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

    Who am I?

    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.


    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 interested in the convergence of French and English medical informatics ontology-based methods and tools in collaboration with Stanford BMIR. Especially in the use of ontologies and terminologies for knowledge extraction from text data e.g., French biomedical data or clinical notes. I develop and maintain an expertise on the BioPortal technology originally developed at Stanford with the vision to standardize ontology repositories and ontology-based services and promote data interoperability and FAIR ontologies. I am also interested in generalizing my work on semantic indexing and data annotation to other domain such as agronomy or biodiversity. I investigate new methods and knowledge engineering approaches in the context of designing a vocabulary and ontology repository for agronomy and related domains (AgroPortal project) as well as a semantic annotation workflow for French biomedical text data (SIFR project) used on real clinical data (PractiKPharma project). I lead the D2KAB project which focus on implementing methods to transform data into knowledge for agronomy and biodiversity. I am also interested in using ontologies for linked open data, knowledge graphs, automatic terminology extraction, text mining and natural language processing, ontology alignment, semantic similarity and graph-based approach for knowledge representation and collaborative learning. The Semantic Web in general.

    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 automatically populated Web profiles.


    English version of my current CV (33 pages) as of February 2020. Also available in HTML.



    161 rue Ada
    34095 Montpellier Cdx 5
    I am located in building 5 (Office 3.159 (level 3, East wing))
    +33/0 4 67 14 97 43

    Scientific council PhD program

    PICS program

    IRL program

    MSCA program

    PIA program

    PIA program

    BSN-10 Program

    H2020 OpenMinTed call for tender 2018

    #DigitAg Convergence Institute


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