C. Goble and R. Stevens, State of the nation in data integration for bioinformatics, Journal of Biomedical Informatics, vol.41, issue.5, pp.687-693, 2008.
DOI : 10.1016/j.jbi.2008.01.008

D. L. Rubin, N. H. Shah, and N. F. Noy, Biomedical ontologies: a functional perspective, Briefings in Bioinformatics, vol.9, issue.1, pp.75-90, 2008.
DOI : 10.1093/bib/bbm059
URL : https://academic.oup.com/bib/article-pdf/9/1/75/827967/bbm059.pdf

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000.
DOI : 10.1091/mbc.9.12.3273

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 and Cell Physiology, vol.296, issue.1, p.1, 2012.
DOI : 10.1126/science.1068037

R. Shrestha, E. Arnaud, R. Mauleon, M. Senger, G. F. Davenport et al., Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature, AoB Plants, vol.116, issue.4, 2010.
DOI : 10.1104/pp.108.119560

P. L. Buttigieg, N. Morrison, . Smith, C. J. Mungall, and S. E. Lewis, The environment ontology: contextualising biological and biomedical entities, Journal of Biomedical Semantics, vol.4, issue.1, p.43, 2013.
DOI : 10.1093/bioinformatics/btm112
URL : https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/2041-1480-4-43?site=jbiomedsem.biomedcentral.com

M. Devare, C. Aubert, M. Laporte, L. Valette, E. Arnaud et al., Datadriven agricultural research for development -a need for data harmonization via semantics, 7th International Conference on Biomedical Ontologies, ICBO'16 of CEUR Workshop Proceedings, 2016.

E. Garnier, U. Stahl, M. Laporte, J. Kattge, I. Mougenot et al., Towards a thesaurus of plant characteristics: an ecological contribution, Journal of Ecology, vol.9, issue.2, pp.298-309
DOI : 10.1371/journal.pone.0089606

E. Griffiths, F. Brinkman, P. L. Buttigieg, D. Dooley, W. Hsiao et al., FoodON: a global farm-to-fork food ontology -the development of a universal food vocabulary, 7th International Conference on Biomedical Ontologies, ICBO'16 of CEUR Workshop Proceedings, 2016.

R. Musker, M. Lange, A. Hollander, P. Huber, N. Springer et al., Towards designing an ontology encompassing the environmentagriculture-food-diet-health knowledge spectrum for food system sustainability and resilience, 7th International Conference on Biomedical Ontologies, ICBO'16 of CEUR Workshop Proceedings, p.5, 2016.

L. M. Hughes, J. Bao, Z. Hu, V. Honavar, and J. M. Reecy, Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species, Journal of Animal Science, vol.86, issue.6, pp.1485-1491, 2014.
DOI : 10.2527/jas.2008-0930

X. Meng, Special Issue ??? Agriculture Ontology, Journal of Integrative Agriculture, vol.11, issue.5, 2012.
DOI : 10.1016/S2095-3119(12)60057-4

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.23, issue.1, 2014.
DOI : 10.1371/journal.pone.0089606.s001

Y. Wang, Y. Wang, J. Wang, Y. Yuan, and Z. Zhang, An ontology-based approach to integration of hilly citrus production knowledge, Computers and Electronics in Agriculture, vol.113, pp.24-43, 2015.
DOI : 10.1016/j.compag.2015.01.009

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, Computers and Electronics in Agriculture, vol.127, pp.351-367, 2016.
DOI : 10.1016/j.compag.2016.06.020
URL : https://hal.archives-ouvertes.fr/lirmm-01346685

R. J. Lehmanna, R. Reichea, and G. Schiefera, Future internet and the agri-food sector: State-of-the-art in literature and research, Computers and Electronics in Agriculture, vol.89, pp.158-174, 2012.
DOI : 10.1016/j.compag.2012.09.005

P. Jaiswal, Plant Reverse Genetics: Methods and Protocols, ch. Gramene Database: A Hub for Comparative Plant Genomics, pp.247-275, 2011.

J. K. Sachit-rajbhandari, The AGROVOC Concept Scheme ??? A Walkthrough, Journal of Integrative Agriculture, vol.11, issue.5, pp.694-699, 2012.
DOI : 10.1016/S2095-3119(12)60058-6

M. Aquin and N. F. Noy, Where to publish and find ontologies? a survey of ontology libraries, Web Semantics, vol.11, pp.96-111, 2012.

O. Bodenreider, The Unified Medical Language System (UMLS): integrating biomedical terminology, Nucleic Acids Research, vol.32, issue.90001, pp.267-270, 2004.
DOI : 10.1093/nar/gkh061
URL : https://academic.oup.com/nar/article-pdf/32/suppl_1/D267/7621558/gkh061.pdf

B. Smith, M. Ashburner, C. Rosse, J. Bard, W. Bug et al., The OBO foundry: coordinated evolution of ontologies to support biomedical data integrationNat, Biotechnol, vol.25, pp.1251-1255, 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 Research, vol.36, issue.suppl_2, pp.170-173, 2009.
DOI : 10.1093/nar/gkn317
URL : https://hal.archives-ouvertes.fr/hal-00492020

P. L. Whetzel, N. F. Noy, N. H. Shah, P. R. Alexander, C. Nyulas et al., BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications, Nucleic Acids Research, vol.140, issue.1, pp.541-545, 2011.
DOI : 10.1104/pp.105.063008

P. L. Whetzel and N. Team, NCBO Technology: Powering semantically aware applications, Journal of Biomedical Semantics, vol.4, issue.Suppl 1, pp.4-5, 2013.
DOI : 10.1186/2041-1480-4-S1-S8
URL : https://doi.org/10.1186/2041-1480-4-s1-s8

Y. Ding and D. Fensel, Ontology library systems: the key to successful ontology re-use, 1st Semantic Web Working Symposium, SWWS'01, pp.93-112, 2001.

K. Baclawski, T. Schneider, T. Tudorache, G. Correndo, N. Noy et al., The open ontology repository initiative: Requirements and research challenges, Workshop on Collaborative Construction, Management and Linking of Structured Knowledge, CK'09 of CEUR Workshop Proceedings, p.10, 2009.

S. Sansone, P. Rocca-serra, D. Field, E. Maguire, C. Taylor et al., Toward interoperable bioscience data, Nature Genetics, vol.27, issue.2, pp.121-126, 2012.
DOI : 10.1038/nbt1109-984a
URL : https://hal.archives-ouvertes.fr/hal-00695792

V. Pesce, G. Geser, V. Protonotarios, C. Caracciolo, and J. Keizer, Towards linked agricultural metadata: directions of the agINFRA project, 7th Metadata and Semantics Research Conference, AgroSem track, p.12, 2013.

Z. Xiang, C. Mungall, A. Ruttenberg, and Y. He, Ontobee: a linked data server and browser for ontology terms, 2nd International Conference on Biomedical Ontology CEUR Workshop Proceedings, p.3, 2011.

R. G. Côté, P. Jones, R. Apweiler, and H. Hermjakob, The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries, 2006.

R. Hoehndorf, L. Slater, P. N. Schofield, and G. V. Gkoutos, Aber-OWL: a framework for ontology-based data access in biology, BMC Bioinformatics, vol.25, issue.1-2, pp.1-9, 2015.
DOI : 10.1007/s00335-013-9481-z

P. Vandenbussche, G. A. Atemezing, M. Poveda-villalón, and B. Vatant, Linked Open Vocabularies (LOV): A gateway to reusable semantic vocabularies on the Web, Semantic Web, vol.39, issue.Suppl, 2014.
DOI : 10.1093/nar/gkr469

M. Till, O. Kutz, and M. Codescu, Ontohub: A semantic repository for heterogeneous ontologies, In: Theory Day in Computer Science, 2014.

J. Graybeal, A. W. Isenor, and C. Rueda, Semantic mediation of vocabularies for ocean observing systems, Computers & Geosciences, vol.40, pp.120-131, 2012.
DOI : 10.1016/j.cageo.2011.08.002

E. Ong, Z. Xiang, B. Zhao, Y. Liu, Y. Lin et al., Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration, Nucleic Acids Research, vol.4, issue.D1, pp.347-352, 2016.
DOI : 10.1016/j.websem.2011.06.005
URL : https://academic.oup.com/nar/article-pdf/45/D1/D347/8847158/gkw918.pdf

C. Jonquet, N. H. Shah, and M. A. Musen, The open biomedical annotator, American Medical Informatics Association Symposium on Translational BioInformatics, AMIA-TBI'09, pp.56-60, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00492024

C. Jonquet, P. Lependu, S. Falconer, A. Coulet, N. F. Noy et al., NCBO Resource Index: Ontology-based search and mining of biomedical resources, 1st Prize of Semantic Web Challenge at the 9th International Semantic Web Conference, ISWC'10, pp.316-324, 2011.
DOI : 10.1016/j.websem.2011.06.005
URL : https://hal.archives-ouvertes.fr/hal-00557982

M. Salvadores, P. R. Alexander, M. A. Musen, and N. F. Noy, BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF, Semantic Web, vol.4, issue.3, pp.277-284, 2013.

C. Rueda, L. Bermudez, and J. Fredericks, The MMI ontology registry and repository: a portal for marine metadata interoperability In: MTS/IEEE Biloxi -Marine Technology for Our Future: Global and Local Challenges, OCEANS'09, p.6, 2009.

D. A. Pouchard, L. Huhns, and M. , Lessons learned in deploying a cloud-based knowledge platform for the ESIP Federation. In: American Geo-physical Union Fall Meeting, poster session, 2012.

C. Jonquet, A. Annane, K. Bouarech, V. Emonet, and S. Melzi, SIFR BioPortal: Un portail ouvert et générique d'ontologies et de terminologies biomédicales françaises au service de l'annotation sémantique, 16th Journées Francophones d'Informatique Médicale, JFIM'16, p.16, 2016.

C. Jonquet, V. Emonet, and M. A. Musen, Roadmap for a multilingual BioPortal, 4th Workshop on the Multilingual Semantic Web, MSW4'15 CEUR Workshop Proceedings, Portoroz, Slovenia, pp.15-26, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01172218

L. Matteis, P. Chibon, H. Espinosa, M. Skofic, R. Finkers et al., Crop ontology: vocabulary for crop-related concepts, 1st International Workshop on Semantics for Biodiversity CEUR Workshop Proceedings, pp.37-46, 2015.

N. F. Noy, T. Tudorache, C. Nyulas, and M. A. Musen, The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies, AMIA Annual Symposium, pp.552-556, 2010.

P. Jaiswal, L. Cooper, J. L. Elser, A. Meier, M. Laporte et al., Planteome: A resource for Common Reference Ontologies and Applications for Plant Biology, 24th Plant and Animal Genome Conference, PAG'16, 2016.

S. Carbon, A. Ireland, C. J. Mungall, S. Shu, B. Marshall et al., AmiGO: online access to ontology and annotation data, Bioinformatics, vol.25, issue.2, pp.288-289, 2009.
DOI : 10.1038/75556
URL : https://academic.oup.com/bioinformatics/article-pdf/25/2/288/16889779/btn615.pdf

M. Schmachtenberg, C. Bizer, H. Paulheim, P. Mika, T. Tudorache et al., Adoption of the Linked Data Best Practices in Different Topical Domains, 13th International Semantic Web Conference, ISWC'14, pp.245-260, 2014.
DOI : 10.1007/978-3-319-11964-9_16

F. Belleau, M. Nolin, N. Tourigny, P. Rigault, and J. Morissette, Bio2RDF: Towards a mashup to build bioinformatics knowledge systems, Journal of Biomedical Informatics, vol.41, issue.5, pp.706-716, 2008.
DOI : 10.1016/j.jbi.2008.03.004
URL : https://doi.org/10.1016/j.jbi.2008.03.004

S. Jupp, J. Malone, J. Bolleman, M. Brandizi, M. Davies et al., The EBI RDF platform: linked open data for the life sciences, Bioinformatics, vol.37, issue.8, pp.1338-1339, 2014.
DOI : 10.1093/bioinformatics/btq099

P. Groth, A. Loizou, A. J. Gray, C. Goble, L. Harland et al., API-centric Linked Data integration: The Open PHACTS Discovery Platform case study, Web Semantics: Science, Services and Agents on the World Wide Web, vol.29, pp.12-18, 2014.
DOI : 10.1016/j.websem.2014.03.003
URL : http://www.websemanticsjournal.org/index.php/ps/article/viewFile/359/380/

A. Venkatesan, N. E. Hassouni, F. Philippe, C. Pommier, H. Quesneville et al., Exposing French agronomic resources as linked open data, 8th Semantic Web Applications and Tools for Life Sciences International Conference, SWAT4LS'15 CEUR Workshop Proceedings, pp.205-207, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01274884

K. Hassani-pak, M. Zorc, J. Taubert, and C. Rawlings, QTLNetMiner -candidate gene discovery in plant and animal knowledge networks, 21st Plant & Animal Genome Conference, poster session, p.980, 2013.

E. Dzalé-yeumo, Developing data interoperability using standards: A wheat community use case, F1000 Research, pp.6-1843, 2017.

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 developed by the crop communities of practice, Frontiers in Physiology, vol.3, 2012.
DOI : 10.3389/fphys.2012.00326

R. Coletta, E. Castanier, P. Valduriez, C. Frisch, D. Ngo et al., Public data integration with WebSmatch, Proceedings of the First International Workshop on Open Data, WOD '12, pp.5-12, 2012.
DOI : 10.1145/2422604.2422606
URL : https://hal.archives-ouvertes.fr/lirmm-00750927

N. F. Noy, P. R. Alexander, R. Harpaz, P. L. Whetzel, R. W. Fergerson et al., Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking, 12th International Semantic Web Conference, ISWC'13, pp.444-459, 2013.
DOI : 10.1007/978-3-642-41335-3_28

A. Ghazvinian, N. F. Noy, C. Jonquet, N. H. Shah, and M. A. Musen, What Four Million Mappings Can Tell You about Two Hundred Ontologies, 8th International Semantic Web Conference, ISWC'09, pp.229-242, 2009.
DOI : 10.1007/978-3-642-04930-9_15
URL : https://hal.archives-ouvertes.fr/hal-00489094

D. Faria, E. Jiménez-ruiz, C. Pesquita, E. Santos, and F. M. Couto, Towards Annotating Potential Incoherences in BioPortal Mappings, 13th International Semantic Web Conference, ISWC'13, pp.17-32, 2014.
DOI : 10.1007/978-3-319-11915-1_2
URL : http://www.cs.ox.ac.uk/files/6655/paper_ISWC_BioPortal.pdf

J. Pathak and C. G. Chute, Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal Mapping Repository, International Conference on Biomedical Ontology, pp.95-98, 2009.
DOI : 10.1038/npre.2009.3456
URL : https://doi.org/10.1038/npre.2009.3456

A. Ghazvinian, N. F. Noy, and M. A. Musen, Creating mappings for ontologies in biomedicine: simple methods work, American Medical Informatics Association Annual Symposium, AMIA'09, pp.198-202, 2009.

N. F. Noy, M. Dorf, N. B. Griffith, C. Nyulas, and M. A. Musen, Harnessing the power of the community in a library of biomedical ontologies, Workshop on Semantic Web Applications in Scientific Discourse, SWASD'09 CEUR Workshop Proceedings, 2009.

N. F. Noy, N. B. Griffith, and M. A. Musen, Collecting Community-Based Mappings in an Ontology Repository, 7th International Semantic Web Conference, ISWC'08, pp.368-371, 2008.
DOI : 10.1007/11762256_6
URL : http://bmir.stanford.edu/file_asset/index.php/1375/BMIR-2008-1343.pdf

A. T. Mccray, An Upper-Level Ontology for the Biomedical Domain, Comparative and Functional Genomics, vol.28, issue.1, pp.80-84, 2003.
DOI : 10.1002/cfg.255

M. Dai, N. H. Shah, W. Xuan, M. A. Musen, S. J. Watson et al., An efficient solution for mapping free text to ontology terms, AMIA Symposium on Translational BioInformatics, AMIA-TBI'08, 2008.

M. Martinez-romero, C. Jonquet, M. J. O-'connor, J. Graybeal, A. Pazos et al., NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation, Journal of Biomedical Semantics, vol.3, issue.PART 1, 2017.
DOI : 10.1007/978-3-540-92673-3_25
URL : https://hal.archives-ouvertes.fr/lirmm-01598848

C. Jonquet, M. A. Musen, and N. H. Shah, Building a biomedical ontology recommender web service, biomedical semantics, 2010.
DOI : 10.1186/2041-1480-1-s1-s1
URL : https://doi.org/10.1186/2041-1480-1-s1-s1

M. Salvadores, M. Horridge, P. R. Alexander, R. W. Fergerson, M. A. Musen et al., Using SPARQL to Query BioPortal Ontologies and Metadata, 11th International Semantic Web Conference, ISWC'12, pp.180-195, 2012.
DOI : 10.1007/978-3-642-35173-0_12

E. Maguire, A. González-beltrán, P. L. Whetzel, S. Sansone, and P. Rocca-serra, OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets, Bioinformatics, vol.5, issue.14, pp.525-527, 2013.
DOI : 10.1186/1471-2105-5-80
URL : https://academic.oup.com/bioinformatics/article-pdf/29/4/525/504231/bts718.pdf

S. Jupp, D. Welter, T. Burdett, H. Parkinson, and J. Malone, Collaborative ontology development using the webulous architecture and google app, 8th International Conference on Semantic Web Applications and Tools for Life Sciences, SWAT4LS'15, pp.120-121, 2015.

K. Wolstencroft, M. Horridge, S. Owen, W. Mueller, F. Bacall et al., Rightfield: embedding ontology term selection into spreadsheets for the annotation of biological data, 9th International Semantic Web Conference, Posters & Demonstrations, ISWC'10 of CEUR Workshop Proceedings, pp.141-144, 2010.

C. Roeder, C. Jonquet, N. H. Shah, W. A. Jr, and L. Hunter, A UIMA wrapper for the NCBO annotator, Bioinformatics, vol.25, issue.15, pp.1800-1801, 2010.
DOI : 10.1093/bioinformatics/btp289
URL : https://hal.archives-ouvertes.fr/hal-00504107

T. Adamusiak, T. Burdett, K. J. Van-der-velde, N. Abeygunawardena, D. Antonakaki et al., OntoCAT ??? a simpler way to access ontology resources, ISMB Conference, Poster session, 2010.
DOI : 10.1038/npre.2010.4666
URL : https://doi.org/10.1038/npre.2010.4666

J. A. Miñarro-giménez, J. T. Mikel, F. Aranguren, E. Antezana, and E. , NCBO-galaxy: bridging the BioPortal web services and the Galaxy platform, 3rd International Conference on Biomedical Ontologies, ICBO'12 of CEUR Workshop Proceedings, 2012.

S. M. Falconer, C. Callendar, and M. Storey, FLEXVIZ: visualizing biomedical ontologies on the web, International Conference on Biomedical Ontology, ICBO'09, 2009.

L. Slater, G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, Using AberOWL for fast and scalable reasoning over BioPortal ontologies, Journal of Biomedical Semantics, vol.4, issue.1, p.49, 2016.
DOI : 10.1186/2041-1480-4-44
URL : https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-016-0090-0?site=jbiomedsem.biomedcentral.com

S. Melzi, C. Jonquet, A. Paschke, A. Burger, P. Romano et al., Scoring semantic annotations returned by the NCBO Annotator, 7th International Semantic Web Applications and Tools for Life Sciences, SWAT4LS'14 CEUR Workshop Proceedings, p.15, 2014.
URL : https://hal.archives-ouvertes.fr/lirmm-01099860

J. Park, S. Oh, and J. Ahn, Ontology selection ranking model for knowledge reuse, Expert Systems with Applications, vol.38, issue.5, pp.5133-5144, 2011.
DOI : 10.1016/j.eswa.2010.10.002

A. Toulet, V. Emonet, and C. Jonquet, Modèle de métadonnées dans un portail d'ontologies, 6èmes Journées Francophones sur les Ontologies, JFO'16, 2016.

D. Ngo, Z. Bellahsene, A. Teije, J. Völker, S. Handschuh et al., YAM++ : A Multi-strategy Based Approach for Ontology Matching Task, 18th International Conference on Knowledge Engineering and Knowledge Management,EKAW'12, pp.421-425, 2012.
DOI : 10.1007/978-3-642-33876-2_38
URL : https://hal.archives-ouvertes.fr/lirmm-00720639

V. Pesce, A. Maru, and J. Keizer, The CIARD RING, an infrastructure for interoperability of agricultural research information services, Agric. Inf. Worldwide, vol.4, issue.1, pp.48-53, 2011.

T. Baker, C. Caracciolo, and E. Arnaud, Global agricultural concept scheme (GACS)a hub for agricultural vocabularies, 7th International Conference on Biomedical Ontologies, ICBO'16, Poster Session CEUR Workshop Proceedings, 2016.
DOI : 10.1007/978-3-319-49157-8_27
URL : http://eprints.rclis.org/30221/1/GACS-Baker-34-MTSR2016%20%28002%29.pdf

D. L. Mcguinness, Spinning the Semantic Web: Bringing the World Wide Web to its Full Potential, ch. Ontologies Come of Age, pp.171-194, 2003.

C. Jonquet, AgroPortal: A vocabulary and ontology repository for agronomy, Computers and Electronics in Agriculture, vol.144, pp.126-143, 2018.
DOI : 10.1016/j.compag.2017.10.012
URL : https://hal.archives-ouvertes.fr/lirmm-01679502