1998.

• J. Pustejovsky, J. Castano, and J. Zhang. Robust relational parsing over biomedical literature: Extracting inhibit relations. In Proceedings of the Pacific Symposium on Biocomputing, pages 362-373, 2002.

• S. Ray and M. Craven. Representing sentence structure in hidden markov models for information extraction. In Proc. of the Int. Joint Conf. on Artificial Intelligence, 2001.

• T. C. Rindflesch, L. Tanabe, J. N. Weinstein, and L. Hunter. EDGAR: Extraction of drugs, genes, and relations from the biomedical literature. In Proc. Pacific Symposium on Biocomputing, pages 514-525, 2000.

• T. C. Rindflesch, L. Bisharah, H. Dimitar, and A. R. Aronson;and H. Kilicoglu. Semantic relations asserting the etiology of genetic diseases. In Proceedings of the AMIA Annual Symposium, 2003.

• Barbara Rosario and Marti Hearst. Classifying the semantic relations in noun compounds via a domain-specific lexical hierarchy. In Proceedings of 2001 Conference on Empirical Methods in Natural Language Processing, Pittsburgh, PA (EMNLP 2001), 2001.

• A. Rzhetsky, T. Koike, S. Kalachikov, SM. Gomez, M. Krauthammer, SH. Kaplan, P. Kra, JJ. Russo, and C. Friedman. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics, 16(12):1120-1128, 2000.

• T. Sekimizu, H. S. Park, and J. Tsujii. Identifying the interaction between genes and gene products based on frequently seen verbs in medline abstracts. Genome Informatics, pages 62-71, 1998.

• H. Shatkay and R. Feldman. Mining the biomedical literature in the genomic era: An overview. Journal of Computational Biology (JCB), 10(6):821-856, December 2003.

• Dan Shen, Jie Zhang, Guodong Zhou, Jian Su, and Chew-Lim Tan. Effective adaptation of hidden Markov model-based named entity recognizer for biomedical domain. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 49-56, 2003. (PDF)

• M. Skounakis, M. Craven, and S. Ray. Hierarchical Hidden Markov Models for information extraction. In Proceedings of the 18th International Joint Conference on Artificial Intelligence, Acapulco, Mexico. Morgan Kaufmann., 2003., 2003.

• L. Smith, T. Rindflesch, and W. J. Wilbur. Medpost: a part-of-speech tagger for biomedical text. Bioinformatics, 20(14), 2004.

• Koichi Takeuchi and Nigel Collier. Bio-medical entity extraction using support vector machines. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 57-64, 2003. (PDF)

• L. Tanabe, U. Scherf, L. H. Smith, J. K. Lee, L. Hunter, and J. N. Weinstein. Medminer: an internet text-mining tool for biomedical information, with application to gene expression profiling. BioTechniques, 27:1210-1217, 1999.

• Y. Tateisi and J. Tsujii. Part-of-speech annotation of biology research abstracts. In Proceedings of 4th International Conference on Language Resource and Evaluation (LREC2004), pages 1267-1270, 2004.

• Y. Tateisi, T. Ohta, and J. Tsujii. Annotation of predicate-argument structure of molecular biology text. In JCNLP-04 workshop on Beyond Shallow Analyses, 2004. (PDF)

• James Thomas, David Milward, Christos Ouzounis, Stephen Pulman, and Mark Carroll. Automatic extraction of protein interactions from scientific abstracts. In Proceedings of the Pacific Symposium on Biocomputing, pages 538-549, 2000.

• Manabu Torii, Sachin Kamboj, and K. Vijay-Shanker. An investigation of various information sources for classifying biological names. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 113-120, 2003. (PDF)

• Yoshimasa Tsuruoka and Jun'ichi Tsujii. Boosting precision and recall of dictionary-based protein name recognition. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 41-48, 2003. (PDF)

• N. Uramoto, H. Matsuzawa, T. Nagano, A. Murakami, H. Takeuchi, , and K. Takeda. A text-mining system for knowledge discovery from biomedical documents. IBM Systems Journal, 43(3):516-533, 2004.

• A. Yakushiji, Y. Tateisi Y. Miyao, and J. Tsujii. Event extraction from biomedical papers using a full parser. In Proceedings of the sixth Pacific Symposium on Biocomputing (PSB 2001), pages 408-419, 2001. (PDF)

• Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, and Yuji Matsumoto. Protein name tagging for biomedical annotation in text. In Sophia Ananiadou and Jun'ichi Tsujii, editors, Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pages 65-72, 2003. (PDF)

• H. Yu, C. Friedman, and A. Rhzetsky abd P. Kra. Representing genomic knowledge in the UMLS semantic network. In Proc AMIA Symp., pages 181-185, 1999.