K. Oda, Y. Matsuoka, A. Funahashi, and H. Kitano, A comprehensive pathway map of epidermal growth factor receptor signaling, Molecular Systems Biology, vol.1, issue.1, p.10, 2005.

L. Calzone, A. Gelay, A. Zinovyev, F. Radvanyi, and E. Barillot, A comprehensive modular map of molecular interactions in rb/e2f pathway, Molecular Systems Biology, vol.4, issue.1, p.174, 2008.

E. Caron, A comprehensive map of the mtor signaling network, Molecular Systems Biology, vol.6, issue.1, p.453, 2010.

P. Gloaguen, P. Crépieux, D. Heitzler, A. Poupon, and E. Reiter, Mapping the follicle-stimulating hormone-induced signaling networks, Frontiers in endocrinology, vol.2, p.45, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01129612

S. Moodie, N. Le-novere, E. Demir, H. Mi, and A. Villeger, Systems biology graphical notation: process description language level 1 version 1.3, Journal of integrative bioinformatics, vol.12, pp.213-280, 2015.

N. Le-novere, The systems biology graphical notation, Nature Biotechnology, vol.27, pp.735-741, 2009.

H. Chen and B. M. Sharp, Content-rich biological network constructed by mining pubmed abstracts, BMC Bioinformatics, vol.5, p.147, 2004.

A. Yuryev, Automatic pathway building in biological association networks, BMC Bioinformatics, vol.7, p.171, 2006.

B. M. Gyori, From word models to executable models of signaling networks using automated assembly, Molecular Systems Biology, vol.13, p.954, 2017.

M. Bansal, V. Belcastro, A. Ambesi-impiombato, and D. Di-bernardo, How to infer gene networks from expression profiles, Molecular Systems Biology, vol.3, p.78, 2007.

F. Markowetz and R. Spang, Inferring cellular networks-a review, BMC Bioinformatics, vol.8, p.5, 2007.

S. Roy and P. H. Guzzi, Biological network inference from microarray data, current solutions, and assessments, Microarray Data Analysis: Methods and Applications, pp.155-167, 2016.

D. Pe'er, A. Regev, G. Elidan, and N. Friedman, Inferring subnetworks from perturbed expression profiles, Bioinformatics, vol.17, pp.215-224, 2001.

D. Zhu, A. O. Hero, H. Cheng, R. Khanna, and A. Swaroop, Network constrained clustering for gene microarray data, Bioinformatics, vol.21, pp.4014-4020, 2005.

H. Fröhlich, M. Fellmann, H. Sültmann, A. Poustka, and T. Beißbarth, Large scale statistical inference of signaling pathways from rnai and microarray data, BMC bioinformatics, vol.8, p.386, 2007.

L. L. Elo, H. Järvenpää, M. Ore?i?, R. Lahesmaa, and T. Aittokallio, Systematic construction of gene coexpression networks with applications to human t helper cell differentiation process, Bioinformatics, vol.23, pp.2096-2103, 2007.

K. Sachs, O. Perez, D. Pe'-er, D. A. Lauffenburger, and G. P. Nolan, Causal protein-signaling networks derived from multiparameter single-cell data, Science, vol.308, pp.523-529, 2005.

T. Xu, Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species, Science Signaling, vol.3, pp.20-20, 2010.

S. M. Hill, Bayesian inference of signaling network topology in a cancer cell line, Bioinformatics, vol.28, pp.2804-2810, 2012.

B. Zupan, Genepath: a system for automated construction of genetic networks from mutant data, Bioinformatics, vol.19, pp.383-389, 2003.

V. Nigam, R. Donaldson, M. Knapp, T. Mccarthy, and C. Talcott, Inferring executable models from formalized experimental evidence, Computational Methods in Systems Biology, pp.90-103, 2015.

S. Eker, Pathway logic: Symbolic analysis of biological signaling, Pacific Symposium on Biocomputing, vol.7, pp.400-412, 2002.

P. Crépieux, The erk-dependent signalling is stage-specifically modulated by fsh, during primary sertoli cell maturation, Oncogene, vol.20, pp.4696-4709, 2001.

C. F. Schaefer, Pid: the pathway interaction database, Nucleic acids research, vol.37, pp.674-679, 2008.

S. P. Davies, H. Reddy, M. Caivano, and P. Cohen, Specificity and mechanism of action of some commonly used protein kinase inhibitors, Biochemical Journal, vol.351, pp.95-105, 2000.

A. Sorokin, Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2, J Integr Bioinform, vol.12, p.264, 2015.

E. Demir, The biopax community standard for pathway data sharing, Nature biotechnology, vol.28, p.935, 2010.

J. R. Faeder, M. L. Blinov, and W. S. Hlavacek, Rule-based modeling of biochemical systems with, BioNetGen. Methods Mol. Biol, vol.500, pp.113-167, 2009.

L. Calzone, F. Fages, and S. Soliman, Biocham: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, pp.1805-1807, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01431364

, ScIeNtIfIc RepORTS |, 2018.

F. Büchel, Path2models: large-scale generation of computational models from biochemical pathway maps, BMC Systems Biology, vol.7, p.116, 2013.

A. Rougny, C. Froidevaux, L. Calzone, and L. Paulevé, Qualitative dynamics semantics for sbgn process description, BMC systems biology, vol.10, p.42, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01332679

M. Hucka, The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, pp.524-531, 2003.

F. Landomiel, A. Gupta, D. Maurel, and A. Poupon, Préliminaire à la construction d'un réseau de signalisation en biologie systémique, Atelier sur la Fouille de Textes, 2017.

N. Friburger and D. Maurel, Finite-state transducer cascades to extract named entities in texts, Theoretical Computer Science, vol.313, pp.93-104, 2004.

K. Inoki, Y. Li, T. Xu, and K. Guan, Rheb gtpase is a direct target of tsc2 gap activity and regulates mtor signaling, Genes & development, vol.17, pp.1829-1834, 2003.

A. F. Castro, J. F. Rebhun, G. J. Clark, and L. A. Quilliam, Rheb binds tuberous sclerosis complex 2 (tsc2) and promotes s6 kinase activation in a rapamycin-and farnesylation-dependent manner, Journal of Biological Chemistry, vol.278, pp.32493-32496, 2003.

D. Nie, Tsc2-rheb signaling regulates epha-mediated axon guidance, Nature neuroscience, vol.13, p.163, 2010.

M. Roccio, J. Bos, and F. Zwartkruis, Regulation of the small gtpase rheb by amino acids, Oncogene, vol.25, p.657, 2006.

J. Huang and B. D. Manning, The tsc1-tsc2 complex: a molecular switchboard controlling cell growth, Biochemical Journal, vol.412, pp.179-190, 2008.

D. Pratt, Ndex, the network data exchange, Cell systems, vol.1, pp.302-305, 2015.

M. Gebser, R. Kaminski, B. Kaufmann, T. Schaub, =. Clingo et al., Theory and Practice of Logic Programming, Technical Communications of the Thirtieth International Conference on Logic Programming (ICLP'14), 2014.

H. Nabeshima, K. Iwanuma, K. Inoue, and O. Ray, Solar: An automated deduction system for consequence finding, AI communications, vol.23, pp.183-203, 2010.

H. Mi, Systems biology graphical notation: activity flow language level 1 version 1.2, Journal of integrative bioinformatics, vol.12, pp.340-381, 2015.