AIMS

RDA/IGAD Webinar Series: ‘AgroPortal: a vocabulary and ontology repository for agronomy’

As part of The Research Data Alliance (RDA) Interest Group on Agricultural Data (IGAD) meeting focusing on IGAD/RDA : Sharing Experiences and Creating Digital Dialogues, Clement Jonquet, LIRMM, University of Montpellier presented a webinar during the ‘Semantics’ group of presentations on May 26. 

The webinar focused on ‘AgroPortal: a vocabulary and ontology repository for agronomy.’ The AgroPortal project, is a community effort started by the Montpellier scientific community (LIRMM, IRD, CIRAD, INRAE, Bioversity International) to build an ontology repository for agronomy and related domains. Our goal is to facilitate the adoption of metadata and semantics to facilitate open science and the production of FAIR data. By enabling straightforward use of ontologies, we expect data managers and researchers to focus on their tasks, without requiring them to deal with the complex engineering work needed for ontology management. 

The Research Data Alliance (RDA) Interest Group on Agricultural Data (IGAD) meeting was set to be held in Rome (Italy) in April 2020 but instead, took place as a virtual meeting from May 25 to 28.  The virtual meeting provided an online platform to continue to build upon collaborations, knowledge sharing and developing innovations with activities including panel sessions, group discussions and presentations.

Authors:

  • Clement Jonquet

    I am associate professor (HDR) at University of Montpellier, France since September 2010. I am a member of the Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM) and do research on ontologies, ontology repositories, ontology metadata, semantic data indexing and annotation, semantic Web, text mining, knowledge representation.

    From 2015 to 2018, I was a visiting scholar (under a H2020 Marie-Skłodowska Curie fellowship) at the Stanford Center for Biomedical Informatics Research (BMIR) within Pr. Mark A. Musen's group. I am currently visiting scholar at Inria Wimmics in Dr. Fabien Gandon's group.

    I obtained a BSc, MSc, and PhD in Informatics from University of Montpellier in Nov. 2006 working on multi-agent systems, grid and service-oriented computing in the context of the European FP6-IST ELeGI project. Then I served as a postdoc for 3 years (2007-2010) at the Stanford Center for BioMedical Informatics Research (Stanford BMIR) within Pr. Mark A. Musen’s group where I was working closely with Pr. Nigam H. Shah, on semantic annotations of biomedical data using biomedical ontologies in the context of the National Center for Biomedical Ontology (NCBO) project. I contributed actively to the design, evolution and development of the NCBO BioPortal, an ontology repository widely used in the biomedical community.

    From 2013 to 2019, I was the principal investigator of the SIFR project (Semantic Indexing of French Biomedical Data Resources) interested in designing ontology-based services first for French biomedicine but also in agronomy. The project was mainly funded by the French ANR Young Researcher –JCJC– program and the H2020 Marie Sklodowska-Curie program. I was also the co-PI of ANR PractiKPharma project (Practice-based evidences for actioning Knowledge in Pharmacogenomics) working on semantic annotation of French clinical notes with terminologies and ontologies to encode pharmacogenomics relations (disease-gene profile-adverse effect).

    Since 2015, I lead the AgroPortal project, a repository of ontologies and vocabularies for agri-food ; this project gathers several national research institutions (INRAE, CIRAD, IRD) but also involve important international organizations (FAO, CGIAR, H2020 eRosa, RDA AgriSemantics). From June 2019 I am the principal investigator of ANR project D2KAB (Data to Knowledge in Agronomy and Biodiversity). D2KAB is a 4-year, 12 partners, 35 people, 950K€ (without salaries) multidisciplinary project which objective is to create a framework to turn agronomy and biodiversity data into knowledge –semantically described, interoperable, actionable, open– and investigate scientific methods and tools to exploit this knowledge for applications in science & agriculture.

    I am the (co)author of 88 publications (+27 posters-demos) cumulating more than 2650 citations, including 23 international journals in multiple domains (biomedical informatics, semantic web, distributed systems & AI), 6 as first author, 3 as last.

    Since 2012, I co-supervised 3 PhD students (J-A Lossio, G. Surroca, A. Annane), 6 postdocs, 3 research engineers and 12 MSc students.