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UM2

LIRMM

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

GT MFI

In France, I was a member of the French MFI working group (Modèles Formels de l'Interaction).

The working group is unfortunaltly suspended for a while.

Informatics vs. Computer Science

I rather prefer the term ’Informatics’ to the term ’Computer Science’.

As the School of Informatics at the University of Edinburgh defines it, Informatics is the study of the structure, behaviour, and interactions of natural and engineered computational systems (i.e., representation, processing and communication of information in natural and artificial systems.). The central notion is the transformation of information – whether by computation or communication, whether by organisms or artifacts.

See also Wikipedia definition and the Indiana University School of Informatics and the Departement of Informatics, University of California, Irvine, definitions.

Current Research Activity

I have been recently interested about the convergence of French and English medical informatics ontology-based tools and services in collaboration with CISMeF and BMIR. I like to export (and contribute to) NCBO research and technologies in order to standardize ontology-based portals and promote interoperability. I am also interested in generalizing my work on semantic indexing and data annotation to other domain such as agronomy or plant sceinces. I am working to deploy at LIRMM a local repository of ontologies and offering custom annotation workflows such as French version of the Annotator. I am also interested in publishing ontology-indexed data into the open linked data cloud, automatic terminology extraction, multilingual ontology alignments, semantic similarity and graph-based approach for knowledge representation and collaborative learning.

Research Activity

I have different experiences and interests for research in Informatics (cf. note on the left for the Informatics vs. Computer Science discussion) from artificial intelligence to biomedical informatics. I made my PhD thesis at the crossing of 3 mains approaches of distributed systems and from 2007 to 2010, as a postdoc in Stanford, I was involved in a more applied research context: annotation using biomedical ontologies.

This page describes and links to the different activities I am (or I was) involved in.

[Research Projects]

[PhD Thesis]

For more detail see also the "Research Activity" section of my online CV.

Research Topics

  • Ontologies,
  • Semantic Web,
  • Semantic annotation,
  • Biomedical Informatics,
  • Data integration,
  • Knowledge representation,
  • Information Retrieval,
  • Text mining,
  • Linked data,
  • Service-oriented computing,
  • Web Services,
  • Web Science,
  • Distributed systems,
  • Multi-Agents Systems,
  • Web 2.0,
  • Virtual communities,
  • Collaborative and learning systems

Teams & Research Projects

  • 2013-2017: Semantic Indexing of French Biomedical Data Resources (SIFR) project, – ANR Young Researcher program. Also funded by UM2, CNRS & the IBC project.
  • 2012-2017: Institut de Biologie Computationnelle (IBC), axe 5 (workflow & data integration) – French Inv. d’Avenir BioInfo.
  • 2011-2016: CR2i DiagnosTIC-Santé project (Centre de Recherche et d'Innovation Industrielle) – French Inv. d’Avenir PFMI. Member of the metadata repository group (multi-omics platform development).
  • Since 2010: Member of the LIRMM’s Smile team (multi-agent systems, interaction, Web science, service-oriented computing, ontologies, collaboration, serious game).
  • 2007-2010: Stanford Center BioMedical Informatics Research (BMIR) – Within Pr. Mark A. Musen’s group. Leading lab in medical informatics, knowledge representation and semantic Web (developing the Protégé ontology editor).
  • 2007-2010: National Center for Biomedical Ontology (NCBO) – Part of the National Centers for Biomedical Computing supported by the NIH Roadmap.
  • 2003-2007: European Learning Grid Infrastructure (ELeGI) – IST IP EU (FP6).
  • 2003-2004: Learning Grid of Excellence Working Group (LeGE-WG) – IST STREP EU (FP6).
  • 2003-2007: Member of the LIRMM’s Kayou team (multi-agent systems, constraints, Web, Grid, service-oriented computing, ontologies, collaborative learning).

Awards & Distinctions

  • I am holder of the French ministry distinction, Prime d'Excellence Scientifique (PES) since 2013.
  • Selection & funding of young researcher project by French National Research Agency (ANR), 2012.
  • Honorable mention award at 3rd ACM International Conference on Web Science, WebSci’11 for our paper “Negotiating the Web Science Curriculum through Shared Educational Artefacts”.
  • Winner (with the NCBO team) of the Semantic Web Challenge 2010 with an ontology-based Web application for searching and mining biomedical data. International Semantic Web Conference, Shanghai, China, November 2010.
  • Selected in Pr. Russ Altman’s 2011 Year in Review for journal article about biomedical ontology recommendation. AMIA Translational Bioinformatics Summit, 2011, San Francisco, USA, March 2011.

They are talking about us...

Past Research Activity

NCBO project & postdoctoral research:

Within NCBO I worked on semantic annotation of biomedical data with biomedical ontologies. I actively contributed to the NCBO BioPortal web application well used in the biomedical community. I designed an ontology-based annotation workflow. This workflow plugs different components (e.g., concept recognition tool, semantic expansion algorithms) in order to leverage the knowledge represented in ontologies and facilitate biomedical data integration. Based on this workflow, I conceptualized, designed, developed and experiment 3 research applications: (i) the NCBO Annotator, an ontology-based web service that can be used by the life sciences community to tag their data automatically with ontology concepts; (ii) the NCBO Resource Index, an database of 20+ open biomedical resources annotated and indexed with ontology concepts (from 200+ ontologies) which can be used to search and integrate data; (iii) the NCBO Recommender, a service which informs the user of the most appropriate ontologies relevant for their given dataset.

BioPortal services that I have developped

For more detail see also the "Research Activity" section of my online CV.

Doctoral research:

Situated at the crossing of 3 important domains: service-oriented computing (web service, components, business process, etc.), multi-agent systems (modeling, interaction, architecture) and Grid (resources sharing, Grid service, Grid computing). I propose in my thesis a new vision, called dynamic service generation, of the concept of service. This vision leverages agent (human or artificial) conversations and the Grid infrastructure to enable the dynamic construction of services based on the conversation between user & provider. Two important contributions are: (i) Strobe: an agent communication and representation model based on conversation contexts to enable interactive specification of agent capabilities; (2) Agent-Grid Integration Language (AGIL): a GRID-MAS integrated model formalized with a description language which leverages the stateful and dynamic aspect of Grid services. More details...

ELeGI project research:

Within ELeGI I worked on a collaborative environment constructed over a Grid infrastructure based shared desktops. We experiment the environment with a community of chemists tackling the problem of collaborative construction of an ontology.

Program Chairing & Organization

  • Co-program chair (with Pr. David Cassagne) of the “return of experience” track of the French ICT in Education Conference, TICE 2014, November 2014, Beziers, France.
  • Local chair (with Francois Scharffe) of 10th Extended Semantic Web Conference (ESWC) 2013, May 26-30 2013, Montpellier, France.
  • Organization comitee of 1st International Workshop on Semantics for Biodiversity (S4BIODIV 2013) in conjunction with ESWC 2013, May 2013, Montpellier,France.
  • Organization of 1st Web Science Montpellier Meetup workshop, in Montpellier May 13th 2011, 25 participants.

Program Committees & Article Reviewing

I am/was a member of the following international program committees:

I am/was a member of the following national program committees:

  • Workshop Knowledge Engineering and Health (ICSanté 2014).
  • 24th- &25th Knowledge Engineering conference “Ingénierie des Connaissances” (IC 2013, IC 2014).
  • 1st Workshop Ontologies et Jeux de Données pour évaluer le web sémantique (OJD 2012).
  • Workshop IC pour l'Interopérabilté Sémantique dans les applications en e-Santé (ICISanté 2012).
  • 1st & 2nd Workshop Quantité et Robustesse pour le Web de données (QetR 2011 & QetR 2012).
  • 1st Workshop Extraction des Connaissances et Contextualisation (ExCoco 2011)

I have reviewed articles for the previous listed conferences and journals plus:

Detailled Seminars & Invited presentations

3 most important presentations (cumulating 3730 views) on SlideShare.
  • SPIM team at INSERM Paris, June 2011 (invited by Dr. M-C. Jaulent).
  • LIM team at Rennes Univ., April 2011 (invited by Dr. O. Dameron).
  • CISMeF team at Rouen School of Medicine, March 2011 (invited by Pr. S. J. Darmoni).
  • Research seminar on ICT & Health, LIRMM, Montpellier, February 2011.
  • EXMO team at INRIA Grenoble, France, March 2010 (invited by Dr. J. Euzenat).
  • Smile team at LIRMM, UM2, France, February 2009 (invited by Pr. S. A. Cerri).
  • EDELWEISS team at INRIA Sophia, France, January 2009 (invited by Dr. F. Gandon).
  • Talk at the NCBO Developer Conference, Stanford Univ., USA, December 2007.
  • Intelligent Interactive Distributed Systems group, Vrije Univ., Amsterdam (invited by Pr. F. Brazier). May 2007.
  • LIRMM's Informatics department day, UM2, France. July 2005.
  • Protégé group, Stanford Medical Informatics, Stanford Univ., CA, USA (invited by Dr. M. Crubezy). June 2005.
  • E-LeGI WP6 (Work Package 6) seminar, LIRMM, UM2, France. June 2004.
  • Computer Science PhD students seminar, LIRMM, UM2, France. January 2004.
  • Talk within the GT MFI (Groupe de Travail Modèles Formels de l'Interaction) working group, LIP6, Université Paris 6, France. December 2003.
  • Social Informatics seminar, LIRMM, UM2, France. June 2003.
 
                                                         Clement Jonquet's homepage - July 2014