G. Sempéré, J. Pétel-a-;-rouard-m-;-frouin, and Y. Hueber,

D. Bellis and F. ,

P. Larmande, Gigwa v2 -Extended and improved genotype investigator

Y. Nti-addae, D. Matthews, R. Victor-jun-ulat, G. Syed, A. Sempere et al., Benchmarking Database Systems for Genomic Selection Implementation, 2019.

R. Abbeloos, J. E. Backlund, B. Salido, M. Bauchet, G. Benites-alfaro et al., Verouden M BrAPI -an Application Programming Interface for Plant Breeding Applications, BioInformatics, 2019.

A. Venkatesan, G. Tagny, N. El-hassouni, I. Chentli, V. Guignon et al.,

, Agronomic Linked Data (AgroLD) : a Knowledge-based System to Enable Integrative Biology in Agronomy, PLoS ONE, vol.13, issue.11

V. M. Juanillas, A. Dereeper, N. Beaume, G. Droc, J. Dizon et al., Rice Galaxy : an open resource for plant science, Giga Science, 2018.

P. Cubry, C. Tranchant-dubreuil, A. C. Thuillet, C. Monat, M. N. Ndjiondjop et al., The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes, Curr Biol, vol.28, pp.2274-2282, 0201.
URL : https://hal.archives-ouvertes.fr/hal-01996543

L. ;. Harper, J. ;. Campbell, . Cannon, K. S. Ethalinda, S. ;. Jung et al.,

R. ;. Walls, C. ;. Andorf, E. ;. Arnaud, T. Z. Berardini, C. ;. Birkett et al., Nathan

C. G. Elsik, A. ;. Farmer, S. P. Ficklin, and D. Grant,

E. Grau,

N. ;. Herndon, . Hu, and . Zhi-liang,

J. ;. Humann, . Jaiswal, ;. Pankaj, C. ;. Jonquet, and M. Laporte,

P. ;. Larmande, G. ;. Lazo, F. ;. Mccarthy, . Menda, ;. Naama et al.,

T. Z. Sen, M. ;. Staton, . Subramaniam, ;. Sabarinath, M. Tello-ruiz et al.,

D. Unni, . Wang, ;. Liya, D. ;. Ware, J. ;. Wegrzyn et al., AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture, Database, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-01964769

A. Scheben, A. Chan, K. Mansueto, L. Mauleon, R. Larmande et al., Progress in single access information systems for wheat and rice crop improvement, Briefing in Bioinformatics, vol.4, 2018.

C. Jonquet, A. Toulet, E. Arnaud, E. Aubin, E. Dzalé-yeumo et al., AgroPortal : an ontology repository for agronomy, Comput. Electron. Agric, vol.144, pp.126-143, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-01598854

D. Yeumo, ;. Esther, . Alaux, ;. Michael, E. ;. Arnaud et al.,

P. ;. Buche, . Cooper, ;. Laurel, . Kupczy´nska, ;. Hanna et al.,

C. Jonquet,

M. Laporte,

P. ;. Larmande, C. ;. Pommier, and V. Protonotarios,

C. ;. Reverte, R. ;. Shrestha, . Subirats, ;. Imma, . Venkatesan et al., Developing data interoperability using standards : A wheat community use case, vol.6, p.1843, 2017.
URL : https://hal.archives-ouvertes.fr/lirmm-01652022

S. ;. Cohen-boulakia, . Belhajjame, ;. Khalid, . Collin, ;. Olivier et al., Scientific workflows for computational reproducibility in the life sciences : Status, challenges and opportunities, Futur. Gener. Comput. Syst, vol.75, pp.284-298, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01516082

, The South Green portal : a comprehensive resource for tropical and Mediterranean crop genomics, Curr. Plant Biol, pp.7-8, 2016.

G. Sempéré, P. F. Dereeper, A. Ruiz, M. Sarah, G. Larmande et al., Gigwa-Genotype investigator for genome-wide analyses, Gigascience, vol.5, 2016.

F. Al-tam, H. Adam, A. Dos-anjos, M. Lorieux, P. Larmande et al., Panicle Traits Phenotyping Tool, vol.13, pp.122-136, 2013.

J. Wollbrett, P. Larmande, F. De-lamotte, and M. Ruiz, Clever generation of rich SPARQL queries from annotated relational schema : application to Semantic Web Service creation for biological databases, BMC Bioinformatics, vol.14, pp.126-141, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268129

M. ;. Lorieux, . Blein, ;. Mélisande, J. ;. Lozano, . Bouniol et al.,

A. ;. Ghesquière, . Gantet, ;. Pascal, J. ;. Tohme, J. Morel et al.,

E. Guiderdoni, In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches. Plant Biotechnol, J, vol.10, pp.555-568, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00821958

G. Droc, C. Périn, S. Fromentin, and L. P. Orygenesdb, update : database interoperability for functional genomics of rice, Nucleic Acids Res, vol.37, p.202, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01218997

P. Larmande, C. Gay, M. Lorieux, C. Périn, M. Bouniol et al.,

A. Manel, Z. Bellahsene, T. Konstantin, and . Legato, Proceedings of the 12th International Workshop on Ontology Matching co-located with the 16th International Semantic Web Conference, pp.146-152, 2017.

A. Manel, Automatic Key Selection for Data Linking, 20th International Conference on Knowledge Engineering and Knowledge Management, vol.10024, pp.3-18, 2016.

A. Manel, Doing Web Data : from Dataset Recommendation to Data Linking, NoSQL Data Models. willey. T. 1. Databases and Big Data SET. Olivier Pivert, juil, pp.57-91, 2018.

A. Stein, « Gene prioritization through genomic data fusion, Nature Biotechnology, vol.24, p.537, 2006.

A. Alexa, J. Rahnenfuhrer, and . Topgo, Enrichment Analysis for Gene Ontology, 2016.

R. Aniceto and R. Xavier, Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency, 2015.

A. Erick, K. Martin, and M. Vladimir, « Biological knowledge management : the emerging role of the Semantic Web technologies, Briefings in Bioinformatics, vol.10, pp.392-407, 2009.

A. Grigoris and F. Harmelen, « Web ontology language : Owl, Handbook on ontologies, 2009.

M. Ashburner, « Gene ontology : tool for the unification of biology, Nat Genet, vol.25, pp.25-29, 2000.

J. Baran, GFVO : the Genomic Feature and Variation Ontology, PeerJ, vol.3, 2015.

B. Daniel, « The GOA database in 2009 -An integrated Gene Ontology Annotation resource, Nucleic Acids Research, vol.37, p.1, 2009.

B. Marco, D. E. Dario, C. Nart, and . Tasso, « Introducing Distiller : A Unifying Framework for Knowledge Extraction, 2015.

B. Marco, Entity recognition in the biomedical domain using a hybrid approach, Journal of Biomedical Semantics, vol.8, issue.1, pp.1-14, 2017.

B. François, Bio2RDF : towards a mashup to build bioinformatics knowledge systems, » In : Journal of biomedical informatics, vol.41, pp.706-722, 2008.

K. Michael and . Bergman, Sources and Classification of Semantic Heterogeneities, AI3 : : :Adaptive Information, 2006.

B. Tim, The semantic web, Scientific american, vol.284, pp.29-37, 2001.

A. Birkland and Y. Golan, BIOZON : a system for unification, management and analysis of heterogeneous biological data, BMC bioinformatics, vol.7, 2006.

B. Christian, « D2R MAP -A Database to RDF Mapping Language, Proceedings of the 12th International World Wide Web Conference, 2003.

B. Christian and S. Andy, « D2RQ -treating non-RDF databases as virtual RDF graphs, the 3rd International Semantic Web Conference, 2004.

J. A. Blake, Gene ontology annotations and resources, vol.41, p.1, 2013.

I. Elizabeth and . Boyle, TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes, Bioinformatics, vol.In, pp.1367-4803

B. Richard, Generation Challenge Programme (GCP) : standards for crop data, Omics : A Journal of Integrative Biology, vol.10, issue.2, pp.215-219, 2006.

S. William, . Bush, M. Scott, . Dudek, D. Marylyn et al., Biofilter : a knowledge-integration system for the multi-locus analysis of genome-wide association studies, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp.2335-6928, 2009.

P. Luigi and B. , The environment ontology in 2016 : bridging domains with increased scope, semantic density, and interoperation, Journal of Biomedical Semantics, vol.7, issue.1, 2016.

M. Elaine, C. Raymond, and J. Mooney, « Relational learning of pattern-match rules for information extraction, Computational Linguistics, vol.4, pp.9-15, 1999.

A. Callahan, C. José, . Toledo, and D. Michel, « Ontology-Based Querying with Bio2RDF's Linked Open Data, In : Journal of biomedical semantics, vol.4, issue.1, p.1, 2013.

C. Emmanuel, Workshop on Crop Ontology and Phenotyping Data Interoperability, p.1, 2014.

C. Dijun, Approaches in Integrative Bioinformatics -Towards the Virtual Cell, pp.299-333, 2014.

C. Jing, ToppGene Suite for gene list enrichment analysis and candidate gene prioritization, Nucleic acids research 37, 2009.

F. Ciravegna, LearningPinocchio : adaptive information extraction for real world applications, Natural Language Engineering, vol.10, pp.145-165, 1999.

C. Michael, Global RDF Vector Space Embeddings. » In : The Semantic Web -ISWC 2017 -16th International Semantic Web Conference, pp.190-207, 2017.

C. Sarah and L. Ulf, « Next generation data integration for Life Sciences, pp.1366-1369, 2011.

C. Sarah and L. Ulf, « Next Generation Data Integration for the Life Sciences, p.ICDE, 2010.

C. Remi, Public Data Integration with WebSmatch, Proceedings of the First International Workshop on Open Data. WOD '12, pp.5-12, 2012.

C. Bradford, Tripal Developer Toolkit ». eng. In : Database : The Journal of Biological Databases and Curation, 2018.

C. Laurel, The Planteome database : An integrated resource for reference ontologies, plant genomics and phenomics, Nucleic Acids Research, vol.46, p.1, 2018.

C. Olivier, D. Rose, and F. Et-catherine, Querying the Semantic Web with Corese Search Engine, Proceedings of the 16th Eureopean Conference on Artificial Intelligence, ECAI'2004, including Prestigious Applicants of Intelligent Systems, pp.705-709, 2004.

G. Richard and . Côté, The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries, BMC bioinformatics, vol.7, p.97, 2006.

C. Nadine, G. Raji, Y. Kokou, and . Db2owl, A Tool for Automatic Database-to-Ontology Mapping 2 Database to Ontology Mappings : DB2OWL Tool, pp.1-4, 2007.

R. , CYGANIAK et Christian BIZER. « Pubby -A Linked Data Frontend for SPARQL Endpoints, 2008.

D. Hanjun, Sequence2Vec : a novel embedding approach for modeling transcription factor binding affinity landscape, Bioinformatics, vol.33, pp.1367-4811, 2017.

D. Petr, The variant call format and VCFtools. » In : Bioinformatics, vol.27, pp.2156-2164, 2011.

S. B. Davidson, K2Kleisli and GUS : Experiments in Integrated Access to Genomic Data Sources, IBM Systems Journal, vol.40, pp.512-543, 2001.

K. H. Davis and A. K. Arora, « Converting A Relational Database Model into an EntityRelationship Model, Proceedings of the Sixth International Conference on Entity-Relationship Approach, 1987.

C. Rahul and . Deo, Prioritizing causal disease genes using unbiased genomic features, Genome biology 15.12 (déc. 2014), pp.534-534

A. Dereeper, SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations, Nucleic acids research, vol.43, pp.295-300, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01279141

A. Dereeper, SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations, Nucleic acids research, vol.43, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01279141

G. Droc, update : database interoperability for functional genomics of rice, Nucleic Acids Research, vol.37, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01218997

D. Esther and . Yeumo, Developing data interoperability using standards : A wheat community use case, p.1843, 2017.

. Ramez-elmasri, B. Shamkant, and . Navathe, Fundamentals of Database Systems

M. A. Boston and . Usa, , pp.0-321, 2006.

E. Sarah, From literature mining to disease-gene discovery, Nucleic Acids Research, vol.44, p.18, 2016.

T. Etzold, A. Ulyanov, and P. A. , SRS : information retrieval system for molecular biology data banks. » In, vol.266, pp.114-142, 1996.
DOI : 10.1016/s0076-6879(96)66010-8

F. Daniel, The AgreementMakerLight ontology matching system, Lecture Notes in Computer Science, vol.8185, pp.527-541, 2013.

F. Farzad, K. Minji, and M. Olgica, HyDRA : gene prioritization via hybrid distance-score rank aggregation, Bioinformatics 31.7 (nov. 2014), pp.1034-1043

F. Alfio, N. Andriy, and S. François, « Data Linking for the Semantic Web, International Journal on Semantic Web and Information Systems (IJSWIS), vol.7, issue.3, pp.46-76, 2011.

S. P. Ficklin, Tripal : a construction toolkit for online genome databases
DOI : 10.1093/database/bar044

URL : https://academic.oup.com/database/article-pdf/doi/10.1093/database/bar044/1269207/bar044.pdf

F. Kristofer, « Protein names and how to find them, International journal of medical informatics, vol.67, pp.49-61, 2002.

L. Matthew and . Freedman, Principles for the post-GWAS functional characterization of cancer risk loci, Nature Genetics, vol.43, p.513, 2011.

G. Chiara, D. Christine, and A. Et-ron, « Funding knowledgebases : Towards a sustainable funding model for the UniProt use case ». en, pp.2046-1402

G. Matteo, BigQ : a NoSQL based framework to handle genomic variants in i2b2, Publisher : BMC Bioinformatics, vol.16, pp.1471-2105, 2015.

S. Kumar and G. , A Survey on NoSQL Databases, 2012.

G. Fabien, F. Catherine, and C. Olivier, Le Web sémantique : comment lier les données et les schémas sur le web ? Dunod, pp.163-166, 2012.

G. Martin, N. Goran, M. Casey, . «. Bergman, and . Linnaeus, A species name identification system for biomedical literature, BMC Bioinformatics, vol.11, issue.1, p.85, 2010.

G. Belinda, Galaxy : A platform for interactive large-scale genome analysis, Genome Research, vol.15, pp.1451-1455, 2005.

G. Jeremy, A. Nekrutenko, and T. James, « Galaxy : a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biology, vol.11, pp.1-13, 2010.

G. Christine, Leveraging Semantic Web Technologies for the Life Sciences, pp.169-182, 2007.

G. Katarina, Data management in cloud environments : NoSQL and NewSQL data stores, Journal of Cloud Computing : Advances, Systems and Applications, vol.2, pp.2192-113, 2013.

L. M. Haas, DiscoveryLink : a system for integrated access to life sciences data sources, IBM Syst. J, vol.40, pp.18-8670, 2001.

H. Maryam, Deep learning with word embeddings improves biomedical named entity recognition, Bioinformatics, vol.33, pp.37-48, 2017.

Y. Alon and . Halevy, Answering queries using views : A survey, The VLDB Journal, 2001.

C. Hamelin, the multi-tropical crop information system updated and extended, Nucleic acids research, 2012.

H. Ian, Matching disease and phenotype ontologies in the ontology alignment evaluation initiative, Journal of Biomedical Semantics, vol.8, 2017.

H. Keywan, Developing integrated crop knowledge networks to advance candidate gene discovery, Applied & Translational Genomics, vol.11, pp.18-26, 2016.

C. Theil, H. , L. Juhl, and J. , « Databases and ontologies Are graph databases ready for bioinformatics ?, In : Bioinformatics 29, vol.24, pp.3107-3108, 2013.

H. Philipp, Revealing relationships in RDF knowledge bases, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). T. 5887 LNCS. Citation Key : Heim2009 ISSN : 03029743, pp.182-187, 2009.

K. M. Hettne, « A dictionary to identify small molecules and drugs in free text, Bioinformatics, vol.25, pp.2983-2991, 2009.

L. Hirschman and R. G. , Natural Language Question Answering : The View from Here, Nat. Lang. Eng, vol.7, issue.4, pp.275-300, 2001.

. Lin-hou and Z. Hongyu, A review of post-GWAS prioritization approaches, Frontiers in Genetics, vol.4, pp.1664-8021, 2013.

D. Houle, R. Diddahally, . Govindaraju, and O. Stig, « Phenomics : the next challenge, Nature Reviews Genetics, vol.11, p.855, 2010.

J. Anja, Silk -Generating RDF Links while publishing or consuming Linked Data, Proceedings of ISWC, 2010.

J. Clément, AgroPortal : A vocabulary and ontology repository for agronomy, Computers and Electronics in Agriculture 144, pp.126-143, 2016.

J. Clément, Indexation et intégration de ressources textuelles à l ' aide d ' ontologies : application au domaine biomédical, pp.1-12, 2010.

L. Insuk, Prioritizing candidate disease genes by network-based boosting of genomewide association data, Genome research 21.7 (juil. 2011), pp.1549-5469

L. Maurizio, « Data Integration : A Theoretical Perspective, Proceedings of the Twenty-first ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, pp.233-246, 2002.

L. Sabina, « Data management and best practice for plant science, vol.3, pp.1-4, 2017.

, Sous la dir. d'Ulf LESER, « Data Integration in the Life Sciences, Third International Workshop, vol.4075, 2006.

L. I. Yongjin and L. I. Et-jinyan, Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data, BMC genomics 13 Suppl 7

L. I. Yongjin, C. Jagdish, and . Patra, « Integration of multiple data sources to prioritize candidate genes using discounted rating system, BMC bioinformatics 11

. S20-s20 and . Issn, , pp.1471-2105

L. I. Yu, DEEPre : sequence-based enzyme EC number prediction by deep learning ». eng, Bioinformatics, vol.34, pp.1367-4811, 2018.

L. Vanessa, « Is Question Answering Fit for the Semantic Web ? : A Survey, Semant. web, vol.2, pp.125-155, 2011.

L. Luyen, Development of a Knowledge System for Big Data : Case Study to Plant Phenotyping Data, Proceedings of the 6th International Conference on Web Intelligence, Mining and Semantics. T. 27. WIMS '16, pp.1-9, 2016.

L. Artem, Representing and querying disease networks using graph databases, BioData Mining, vol.9, p.23, 2016.

M. Michele, C. Et-uni-prot, and . Uniprot-knowledgebase, A hub of integrated protein data, Database 2011, 2011.

M. Ioana, « Efficient Querying of Distributed Resources in Mediator Systems, pp.468-485, 2002.

T. A. Manolio, « Finding the missing heritability of complex diseases, Nature, vol.461, p.747, 2009.

M. Ganiraju, Relax with CouchDB -Into the non-relational DBMS era of bioinformatics, In : Genomics, vol.100, issue.1, pp.1-7, 2012.

M. Takashi, The Nipponbare genome and the next-generation of rice genomics research in Japan, Rice 9.1 (juil. 2016), p.33

M. Soumia and J. Clement, « Scoring semantic annotations returned by the NCBO Annotator, 7th International Semantic Web Applications and Tools for Life Sciences, SWAT4LS'14. CEUR Workshop Proceedings, vol.1320, p.15, 2014.

M. Franck, J. M. , and C. Faron-zucker, « A survey of RDB to RDF translation approaches and tools, HAL May, 2014.

M. Franck, Non-Relational Databases to RDF Mapping Language, vol.2, p.HAL, 2015.

M. Iain, Flapjack-graphical genotype visualization, Bioinformatics, vol.26, pp.3133-3137, 2010.

M. Dan, « Performance Issues and Error Analysis in an Open-Domain Question Answering System, Proceedings of 40th Annual Meeting of the Association for Computational Linguistics, pp.33-40, 2002.

M. Cécile, TOGGLE : toolbox for generic NGS analyses, BMC bioinformatics, vol.16, p.374, 2015.

A. Moniruzzaman, H. Syed-akhter, and . Nosql-database, New Era of Databases for Big data Analytics -Classification, Characteristics and Comparison, pp.2005-4270, 2013.

M. Fantine, V. Jean-philippe, and . Prodige, Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples, BMC bioinformatics, vol.12, pp.1471-2105, 2011.

Y. Moreau-et-léon-charles and T. , Computational tools for prioritizing candidate genes : Boosting disease gene discovery, Nature Reviews Genetics, vol.13, pp.523-536, 2012.

N. Nagarajan, S. Inderjit, and . Dhillon, Inductive matrix completion for predicting gene-disease associations ». eng, Bioinformatics, vol.30, pp.1367-4811

H. Theodor and . Nelson, From Memex to Hypertext, pp.245-260, 1991.

N. Mariana and L. Ulf, « Question answering for Biology, Methods, vol.74, pp.36-46, 2015.

N. Pascal, Dealing with multi-source and multi-scale information in plant phenomics : the ontology-driven Phenotyping Hybrid Information System, New Phytologist 0.0 (

.. C. Ngomo and A. Sörer, « Limes-a time-efficient approach for large-scale link discovery on the web of data, Proceedings of IJCAI, pp.2312-2317, 2011.

N. Andriy, Combining RDF Graph Data and Embedding Models for an Augmented Knowledge Graph, Companion of the The Web Conference 2018 on The Web Conference 2018. International World Wide Web Conferences Steering Committee, pp.977-980, 2018.

N. Henrik, A Hadoop-based analytic toolkit for large-scale sequence data, Bioinformatics, vol.29, p.13674803, 2013.

F. Natalya and . Noy, BioPortal : ontologies and integrated data resources at the click of a mouse, Nucleic Acids Research, vol.37, pp.170-173, 2009.

N. Yaw, Benchmarking Database Systems for Genomic Selection Implementation, bioRxiv (jan. 2019), p.519017

E. Ong, A linked ontology data server to support ontology term dereferencing, linkage, query and integration, Nucleic Acids Research, p.918, 2016.

M. James, . Ostell, and . Entrez, The NCBI Search and Discovery Engine, pp.1-4, 2012.

L. Otero-cerdeira, F. J. Rodríguez-martínez, and A. Gómez-rodríguez, « Ontology matching : A literature review, Expert Systems with Applications, vol.42, pp.949-971, 2015.

O. Paul, « Traité de documentation, vol.205, pp.377-381, 1934.

P. Pablo, Bio4j : a high-performance cloud-enabled graph-based data platform, BioXriv, pp.1-11, 2015.

P. Muller and G. Et-nathalie, Modelisation Objet Avec Uml -Muller -2ème édition -Librairie Eyrolles. fr. Eyrolles, 2002.

P. The and C. Ontology, « The Plant Ontology Consortium and plant ontologies, Comparative and functional genomics, vol.3, issue.2, pp.1531-6912, 2002.

L. R. Rabiner, A tutorial on hidden Markov models and selected applications in speech recognition, Proceedings of the IEEE, vol.77, pp.257-286, 1989.

A. Rao, Phenotype-driven gene prioritization for rare diseases using graph convolution on heterogeneous networks, BMC medical genomics 11.1 (juil. 2018), pp.1755-8794

N. Redaschi, . The, and . Consortium, Uniprot in RDF : Tackling data integration and distributed annotation with the semantic web, Nature Prec, 2009.

L. Reiser, Sustainable funding for biocuration : The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model, Database : The Journal of Biological Databases and Curation, 2016.

R. Laurens and H. Et-rinke, « The YASGUI Family of SPARQL Clients, Citation Key : Rietveld2015YASGUI, 2015.

J. Daniel, . Rigden, and M. F. Xosé, The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection, Nucleic Acids Research, vol.47, pp.1362-4962, 2019.

. Petar-ristoski, P. Heiko, and . Rdf2vec, RDF Graph Embeddings for Data Mining. » In : The Semantic Web -ISWC 2016 -15th International Semantic Web Conference, pp.498-514, 2016.

R. Tim, W. Michael, and L. Ulf, ChemSpot : a hybrid system for chemical named entity recognition, Bioinformatics, vol.28, pp.1633-1640, 2012.

R. Mariano, Query Rewriting and Optimisation with Database Dependencies in Ontop, Citation Key

M. Mart\ and &. Romero, « NCBO Ontology Recommender 2.0 : An Enhanced Approach for Biomedical Ontology Recommendation, 2016.

R. Mathieu, GreenPhylDB v2.0 : comparative and functional genomics in plants, Nucleic acids research, vol.39, 2011.

L. Sanderson, Tripal v1.1 : a standards-based toolkit for construction of online genetic and genomic databases, Database 2013.0 (oct. 2013)

S. Max, B. Christian, and P. Heiko, « Adoption of the Linked Data Best Practices in Different Topical Domains, Semantic Web Conference, vol.1, pp.245-260, 2014.

S. André, Simple and scalable scripting for large sequencing data sets in hadoop, Electronic)\r1367-4803 (Linking), vol.30, 2014.

S. Dominik, J. Marie, S. Et-markus, and S. , « GeneDistiller-distilling candidate genes from linkage intervals, PloS one 3.12 (déc. 2008)

I. Segura-bedmar, S. Víctor, and M. Paloma, « Combining Conditional Random Fields and Word Embeddings for the CHEMDNER-patents task, Proceedings of the fifth BioCreative challenge evaluation workshop, pp.90-93, 2015.

S. Guilhem, « Gigwa-Genotype investigator for genome-wide analyses, » In : GigaScience, vol.5, p.25, 2016.

F. Juan and . Sequeda, Survey of Directly Mapping SQL Databases to the Semantic Web, pp.1-33, 2011.

B. Settles, ABNER : an open source tool for automatically tagging genes, proteins and other entity names in text, Bioinformatics, vol.21, pp.3191-3192, 2005.

S. Burr, « Biomedical named entity recognition using conditional random fields and rich feature sets, International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, pp.104-107, 2004.

P. Sohrab and . Shah, Atlas -a data warehouse for integrative bioinformatics, BMC Bioinformatics, vol.6, p.34, 2005.

B. Sheehan, A relation based measure of semantic similarity for Gene Ontology annotations, » In : BMC bioinformatics 9, p.468, 2008.

U. Martin and S. , Prediction and validation of gene-disease associations using methods inspired by social network analyses, PloS one, vol.8, issue.5, 2013.

F. Zohra, S. Robert, H. Xin, and G. , « Onto2Vec : joint vector-based representation of biological entities and their ontology-based annotations, Bioinformatics, vol.34, 2018.

F. Zohra, S. Robert, H. Xin, and G. , « OPA2Vec : combining formal and informal content of biomedical ontologies to improve similarity-based prediction, 2018.

S. Damian, BioMart -biological queries made easy, BMC Genomics, vol.10, pp.1471-2164, 2009.

S. Barry, The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration, Nat Biotech, vol.25, pp.1251-1255, 2007.

N. Richard and . Smith, InterMine : a flexible data warehouse system for the integration and analysis of heterogeneous biological data, Bioinformatics, vol.In, pp.1367-4811

S. Das, S. Sundara, and R. Cyganiak, R2RML : RDB to RDF Mapping Language

R. Stevens, TAMBIS : transparent access to multiple bioinformatics information sources. » In : Bioinformatics 16.2 (fév. 2000), pp.184-185
DOI : 10.1093/bioinformatics/16.2.184

URL : https://academic.oup.com/bioinformatics/article-pdf/16/2/184/630554/160184.pdf

S. Danai, Scalable Almost Key Discovery in RDF Data, The Semantic Web -ISWC 2014 -13th International Semantic Web Conference, pp.33-49, 2014.

T. Jan, « ONDEX -a data integration framework for the life sciences, 2011.

T. Jan, Ondex Web : Web-based visualization and exploration of heterogeneous biological networks, Bioinformatics, vol.30, 2014.

C. Ronald and . Taylor, « An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics, BMC Bioinformatics 11.Suppl, vol.12, 2010.

M. K. Tello-ruiz, Unifying comparative genomics and pathway resources for plant research, Nucleic Acids Research, 2018.
DOI : 10.1093/nar/gkx1111

URL : https://academic.oup.com/nar/article-pdf/46/D1/D1181/23162362/gkx1111.pdf

. The-gene-ontology-consortium, Gene Ontology Consortium : going forward. » In : Nucleic acids research, vol.43, pp.1049-1056, 2014.

S. Hamid, T. , J. Sequeda, and M. Daniel, « Translating SQL Applications to the Semantic Web, pp.450-464, 2008.

S. Hamid and T. , Mapping between the OBO and OWL ontology languages, J. Biomedical Semantics, vol.2, 2011.

T. Anthony, R. Louiqa, and V. Patrick, « Scaling Access to Heterogeneous Data Sources with DISCO, Knowledge and Data Engineering, vol.10, pp.808-823, 1998.

T. Anne, E. Vincent, and J. Clement, Modele de metadonnees dans un portail d'ontologies, 2016.

L. Charles and T. , « Candidate gene prioritization with Endeavour, Nucleic acids research, vol.44, pp.117-121, 2016.

L. Tranchevent, Kernel-based data fusion for gene prioritization, Bioinformatics 23.13 (juil. 2007), pp.125-132

T. Silke, Columba : an integrated database of proteins, structures, and annotations, BMC Bioinformatics, vol.6, p.81, 2005.

T. Thoralf, BioDWH : a data warehouse kit for life science data integration, Journal of Integrative Bioinformatics, vol.5, issue.2, 2008.

U. Özlem, i2b2/VA challenge on concepts, assertions, and relations in clinical text, » In : Journal of the American Medical Informatics Association : JAMIA, vol.18, pp.552-558, 2010.

V. Alfonso, . Search, and . Retrieve, Large-scale data generation is becoming increasingly important in biological research, EMBO reports, vol.3, issue.5, pp.1469-221, 2002.

V. Pierre-yves and . Thèse, Définition d'un cadre formel de représentation des Systèmes d'Organisation de la Connaissance, pp.58-61, 2011.

W. Samart, « The Generation Challenge Programme comparative plant stressresponsive gene catalogue, Nucleic Acids Research, vol.36, pp.943-946, 2008.

W. Wensheng, Genomic variation in 3,010 diverse accessions of Asian cultivated rice, Nature, vol.557, pp.43-49, 2018.

L. Patricia and . Whetzel, The MGED ontology : A Resource for semantics-based description of microarray experiments, pp.866-873, 2006.

G. Wiederhold, R. Michael, and . Genesereth, « The basis for mediation, Proc. CO-OPIS, 1995.

G. Wiederhold and R. G. Michael, The Conceptual Basis for Mediation Services, IEEE Expert, vol.12, pp.38-47, 1997.
DOI : 10.1109/64.621227

W. Mark, BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case, Plant Physiology, vol.138, pp.5-17, 2005.

D. Mark, . Wilkinson, and L. Matthew, BioMOBY : an open source biological web services proposal, Briefings in Bioinformatics, vol.3, pp.331-341, 2002.

D. Mark and . Wilkinson, « The FAIR Guiding Principles for scientific data management and stewardship, Scientific Data, vol.3, p.160018, 2016.

A. J. Williams, Open PHACTS : Semantic interoperability for drug discovery, 2012.
DOI : 10.1016/j.drudis.2012.05.016

URL : https://doi.org/10.1016/j.drudis.2012.05.016

R. A. Wing, The Oryza Map Alignment Project : The Golden Path to Unlocking the Genetic Potential of Wild Rice Species, Plant Molecular Biology, vol.59, issue.1, pp.1573-5028

W. Julien, Clever generation of rich SPARQL queries from annotated relational schema : application to Semantic Web Service creation for biological databases, BMC bioinformatics, vol.14, pp.126-141, 2013.

X. Zhihao, PolyA : a robust and generic deep learning method for PAS identification, DOI : 10 . 1093 / bioinformatics / bty991, 2018.

Y. U. Haiyuan, G. Natali, and W. Et-xiujuan, « Network-based methods for human disease gene prediction, Briefings in Functional Genomics, vol.10, pp.2041-2649, 2011.

Z. Pooya, Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information, Bioinformatics, vol.34, pp.1367-4811

Z. Pinglei, D. Emmert, Z. Peili, D. «-;-andreas, and . Baxevanis, Using Chado to store genome annotation data, Current Protocols in Bioinformatics / Editoral Board, 2006.

Z. Marinka, A. Monica, and L. Jure, « Modeling polypharmacy side effects with graph convolutional networks, Bioinformatics, vol.34, pp.1367-4811

?. Marinka, Arabidopsis reactome: a foundation knowledgebase for plant systems biology, Gene Prioritization by Compressive Data Fusion and Chaining ». eng, vol.11, pp.1426-1436, 2008.

A. Lysenko, M. M. Hindle, J. Taubert, M. Saqi, and C. J. Rawlings, Data integration for plant genomics-exemplars from the integration of Arabidopsis thaliana databases, Brief Bioinform, vol.10, pp.676-693, 2009.

L. D. Stein, Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges, Nat Rev Genet, vol.9, pp.678-688, 2008.

C. Goble and R. Stevens, State of the nation in data integration for bioinformatics, J Biomed Inform, vol.41, pp.687-693, 2008.

. Rdf/xml, Syntax Specification

, SPARQL Query Language for RDF

, OWL Web Ontology Language Overview

D. Swarbreck and C. Wilks, The Arabidopsis Information Resource (TAIR): gene structure and function annotation, Nucleic Acids Res, vol.36, pp.1009-1014, 2008.

C. Liang and P. Jaiswal, Gramene: a growing plant comparative genomics resource, Nucleic Acids Res, vol.36, pp.947-953, 2008.

C. G. Mclaren and R. M. Bruskiewich, The International Rice Information System. A platform for meta-analysis of rice crop data, Plant Physiol, vol.139, pp.637-642, 2005.

C. J. Lawrence and L. C. Harper, MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research, Int J Plant Genomics, pp.1-10, 2008.

D. Samson and F. Legeai, GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics, Nucleic Acids Res, vol.31, pp.179-182, 2003.

D. L. Rubin and N. H. Shah, Biomedical ontologies: a functional perspective, Brief Bioinform, vol.9, pp.75-90, 2008.

L. L. Chepelev and M. Dumontier, Semantic Web integration of Cheminformatics resources with the SADI framework, J Cheminform, vol.3, p.16, 2011.

R. Bruskiewich, M. Senger, G. Davenport, M. Ruiz, and M. Rouard, The generation challenge programme platform: semantic standards and workbench for crop science, Int J Plant Genomics, p.369601, 2008.

S. A. Goff, S. Mckay, A. E. Stapleton, M. Hanlon, S. Mock et al., The iPlant collaborative: cyberinfrastructure for plant biology, Front Plant Sci, vol.2, p.34, 2011.

M. D. Wilkinson, B. Vandervalk, and L. Mccarthy, SADI Semantic Web Services -' cause you can't always GET what you want! Services Computing Conference, pp.13-18, 2009.
DOI : 10.1109/apscc.2009.5394148

D. Gessler and G. Schiltz, SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services, BMC Bioinformatics, vol.10, p.309, 2009.
DOI : 10.1186/1471-2105-10-309

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-309

M. D. Wilkinson, B. Vandervalk, and L. Mccarthy, The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation, J Biomed Semantics, vol.2, issue.8, 2011.
DOI : 10.1186/2041-1480-2-8

URL : https://doi.org/10.1186/2041-1480-2-8

M. D. Wilkinson, M. Senger, E. Kawas, R. Bruskiewich, J. Gouzy et al., Interoperability with Moby 1.0-it's better than sharing your toothbrush! Brief Bioinform, vol.9, pp.220-231, 2008.

M. Wilkinson and L. Mccarthy, SADI, SHARE, and the in silico scientific method, BMC Bioinform, vol.11, p.7, 2010.

D. Spanos, P. Stavrou, and N. Mitrou, Bringing relational databases into the Semantic Web: A survey, Semantic Web, vol.2012, issue.2, pp.169-209

, Mapping Relational Data to RDF in Virtuoso

A. Miles, J. Zhao, G. Klyne, H. White-cooper, and D. Shotton, OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster, J Biomed Inform, 2010.

K. H. Cheung, K. Y. Yip, A. Smith, R. Deknikker, A. Masiar et al., YeastHub: a semantic web use case for integrating data in the life sciences domain, Bioinformatics, vol.21, issue.1, pp.85-96, 2005.

H. Lam, L. Marenco, G. M. Shepherd, P. L. Miller, and K. Cheung, Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences, AMIA Annu Symp Proc, pp.464-468, 2006.

R. Bruskiewich and G. Davenport, Generation Challenge Programme (GCP): standards for crop data, OMICS, vol.10, pp.215-219, 2006.
DOI : 10.1089/omi.2006.10.215

J. W. Rahayu and E. Chang, A methodology for transforming inheritance relationships in an object-oriented conceptual model to relational tables, Inf Softw Technol, vol.42, pp.571-592, 2000.

S. Tirmizi, J. Sequeda, and D. Miranker, Translating SQL Applications to the Semantic Web, Database and Expert Systems Applications, vol.5181, pp.450-464, 2008.
DOI : 10.1007/978-3-540-85654-2_40

E. Dijkstra, A note on two problems in connexion with graphs, Numerische Mathematik, vol.1, pp.269-271, 1959.

S. Pettifer and J. Ison, The EMBRACE web service collection, Nucleic Acids Res, vol.38, pp.683-688, 2010.
DOI : 10.1093/nar/gkq297

URL : https://hal.archives-ouvertes.fr/in2p3-00573748

J. Kopecký and T. Vitvar, SAWSDL: Semantic Annotations for WSDL and XML Schema, IEEE Internet Comput, vol.11, pp.60-67, 2007.

J. Bhagat, F. Tanoh, E. Nzuobontane, T. Laurent, J. Orlowski et al., BioCatalogue: a universal catalogue of web services for the life sciences, Nucleic Acids Res, pp.689-694, 2010.

M. Ruiz, M. Rouard, L. M. Raboin, M. Lartaud, P. Lagoda et al., TropGENE-DB, a multi-tropical crop information system, Nucleic Acids Res, vol.32, pp.364-367, 2004.
DOI : 10.1093/nar/gkh105

URL : https://academic.oup.com/nar/article-pdf/32/suppl_1/D364/7621926/gkh105.pdf

P. Flicek, M. R. Amode, D. Barrell, K. Beal, S. Brent et al., Nucleic Acids Res, vol.40, pp.84-90, 2011.

C. A. Goble, J. Bhagat, S. Aleksejevs, D. Cruickshank, D. Michaelides et al., myExperiment: a repository and social network for the sharing of bioinformatics workflows, vol.38, pp.677-682, 2010.

G. Droc and C. Périn, OryGenesDB 2008 update: database interoperability for functional genomics of rice, Nucleic Acids Res, vol.37, pp.992-995, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01218997

. Singer,

R. Shrestha and E. Arnaud, Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature, AoB Plants, p.8, 2010.

K. Eilbeck, S. Lewis, C. Mungall, M. Yandell, L. Stein et al., The Sequence Ontology: a tool for the unification of genome annotations, Genome Biology, vol.6, p.44, 2005.

C. Bizer and A. Schultz, The Berlin SPARQL Benchmark, Int J Semantic Web Inf Syst, vol.5, pp.1-24, 2009.
DOI : 10.4018/978-1-60960-593-3.ch004

O. Biological and B. Ontologies, WebSmatch project: an environment for Web Schema Matching

. Wollbrett, Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases, BMC Bioinformatics, vol.14, p.126, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268129

, MR performed beta-testing. PL, GSempéré and AD drafted the manuscript. All authors read and approved the final manuscript

. Umr-intertryp, Campus International de Baillarguet, vol.34398, p.1000

, Avenue Agropolis, 34934 Montpellier, Cedex, vol.5

C. Cali, U. Inra, and . Agap,

. Montpellier,

A. Gheyas, C. Boschiero, L. Eory, H. Ralph, R. Kuo et al., Functional classification of 15 million SNPs detected from diverse chicken populations, DNA Res, vol.22, issue.3, pp.205-222, 2015.

X. Li, A. J. Buitenhuis, M. S. Lund, C. Li, D. Sun et al., Joint genomewide association study for milk fatty acid traits in Chinese and Danish Holstein populations, J Dairy Sci, vol.98, issue.11, pp.8152-63, 2015.
DOI : 10.3168/jds.2015-9383

H. Shinada, T. Yamamoto, H. Sato, E. Yamamoto, K. Hori et al., Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping, Breed Sci, vol.65, issue.5, pp.388-95, 2015.

I. Marcotuli, K. Houston, R. Waugh, G. B. Fincher, R. A. Burton et al., Genome wide association mapping for arabinoxylan content in a collection of tetraploid wheats, PLoS One, vol.10, issue.7, 2015.

, The 3000 rice genomes project. The 3,000 rice genomes project, Gigascience, vol.3, 2014.

S. Ossowski, K. Schneeberger, R. M. Clark, C. Lanz, N. Warthmann et al., Sequencing of natural strains of Arabidopsis thaliana with short reads, Genome Res, vol.18, pp.2024-2057, 2008.

J. Cao, K. Schneeberger, S. Ossowski, T. Günther, S. Bender et al., Wholegenome sequencing of multiple Arabidopsis thaliana populations, Nat Genet, vol.43, issue.10, pp.956-63, 2011.
DOI : 10.1038/ng.911

URL : https://www.nature.com/articles/ng.911.pdf

P. Danecek, A. Auton, G. Abecasis, C. A. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2164, 2011.
DOI : 10.1093/bioinformatics/btr330

URL : https://academic.oup.com/bioinformatics/article-pdf/27/15/2156/1125001/btr330.pdf

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The genome analysis toolkit: a MapReduce framework for analyzing nextgeneration DNA sequencing data, Genome Res, vol.20, issue.9, pp.1297-303, 2010.

J. Casbon, PyVCF -A Variant Call Format Parser for Python, 2012.

V. Obenchain, M. Lawrence, V. Carey, S. Gogarten, P. Shannon et al., VariantAnnotation: a bioconductor package for exploration and annotation of genetic variants, Bioinformatics, vol.30, issue.14, pp.2076-2084, 2014.

U. Wittelsburger, B. Pfeifer, and M. J. Lercher, WhopGenome: high-speed access to whole-genome variation and sequence data in R, Bioinformatics, vol.31, issue.3, pp.413-418, 2015.

M. Bach and A. Werner, Innovative control systems for tracked vehicle platforms, vol.2, pp.163-74, 2014.

S. K. Gajendran, A survey on NoDQL databases, 2012.

A. Moniruzzaman and S. A. Hossain, Nosql database: New era of databases for big data analytics-classification, characteristics and comparison, CoRR [Internet], vol.6, issue.4, pp.1-14, 2013.

B. D. O'connor, B. Merriman, and S. F. Nelson, SeqWare query engine: storing and searching sequence data in the cloud, S2. Available from, vol.11, 2010.

S. Wang, I. Pandis, C. Wu, S. He, D. Johnson et al., High dimensional biological data retrieval optimization with NoSQL technology, BMC Genomics, vol.15, issue.8, 2014.

B. Langmead, M. C. Schatz, J. Lin, M. Pop, and S. L. Salzberg, Searching for SNPs with cloud computing, Genome Biol, vol.10, issue.11, 2009.

E. Afgan, B. Chapman, and J. Taylor, CloudMan as a platform for tool, data, and analysis distribution, BMC Bioinf, vol.13, issue.1, p.315, 2012.

M. C. Schatz, CloudBurst: highly sensitive read mapping with MapReduce, Bioinformatics, vol.25, issue.11, pp.1363-1372, 2009.

T. A. Russ, C. Ramakrishnan, E. H. Hovy, M. Bota, and G. Burns, Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case, BMC Bioinf, vol.12, issue.1, p.351, 2011.

Z. Ye and S. Li, Arequest skewaware heterogeneous distributed storage systembased on Cassandra. the International Conference on Computer and Management (CAMAN'11), pp.1-5, 2011.

G. Manyam, M. Payton, J. Roth, L. Abruzzo, and K. R. Coombes, Relax with CouchDB -Into the non-relational DBMS era of bioinformatics, Genomics, 2012.

H. Ohyanagi, T. Ebata, X. Huang, H. Gong, M. Fujita et al., Genome Diversity Database of Wild Oryza Species Special Online Collection -Database Paper, vol.0, pp.1-7, 2015.

N. Alexandrov, S. Tai, W. Wang, L. Mansueto, K. Palis et al., SNPSeek database of SNPs derived from 3000 rice genomes, Nucleic Acids Res, vol.63, issue.2, pp.2-6, 2015.

C. Miller, Y. Qiao, T. Disera, D. 'astous, B. et al., Iobio: a Web-based, real-time, sequence alignment file inspector, Nat Methods, vol.11, issue.12, p.1189, 2014.

D. Sera and T. L. Vcf, iobio-A visually driven variant data inspector and real-time analysis web application. NEXT GEN SEEK, 2015.

M. E. Skinner, A. V. Uzilov, L. D. Stein, C. J. Mungall, and I. H. Holmes, JBrowse: a nextgeneration genome browser, Genome Res, vol.19, pp.1630-1638, 2009.

P. Cingolani, A. Platts, L. L. Wang, M. Coon, T. Nguyen et al., A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w 1118; iso-2; iso-3, Fly (Austin), vol.6, pp.80-92, 2012.

B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski et al., Galaxy: a platform for interactive large-scale genome analysis, Genome Res, vol.15, issue.10, pp.1451-1456, 2005.

H. Thorvaldsdóttir, J. T. Robinson, and J. P. Mesirov, Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration, Brief Bioinform, vol.14, issue.2, pp.178-92, 2013.

, The jQuery Foundation. JQuery, 2015.

, The Broad Institute. SamTools API. Available

. Highsoft and A. Highcharts, , 2015.

, Rice genomes datasets, 2015.

. Oracle and . Mysql, Platform as a Service. Available, 2015.

, South Green Bioinformatic Platform. Gigwa code repository, 2015.

G. Sempere, F. Philippe, A. Dereeper, M. Ruiz, G. Sarah et al., Supporting information for "Gigwa -Genotype Investigator for Genome Wide Analyses, GigaScience Database, 2016.

, Oryza Tag Line and GreenPhylDB. predicate "has_dbxref'. This greatly increases the number of outbound links, making AgroLD more integrated with other Linked Open Data. In the future, we will implement a "similarity-based approach" to identify correspondences between entities which have different URIs. To map the various data types and properties, we developed a lightweight schema, ? We accept pre-submission inquiries ? Our selector tool helps you to find the most relevant journal such as GOA, Gramene, and complementary information hosted by the local research community, for instance

, It is mapped to a more generic property, causally related to in the Relations Ontology [43]. For now, 55 mappings were identified. Furthermore, mappings are both stored side by side with ontologies in AgroPortal, which allows direct links between classes and instances of these classes in AgroLD. For example, the following link will show the external mappings for SO:0000104 (polypeptide) stored in Agro, p=classes&conceptid=http%3A%2F% 2Fpurl.obolibrary.org%2Fobo%2FSO_0000104&jump_to_nav=true#mappings. Additionally, classes, properties and resources

. User-interface, co), to enabling Quick Search retrieving more textual information and hiding the technical details. Further, we will improve the performance and expand the API suite to cover other entities represented in AgroLD

, Gene Expression Atlas [52], on gene regulatory networks such as RiceNetDB [53] and explore linking textAgroLD PLOS ONE, vol.51, p.17, 2018.

C. Goble and R. Stevens, State of the nation in data integration for bioinformatics, J Biomed Inform, vol.41, p.18358788, 2008.

L. Harper, J. Campbell, E. K. Cannon, S. Jung, D. Main et al., AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture, Database, pp.1-7, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-01964769

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat Genet, vol.25, p.10802651, 2000.

L. Cooper, R. L. Walls, J. Elser, M. A. Gandolfo, D. W. Stevenson et al., The plant ontology as a tool for comparative plant anatomy and genomic analyses, Plant Cell Physiol, vol.54, p.23220694, 2013.

R. Shrestha, L. Matteis, M. Skofic, A. Portugal, G. Mclaren et al., Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the, Crop Ontology AgroLD PLOS ONE, vol.14, p.17, 2018.

, Front Physiol, vol.3, p.22934074, 2012.

P. L. Buttigieg, N. Morrison, B. Smith, C. J. Mungall, S. E. Lewis et al., The environment ontology: contextualising biological and biomedical entities, J Biomed Semantics, vol.4, p.24330602, 2013.

R. L. Walls, J. Deck, R. Guralnick, S. Baskauf, R. Beaman et al., Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies, PLoS One, vol.9, p.24595056, 2014.

A. Oellrich, R. L. Walls, E. K. Cannon, S. B. Cannon, L. Cooper et al., An ontology approach to comparative phenomics in plants, Plant Methods, vol.11, issue.10, p.25774204, 2015.

Y. Wang, Y. Wang, J. Wang, Y. Yuan, and Z. Zhang, An ontology-based approach to integration of hilly citrus production knowledge, Comput Electron Agric, vol.113, pp.24-43, 2015.

C. Lousteau-cazalet, A. Barakat, J. Belaud, P. Buche, G. Busset et al., 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

C. Jonquet, A. Toulet, E. Arnaud, S. Aubin, D. Yeumo et al., 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

T. Berners-lee, J. Hendler, and O. Lassila, The Semantic Web. Sci Am, vol.284, pp.35-43, 2001.

, W3C. Resource Description Framework (RDF): Concepts and Abstract Syntax, 2010.

. W3c, OWL 2 Web Ontology Language Structural Specification and Functional-Style Syntax

W. The, . Sparql-working, and . Group, , p.15, 2013.

J. S. Luciano, B. Andersson, C. Batchelor, O. Bodenreider, T. Clark et al., 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.

A. Venkatesan, S. Tripathi, A. Sanz-de-galdeano, W. Blondé, A. Laegreid et al., Finding gene regulatory network candidates using the gene expression knowledge base, BMC Bioinformatics, vol.15, p.25490885, 2014.

R. N. Smith, J. Aleksic, D. Butano, A. Carr, S. Contrino et al., InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data, Bioinformatics, vol.28, p.23023984, 2012.

B. Smith, M. Ashburner, C. Rosse, J. Bard, W. Bug et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nat Biotechnol. Nature Publishing Group, vol.25, p.17989687, 2007.

N. F. Noy, N. H. Shah, P. L. Whetzel, B. Dai, M. Dorf et al., BioPortal: ontologies and integrated data resources at the click of a mouse, Nucleic Acids Res, vol.37, p.19483092, 2009.

F. Belleau, M. Nolin, N. Tourigny, P. Rigault, and J. Morissette, Bio2RDF: towards a mashup to build bioinformatics knowledge systems, J Biomed Inform, vol.41, p.18472304, 2008.

A. J. Williams, L. Harland, P. Groth, S. Pettifer, C. Chichester et al., Open PHACTS: Semantic interoperability for drug discovery. Drug Discovery Today, p.22683805, 2012.

A. Venkatesan, N. El-hassouni, P. F. Pommier, C. Quesneville, H. Ruiz et al., 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

S. Leonelli, R. P. Davey, E. Arnaud, G. Parry, and R. Bastow, Data management and best practice for plant science, vol.3, p.28585570, 2017.

L. Cooper, A. Meier, M. A. Laporte, J. L. Elser, C. Mungall et al., The Planteome database: An integrated resource for reference ontologies, plant genomics and phenomics, Nucleic Acids Res, 2018.

, , p.29186578

M. K. Monaco, J. Stein, S. Naithani, S. Wei, P. Dharmawardhana et al., Comparative plant genomics resources, Nucleic Acids Res, vol.42, p.24217918, 2013.

M. Magrane and U. P. Consortium, UniProt Knowledgebase: A hub of integrated protein data, Database, p.21447597, 2011.

D. Barrell, E. Dimmer, R. P. Huntley, D. Binns, C. O'donovan et al., The GOA database in 2009-An integrated Gene Ontology Annotation resource, Nucleic Acids Res, vol.37, p.18957448, 2009.

C. Hamelin, G. Sempere, V. Jouffe, and M. Ruiz, TropGeneDB, the multi-tropical crop information system updated and extended, Nucleic Acids Res, vol.41, p.23161680, 2013.

G. Droc, M. Ruiz, P. Larmande, A. Pereira, P. Piffanelli et al., OryGenesDB: a database for rice reverse genetics, Nucleic Acids Res, vol.34, p.16381969, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01218996

P. Larmande, C. Gay, M. Lorieux, C. Pé-rin, M. Bouniol et al., Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library, Nucleic Acids Res, vol.36, p.17947330, 2008.

M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, and C. Périn, GreenPhylDB: a database for plant comparative genomics, Nucleic Acids Res, vol.36, p.17986457, 2008.

A. Dereeper, F. Homa, G. Andres, G. Sempere, G. Sarah et al., 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

R. A. Gibbs, J. W. Belmont, P. Hardenbol, T. D. Willis, F. Yu et al., The International HapMap Project, Nature, vol.426, p.14685227, 2003.

P. Danecek, A. Auton, G. Abecasis, C. A. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, p.21653522, 2011.

N. Juty, L. Novère, N. Laibe, and C. , Identifiers.org and MIRIAM Registry: community resources to provide persistent identification, Nucleic Acids Res, vol.40, p.22140103, 2012.

B. Smith, W. Ceusters, B. Klagges, J. Kohler, A. Kumar et al.,

, Genome Biol, vol.6, p.15892874, 2005.

I. Cyganiak-r-(national-u-of and C. Bizer, Pubby-A Linked Data Frontend for SPARQL Endpoints, 2008.

P. Heim, S. Hellmann, J. Lehmann, S. Lohmann, and T. Stegemann, 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.

L. Rietvelda and R. Hoekstraa, The YASGUI Family of SPARQL Clients, Semant Web J, vol.0, pp.1-10, 2015.

K. Elbedweihy, S. N. Wrigley, F. Ciravegna, R. D. Bernstein, and A. , Evaluating semantic search systems to identify future directions of research. The Semantic Web: ESWC 2012 Satellite Events, pp.148-162, 2012.

J. Brooke, SUS-A quick and dirty usability scale, Usability Eval Ind. London, vol.189, pp.4-7, 1996.

M. D. Wilkinson, M. Dumontier, A. Ijj, G. Appleton, M. Axton et al., The FAIR Guiding Principles for scientific data management and stewardship, Sci Data, vol.3, p.26978244, 2016.

, AgroLD PLOS ONE, 2018.

A. Venkatesan, J. Kim, F. Talo, M. Ide-smith, J. Gobeill et al., 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.

. Ic4r-project-consortium, L. Hao, H. Zhang, Z. Zhang, S. Hu et al., Information Commons for Rice (IC4R), Nucleic Acids Res, vol.44, 2016.

R. Petryszak, M. Keays, Y. A. Tang, N. A. Fonseca, E. Barrera et al., Expression Atlas update-An integrated database of gene and protein expression in humans, animals and plants, Nucleic Acids Res, vol.44, p.26481351, 2016.

T. Lee, T. Oh, S. Yang, J. Shin, S. Hwang et al., RiceNet v2: An improved network prioritization server for rice genes, Nucleic Acids Res, vol.43, p.25813048, 2015.

P. Agrold and . One-|, , vol.17, p.17, 2018.