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July 2015, check our local reuse of the NCBO tecnhology
bioportal.lirmm.fr (French biomedical terminologies and SIFR Annotator) and agroportal.lirmm.fr (agronomic/plant ontologies portal)

November 2012, the SIFR project is accepted!
The ANR JCJC project that I have submitted is finally accepted for funding. This is great news!.

Thanks Russ!
Our paper in Journal of Biomedical Semantics [this one] has been selected by Pr. Russ Altman's 2011 Year in Review at AMIA TBI.

November 2010, NCBO Resource Index wins ISWC Semantic Web Challenge !
SWC 2010

January 2010, new release!
A new version of the NCBO Annotator is released within BioPortal 2.3 (learn more).

September 2010, new release of NCBO Resource Index
With a brand new UI and backend. Check it out in BioPortal.

September 2009, new release!
New release of the NCBO Resource Index within BioPortal 2.2 (learn more).

Genome Web news article about us!
There is a post in March 2009 on the GenomeWeb web site about the NCBO Annotator.


Welcome on my homepage!

Dr. Clement Jonquet, PhD in Informatics

Assistant Professor, Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM), University of Montpellier.

Informatics teacher at Polytech’Montpellier Engineering School.

Clement Jonquet's picture

Short Bio

I am assistant professor at University of Montpellier, France since September 2010. I teach Informatics to the students of the Polytech’Montpellier Engineering School.

I am a member of the Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM) and do my research within the SMILE research group on (biomedical)ontologies, semantic data indexing and annotation, semantic Web, text mining, knowledge representation, collaborative and learning systems, agents and services.

I obtained a BSc, MSc, and PhD in Informatics from the same university in November 2006, supervised by Pr. Stefano A. Cerri. I worked on multi-agent systems, grid and service-oriented computing.

I served as a postdoc for 3 years at the Stanford Center for Biomedical Informatics Research (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 web repository widely used in the biomedical informatics community.

With NCBO team, we won the 1st prize at ISWC – Semantic Web Challenge in 2010 with our ontology-based Web application for searching and mining biomedical data.

Since beginig of 2013, I am the PI of the SIFR project (Semantic Indexing of French Biomedical Data Resources) mainly funded by the ANR Young Researcher program. And since 2015 I coordinate the AgroPortal project, which goals is to affer an ontology repository for agronomy and plant sciences.

I co-supervises 2 PhD candidates, Juan-Antonio Lossio Ventura and Guillaume Surroca.

I am interested and I have experience in several domains such as biomedical informatics, ontology and semantic Web, data integration and annotation, information retrieval and text mining, distributed systems, agents, service-oriented computing, collaborative systems.

I am the (co)author of 51 publications, cumulating 1350+ citations, including 11 international journals in multiple domains (biomedical informatics, semantic Web, distributed systems & AI).

I am also interested in Web Science and organizer of the Web Science Montpellier Meetup.

I am also interested in the use of ICT in Education and especially the use of iPads within the classrom. I am the representative for Polytech’Montpellier within UM2 council for Information and Communication Technologies in Education (TICE). I co-chair the “return of experience” track of TICE 2014.


Public web profiles


  • English version one (32 pages) [PDF] or [HTML] (as of September 2015).

How to contact me?

+33/0 4 67 14 97 43
+33/4 67 41 85 00

University of Montpellier
161 rue Ada
34095 Montpellier Cdx 5






How to find me?

I am in office 3.141 level 3, LIRMM. Maps and Information.

                                                         Clement Jonquet's homepage - July 2015