S. Ananiadou, S. Pyysalo, D. B. Jun'ichi-tsujii, and . Kell, Event extraction for systems biology by text mining the literature, Trends in Biotechnology, vol.28, issue.7, pp.381-390, 2010.

S. Ananiadou, D. Sullivan, W. Black, G. Levow, J. J. Gillespie et al., Named entity recognition for bacterial type IV secretion systems, PLoS ONE, vol.6, issue.3, p.14780, 2011.

M. Ashburner, J. A. Ball, . Blake, H. Botstein, . Butler et al., Gene ontology: tool for the unification of biology, Nature genetics, vol.25, pp.25-29, 2000.

J. Björne and T. Salakoski, Generalizing biomedical event extraction, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

E. Charniak and M. Johnson, Coarseto-Fine n-Best Parsing and MaxEnt Discriminative Reranking, Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pp.173-180, 2005.

P. Corbett and P. Murray-rust, Highthroughput identification of chemistry in life science texts, Computational Life Sciences II, pp.107-118, 2006.

M. De-marneffe, B. Maccartney, and C. D. Manning, Generating Typed Dependency Parses from Phrase Structure Parses, Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC'06), pp.449-454, 2006.

M. Gerner, G. Nenadic, and C. M. Bergman, LINNAEUS: a species name identification system for biomedical literature, BMC bioinformatics, vol.11, issue.1, p.85, 2010.

Y. Gotoh, Y. Eguchi, T. Watanabe, S. Okamoto, A. Doi et al., Two-component signal transduction as potential drug targets in pathogenic bacteria, Cell regulation, vol.13, pp.232-239, 2010.

H. Kilicoglu and S. Bergler, Adapting a general semantic interpretation approach to biological event extraction, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

J. Kim, T. Ohta, and Y. Tsuruoka, Introduction to the bio-entity recognition task at JNLPBA, 2004.

J. Kim, T. Ohta, and J. Tsujii, Corpus annotation for mining biomedical events from lterature, BMC Bioinformatics, vol.9, issue.1, p.10, 2008.

J. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, Overview of BioNLP'09 Shared Task on Event Extraction, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pp.1-9, 2009.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

J. Kim, Y. Wang, T. Takagi, and A. Yonezawa, Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

M. Krallinger, A. Morgan, L. Smith, F. Leitner, L. Tanabe et al., Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge, Genome biology, vol.9, issue.2, p.1, 2008.

T. Krell, J. Lacal, A. Busch, H. Silva-jimnez, M. Guazzaroni et al., Bacterial sensor kinases: Diversity in the recognition of environmental signals. Annual Review of Microbiology, vol.64, pp.539-559, 2010.

T. Mascher and D. John, Stimulus perception in bacterial signaltransducing histidine kinases. Microbiol, Mol. Biol. Rev, vol.70, issue.4, pp.910-938, 2006.

D. Mcclosky, M. Surdeanu, and C. Manning, Event extraction as dependency parsing for bionlp 2011, Proceedings of the BioNLP, 2011.

, Workshop Companion Volume for Shared Task

D. Mcclosky, Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2009.

L. Mcgrath, K. Domico, C. Corley, and B. Webb-robertson, Complex biological event extraction from full text using signatures of linguistic and semantic features, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

M. Miwa, S. Pyysalo, T. Hara, and J. Tsujii, Evaluating dependency representation for event extraction, Proceedings of COL-ING'10, pp.779-787, 2010.

T. Ohta, J. Kim, S. Pyysalo, Y. Wang, and J. Tsujii, Incorporating GENETAG-style annotation to GENIA corpus, Proceedings of BioNLP'09, pp.106-107, 2009.

T. Ohta, S. Pyysalo, and J. Tsujii, Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

S. Pyysalo, T. Ohta, H. Cho, D. Sullivan, C. Mao et al., Towards event extraction from full texts on infectious diseases, Proceedings of BioNLP'10, pp.132-140, 2010.

S. Pyysalo, T. Ohta, R. Rak, D. Sullivan, C. Mao et al., Annotation guidelines for infectious diseases event corpus, 2011.

S. Riedel and A. Mccallum, Robust biomedical event extraction with dual decomposition and minimal domain adaptation, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

S. Riedel, D. Mcclosky, M. Surdeanu, A. Mccallum, and C. Manning, Model combination for event extraction in bionlp, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

Y. Sasaki, Y. Tsuruoka, J. Mcnaught, and S. Ananiadou, How to make the most of NE dictionaries in statistical NER, BMC bioinformatics, issue.9, 2008.

P. Stenetorp, G. Topi?, S. Pyysalo, T. Ohta, J. Kim et al., BioNLP Shared Task 2011: Supporting Resources, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

P. Thomason and R. Kay, Eukaryotic signal transduction via histidine-aspartate phosphorelay, J Cell Sci, vol.113, issue.18, pp.3141-3150, 2000.

Y. Wang, J. Kim, R. Saetre, S. Pyysalo, and J. Tsujii, Investigating heterogeneous protein annotations toward cross-corpora utilization, BMC Bioinformatics, issue.403, p.10, 2009.

C. Wang, J. Kemp, I. O. Da-fonseca, R. C. Equi, X. Sheng et al., Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvi and its phenotypic characteristics, Molecular Plant-Microbe Interactions, vol.23, issue.2, pp.153-160, 2010.

S. Dingare, D. Christopher, M. Manning, B. A. Nissim, and C. Grover, Exploring the Boundaries: Gene and Protein Identification in Biomedical Text, References References References Jenny Finkel, vol.6, p.5, 2005.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

T. Kudoh, , 2007.

R. Mcdonald and F. Pereira, Identifying Gene and Protein Mentions in Text Using Conditional Random Fields, BMC Bioinformatics, vol.6, p.6, 2005.

Y. Miyao and J. Tsujii, Feature Forest Models for Probabilistic HPSG Parsing, Computational Linguistics, vol.34, issue.1, pp.35-80, 2008.

L. T. Ngan, J. Nguyen, and . Kim, Exploring Domain Differences for the Design of Pronoun Resolution Systems for Biomedical Text, Proceedings of COLING, pp.625-632, 2008.

L. T. Ngan, J. Nguyen, J. Kim, and . Tsujii, Challenges in Pronoun Resolution System for Biomedical Text, Proceedings of LREC, 2008.

L. T. Ngan, J. Nguyen, J. Kim, and . Tsujii, Overview of the Protein Coreference task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

M. Poesio and M. A. Kabadjov, A general-purpose, off-the-shelf anaphora resolution module: implementation and preliminary evaluation, Proceedings of LREC, 2004.

L. Qiu, M. Kan, and T. Chua, A Public Reference Implementation of the Rap Anaphora Resolution Algorithm, Proceedings of LREC, 2004.

V. Stoyanov, C. Cardie, N. Gilbert, E. Riloff, D. Buttler et al., Reconcile: A Coreference Resolution Platform, 2010.

V. Stoyanov, C. Cardie, N. Gilbert, E. Riloff, D. Buttler et al., Coreference Resolution with Reconcile. Proceedings of ACL, 2010.

V. Stoyanov, N. Gilbert, C. Cardie, and E. Riloff, Conundrums in Noun Phrase Coreference Resolution: Making Sense of the Stateof-the-Art, Proceedings of ACL-IJCNLP, 2009.

Y. Tsuruoka and J. Tsujii, Bidirectional Inference with the Easiest-First Strategy for Tagging Sequence Data, Proceedings of HLT/EMNLP 2005, pp.467-474, 2005.

Y. Versley, S. P. Ponzetto, M. Poesio, V. Eidelman, A. Jern et al., BART: A modular toolkit for coreference resolution, Proceedings of LREC, 2008.

X. Yang, J. Su, G. Zhou, and C. Tan, A NP-Cluster Based Approach to Coreference Resolution, Proceedings of COLING, pp.226-232, 2004.

X. Yang, G. Zhou, J. Su, and C. Tan, Improving Noun Phrase Coreference Resolution by Matching Strings, Proceedings of IJCNLP, pp.226-333, 2004.

G. Zhou, D. Shen, J. Zhang, J. Su, and S. Tan, Recognition of Protein/Gene Names from Text Using an Ensemble of Classifiers, BMC Bioinformatics, vol.6, p.7, 2005.

R. References, C. Bossy, J. Nedellec, and . Jourde, Guidelines for Annotation of Bacteria Biotopes, 2010.

R. Bossy, J. Jourde, P. Bessières, C. Marteen-van-de-guchte, and . Nédellec, BioNLP Shared Task 2011 -Bacteria Biotope, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task. Portland, Oregon, Association for Computational Linguistics, 2011.

H. Daumé, I. , and D. Marcu, A Large-scale Exploration of Effective Global Features for a Joint Entity Detection and Tracking Model, Proceedings of HLT-EMNLP 2005, pp.97-104, 2005.

S. M. Harabagiu, C. Razvan, S. J. Bunescu, and . Maiorano, Text and Knowlegde Mining for Coreference Resolution, Proceedings of NAACL 2001, pp.1-8, 2001.

Y. Jun'ichi-kazama, J. Miyao, and . Tsujii, A Maximum Entropy Tagger with Unsupervised Hidden Markov Models, Proceedings of NL-PRS, pp.333-340, 2001.

T. Koo, X. Carreras, and M. Collins, Simple Semi-supervised Dependency Parsing, Proceedings of ACL-08: HLT, pp.595-603, 2008.

J. Lafferty, A. Mccallum, and F. Pereira, Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data, Proceedings of ICML'01, pp.282-289, 2001.

P. Liang and D. Klein, Online EM for Unsupervised Models, Proceedings of NAACL 2009, pp.611-619, 2009.

X. Luo, A. Ittycheriah, H. Jing, N. Kambhatla, and S. Roukos, A Mention-Synchronous Co-reference Resolution Algorithm based on the Bell Tree, Proceedings of ACL 2004, pp.135-142, 2004.

K. Markert and M. Nissim, Comparing Knowledge Sources for Nominal Anaphora Resolution, Computational Linguistics, vol.31, pp.367-402, 2005.

S. Pyysalo, J. Björne, T. Pahnikkala, F. Ginter, and T. Salakoski, A Graph Kernel for Protein-Protein Interaction Extraction, BioNLP2008: Current Trends in Biomedical Natural Language Processing, pp.1-9, 2008.

R. Alan and . Aronson, Effective mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program, Proceedings of AMIA Symposium, pp.17-21, 2001.

E. Desmontils, C. Jacquin, and L. Simon, Ontology enrichment and indexing process, 2003.

J. Euzenat and P. Shvaiko, Ontology matching, p.333, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00817824

D. Field, Towards a richer description of our complete collection of genomes and metagenomes: the Minimum Information about a Genome Sequence (MIGS) specification, Nature Biotechnology, vol.26, pp.541-547, 2008.

, GeoNames

G. Grefenstette, Explorations in Automatic Thesaurus Discovery. Natural Language Processing and Machine Translation, 1994.

B. J. Grosz, A. K. Joshi, and S. Weinstein, Centering: A Framework for Modelling the Local Coherence of Discourse. University of Pennsylvania Institute for Research in, Cognitive Science Technical Reports Series, 1995.

G. Erkan, A. Özgür, and D. R. Radev, Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing, Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, pp.228-237, 2007.

T. Hamon and S. Aubin, Improving term extraction with terminological resources, Advances in Natural Language Processing 5th International Conference on NLP (Fin-TAL'06), pp.380-387, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00091444

T. Hamon and A. Nazarenko, Detection of synonymy links between terms: experiment and results, Recent Advances in Computational Terminology, 2001.

A. Marti and . Hearst, Automatic acquisition of hyponyms from large text corpora, Proceedings of the 14 th COLING, pp.539-545, 1992.

C. Jacquemin and E. Tzoukermann, NLP for term variant extraction: A synergy of morphology, lexicon, and syntax, Natural language information retrieval, vol.7, pp.25-74, 1999.

M. A. Jaro, Advances in record linkage methodology as applied to matching the 1985 census of, Journal of the American Statistical Association, vol.84, issue.406, pp.414-434, 1989.

J. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, Extracting bio-molecular events from literature -the Bi-oNLP'09 shared task, Special issue of the International Journal of Computational Intelligence

V. I. Levenshtein, Binary codes capable of correcting deletions, insertions and reversals. Doklady akademii nauk SSSR, Russian. English translation in Soviet Physics Doklady, vol.163, pp.707-710, 1965.

Y. Lin and T. Liang, Pronomial and Sortal Anaphora Resolution for Biomedical Literature, Proceedings of ROCLING XVI: Conference on Computational Linguistics and Speech Processing, 2004.

K. Liolios, A. I-min, K. Chen, N. Mavromatis, P. Tavernarakis et al., The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata, 2009.

A. Manine, E. A. , and P. Bessières, Information extraction as an ontology population task and its application to genic interactions, 20th IEEE Intl. Conf. Tools with Artificial Intelligence, ICTAI'08, vol.II, pp.74-81, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02756569

C. Nédellec, W. Golik, S. Aubin, and R. Bossy, Building Large Lexicalized Ontologies from Text: a Use Case in Indexing Biotechnology Patents, International Conference on Knowledge Engineering and Knowledge Management, 2010.

M. Daniel and . Bikel, Intricacies of Collins' Parsing Model, Computational Linguistics, vol.30, issue.4, pp.479-511, 2004.

J. Björne, F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski, Complex event extraction at PubMed scale, Bioinformatics, vol.26, issue.12, p.382, 2010.

R. Bossy, J. Jourde, P. Bessières, C. Marteen-van-de-guchte, and . Nédellec, BioNLP Shared Task 2011 -Bacteria Biotope, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

S. Buchholz and E. Marsi, CoNLL-X shared task on multilingual dependency parsing, Proceedings of the Tenth Conference on Computational Natural Language Learning, pp.149-164, 2006.

E. Buyko and U. Hahn, Evaluating the impact of alternative dependency graph encodings on solving event extraction tasks, Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, pp.982-992, 2010.

E. Charniak and M. Johnson, Coarseto-Fine n-Best Parsing and MaxEnt Discriminative Reranking, Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pp.173-180, 2005.

P. Choudhury, M. Gamon, C. Quirk, and L. Vanderwende, MSR-NLP entry in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

S. Clark and J. R. Curran, Parsing the WSJ using CCG and log-linear models, Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, page 103. Association for Computational Linguistics, 2004.

M. and C. , A new statistical parser based on bigram lexical dependencies, Proceedings of the 34th Annual Meeting of the Association for Computational Linguistics, pp.184-191, 1996.

M. De-marneffe, B. Maccartney, and C. D. Manning, Generating Typed Dependency Parses from Phrase Structure Parses, Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC'06), pp.449-454, 2006.

H. L. Dickensheets, C. Venkataraman, U. Schindler, and R. P. Donnelly, Interferons inhibit activation of STAT6 by interleukin 4 in human monocytes by inducing SOCS-1 gene expression, Proceedings of the National Academy of Sciences of the United States of America, vol.96, p.10800, 1999.

E. Emadzadeh, A. Nikfarjam, and G. Gonzalez, A generalizable and efficient machine learning approach for biological event extraction from text, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

C. J. Fillmore, Frame semantics and the nature of language, Annals of the New York Academy of Sciences, vol.280, issue.1, pp.20-32, 1976.

R. Johansson and P. Nugues, Extended constituent-to-dependency conversion for English, Proc. of the 16th Nordic Conference on Computational Linguistics (NODALIDA), 2007.

J. Jourde, A. Manine, P. Veber, K. Fort, and R. Bossy, BioNLP Shared Task 2011 -Bacteria Gene Interactions and Renaming, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00641586

Y. Kano, W. Baumgartner, L. Mccrohon, S. Ananiadou, K. Cohen et al., U-Compare: share and compare text mining tools with UIMA, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, vol.25, pp.1-9, 2009.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

J. Kim, Y. Wang, T. Takagi, and A. Yonezawa, Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

D. Klein and C. D. Manning, Fast exact inference with a factored model for natural language parsing, Advances in neural information processing systems, pp.3-10, 2003.

M. Marcus, B. Santorini, and M. Marcinkiewicz, Building a large annotated corpus of English: The Penn Tree Bank, Computational Linguistics, pp.313-318, 1993.

D. Mcclosky, Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2009.

M. Miwa, S. Pyysalo, T. Hara, and J. Tsujii, Evaluating Dependency Representation for Event Extraction, the 23rd International Conference on Computational Linguistics (COLING 2010), pp.779-787, 2010.

Y. Miyao and J. Tsujii, Feature forest models for probabilistic HPSG parsing, Computational Linguistics, vol.34, issue.1, pp.35-80, 2008.

Y. Miyao, R. Saetre, and K. Sagae, Task-oriented evaluation of syntactic parsers and their representations, Takuya Matsuzaki, and Jun'ichi Tsujii, pp.46-54, 2008.

R. Morante, V. Van-asch, and W. Daelemans, Memory-based resolution of in-sentence scopes of hedge cues, CoNLL-2010: Shared Task, p.40, 2010.

N. Nguyen, J. Kim, and J. Tsujii, Overview of the Protein Coreference task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

T. Ohta, S. Pyysalo, and J. Tsujii, Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

S. Petrov, L. Barrett, R. Thibaux, and D. Klein, Learning accurate, compact, and interpretable tree annotation, Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics, pp.433-440, 2006.

H. Poon and L. Vanderwende, Joint inference for knowledge extraction from biomedical literature, Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, pp.813-821, 2010.

S. Pyysalo, T. Ohta, R. Rak, D. Sullivan, C. Mao et al., Overview of the Infectious Diseases (ID) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

S. Pyysalo, T. Ohta, and J. Tsujii, Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

L. Rimell and S. Clark, Porting a lexicalized-grammar parser to the biomedical domain, Journal of Biomedical Informatics, vol.42, issue.5, pp.852-865, 2009.

, Biomedical Natural Language Processing

K. Saetre, A. Yoshida, Y. Yakushiji, Y. Miyao, T. Matsubyashi et al., AKANE system: proteinprotein interaction pairs in BioCreAtIvE2 challenge, PPI-IPS subtask, Proceedings of the Second BioCreative Challenge Workshop, pp.209-212, 2007.

K. Sagae and J. Tsujii, Dependency parsing and domain adaptation with LR models and parser ensembles, Proceedings of the CoNLL, 2007.

G. Schneider, M. Hess, and P. Merlo, Hybrid long-distance functional dependency parsing, 2007.

G. Szarvas, V. Vincze, R. Farkas, and J. Csirik, The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts, Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, pp.38-45, 2008.

Y. Tateisi, A. Yakushiji, T. Ohta, and J. Tsujii, Syntax Annotation for the GENIA corpus, Proceedings of the IJCNLP, pp.222-227, 2005.

A. References, R. Bairoch, and . Apweiler, The SWISS-PROT protein sequence data bank and its new supplement TREMBL, Nucleic Acids Research, vol.24, issue.1, p.21, 1996.

A. Bairoch, R. Apweiler, C. H. Wu, W. C. Barker, B. Boeckmann et al., The universal protein resource (UniProt), vol.33, p.154, 2005.

D. A. Benson, I. Karsch-mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, GenBank. Nucleic acids research, vol.36, p.25, 2008.

M. Caropreso and S. Matwin, Beyond the Bag of Words: A Text Representation for Sentence Selection, Advances in Artificial Intelligence, pp.324-335, 2006.

J. L. Fagan, Experiments in automatic phrase indexing for document retrieval: a comparison of syntactic and non-syntactic methods, 1987.

. La-flórez, A. G. Roppel, C. R. Schmeisky, J. Lammers, B. Stülke-;-a-goelzer et al., A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database: The Journal of Biological Databases and Curation, BMC systems biology, vol.2, issue.1, p.20, 2008.

M. Hall, . Frank, B. Holmes, P. Pfahringer, I. Reutemann et al., The WEKA data mining software: an update, ACM SIGKDD Explorations Newsletter, vol.11, issue.1, pp.10-18, 2009.

L. Hirschman, A. Yeh, C. Blaschke, and A. Valencia, Overview of BioCre-AtIvE: critical assessment of information extraction for biology, BMC bioinformatics, vol.6, 2005.

P. Lechat, L. Hummel, S. Rousseau, and I. Moszer, GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Research, vol.36, p.469, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-02634892

C. Nedellec, M. Vetah, and P. Bessières, Sentence filtering for information extraction in genomics, a classification problem. Principles of Data Mining and Knowledge Discovery, pp.326-337, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02764043

C. Nédellec, R. Nazarenko, and . Bossy, Information Extraction. Handbook on Ontologies, pp.663-685, 2009.

I. K-e-nelson, J. Paulsen, C. Heidelberg, and . Fraser, Status of genome projects for nonpathogenic bacteria and archaea, Nature biotechnology, vol.18, issue.10, pp.1049-54, 2000.

A. Ogiwara, N. Ogasawara, M. Watanabe, and T. Takagi, Construction of the Bacillus subtilis ORF database (BSORF DB), Genome Informatics, pp.228-229, 1996.

H. Schmid, Probabilistic part-of-speech tagging using decision trees, 1994.

P. J. Sterk, R. Kersey, and . Apweiler, Genome reviews: standardizing content and representation of information about complete genomes, Omics: a journal of integrative biology, vol.10, issue.2, pp.114-118, 2006.

D. Weissenbacher, La relation de synonymie en Génomique, 2004.

S. Weston, . Mukherjee, M. Chapelle, T. Pontil, V. Poggio et al., Feature selection for SVMs, Advances in neural information processing systems, pp.668-674, 2001.

H. Yu, V. Hatzivassiloglou, C. Friedman, A. Rzhetsky, and W. J. Wilbur, Automatic extraction of gene and protein synonyms from MED-LINE and journal articles, Proceedings of the AMIA Symposium, p.919, 2002.

F. Alan-r-aronson and . Lang, An overview of metamap: historical perspective and recent advances, J Am Med Inform Assoc, vol.17, issue.3, pp.229-265, 2010.

J. Bjorne, . Ginter, . Pyysalo, T. Tsujii, and . Salakoski, Complex event extraction at pubmed scale, Bioinformatics, vol.26, issue.12, pp.382-390, 2010.

O. Bodenreider, The unified medical language system (UMLS): integrating biomedical terminology, Nucleic acids research, vol.32, issue.1, p.267, 2004.

M. C. Demarneffe, B. Maccartney, and C. D. Manning, Generating typed dependency parses from phrase structure parses, Proceedings of LREC, 2006.

D. Gildea and D. Jurafsky, Automatic labeling of semantic roles, Computational Linguistics, vol.28, issue.3, pp.245-288, 2002.

T. Joachims, Making large scale SVM learning practical, Advances in Kernel Methods -Support Vector Learning, 1999.

D. Kim, H. Yu-;-e15338, J. Kim, . Ohta, Y. Pyysalo et al., Overview of bionlp'09 shared task on event extraction, Proceedings of the Workshop on BioNLP: Shared Task, vol.6, pp.1-9, 2009.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

D. Klein and C. D. Manning, Accurate unlexicalized parsing, Proceedings of the 41st Annual Meeting on Association for Computational Linguistics, vol.1, pp.423-430, 2003.

A. Mackinlay, T. Martinez, and . Baldwin, Biomedical event annotation with crfs and precision grammars, Proceedings of the Workshop on BioNLP: Shared Task, pp.77-85, 2009.

M. Miwa, R. Saetre, J. Kim, and J. Tsujii, Simple tricks for improving pattern-based information extraction from the biomedical literature, J. Bioinform. Comput. Biol, vol.8, issue.1, p.9, 2010.

S. Pyysalo, T. Ohta, H. C. Cho, D. Sullivan, C. Mao et al., Towards event extraction from full texts on infectious diseases, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.132-140, 2010.

S. Pyysalo, T. Ohta, R. Rak, D. Sullivan, C. Mao et al., Overview of the Infectious Diseases (ID) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

P. Stenetorp, G. Topi?, S. Pyysalo, T. Ohta, J. Kim et al., BioNLP Shared Task 2011: Supporting Resources, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

M. Torii, L. Yin, T. Nguyen, T. Chand, H. Mazumdar et al., An exploratory study of a text classification framework for internet-based surveillance of emerging epidemics, International Journal of Medical Informatics, vol.80, issue.1, pp.56-66, 2011.

J. Van-rijsbergen, S. E. Robertson, and M. F. Porter, New models in probabilistic information retrieval, 1980.

V. Vapnik, The Nature of Statistical Learning Theory, 1995.

P. References-wauter-bosma, A. Vossen, G. Soroa, M. Rigau, A. Tesconi et al., KAF: a generic semantic annotation format Proceedings of the 5th International Conference on Generative Approaches to the Lexicon GL, 2009.

K. Bretonnel-cohen, K. Verspoor, H. L. Johnson, C. Roeder, P. V. Ogren et al., High-precision biological event extraction: Effects of system and data, Computational Intelligence, pp.89-96, 2009.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task. Association for Computational Linguistics, 2011.

A. Vlachos, Two Strong Baselines for the BioNLP 2009 Event Extraction Task, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.1-9, 2010.

P. Vossen, E. Agirre, N. Calzolari, C. Fellbaum, S. Hsieh et al., BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing, A System for Mining, Structuring, and Distributing Knowledge Across Languages and Cultures. Proceedings of LREC, pp.99-102, 2008.

G. Móra, Exploring ways beyond the simple supervised learning approach for biological event extraction, Proceedings of the Workshop on Bi-oNLP'09 Shared Task, pp.137-140, 2009.

J. Kim, Overview of BioNLP?09 shared task on event extraction, Proceedings of the Workshop on BioNLP'09 Shared Task, pp.1-9, 2009.

K. Kaljurand, UZurich in the BioNLP 2009 shared task, Proceedings of the Workshop on Bi-oNLP'09 Shared Task, pp.28-36, 2009.

H. Kilicoglu and S. Bergler, Syntactic dependency based heuristics for biological event extraction, Proceedings of the Workshop on BioNLP'09 Shared Task, pp.119-127, 2009.

Q. C. Bui, S. Katrenko, and P. M. Sloot, A hybrid approach to extract protein-protein interactions, Bioinformatics, vol.27, issue.2, pp.259-265, 2011.

M. Miwa, R. Saetre, J. Kim, and J. Tsujii, Event Extraction with Complex Event Classification Using Rich Features, Journal of Bioinformatics and Computational Biology, vol.8, pp.131-146, 2010.

J. Björne, F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski, Complex event extraction at PubMed scale, Bioinformatics, vol.26, pp.382-390, 2010.

, Event Class Recall Precision Fscore Gene_expression References David Jurgens and Keith Stevens. 2010. The S-Space package: an open source package for word space models, Proceedings of the ACL 2010 System Demonstrations, ACLDemos '10, pp.30-35

J. Kim, T. Ohta, and J. Tsujii, Corpus annotation for mining biomedical events from literature, BMC Bioinformatics, vol.9, issue.1, p.10, 2008.

S. Pyysalo, T. Ohta, and J. Tsujii, Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2000.

S. Van-landeghem, S. Pyysalo, T. Ohta, and Y. Van-de-peer, Integration of static relations to enhance event extraction from text, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.144-152, 2010.

E. References, E. Buyko, J. Faessler, U. Wermter, and . Hahn, Event Extraction from Trimmed Dependency Graphs, Proceedings of the Workshop on BioNLP: Shared Task, pp.19-27, 2009.

J. Bjorne, J. Heimonen, F. Ginter, A. Airola, T. Pahikkala et al., Extracting Complex Biological Events with Rich Graph-Based Feature Sets, Proceedings of the Workshop on BioNLP: Shared Task, pp.10-18, 2009.

M. References, D. Klenner, A. Tuggener, and . Fahrni, Inkrementelle koreferenzanalyse für das deutsche, Proceedings der 10. Konferenz zur Verarbeitung Natürlicher Sprache, 2010.

S. Lappin, J. Herbert, and . Leass, An algorithm for pronominal anaphora resolution, Computational Linguistics, vol.20, pp.535-561, 1994.

X. Luo, A. Ittycheriah, H. Jing, N. Kambhatla, and S. Roukos, A mention-synchronous coreference resolution algorithm based on the bell tree, Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, 2004.

A. Rahman and V. Ng, Supervised models for coreference resolution, Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing, vol.2, pp.968-977, 2009.

F. Rinaldi, G. Schneider, K. Kaljurand, M. Hess, and M. Romacker, An Environment for Relation Mining over Richly Annotated Corpora: the case of GENIA, BMC Bioinformatics, vol.7, p.3, 2006.

F. Rinaldi, T. Kappeler, K. Kaljurand, G. Schneider, M. Klenner et al., OntoGene in BioCreative II, vol.9, p.13, 2008.

F. Rinaldi, G. Schneider, K. Kaljurand, S. Clematide, T. Vachon et al., OntoGene in BioCreative II.5, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.3, pp.472-480, 2010.

G. Schneider, Hybrid Long-Distance Functional Dependency Parsing, 2008.

X. Yang, J. Su, G. Zhou, and C. Tan, An np-cluster based approach to coreference resolution, Proceedings of the 20th international conference on Computational Linguistics, 2004.

J. References-jari-bjorne, F. Heimonen, A. Ginter, T. Airola, T. Pahikkala et al., Extracting Complex Biological Events with Rich Graph-Based Feature Sets, Computational Linguistics, pp.10-18, 2009.

M. Hall, E. Frank, G. Holmes, B. Pfahringer, P. Reutemann et al., The WEKA data mining software: an update, ACM SIGKDD Explorations Newsletter, vol.11, issue.1, pp.10-18, 2009.

T. Joachims, Making large scale SVM learning practical, Advances in Kernel Methods -Support Vector Learnin, 1999.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

J. Kim, Y. Wang, T. Takagi, and A. Yonezawa, Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

P. Stenetorp, G. Topi?, S. Pyysalo, T. Ohta, J. Kim et al., BioNLP Shared Task 2011: Supporting Resources, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

J. References-jari-björne, F. Heimonen, A. Ginter, T. Airola, T. Pahikkala et al., Extracting Complex Biological Events with Rich Graph-Based Feature Sets, Proceedings of the Workshop on BioNLP: Shared Task, 2009.

T. Cormen, C. Leiserson, and R. Rivest, Introduction to Algorithms, 2002.

T. Dunning, Accurate methods for the statistics of surprise and coincidence, Computational Linguistics, vol.19, issue.1, pp.61-74, 1993.

G. E. Heidorn, Intelligent Writing Assistance, Handbook of Natural Language Processing, 2000.

K. Jensen, K. Jensen, G. E. Heidorn, and S. D. Richardson, PEGASUS: Deriving Argument Structures after Syntax, Natural Language Processing: the PLNLP approach, 1993.

M. De-marneffe, B. Maccartney, D. Christopher, and . Manning, Generating Typed Dependency Parses from Phrase Structure Parses, LREC, 2006.

Y. Miyao and J. Tsujii, Feature forest models for probabilistic HPSG parsing, Computational Linguistics, vol.34, issue.1, pp.35-80, 2008.

D. Mcclosky and E. Charniak, Self-Training for Biomedical Parsing, Proceedings of the Association for Computational Linguistics, 2008.

D. Mcclosky, Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2010.

R. Mcdonald, Discriminative training and spanning tree algorithms for dependency parsing, 2006.

H. Mi, L. Huang, and Q. Liu, Forestbased Translation, Proceedings of ACL, 2008.

P. Pantel, E. Crestan, A. Borkovsky, A. Popescu, and V. Vyas, Web-Scale Distributional Similarity and Entity Set Expansion, Proceedings of EMNLP, 2009.

H. Poon and L. Vanderwende, Joint inference for knowledge extraction from biomedical literature, Proceedings of NAACL-HLT 2010, 2010.

.. F. Martin and . Porter, An algorithm for suffix stripping, vol.14, pp.130-137, 1980.

I. Tsochantaridis, T. Hofmann, T. Joachims, and Y. Alton, Support vector machine learning for interdependent and structured output spaces, 2004.

M. Abulaish and L. Dey, Biological relation extraction and query answering from medline abstracts using ontology-based text mining, Data & Knowledge Engineering, vol.61, issue.2, pp.228-262, 2007.

S. Ananiadou and J. Mcnaught, Text Mining for Biology And Biomedicine, 2005.

S. Ananiadou, S. Pyysalo, D. B. Jun'ichi-tsujii, and . Kell, Event extraction for systems biology by text mining the literature, Trends in Biotechnology, vol.28, issue.7, pp.381-390, 2010.

E. Buyko, E. Faessler, J. Wermter, and U. Hahn, Event extraction from trimmed dependency graphs, BioNLP '09: Proceedings of the Workshop on BioNLP, pp.19-27, 2009.

L. P. Cordella, P. Foggia, C. Sansone, and M. Vento, A (sub)graph isomorphism algorithm for matching large graphs, IEEE Trans. Pattern Anal. Mach. Intell, vol.26, issue.10, pp.1367-1372, 2004.

H. Thomas, C. E. Cormen, R. L. Leiserson, C. Rivest, and . Stein, Introduction to Algorithms, 2001.

C. Fellbaum, WordNet: An Electronic Lexical Database, 1998.

C. Gasperin and T. Briscoe, Statistical anaphora resolution in biomedical texts, COLING '08: Proceedings of the 22nd International Conference on Computational Linguistics, pp.257-264, 2008.

P. Gérard and . Huet, A unification algorithm for typed lambda-calculus, Theor. Comput. Sci, vol.1, issue.1, pp.27-57, 1975.

L. Hunter, The Processes of Life: An Introduction to Molecular Biology, 2009.

H. Kilicoglu and S. Bergler, Syntactic dependency based heuristics for biological event extraction, Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task, BioNLP '09, pp.119-127, 2009.

J. Kim, Y. Ohta, S. Pyysalo, and J. Tsujii, Overview of bionlp'09 shared task on event extraction, Proceedings of the NAACL-HLT 2009 Workshop on Natural Language Processing in Biomedicine (BioNLP'09), pp.1-9, 2009.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

, Workshop Companion Volume for Shared Task

J. Kim, Y. Wang, T. Takagi, and A. Yonezawa, Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

H. Liu, V. Keselj, and C. Blouin, Evaluating contributions of natural language parsers to protein-protein interaction extraction, Proceedings of the 4th International Symposium on Semantic Mining in Biomedicine (SMBM-2010), October. Yusuke Miyao, Kenji Sagae, Rune Saetre, Takuya Matsuzaki, and Jun'ichi Tsujii, vol.25, pp.394-400, 2009.

T. Ohta, Y. Tateisi, and J. Tsujii, Syntax annotation for the genia corpus, Proceedings of the IJCNLP 2005, pp.222-227, 2005.

T. Ohta, S. Pyysalo, and J. Tsujii, Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

M. Ongenaert, T. D. Leander-van-neste, G. Meyer, S. Menschaert, W. Bekaert et al., Pubmeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Research, pp.1-5, 2007.

M. Pelillo, K. Siddiqi, and S. W. Zucker, Matching hierarchical structures using association graphs, IEEE Trans. Pattern Anal. Mach. Intell, vol.21, issue.11, pp.1105-1120, 1999.

M. F. Porter, An algorithm for suffix stripping, pp.313-316, 1997.

Y. Tian, R. C. Mceachin, C. Santos, D. J. States, and J. M. Patel, Saga: a subgraph matching tool for biological graphs, Bioinformatics, vol.23, issue.2, pp.232-239, 2007.

J. R. Ullmann, An algorithm for subgraph isomorphism, J. ACM, vol.23, issue.1, pp.31-42, 1976.

X. Yan, F. Zhu, J. Han, and P. S. Yu, Searching substructures with superimposed distance, Association for Computational Linguistics References Robert Bossy, Julien Jourde, Philippe Bessières, Marteen van de Guchte, and Claire Nédellec, vol.88, pp.173-182, 2006.

E. Charniak and M. Johnson, Coarse-tofine n-best parsing and maxent discriminative reranking, Proceedings of the 43rd Meeting of the Association for Computational Linguistics, pp.173-180, 2005.

H. L. K-bretonnel-cohen, K. Johnson, C. Verspoor, L. E. Roeder, and . Hunter, The structural and content aspects of abstracts versus bodies of full text journal articles are different, BMC Bioinformatics, vol.11, p.492, 2010.

L. Danlos, Discourse verbs" and discourse periphrastic links, Second Workshop on Constraints in Discourse (CID06), pp.59-65, 2006.

M. De-marneffe, B. Maccartney, and C. Manning, Generating typed dependency parses from phrase structure parses, Proceedings of the 5th International Conference on Language Resources and Evaluation, pp.449-454, 2006.

J. Jourde, A. Manine, P. Veber, K. Fort, and R. Bossy, BioNLP Shared Task 2011 -Bacteria Gene Interactions and Renaming, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00641586

H. Kilicoglu and S. Bergler, Recognizing speculative language in biomedical research articles: a linguistically motivated perspective, BMC Bioinformatics, vol.9, issue.11, p.10, 2008.

H. Kilicoglu and S. Bergler, Syntactic dependency based heuristics for biological event extraction, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pp.119-127, 2009.

J. Kim, T. Ohta, and J. Tsujii, Corpus annotation for mining biomedical events from literature, BMC Bioinformatics, vol.9, p.10, 2008.

J. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, Overview of BioNLP'09 Shared Task on Event Extraction, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pp.1-9, 2009.

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

J. Kim, Y. Wang, T. Takagi, and A. Yonezawa, Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

C. William, S. A. Mann, and . Thompson, Rhetorical structure theory: Toward a functional theory of text organization, Text, vol.8, issue.3, pp.243-281, 1988.

D. Mcclosky and E. Charniak, Selftraining for biomedical parsing, Proceedings of the 46th Meeting of the Association for Computational Linguistics, pp.101-104, 2008.

N. Nguyen, J. Kim, and J. Tsujii, Overview of the Protein Coreference task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

T. Ohta, S. Pyysalo, and J. Tsujii, Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.

;. Frank-r-palmer, T. Sampo-pyysalo, R. Ohta, D. Rak, C. Sullivan et al., Overview of the Infectious Diseases (ID) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 1986.

S. Pyysalo, T. Ohta, and J. Tsujii, ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, vol.21, pp.3191-3192, 2005.

T. Wilson, J. Wiebe, and P. Hoffmann, Extracting complex biological events with rich graph-based feature sets, Association for Computational Linguistics References Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, and Tapio Salakoski, pp.10-18, 2005.

J. Björne, F. Ginter, S. Pyysalo, T. Jun'ichi-tsujii, and . Salakoski, Scaling up biomedical event extraction to the entire PubMed, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.28-36, 2010.

J. Björne, J. Heimonen, F. Ginter, A. Airola, T. Pahikkala et al., Extracting contextualized complex biological events with rich graph-based feature sets, Computational Intelligence, Special issue on Extracting Bio, 2009.

E. Buyko, E. Faessler, J. Wermter, and U. Hahn, Event extraction from trimmed dependency graphs, Proceedings of the BioNLP, 2009.

, Workshop Companion Volume for Shared Task, pp.19-27

E. Charniak and M. Johnson, Coarse-tofine n-best parsing and maxent discriminative reranking, Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pp.173-180, 2005.

M. De-marneffe, B. Maccartney, and C. Manning, Generating typed dependency parses from phrase structure parses, Proceedings of LREC-06, pp.449-454, 2006.

J. P. Euzéby, List of bacterial names with standing in nomenclature: a folder available on the internet, Int J Syst Bacteriol, vol.47, issue.2, pp.590-592, 1997.

, WordNet: an electronic lexical database, 1998.

J. Heimonen, J. Björne, and T. Salakoski, Reconstruction of semantic relationships from their projections in biomolecular domain, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.108-116, 2010.

H. Kilicoglu and S. Bergler, Syntactic dependency based heuristics for biological event extraction, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.119-127, 2009.

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

J. Kim, S. Pyysalo, T. Ohta, R. Bossy, and J. Tsujii, Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02745923

M. De-marneffe and C. Manning, The Stanford typed dependencies representation, COLING Workshop on Cross-framework and Cross-domain Parser Evaluation, 2008.

D. Mcclosky, Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2010.

M. Miwa, S. Pyysalo, T. Hara, and J. Tsujii, A comparative study of syntactic parsers for event extraction, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, BioNLP '10, pp.37-45, 2010.

M. Miwa, R. Saetre, J. Kim, and J. Tsujii, Event extraction with complex event classification using rich features, J Bioinform Comput Biol, vol.8, pp.131-146, 2010.

M. F. Porter, An algorithm for suffix stripping, vol.14, pp.130-137, 1980.

S. Riedel, H. Chun, T. Takagi, and J. Tsujii, A markov logic approach to bio-molecular event extraction, Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task, BioNLP '09, pp.41-49, 2009.

I. Tsochantaridis, T. Joachims, T. Hofmann, and Y. Altun, Large margin methods for structured and interdependent output variables, Journal of Machine Learning Research, vol.6, pp.1453-1484, 2005.

S. Van-landeghem, Y. Saeys, B. D. Baets, and Y. Van-de-peer, Analyzing text in search of bio-molecular events: a high-precision machine learning framework, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.128-136, 2009.

, Author Index