• Check my ORCID profile:


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

    Who am I?

    Since Jan. 2022, I am senior researcher (directeur de recherche) at INRAE (French National Research Institute for Agriculture, Food and Environment) in the MISTEA (Mathematics, Informatics and STatistics for Environment and Agronomy) research unit. I was previously associate researcher at INRAE since Sept. 2020 and before (2010-2020) Assistant then Associate Professor (HDR) at University of Montpellier, France. I am still 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, knowledge graphs.


    I lead the AgroPortal project, a repository of ontologies and vocabularies for agri-food ; this project, started in 2015, gathers several national research institutions (INRAE, CIRAD, IRD) but also involve important international organizations (FAO, CGIAR, HEU projects, RDA AgriSemantics, GO FAIR Food System IN). I also collaborate on ontology repositories with Stanford, LifeWatch and others in the context of the OntoPortal Alliance.


    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 now involved in two other ANR projects: FooSIN and DACE-DL.


    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 125 publications or communications cumulating more than 3500 citations, including 26 international journals in multiple domains (biomedical informatics, semantic Web, distributed systems & AI), 6 as first author, 4 as last, and 63 conference or workshop articles.


    Since 2012, I co-supervised 15+ MSc. Students & 4 PhD students (J-A Lossio, G. Surroca, A. Annane, B. Darnala), 6 postdocs, 4 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 aught Informatics at the Polytech Montpellier Engineering School. In 2012, I uploaded a course called "Internet Application and Interoperability (AIOP)" on iTunesU.


    I was 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).

    Expanding FAIR Solutions across EOSC


    Information System to explore the agronomic and oenological potential of vine genotypes


    DAta-CEntric AI-driven Data Linking

    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

    European Learning Grid Infrastructure

    Learning Grid of Excellence Working Group


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


    English version of my current CV (39 pages) as of July 2022. Also available in HTML.


  • MISTEA – INRAE Montpellier
    2, place Pierre Viala
    34060 Montpellier Cedex 2
    MONDAY-THURSDAY: I am located in building 21 (Office 412, level 4)
    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

    OntoCommons Workshop

    OntoPortal technology and partnership for co-developing ontology repositories

    Online, Nov. 3rd, 2021

    Tutorial @SemTech 2021

    How to use ontology repositories and ontology-based services

    Online, Feb. 24th, 2021

    Presentation @RDA-IGAD

    AgroPortal: a vocabulary and ontology repository for agronomy

    Online, May 26, 2020

    Keynote @IB2019

    Agricultural semantics interoperability and ontology-based annotations with AgroPortal

    Paris, Sep. 20th, 2019

    HDR defense jury

    Ontology Repository and Ontology-Based Services – Challenges, contributions and applications to biomedicine & agronomy

    Montpellier, May 28th, 2019

    Tutorial @ENVRI-FAIR Data FAIRness Summer School

    How to use ontology repositories and ontology-based services

    Lecce, July 5th, 2019

    JNSO 2018

    RDA Vocabulary Services Interest Group

    Paris, Dec. 6th, 2018

    Interview @SIMBig 2017

    4th Int. Symp. on INformation Management and Big Data

    Lima, Sep. 5th, 2017

    Interview @INIST

    Séquence de com

    Nancy, Dec. 5th, 2017

    2nd IBC-NUMEV AgroHackathon 2017

    Ending the competition, partnered with the DigitAg Challenge

    Montpellier, July 2nd, 2017

    GODAN Summit 2016

    Booth with INRA

    New York, Sep. 16th, 20016

    1st IBC-NUMEV AgroHackathon

    Group photo

    Montpellier, June 29th, 2016

    2nd BD2K, 4th Network of BioThings Hackathon

    Wining the hackathon with the NCBO/CEDAR team

    Stanford, Nov. 20th, 2015

    ESWC 2013

    Closing ceremony

    Montpellier, May 30th, 2013

    PhD defense

    Dynamic Service Generation: Agent interactions for service exchange on the Grid

    Montpellier, Nov. 16th, 2006


    Horizon Europe

    Grant No 101057344

    Support for FAIR-IMPACT.

    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.

    #DigitAg Convergence Institute

    Support for D2KAB and AgroHackathons.

    Plan National Dépérissement du Vignoble

    Support for VitisExplorer project.

    Labex Agro

    Support for AgroPortal.

    BSN-10 Program

    Support for VisaTM.

    H2020 OpenMinTed call for tender 2018

    Support for VisaTM.

    PIA program

    Support for AgroPortal.

    PICS program

    IRL program

    Support for SIFR.

    Scientific council PhD program

    Support for SIFR and other infrastructure.


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