C. Nédellec, Learning Language in Logic -Genic Interaction Extraction Challenge, Proc 4th Learning Language in Logic Workshop (LLL'05) 2005, pp.31-38

M. Krallinger, F. Leitner, C. Rodriguez-penagos, and A. Valencia, Overview of the protein-protein interaction annotation extraction task of BioCreative II

, Genome Biology, vol.9, issue.2, p.4, 2008.

D. Demner-fushman, S. Ananiadou, K. B. Cohen, J. Pestian, J. Tsujii et al., Themes in biomedical natural language processing: BioNLP08. BMC Bioinformatics, vol.9, p.1, 2008.

J. D. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, Overview of BioNLP'09 shared task on event extraction, Proc Workshop on BioNLP: Shared Task (BioNLP'09, pp.1-9, 2009.

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

A. P. Manine, A. E. Bessières, and P. , Extraction of genic interactions with the recursive logical theory of an ontology, Lecture Notes in Computer Sciences, vol.6008, pp.549-63, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02758320

A. P. Manine, A. E. Bessières, and P. , Learning ontological rules to extract multiple relations of genic interactions from text, Int J Medical Informatics, vol.78, issue.12, pp.31-39, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02660738

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

L. Hirschman, C. Clark, K. B. Cohen, S. Mardis, J. Luciano et al., Habitat-Lite: a GSC case study based on free text terms for environmental metadata, OMICS, vol.12, issue.2, pp.129-136, 2008.

J. Tamames and V. De-lorenzo, EnvMine: A text-mining system for the automatic extraction of contextual information, BMC Bioinformatics, vol.11, p.294, 2010.

K. Liolios, I. M. Chen, K. Mavromatis, N. Tavernarakis, P. Hugenholtz et al., Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Research, pp.346-54, 2010.

J. Jourde, A. P. Manine, P. Veber, K. Fort, R. Bossy et al., BioNLP Shared Task 2011 -Bacteria Gene Interactions and Renaming
URL : https://hal.archives-ouvertes.fr/hal-00641586

, Proc BioNLP Shared Task 2011 Workshop Portland, pp.65-73, 2011.

M. M. Floyd, J. Tang, M. Kane, and D. Emerson, Captured Diversity in a Culture Collection: Case Study of the Geographic and Habitat Distributions of Environmental Isolates Held at the American Type Culture Collection, Applied and Environmental Microbiology, vol.71, issue.6, pp.2813-2823, 2005.

C. Nédellec and A. Nazarenko, Bossy R: Information Extraction, Ontology Handbook

S. Staab and R. Studer, , pp.663-686, 2008.

L. A. Flórez, S. F. Roppel, A. G. Schmeisky, C. R. Lammers, and J. Stülke, A communitycurated consensual annotation that is continuously updated: The Bacillus subtilis centred wiki SubtiWiki, p.12, 2009.

C. R. Lammers, L. A. Flórez, A. G. Schmeisky, S. F. Roppel, U. Mäder et al., Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis, Microbiology, vol.2010, issue.3, pp.849-59

S. Muggleton and L. D. Raedt, Inductive Logic Programming: Theory and Methods, J Logic Programming, pp.629-79, 1994.

J. Björne, F. Ginter, and T. Salakoski, Generalizing Biomedical Event Extraction, BMC Bioinformatics, vol.2012, issue.8, p.4

N. Nguyen and Y. Tsuruoka, Extracting Bacteria Biotopes with Semisupervised Named Entity Recognition and Coreference Resolution, Proceedings of BioNLP Shared Task 2011 Workshop, pp.94-101, 2011.

Z. Ratkovic, W. Golik, and P. Warnier, Event Extraction of Bacteria Biotopes: A knowledge intensive NLP-based approach, BMC Bioinformatics, vol.13, issue.8, p.8, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02651077

P. Sneath and D. J. Brenner, Official" Nomenclature Lists, vol.58, 1992.

. Bossy, BioNLP Shared Task -The Bacteria Track, BMC Bioinformatics, issue.11, p.3, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01190775