H. Ji, Improving bioinformatic pipelines for exome variant calling, Genome Medicine, vol.4, issue.1, p.7, 2012.
DOI : 10.1101/gr.112326.110

D. Challis, J. Yu, U. Evani, A. Jackson, S. Paithankar et al., An integrative variant analysis suite for whole exome next-generation sequencing data, BMC Bioinformatics, vol.13, issue.1, pp.1-3, 2012.
DOI : 10.1038/nature08250

W. Mclaren, B. Pritchard, D. Rios, Y. Chen, P. Flicek et al., Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor, Bioinformatics, vol.26, issue.16, pp.2069-2070, 2010.
DOI : 10.1093/bioinformatics/btq330

R. Cotton, A. Auerbach, J. Beckmann, O. Blumenfeld, A. Brookes et al., Recommendations for locus-specific databases and their curation, Human Mutation, vol.21, issue.1, pp.2-5, 2008.
DOI : 10.1002/humu.20650

J. Den-dunnen, R. Sijmons, P. Andersen, M. Vihinen, J. Beckmann et al., Sharing data between LSDBs and central repositories, Human Mutation, vol.17, issue.4, pp.493-495, 2009.
DOI : 10.1002/humu.20977

C. Mitropoulou, A. Webb, K. Mitropoulos, A. Brookes, and G. Patrinos, Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea, Human Mutation, vol.28, issue.10, pp.1109-1116, 2010.
DOI : 10.1002/humu.21332

J. Kuntzer, D. Eggle, S. Klostermann, and H. Burtscher, Human variation databases. Oxford): Database, p.15, 2010.
DOI : 10.1093/database/baq015

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911800

G. Patrinos and A. Brookes, DNA, diseases and databases: disastrously deficient, Trends in Genetics, vol.21, issue.6, pp.333-338, 2005.
DOI : 10.1016/j.tig.2005.04.004

J. Celli, R. Dalgleish, M. Vihinen, P. Taschner, and J. Den-dunnen, Curating gene variant databases (LSDBs): Toward a universal standard, Human Mutation, vol.29, issue.2, pp.291-297, 2012.
DOI : 10.1002/humu.21626

L. Ding, M. Wendl, D. Koboldt, and E. Mardis, Analysis of next-generation genomic data in cancer: accomplishments and challenges, Human Molecular Genetics, vol.19, issue.R2, pp.188-196, 2010.
DOI : 10.1093/hmg/ddq391

J. Kaput, R. Cotton, L. Hardman, M. Watson, A. Aqeel et al., Planning the Human Variome Project: The Spain report, Human Mutation, vol.381, issue.Pt 1, pp.496-510, 2009.
DOI : 10.1002/humu.20972

A. Brookes, H. Lehvaslaiho, J. Muilu, Y. Shigemoto, T. Oroguchi et al., The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation, Human Mutation, vol.29, issue.Database issue, pp.968-977, 2009.
DOI : 10.1002/humu.20973

T. Adamusiak, H. Parkinson, J. Muilu, E. Roos, K. Van-der-velde et al., Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information, Human Mutation, vol.9, issue.5, pp.867-73
DOI : 10.1002/humu.22070

G. Tyrelle and G. King, A platform for the description, distribution and analysis of genetic polymorphism data, Bioinformatics: Proceedings of the First Asia- Pacific bioinformatics conference on, 2003.

J. Nakaya, M. Kimura, K. Hiroi, K. Ido, W. Yang et al., Genomic Sequence Variation Markup Language (GSVML), International Journal of Medical Informatics, vol.79, issue.2, pp.130-142, 2010.
DOI : 10.1016/j.ijmedinf.2009.11.003

P. Danecek, A. Auton, G. Abecasis, C. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2158, 2011.
DOI : 10.1093/bioinformatics/btr330

T. Rayner, P. Rocca-serra, P. Spellman, H. Causton, A. Farne et al., A simple spreadsheet-based, MIAME-supportive format for microarray data, BMC Bioinformatics, vol.7, issue.1, pp.489-489, 2006.
DOI : 10.1186/1471-2105-7-489

R. Jeliffe, The Schematron Assertion Language

I. Fokkema, P. Taschner, G. Schaafsma, J. Celli, and J. Laros, LOVD v.2.0: the next generation in gene variant databases, Human Mutation, vol.29, issue.5, pp.557-563, 2011.
DOI : 10.1002/humu.21438

M. Swertz, K. Velde, B. Tesson, R. Scheltema, D. Arends et al., XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments, Genome Biology, vol.11, issue.3, p.27, 2010.
DOI : 10.1186/gb-2008-9-6-r102

M. Vihinen, J. Den-dunnen, R. Dalgleish, and R. Cotton, Guidelines for establishing locus specific databases, Human Mutation, vol.79, issue.2, pp.298-305, 2012.
DOI : 10.1002/humu.21646

M. Kohonen-corish, J. Aama, A. Auerbach, M. Axton, C. Barash et al., How to catch all those mutations-the report of the Third Human Variome Project Meeting, UNESCO Paris, May 2010, Human Mutation, vol.7, issue.12, pp.1374-1381, 2010.
DOI : 10.1002/humu.21379

P. Robinson and S. Mundlos, The Human Phenotype Ontology, Clinical Genetics, vol.37, issue.2, pp.525-534, 2010.
DOI : 10.1111/j.1399-0004.2010.01436.x

URL : https://hal.archives-ouvertes.fr/inserm-00854299

K. Eilbeck, S. Lewis, C. Mungall, M. Yandell, L. Stein et al., Sequence Ontology, Genome Biol, vol.6, pp.441-453, 2005.
DOI : 10.1007/978-1-4419-9863-7_1107

A. Bizer, D2RQ -Treating Non-RDF Databases as Virtual RDF Graphs, 2004.

M. Dumontier and N. Villanueva-rosales, Towards pharmacogenomics knowledge discovery with the semantic web, Briefings in Bioinformatics, vol.10, issue.2, pp.153-163, 2009.
DOI : 10.1093/bib/bbn056

M. Fenner, . Identifiers, . Authors, and . Contributors, ORCID: Unique Identifiers for Authors and Contributors, Information Standards Quarterly, vol.23, issue.3, pp.10-13, 2011.
DOI : 10.3789/isqv23n3.2011.03

B. Giardine, J. Borg, D. Higgs, K. Peterson, S. Philipsen et al., Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach, Nature Genetics, vol.64, issue.4, pp.295-301, 2011.
DOI : 10.1111/j.1365-2257.2004.00606.x

J. Den-dunnen, Nomenclature for the description of sequence variants

J. Laros, A. Blavier, J. Den-dunnen, and P. Taschner, A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form, BMC Bioinformatics, vol.12, issue.Suppl 4, p.5, 2011.
DOI : 10.1093/bioinformatics/btg279

N. Juty, L. Novère, N. Laibe, and C. , Identifiers.org and MIRIAM Registry: community resources to provide persistent identification, Nucleic Acids Research, vol.40, issue.D1, pp.580-586, 2012.
DOI : 10.1093/nar/gkr1097

R. Dalgleish, P. Flicek, F. Cunningham, A. Astashyn, R. Tully et al., Locus Reference Genomic sequences: an improved basis for describing human DNA variants, Genome Medicine, vol.2, issue.4
DOI : 10.1186/gm145

URL : https://hal.archives-ouvertes.fr/inserm-00668222

J. D. Bell, E. Sistermans, and S. Ramsden, Practice guidelines for the interpretation and reporting of unclassified variants (UVs) in clinical molecular genetics. Guidelines ratified by the UK CMGS); 2007. A CMGS e-publication, ) and the VGKL, 2007.

S. Pathogenicity, Turtle RDF file

A. Jenkinson, M. Albrecht, E. Birney, H. Blankenburg, T. Down et al., Integrating biological data ??? the Distributed Annotation System, BMC Bioinformatics, vol.9, issue.Suppl 8, pp.1-7, 2008.
DOI : 10.1186/1471-2105-9-S8-S3

A. Shabo, S. Rabinovici-cohen, and P. Vortman, Revolutionary impact of XML on biomedical information interoperability, IBM Systems Journal, vol.45, issue.2, pp.361-372, 2006.
DOI : 10.1147/sj.452.0361

H. Abelson, J. Sussman, and J. Sussman, Structure and Interpretation of Computer Programs, 1984.

N. Nurseitov, M. Paulson, R. Reynolds, and C. Izurieta, Comparison of JSON and XML Data Interchange Formats: A Case Study, pp.157-162, 2009.

N. Kobayashi, M. Ishii, S. Takahashi, Y. Mochizuki, A. Matsushima et al., Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases, Nucleic Acids Research, vol.39, issue.suppl, pp.533-540, 2011.
DOI : 10.1093/nar/gkr353

P. Lopes, R. Dalgleish, and J. Oliveira, WAVe: web analysis of the variome, Human Mutation, vol.10, issue.7, pp.729-734, 2011.
DOI : 10.1002/humu.21499

C. Mak, CNVs from exome sequencing, Nature Biotechnology, vol.30, issue.7, pp.626-626, 2012.
DOI : 10.1038/nbt.2311

S. Benowitz, When Scientists Don't Share: Is Secrecy a Necessary Evil?, CancerSpectrum Knowledge Environment, vol.94, issue.10, pp.712-713, 2002.
DOI : 10.1093/jnci/94.10.712

S. Ram and G. Shankaranarayanan, Research issues in database schema evolution: the road not taken.I nBoston University School of Management, Department of Information Systems, Working Paper, pp.2003-2018, 2003.

V. Simplified and U. Model, https://raw.github.com/VarioML

. Byrne, VarioML framework for comprehensive variation data representation and exchange, BMC Bioinformatics, vol.13, issue.1, p.254, 2012.
DOI : 10.1186/1471-2105-13-254

URL : https://hal.archives-ouvertes.fr/inserm-00758018