A. B. Abacha and P. Zweigenbaum, Annotation et interrogation sémantiques de textes médicaux, 2010.

S. Agarwal and H. Yu, Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion, Bioinformatics, vol.25, issue.23, pp.3174-3180, 2009.
DOI : 10.1093/bioinformatics/btp548

D. Albright, A. Lanfranchi, A. Fredriksen, W. F. Styler, C. Warner et al., Towards comprehensive syntactic and semantic annotations of the clinical narrative, Journal of the American Medical Informatics Association, vol.20, issue.5, 2013.
DOI : 10.1136/amiajnl-2012-001317

K. H. Ambert, A. M. Cohen, G. A. Burns, E. Boudreau, and K. Sonmez, Virk: an active learning-based system for bootstrapping knowledge base development in the neurosciences, Frontiers in Neuroinformatics, vol.7, 2013.
DOI : 10.3389/fninf.2013.00038

R. Artstein and M. Poesio, Inter-Coder Agreement for Computational Linguistics, Computational Linguistics, vol.27, issue.1, pp.555-596, 2008.
DOI : 10.1037/0033-2909.103.3.374

M. Bada, M. Eckert, D. Evans, K. Garcia, K. Shipley et al., Concept annotation in the CRAFT corpus, BMC Bioinformatics, vol.13, issue.1, 2012.
DOI : 10.1093/bioinformatics/btn158

S. Bethard, S. Finan, M. Palmer, S. Pradhan, P. C. De-groen et al., Temporal annotation in the clinical domain, Proceedings of the Association for Computational Linguistics, pp.143-154, 2014.

R. Ginn, P. Pimpalkhute, A. Nikfarjam, A. Patki, O. Karen et al., Mining Twitter for adverse drug reaction mentions: A corpus and classification benchmark, In: Evaluating Resources for Health and Biomedical Text Processing, 2014.

W. Golik, P. Warnier, and C. Nédellec, Corpus-based extension of termino-ontology by linguistic analysis: a use case in biomedical event extraction, Proc. 9th Intl Conf. Terminology and Artificial Intelligence, pp.37-39, 2011.

R. Grishman and B. Sundheim, Message Understanding Conference-6, Proceedings of the 16th conference on Computational linguistics -, pp.466-471, 1996.
DOI : 10.3115/992628.992709

C. Grouin, S. Rosset, P. Zweigenbaum, K. Fort, O. Galibert et al., Proposal for an extension of traditional named entities: From guidelines to evaluation, an overview, Proceedings of the 5th Linguistic Annotation Workshop, pp.92-100, 2011.

H. Gurulingappa, A. M. Rajput, A. Roberts, J. Fluck, M. Hofmann-apitius et al., Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports, Journal of Biomedical Informatics, vol.45, issue.5, pp.885-892, 2012.
DOI : 10.1016/j.jbi.2012.04.008

K. Haverinen, F. Ginter, V. Laippala, T. Viljanen, and T. Salakoski, Dependency-based propbanking of clinical Finnish, Proceedings of The Fourth Linguistic Annotation Workshop (LAW IV), pp.137-141, 2010.

W. Hersh, J. Kalpathy-cramer, and H. Müller, The ImageCLEFmed Medical Image Retrieval Task Test Collection, Journal of Digital Imaging, vol.188, issue.6, pp.648-655, 2009.
DOI : 10.1007/s10278-008-9154-8

L. Hirschman, P. Robinson, J. Burger, and M. Vilain, Automating coreference: The role of annotated training data, Proceedings of the AAAI Spring Symposium on Applying Machine Learning to Discourse Processing, pp.118-121, 1997.

G. Hripcsak and A. S. Rothschild, Agreement, the F-Measure, and Reliability in Information Retrieval, Journal of the American Medical Informatics Association, vol.12, issue.3, pp.296-298, 2005.
DOI : 10.1197/jamia.M1733

P. Kedzia, M. Piasecki, M. Maziarz, and M. Marci´nczukmarci´nczuk, Recognising Compositionality of Multi-Word Expressions in the Wordnet Oriented Perspective, Advances in Artificial Intelligence and Its Applications, pp.240-251, 2013.
DOI : 10.1007/978-3-642-45114-0_19

H. Kilicoglu, G. Rosemblat, M. Fiszman, and T. C. Rindflesch, Constructing a semantic predication gold standard from the biomedical literature, BMC Bioinformatics, vol.12, issue.1, p.486, 2011.
DOI : 10.1016/S1532-0464(03)00012-1

J. D. Kim, A generalized LCS algorithm and its application to corpus alignment, Proceedings of the 6th International Joint Conference on Natural Language Processing, pp.14-18, 2013.

J. D. Kim, Sharing reference texts for interoperability of literature annotation, Proceedings of the 5th international symposium on languages in biology and medicine, pp.57-61, 2013.

J. D. Kim, T. Ohta, Y. Tateisi, H. Mima, and J. Tsujii, XML-based linguistic annotation of corpus, Proceedings of The First NLP and XML Workshop, pp.47-53, 2001.

J. D. Kim, T. Ohta, Y. Tateisi, and J. Tsujii, GENIA corpus--a semantically annotated corpus for bio-textmining, Bioinformatics, vol.19, issue.Suppl 1, pp.180-182, 2003.
DOI : 10.1093/bioinformatics/btg1023

J. D. Kim and Y. Wang, PubAnnotation: a persistent and sharable corpus and annotation repository, Proceedings of the 2012 Workshop on Biomedical Natural Language Processing, pp.202-205, 2012.

H. J. Lee, S. H. Shim, M. R. Song, H. Lee, and J. C. Park, CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations, BMC Bioinformatics, vol.14, issue.1, p.323, 2013.
DOI : 10.1186/1471-2105-9-S11-S10

L. Levin and M. Stede, Proceedings of LAW VIII -The 8th Linguistic Annotation Workshop, pp.14-49, 2014.

J. Lin, Is searching full text more effective than searching abstracts?, BMC Bioinformatics, vol.10, issue.1, 2009.
DOI : 10.1186/1471-2105-10-46

URL : http://doi.org/10.1186/1471-2105-10-46

Z. Lu, H. Y. Kao, C. H. Wei, M. Huang, J. Liu et al., The gene normalization task in BioCreative III, BMC Bioinformatics, vol.12, issue.Suppl 8, p.2, 2011.
DOI : 10.1197/jamia.M2085

M. P. Marcus, M. A. Marcinkiewicz, and B. Santorini, Building a large annotated corpus of English: the Penn Treebank, Computational Linguistics, vol.19, issue.2, pp.313-330, 1993.

T. Mcintosh and J. R. Curran, Challenges for automatically extracting molecular interactions from full-text articles, BMC Bioinformatics, vol.10, issue.1, 2009.
DOI : 10.1186/1471-2105-10-311

C. Mih?-ail?-a, T. Ohta, S. Pyysalo, and S. Ananiadou, BioCause: Annotating and analysing causality in the biomedical domain, BMC bioinformatics, vol.14, issue.1 2, 2013.

A. Mitchell, S. Strassel, S. Huang, and R. Zakhary, Ace 2004 multilingual training corpus, Linguistic Data Consortium, 2005.

D. Molla and M. E. Santiago-martinez, Development of a corpus for evidence based medicine summarisation, Proceedings of the Australasian Language Technology Association Workshop, pp.86-94, 2011.

A. A. Morgan, L. Hirschman, M. Colosimo, A. S. Yeh, and J. B. Colombe, Gene name identification and normalization using a model organism database, Journal of Biomedical Informatics, vol.37, issue.6, pp.396-410, 2004.
DOI : 10.1016/j.jbi.2004.08.010

A. A. Morgan, Z. Lu, X. Wang, A. M. Cohen, J. Fluck et al., Overview of BioCreative II gene normalization, Genome Biology, vol.9, issue.Suppl 2, p.3, 2008.
DOI : 10.1186/gb-2008-9-s2-s3

A. Névéol, C. Grouin, J. Leixa, S. Rosset, and P. Zweigenbaum, The Quaero French Medical Corpus: A resource for medical entity recognition and normalization, Fourth workshop on building and evaluating resources for health and biomedical text processing, 2014.

M. Neves, An analysis on the entity annotations in biological corpora, F1000Research, vol.3, issue.96, 2014.
DOI : 10.12688/f1000research.3216.1

C. Nobata, P. D. Dobson, S. A. Iqbal, P. Mendes, J. Tsujii et al., Mining metabolites: extracting the yeast metabolome from the literature, Metabolomics, vol.7, issue.Suppl 2, pp.94-101, 2011.
DOI : 10.1007/s11306-010-0251-6

T. Nunes, D. Campos, S. Matos, and J. L. Oliveira, BeCAS: biomedical concept recognition services and visualization, Bioinformatics, vol.29, issue.15, pp.1915-1916, 2013.
DOI : 10.1093/bioinformatics/btt317

P. Ogren, Knowtator, Proceedings of the 2006 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology companion volume: demonstrations -, 2006.
DOI : 10.3115/1225785.1225791

P. Ogren, Knowtator, Proceedings of the 2006 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology companion volume: demonstrations -, pp.73-76, 2006.
DOI : 10.3115/1225785.1225791

T. Ohta, J. D. Kim, S. Pyysalo, Y. Wang, and J. Tsujii, Incorporating GENETAG-style annotation to GENIA corpus, Proceedings of the Workshop on BioNLP, BioNLP '09, pp.106-107, 2009.
DOI : 10.3115/1572364.1572379

T. Ohta, S. Pyysalo, J. Tsujii, and S. Ananiadou, Open-domain anatomical entity mention detection, Proceedings of the Workshop on Detecting Structure in Scholarly Discourse, pp.27-36, 2012.

T. Ohta, Y. Tateisi, J. D. Kim, H. Mima, and J. Tsujii, The GENIA corpus, Proceedings of the second international conference on Human Language Technology Research -, 2002.
DOI : 10.3115/1289189.1289260

A. Pareja-lora, M. Liakata, and S. Dipper, Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse, pp.13-23, 2013.

A. Peñas, E. Hovy, P. Forner, ´. A. Rodrigo, R. Sutcliffe et al., Overview of question answering for machine reading evaluation, Information Access Evaluation. Multilinguality, Multimodality, and Visualization, pp.303-320, 2011.

S. Pradhan, N. Elhadad, B. South, D. Martinez, L. Christensen et al., Task 1: ShARe/CLEF eHealth evaluation lab 2013, Online Working Notes of CLEF, p.230, 2013.

S. Pradhan, L. Ramshaw, M. Marcus, M. Palmer, R. Weischedel et al., CoNLL-2011 shared task: Modeling unrestricted coreference in OntoNotes, Proceedings of the Fifteenth Conference on Computational Natural Language Learning: Shared Task, pp.1-27, 2011.

S. S. Pradhan, L. Ramshaw, R. Weischedel, J. Macbride, and L. Micciulla, Unrestricted Coreference: Identifying Entities and Events in OntoNotes, International Conference on Semantic Computing (ICSC 2007), pp.446-453, 2007.
DOI : 10.1109/ICSC.2007.93

R. Prasad, S. Mcroy, N. Frid, A. Joshi, and H. Yu, The biomedical discourse relation bank, BMC Bioinformatics, vol.12, issue.1, 2011.
DOI : 10.1016/S1532-0464(03)00012-1

J. Pustejovsky and A. Stubbs, Natural language annotation for machine learning, 2012.

S. Pyysalo and S. Ananiadou, Anatomical entity mention recognition at literature scale, Bioinformatics, vol.30, issue.6, 2013.
DOI : 10.1093/bioinformatics/btt580

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957068

S. Pyysalo, T. Ohta, M. Miwa, H. C. Cho, J. Tsujii et al., Event extraction across multiple levels of biological organization, Bioinformatics, vol.28, issue.18, pp.575-581, 2012.
DOI : 10.1093/bioinformatics/bts407

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 Shared Task 2011 Workshop, pp.26-35, 2011.

P. Raghavan, E. Fosler-lussier, and A. M. Lai, Inter-annotator reliability of medical events, coreferences and temporal relations in clinical narratives by annotators with varying levels of clinical expertise, AMIA Annual Symposium Proceedings, p.1366, 2012.

S. Ramanan and P. S. Nathan, Adapting Cocoa, a multi-class entity detector, for the CHEMD- NER task of, BioCreative IV, 2013.

A. Roberts, R. Gaizauskas, M. Hepple, G. Demetriou, Y. Guo et al., Building a semantically annotated corpus of clinical texts, Journal of Biomedical Informatics, vol.42, issue.5, pp.950-66, 2009.
DOI : 10.1016/j.jbi.2008.12.013

K. Roberts, S. M. Harabagiu, and M. A. Skinner, Structuring Operative Notes using Active Learning, Proceedings of BioNLP 2014, pp.68-76, 2014.
DOI : 10.3115/v1/W14-3410

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

K. Roberts, K. Masterton, M. Fiszman, H. Kilicoglu, and D. Demner-fushman, Annotating question decomposition on complex medical questions, Language Resources and Evaluation Conference, 2014.

K. Roberts, K. Masterton, M. Fiszman, H. Kilicoglu, and D. Demner-fushman, Annotating Question Types for Consumer Health Questions, Proceedings of the Fourth LREC Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing, 2014.

S. Guergana-;-pradhan and S. P. , Annotating the clinical text -MiPACQ, ShARe, SHARPn and THYME corpora, 2015.

P. K. Shah, C. Perez-iratxeta, P. Bork, and M. A. Andrade, Information extraction from full text scientific articles: where are the keywords?, BMC Bioinformatics, vol.4, issue.1, 2003.

B. Smith and W. Ceusters, Ontological realism: A methodology for coordinated evolution of scientific ontologies, Applied ontology, vol.5, issue.3, pp.139-188, 2010.

P. Stenetorp, S. Pyysalo, G. Topi´ctopi´c, T. Ohta, S. Ananiadou et al., BRAT: a web-based tool for NLP-assisted text annotation, Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics, pp.102-107, 2012.

A. Stubbs, A methodology for using professional knowledge in corpus annotation, 2013.

A. Stubbs and O. Uzuner, De-identification of medical records through annotation Handbook of Linguistic Annotation, 2015.

L. Tanabe and W. J. Wilbur, Tagging gene and protein names in full text articles, Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain -, pp.9-13, 2002.
DOI : 10.3115/1118149.1118151

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

Y. Tateisi, A. Yakushiji, T. Ohta, and J. Tsujii, Syntax annotation for the GENIA corpus, Second international joint conference on natural language processing: Companion volume, pp.220-225, 2005.

I. P. Temnikova and K. B. Cohen, Recognizing sublanguages in scientific journal articles through closure properties, In: Proceedings of BioNLP, p.2013, 2013.

P. Thompson, S. A. Iqbal, J. Mcnaught, and S. Ananiadou, Construction of an annotated corpus to support biomedical information extraction, BMC Bioinformatics, vol.10, issue.1, p.349, 2009.
DOI : 10.1186/1471-2105-10-349

P. Thompson, R. Nawaz, J. Mcnaught, and S. Ananiadou, Enriching a biomedical event corpus with meta-knowledge annotation, BMC Bioinformatics, vol.12, issue.1, p.393, 2011.
DOI : 10.1016/j.artmed.2004.07.016

E. M. Van-mulligen, A. Fourrier-reglat, D. Gurwitz, M. Molokhia, A. Nieto et al., The EU-ADR corpus: Annotated drugs, diseases, targets, and their relationships, Journal of Biomedical Informatics, vol.45, issue.5, pp.879-884, 2012.
DOI : 10.1016/j.jbi.2012.04.004

K. Verspoor, K. B. Cohen, and L. Hunter, The textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics, vol.10, issue.1, 2009.
DOI : 10.1186/1471-2105-10-183

K. Verspoor, K. B. Cohen, A. Lanfranchi, C. Warner, H. L. Johnson et al., A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools, BMC Bioinformatics, vol.13, issue.1, 2012.
DOI : 10.1093/bioinformatics/bti475

K. Verspoor, A. J. Yepes, L. Cavedon, T. Mcintosh, A. Herten-crabb et al., Annotating the biomedical literature for the human variome, Database, vol.2013, issue.0, 2013.
DOI : 10.1093/database/bat019

N. Xue and M. Poesio, Proceedings of the Fourth Linguistic Annotation Workshop, pp.10-18, 2010.