T. Bernard, A. Bridge, A. Morgat, S. Moretti, I. Xenarios et al., Reconciliation of metabolites and biochemical reactions for metabolic networks, Brief. Bioinform, vol.15, pp.123-135, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00764412

C. E. Blaby-haas and V. De-crécy-lagard, Mining high-throughput experimental data to link gene and function, Trends Biotechnol, vol.29, pp.174-182, 2011.

J. Chambers, M. Davies, A. Gaulton, A. Hersey, S. Velankar et al., UniChem: a unified chemical structure cross-referencing and identifier tracking system, J. Cheminform, vol.5, p.3, 2013.

L. Cottret, D. Wildridge, F. Vinson, M. P. Barrett, H. Charles et al., MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks, Nucleic Acids Res, vol.38, pp.132-137, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00690651

D. J. Creek, W. B. Dunn, O. Fiehn, J. L. Griffin, R. D. Hall et al., Metabolite identification: are you sure? And how do your peers gauge your confidence?, Metabolomics, vol.10, pp.350-353, 2014.

L. Dai, X. Gao, Y. Guo, J. Xiao, and Z. Zhang, Bioinformatics clouds for big data manipulation, Biol. Direct, vol.7, p.43, 2012.

S. Devoid, R. Overbeek, M. Dejongh, V. Vonstein, A. A. Best et al., Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED, Methods Mol. Biol, vol.985, pp.17-45, 2013.

O. Fiehn, J. Kopka, P. Dörmann, T. Altmann, R. N. Trethewey et al., Metabolite profiling for plant functional genomics, Nat. Biotechnol, vol.18, pp.1157-1161, 2000.

J. Galgonek and J. Vondrá?ek, On InChI and evaluating the quality of cross-reference links, J. Cheminform, vol.6, p.15, 2014.

M. Ganter, T. Bernard, S. Moretti, J. Stelling, and M. Pagni, MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks, Bioinformatics, vol.29, pp.815-816, 2013.

F. Giacomoni, G. Le-corguillé, M. Monsoor, M. Landi, P. Pericard et al., Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics, Bioinformatics, vol.31, pp.1493-1495, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01214152

H. S. Haraldsdóttir, I. Thiele, R. M. Fleming, H. S. Haraldsdottir, I. Thiele et al., Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2, J. Cheminform, vol.6, issue.2, 2014.

J. Hastings, P. De-matos, A. Dekker, M. Ennis, B. Harsha et al., The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013, Nucleic Acids Res, vol.41, pp.456-463, 2013.

K. Haug, R. M. Salek, P. Conesa, J. Hastings, P. De-matos et al., MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data, Nucleic Acids Res, vol.41, pp.781-786, 2013.

S. Heller, A. Mcnaught, S. Stein, D. Tchekhovskoi, and I. Pletnev, InChIthe worldwide chemical structure identifier standard, J. Cheminform, vol.5, p.7, 2013.

S. R. Heller and A. D. Mcnaught, The IUPAC International Chemical Identifier, InChI. ACS Style Guid, vol.3, pp.101-102, 2006.

H. Horai, M. Arita, S. Kanaya, Y. Nihei, T. Ikeda et al., MassBank: a public repository for sharing mass spectral data for life sciences, J. Mass Spectrom, vol.45, pp.703-714, 2010.

M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle et al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, pp.524-531, 2003.

M. Kanehisa, S. Goto, Y. Sato, M. Kawashima, M. Furumichi et al., Data, information, knowledge and principle: back to metabolism in KEGG, Nucleic Acids Res, vol.42, pp.199-205, 2014.

P. D. Karp, M. Latendresse, S. M. Paley, M. Krummenacker, Q. D. Ong et al., Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology, Brief. Bioinform, 2015.

S. Kim, P. A. Thiessen, E. E. Bolton, J. Chen, G. Fu et al., PubChem Substance and Compound databases, Nucleic Acids Res, vol.44, pp.1202-1213, 2016.

J. W. May, A. G. James, and C. Steinbeck, Metingear: a development environment for annotating genome-scale metabolic models, Bioinformatics, vol.29, pp.2213-2215, 2013.

J. K. Nicholson, J. C. Lindon, and E. Holmes, Metabonomics": understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data, Xenobiotica, vol.29, pp.1181-1189, 1999.

H. E. Pence, W. , and A. , ChemSpider: an online chemical information resource, J. Chem. Educ, vol.87, pp.1123-1124, 2010.

R. Ramautar, R. Berger, J. Van-der-greef, and T. Hankemeier, Human metabolomics: strategies to understand biology, Curr. Opin. Chem. Biol, vol.17, pp.841-846, 2013.

H. Redestig, M. Kusano, A. Fukushima, F. Matsuda, K. Saito et al., Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis, BMC Bioinformatics, vol.11, p.214, 2010.

S. Rogers and M. Girolami, A Bayesian regression approach to the inference of regulatory networks from gene expression data, Bioinformatics, vol.21, pp.3131-3137, 2005.

R. M. Salek, S. Neumann, D. Schober, J. Hummel, K. Billiau et al., COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access, Metabolomics, vol.11, pp.1587-1597, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01165673

J. Schellenberger, J. O. Park, T. M. Conrad, and B. Ø. Palsson, BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BMC Bioinformatics, vol.11, p.213, 2010.

S. Shameer, F. J. Logan-klumpler, F. Vinson, L. Cottret, B. Merlet et al., TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei, Nucleic Acids Res, vol.43, pp.637-644, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02631222

R. R. Silva, F. Jourdan, D. M. Salvanha, F. Letisse, E. L. Jamin et al., ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS based metabolomics, Bioinformatics, vol.30, pp.1336-1337, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01268715

K. Smallbone, Striking a Balance with Recon 2, 2013.

L. W. Sumner, A. Amberg, D. Barrett, M. H. Beale, R. Beger et al., Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI), Metabolomics, vol.3, pp.211-221, 2007.

I. Thiele and B. Ø. Palsson, A protocol for generating a highquality genome-scale metabolic reconstruction, Nat. Protoc, vol.5, pp.93-121, 2010.

I. Thiele, N. Swainston, R. M. Fleming, A. Hoppe, S. Sahoo et al., A community-driven global reconstruction of human metabolism, Nat. Biotechnol, vol.31, pp.419-425, 2013.

S. M. Wimalaratne, P. Grenon, H. Hermjakob, N. Le-novère, and C. Laibe, BioModels linked dataset, BMC Syst. Biol, vol.8, p.91, 2014.

D. S. Wishart, T. Jewison, A. C. Guo, M. Wilson, C. Knox et al., HMDB 3.0-The Human Metabolome Database in 2013, Nucleic Acids Res, vol.41, pp.801-807, 2013.

G. Wohlgemuth, P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn, The Chemical Translation Service-a web-based tool to improve standardization of metabolomic reports, Bioinformatics, vol.26, pp.2647-2648, 2010.

J. Xia and D. S. Wishart, MetPA: a web-based metabolomics tool for pathway analysis and visualization, Bioinformatics, vol.26, pp.2342-2344, 2010.