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.
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 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.
RESEARCH PROJECTS & TOPICS
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).
DAta-CEntric AI-driven Data Linking
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
AgroPortal: a vocabulary and ontology repository for agronomy
Online, May 26, 2020
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
Interview @SIMBig 2017
4th Int. Symp. on INformation Management and Big Data
Lima, Sep. 5th, 2017
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
Montpellier, June 29th, 2016
2nd BD2K, 4th Network of BioThings Hackathon
Wining the hackathon with the NCBO/CEDAR team
Stanford, Nov. 20th, 2015
Montpellier, May 30th, 2013
Dynamic Service Generation: Agent interactions for service exchange on the Grid
Montpellier, Nov. 16th, 2006
Clement Jonquet's homepage - 2018