BMIR RESEARCH IN PROGRESS – “Challenges for ontology repositories: reusing NCBO technology for other languages (French) and other domains (Agronomy)”

April 21, 2016 @ 12:00 pm – 1:00 pm
MSOB Conference Room X-275
1265 Welch Rd
Stanford, CA 94305
Marta Vitale-Soto
BMIR RESEARCH IN PROGRESS - “Challenges for ontology repositories: reusing NCBO technology for other languages (French) and other domains (Agronomy)” @ MSOB Conference Room X-275 | Stanford | California | United States

Presenter: Clement Jonquet, PhD
Assistant Professor
University of Montpellier

About the Event:


A key aspect to address data integration and semantic interoperability is the use of terminologies and ontologies. Ontology repositories, have been developed to facilitate the identification, reuse and valorization of ontologies. The NCBO BioPortal, for instance, allows anyone to locate, select, browse, search, comment and use for annotation, any of the +500 biomedical ontologies available within the portal. It also stores (and generates some) mappings between these ontologies and indexes relevant biomedical resources. The success of the NCBO BioPortal motivates other domains to actually provide such a resource to their communities (e.g., agronomy, environmental sciences, etc.) and the question of reusing available technology obviously raises first to avoid redeveloping software and tools that have been designed and extensively used and second, to facilitate interoperability between the domains. In this talk, I will review our work achieved within the Semantic Indexing of French Biomedical Data Resources ( and AgroPortal ( projects in which we (i) build ontology-based services to index, mine and retrieve French biomedical data; (ii) develop and support a reference ontology repository for the agronomic domain. In both cases, we are reusing the NCBO technology and identifying new use cases and challenges in managing ontologies and ontology-based services. I will present our platforms, the genericity/specificity of our approach and try to discuss a vision of mutual cooperative efforts that can benefit any users interested in ontologies, in any languages and in any domain.
Clement Jonquet, Esther Dzalé-Yeumo, Elizabeth Arnaud & Pierre Larmande. AgroPortal : a proposition for ontology-based services in the agronomic domain, In 3ème atelier INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement, IN-OVIVE’15. Rennes, France, June 2015. pp. 5.
Clement Jonquet, Vincent Emonet & Mark A. Musen. Roadmap for a multilingual BioPortal, In 4th Workshop on the Multilingual Semantic Web, MSW4’15. Portoroz, Slovenia, June 2015. pp. 12.
Amina Annane, Vincent Emonet, Faical Azouaou & Clement Jonquet. Multilingual Mapping Reconciliation between English-French Biomedical Ontologies, In 6th International Conference on Web Intelligence, Mining and Semantics, WIMS’16. Nimes, France, June 2016. ACM.
Clement Jonquet, Amina Annane, Khedidja Bouarech, Vincent Emonet & Soumia Melzi. SIFR BioPortal : Un portail ouvert et générique d’ontologies et de terminologies biomédicales françaises au service de l’annotation sémantique, In 16th Journées Francophones d’Informatique Médicale, JFIM’16. Genève, Suisse, July 2016.