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Clement Jonquet's Homepage
Clement Jonquet's Homepage
PhD in Informatics
Senior Researcher – INRAE (MISTEA)
Associate Researcher – University of Montpellier (LIRMM)
PhD in Informatics
Senior Researcher – INRAE (MISTEA)
Associate Researcher – University of Montpellier (LIRMM)
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.
Teaching
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...
- Co-head of Informatics Axe within MISTEA.
- Previous co-head of FADO research group at LIRMM with Pr. A. Laurent.
- Organizer of the Web Science Montpellier Meetup and the AgroHackathon series.
- Member of several workshop and conference program committees related to life sciences and informatics.
- Local chair of ESWC 2013, program co-chair of S4BIODIV 2013 & 2017 and TICE 2014.
- Member of the RDA Agrisemantics working group with the IG on agriculture data.
- Co-chair the "Ontology Metadata" task group of the RDA VSSIG working group.
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).
DACE-DL
DAta-CEntric AI-driven Data Linking
Vocabulary and ontology repository for agriculture, plant sciences, nutrition and biodiversity
PUBLICATIONS
Access my consolidated and complete list on on HAL, the French publication archive... or others Web profiles.
- COMPLETE RESUME
English version of my current CV (29 pages) as of June 2024. Also available in HTML.
- CONTACT
(to come to MISTEA see: https://www.institut-agro-montpellier.fr/index.php/campus-de-la-gaillarde-montpellier)
MISTEA – INRAE Montpellier
2, place Pierre Viala
34060 Montpellier Cedex 2
FranceMONDAY-THURSDAY: I am located in building 21 (Office 412, level 4) (to come to LIRMM see: https://www.lirmm.fr/contact-et-acces)
LIRMM
161 rue Ada
34095 Montpellier Cedex 5
FranceFRIDAY: I am located in building 5 (Office 3.159 (level 3, East wing))+33/0 4 67 14 97 43MEDIA
Embrapa's & GO FAIR Agro Seminar
Ontology Repositories�with the OntoPortal Technology�& a deeper look into AgroPortal
Brasilia, April. 24th, 2024
Vocabulary Symposium2023
Ontology Repositories and Semantic Artefact Catalogues with the OntoPortal Technology
Acton & online, Nov. 15th, 2023
NKOS Workshop 2023
State-of-the-art browsing of SKOS resources in AgroPortal
Online and in Daegu, Nov. 9th, 2023
GO FAIR Agro Webminar
FAIR DATA requires FAIR ONTOLOGIES, how do we do?
Online, Oct. 17th, 2023
FAIR-IMPACT All HandsMeeting
Group photo
The Hague, Oct. 4th, 2023
FAIR-IMPACT Semantic Artefact Governance Workshop
Workshop organized in conjunction with the 2nd OntoPortal Worksop
Online and in Lecce, Sept. 28th, 2023
LifeWatch Semantic Academy 2023
Ontology repositories
Lecce, Sept. 26th, 2023
6th Annual AGROVOC editorial community meeting
AgroPortal: a vocabulary and ontology repository for agri-food
Munich, July 13th, 2023
Journées EOSC France
Panel: how to improve the impact of and on the EOSC
Montpellier, June. 14th, 2023
OntoPortal Workshop 2022
Group photo
Montpellier, Sept. 28th, 2022
MISTEA general assembly
Group photo
Juvignac, Nov. 29th, 2022
Horizon EU FAIR-IMPACT kick-off
Contribution to Metadata and Ontologies in EOSC
Amsterdam, June 28th, 2022
CGIAR Ontologies Community of Practice Webinar
AgroPortal Ontology Repository:
What is the value added of indexing the CGIAR
ontologies?
Online, Oct. 4th, 2022
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
2nd Annual GO FAIR Implementation Networks Meeting
Group photo
Hamburg, Jan. 24th, 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
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
FUNDING
JCJC, Generic, MRSEI programs
Support for SIFR, PractiKPharma, eRosa, D2KAB and FooSIN
ARCHIVES
Links to archivesd web pages that describe previous projects or topics.
Clement Jonquet's homepage - 2018