State of the nation in data integration for bioinformatics, J Biomed Inform, vol.41, p.18358788, 2008. ,
AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture, Database, pp.1-7, 2018. ,
DOI : 10.1093/database/bay088
URL : https://hal.archives-ouvertes.fr/lirmm-01964769
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat Genet, vol.25, p.10802651, 2000. ,
The plant ontology as a tool for comparative plant anatomy and genomic analyses, Plant Cell Physiol, vol.54, p.23220694, 2013. ,
Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice, Front Physiol, vol.3, p.22934074, 2012. ,
The environment ontology: contextualising biological and biomedical entities, J Biomed Semantics, vol.4, p.24330602, 2013. ,
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies, PLoS One, vol.9, p.24595056, 2014. ,
An ontology approach to comparative phenomics in plants, Plant Methods, vol.11, issue.10, p.25774204, 2015. ,
An ontology-based approach to integration of hilly citrus production knowledge, Comput Electron Agric, vol.113, pp.24-43, 2015. ,
A decision support system for eco-efficient biorefinery process comparison using a semantic approach, Comput Electron Agric, vol.127, pp.351-367, 2016. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01346685
AgroPortal: A vocabulary and ontology repository for agronomy, Comput Electron Agric, vol.144, pp.126-143, 2018. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01679502
, The Semantic Web. Sci Am, vol.284, pp.35-43, 2001.
, W3C. Resource Description Framework (RDF): Concepts and Abstract Syntax, 2010.
OWL 2 Web Ontology Language Structural Specification and Functional-Style Syntax, 2010. ,
, , p.15, 2013.
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside, J Biomed Semantics, vol.2, p.21624155, 2011. ,
Finding gene regulatory network candidates using the gene expression knowledge base, BMC Bioinformatics, vol.15, p.25490885, 2014. ,
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data, Bioinformatics, vol.28, p.23023984, 2012. ,
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nat Biotechnol. Nature Publishing Group, vol.25, p.17989687, 2007. ,
BioPortal: ontologies and integrated data resources at the click of a mouse, Nucleic Acids Res, vol.37, p.19483092, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00492020
Bio2RDF: towards a mashup to build bioinformatics knowledge systems, J Biomed Inform, vol.41, p.18472304, 2008. ,
Open PHACTS: Semantic interoperability for drug discovery. Drug Discovery Today, p.22683805, 2012. ,
Expanding the Pathway and Interaction Knowledge in Linked Life Data. International Semantic Web Challenge, 2009. ,
Developing a kidney and urinary pathway knowledge base, J Biomed Semantics, vol.2, p.21624162, 2011. ,
URL : https://hal.archives-ouvertes.fr/inserm-00593743
The EBI RDF platform: linked open data for the life sciences, Bioinformatics, vol.1, issue.2, p.24413672, 2014. ,
Towards efficient data integration and knowledge management in the Agronomic domain, APIA'15: premiere Conference Applications Pratiques de l'Intelligence Artificielle, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01176903
Data management and best practice for plant science, vol.3, p.28585570, 2017. ,
The Planteome database: An integrated resource for reference ontologies, plant genomics and phenomics, Nucleic Acids Res, 2018. ,
, , p.29186578
Comparative plant genomics resources, Nucleic Acids Res, vol.42, p.24217918, 2013. ,
UniProt Knowledgebase: A hub of integrated protein data, Database, p.21447597, 2011. ,
The GOA database in 2009-An integrated Gene Ontology Annotation resource, Nucleic Acids Res, vol.37, p.18957448, 2009. ,
TropGeneDB, the multi-tropical crop information system updated and extended, Nucleic Acids Res, vol.41, p.23161680, 2013. ,
OryGenesDB: a database for rice reverse genetics, Nucleic Acids Res, vol.34, p.16381969, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-01218996
Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library, Nucleic Acids Res, vol.36, p.17947330, 2008. ,
GreenPhylDB: a database for plant comparative genomics, Nucleic Acids Res, vol.36, p.17986457, 2008. ,
SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations, Nucleic Acids Res, vol.43, pp.295-300, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01279141
, Gene Annotation File (GAF) specification, 2018.
, Sequence Ontology consortium. GFF3 Specification
The International HapMap Project, Nature, vol.426, p.14685227, 2003. ,
The variant call format and VCFtools, Bioinformatics, vol.27, p.21653522, 2011. ,
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification, Nucleic Acids Res, vol.40, p.22140103, 2012. ,
Relations in biomedical ontologies, Genome Biol, vol.6, p.15892874, 2005. ,
Pubby-A Linked Data Frontend for SPARQL Endpoints, 2008. ,
RelFinder: Revealing relationships in RDF knowledge bases, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, pp.182-187, 2009. ,
The YASGUI Family of SPARQL Clients, Semant Web J, vol.0, pp.1-10, 2015. ,
Evaluating semantic search systems to identify future directions of research. The Semantic Web: ESWC 2012 Satellite Events, pp.148-162, 2012. ,
SUS-A quick and dirty usability scale, Usability Eval Ind. London, vol.189, pp.4-7, 1996. ,
The FAIR Guiding Principles for scientific data management and stewardship, Sci Data, vol.3, p.26978244, 2016. ,
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data, Wellcome Open Res, vol.1, p.28948232, 2016. ,
Information Commons for Rice (IC4R), Nucleic Acids Res, vol.44, 2016. ,
Expression Atlas update-An integrated database of gene and protein expression in humans, animals and plants, Nucleic Acids Res, vol.44, p.26481351, 2016. ,
RiceNet v2: An improved network prioritization server for rice genes, Nucleic Acids Res, vol.43, p.25813048, 2015. ,