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    The persistent URL for this web page is: http://www.lirmm.fr/~jonquet 

    Who am I?

    Since Sept. 2020, I am associate research scientist at INRAE (French National Research Institute for Agriculture, Food and Environment) in the MISTEA (Mathematics, Informatics and STatistics for Environment and Agronomy) research unit.


    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, GO FAIR Food System IN). Since 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 also associate professor (HDR) at University of Montpellier, France since September 2010 and an associated member of the Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM). My research topics include ontologies, ontology repositories, ontology metadata, semantic data indexing and annotation, semantic Web, text mining, knowledge representation.


    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).

    From 2018 to 2020, I was visiting scholar at Inria Wimmics in Dr. Fabien Gandon's group.

    From 2015 to 2018, I was a visiting scholar (H2020 Marie-Skłodowska Curie fellow) at the Stanford Center for Biomedical Informatics Research (BMIR) within Pr. Mark A. Musen's group.


    From 2007 to 2010, I also served I served as a postdoc in the same lab, 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.

    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.


    I am the (co)author of 119 publications or communications cumulating more than 2800 citations, including 24 international journals in multiple domains (biomedical informatics, semantic Web, distributed systems & AI), 6 as first author, 3 as last, and 60 conference or workshop articles.


    Since 2012, I co-supervised 13+ MSc. Students & 3 PhD students (J-A Lossio, G. Surroca, A. Annane), 6 postdocs, 3 research engineers.


    I have 9 years of various academic teaching (~1400h ~TD) to different kind of students of mixed levels. At Polytech, I have taught programming, computer architecture, web applications, semantic web to engineer students.


    I teach Informatics at the Polytech Montpellier Engineering School. In 2012, I uploaded a course called "Internet Application and Interoperability (AIOP)" on iTunesU.


    I am also interested in the use of ICT in Education and especially the use of iPads within the classroom. I was the representative for Polytech Montpellier Information and Communication Technologies in Education (TICE). I co-chair the “return of experience” track of TICE 2014.

    and more...


    I am working in the semantic Web area, designing, implementing, experimenting and evaluating scientific methods and technologies for ontologies and their use. I am interested in knowledge engineering and data interoperability issues, especially in the use of ontologies (or semantic resources) for knowledge representation, extraction and sharing. I am an expert on ontology repositories and ontology-based services (topic of my HDR) and I develop and maintain a scientific and technical expertise on this subject especially through a partnership with Stanford BMIR and the development of the OntoPortal technology with the vision to promote data interoperability and FAIR ontologies. This fairly applicative context allows me to practice science on several sub-fields of knowledge engineering: semantic annotation, terminology extraction, linked-open data, text and data mining, ontology alignment, metadata languages, knowledge graphs. I have experience in the biomedical domain (NCBO & SIFR projects) –for instance on semantic annotation and indexing of biomedical text or clinical notes– and my challenge is to abstract and generalize informatics methods to other languages (e.g., French) and domains (e.g., agronomy, biodiversity). Today, I lead the D2KAB project, a 12-partern and 35-person ANR research action which focus on implementing methods to transform data into knowledge for agronomy and biodiversity and in which we design a vocabulary and ontology repository for agronomy and related domains (AgroPortal project).

    OntoPortal Alliance

    French section of the GO FAIR Food Systems Implementation Network

    Data to Knowledge in Agronomy and Biodiversity

    Visa Text Mining

    Vocabulary and ontology repository for agriculture, plant sciences, nutrition and biodiversity

    Practice-based evidences for actioning Knowledge in Pharmacogenomics project

    Semantic Indexing of French Biomedical Data Resources project

    National Center for Biomedical Ontology


    Access my consolidated and complete list on on HAL, the French publication archive... or others Web profiles.


    English version of my current CV (34 pages) as of September 2020. Also available in HTML.


  • MISTEA – INRAE Montpellier
    2, place Pierre Viala
    34060 Montpellier Cedex 2
    MONDAY-THURSDAY: I am located in building 29 (Office 101, level 1)
    161 rue Ada
    34095 Montpellier Cedex 5
    FRIDAY: I am located in building 5 (Office 3.159 (level 3, East wing))
    +33/0 4 67 14 97 43

    Scientific council PhD program

    Support for SIFR and other infrastructure.

    PICS program

    IRL program

    Support for SIFR.

    JCJC, Generic, MRSEI programs

    Support for SIFR, PractiKPharma, eRosa, D2KAB and FooSIN

    MSCA program

    Support for SIFR

    PIA program

    Support for AgroPortal, AgroHackathons and OntoPortal Alliance.

    PIA program

    Support for AgroPortal.

    BSN-10 Program

    Support for VisaTM.

    H2020 OpenMinTed call for tender 2018

    Support for VisaTM.

    Labex Agro

    Support for AgroPortal.

    #DigitAg Convergence Institute

    Support for D2KAB and AgroHackathons.


    Links to archivesd web pages that describe previous projects or topics.