Journal

Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Daniel L. Rubin, Barry Smith, Margaret-Anne Storey, Christopher G. Chute, Mark A. Musen, BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse, Nucleic Acids Research, Advance Access published online on May 29, 2009. [journal's web site] [link]

Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, Ontology-driven Indexing of Public Datasets for Translational Bioinformatics, BMC Bioinformatics, Vol. 10, February 2009. [journal's web site] [pdf - 651 Kb]

Clement Jonquet, Pascal Dugenie, Stefano A. Cerri, Agent Grid Integration Language, Multiagent and Grid Systems, Vol. 4 (2), pp. 167-211, 2008. [journal's web site] [pdf - 1389 Kb]

Pascal Dugénie, Philippe Lemoisson, Clement Jonquet, Monica Crubézy, Claude Laurenco, The Grid Shared Desktop: A Bootstrapping Environment for Collaboration, Advanced Technology for Learning, Special issue on Collaborative Learning, Vol. 3 (4), pp. 241-249, 2006. [journal's web site] [pdf - 423 Kb (first version)]

Clement Jonquet, Stefano A. Cerri, The STROBE model: Dynamic Service Generation on the Grid, Applied Artificial Intelligence Journal Special issue on Learning Grid Services, Vol. 19 (9-10), p.967-1013, November 2005. [journal's web site] [pdf - 657 Kb]

(to come)

Clement Jonquet, Pascal Dugenie, Stefano A. Cerri, Service-Based Integration of Grid and Multi-Agent Systems Models, Extended version of International Workshop on Service-Oriented Computing: Agents, Semantics, and Engineering, SOCASE'08 accepted for publication in inaugural issue of International Journal of Grid Computing and Multi Agent Systems (GCMAS).

Serie

Clement Jonquet, Marc Eisenstadt and Stefano A. Cerri, Learning Agents and Enhanced Presence for Generation of Services on the Grid, In P. Ritrovato, C. Allison, S.A. Cerri, T. Dimitrakos, M. Gaeta and S. Salerno (eds): Towards the Learning GRID: advances in Human Learning Services, Vol. 127, Frontiers in Artificial Intelligence and Applications, p.203-213, IOS Press, November 2005. [serie's web site] [pdf - 82 Kb]

International Conference

Clement Jonquet, Nigam H. Shah, Mark A. Musen, The Open Biomedical Annotator, AMIA Summit on Translational Bioinformatics, p. 56-60, March 2009, San Francisco, CA, USA. [conference's web site] [pdf - 201Kb]

Clement Jonquet, Mark A. Musen and Nigam H. Shah, A System for Ontology-Based Annotation of Biomedical Data, In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08, Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [conference's web site] [pdf - 431Kb]

Stefano A. Cerri, Monica Crubézy, Pascal Dugénie, Clement Jonquet, Phillippe Lemoisson, The Grid Shared Desktop for CSCL. P. Cunningham and M. Cunningham (eds), Exploiting the Knowledge Economy: Issues, Applications, Case Studies, Vol. 3, Information and Communication Technologies and the Knowledge Economy, p. 1493-1499, IOS Press, Amsterdam, Netherlands, 2006. Proceedings of eChallenges 2006 Conference, October 2006, Barcelona, Spain. [conference's web site] [pdf - 850 Kb]

Clement Jonquet, Stefano A. Cerri, I-Dialogue: Modelling Agent Conversation by Streams and Lazy Evaluation, International Lisp Conference, ILC'05, Stanford University, CA, USA, June 2005. [conference's web site ] [pdf - 216 Kb]

Workshop

Clement Jonquet, Nigam H. Shah, Mark A. Musen, Prototyping a Biomedical Ontology Recommender Service, Bio-Ontologies: Knowledge in Biology, SIG, ISMBECCB 2009, pp. 65-68, Stockholm, Sweden, July 2009. [SIG's web site] [pdf - 152Kb]

Pascal Dugenie, Clement Jonquet, Stefano A. Cerri, The Principle of Immanence in GRID-Multiagent Integrated System, R. Meersman, Z. Tari, P. Herrero (eds.) 4th International Workshop On Agents and Web Services Merging in Distributed Environments, AWeSOMe'08, , OTM 2008 Workshops, Vol. 5333, Lecture Notes in Computer Science, pp. 98-107, Springer-Verlag, Monterrey, Mexico, November 2008. [workshop's web site] [pdf - 590 Kb]

Clement Jonquet, Pascal Dugenie, Stefano A. Cerri, Service-Based Integration of Grid and Multi-Agent Systems Models, International Workshop on Service-Oriented Computing: Agents, Semantics, and Engineering, SOCASE'08, Vol. 5006, Lecture Notes in Computer Science, pp. 56-68, Springer-Verlag, Estoril, Portugal, May 2008. [workshop's web site] [pdf - 270 Kb]

Frédéric Duvert, Clement Jonquet, Pascal Dugénie, Stefano A. Cerri, Agent-Grid Integration Ontology, R. Meersman, Z. Tari, P. Herrero (eds.) International Workshop on Agents, Web Services and Ontologies Merging, AWeSOMe'06, OTM Workshops 2006, Vol. 4277, Lecture Notes in Computer Science, pp. 136-146, Springer-Verlag, Montpellier, France, November 2006. [workshop's web site] [pdf - 408 Kb]

Clement Jonquet, Stefano A. Cerri, Agents Communicating for Dynamic Service Generation, 1st International Workshop on GRID Learning Services, GLS'04, p. 39-53, Maceió, Brazil, September 2004. [pdf - 116 Kb]

Stefano A. Cerri, Marc Eisenstadt, Clement Jonquet, Dynamic Learning Agents and Enhanced Presence on the Grid, 3rd International LeGE-WG Workshop: GRID Infrastructure to Support Future Technology Enhanced Learning, Berlin, Germany, December 2003, Electronic Workshops in Computing (eWiC). [workshop's web site] [pdf - 73 Kb]

National (French) Conference

Clement Jonquet, Nigam H. Shah, Mark A. Musen, Un service Web pour l’annotation sémantique de données biomédicales avec des ontologies, 13èmes Journées Francophones d'Informatique Médicale, JFIM’09, Nice, France, Avril 2009. [conference's web site] [pdf - 645 Kb]

Clement Jonquet, Pascal Dugenie, Stefano A. Cerri, Intégration orientée service des modèles Grid et multi-agents, V. Chevrier and M-P. Huget (eds.), 14èmes Journées Francophones sur les Systèmes Multi-Agents, JFSMA06, p. 271-274, Annecy, France, October 2006, Hermès. [conference's web site] [pdf - 306 Kb]

Clement Jonquet, Stefano A. Cerri, Les Agents comme des interpréteurs Scheme : Spécification dynamique par la communication, 14ème Congrès Francophone AFRIF-AFIA de Reconnaissance des Formes et Intelligence Artificielle, RFIA'04, Vol. 2, p. 779-788, Toulouse, France, January 2004. [conference's web site] [pdf - 71 Kb] [english version - 376 Kb]

Clement Jonquet, Stefano A. Cerri, Apprentissage issu de la communication pour des agents cognitifs, J-P. Briot, K. Ghédira (eds.) 11ème Journées Francophones sur les Systèmes Multi-Agents, JFSMA'03, p. 83-87, Hammamet, Tunisia, November 2003, Hermès. [conference's web site] [pdf - 41 Kb]

Clement Jonquet, Stefano A. Cerri, Cognitive Agents Learning by Communicating, P. Aniorté (ed.), 7ème Colloque Agents Logiciels, Coopération, Apprentissage & Activité humaine, ALCAA'03, Bayonne, France, September 2003. [conference's web site] [pdf - 60 Kb]

Dissertation

Clement Jonquet, Dynamic Service Generation: Agent interactions for service exchange on the Grid, PhD thesis (thèse de doctorat) , Université Montpellier 2, Montpellier, France, November 2006. [internal link] [pdf - 7.08 Mb]

Clement Jonquet, Communication Agent et Interprétation Scheme pour l'apprentissage au méta-niveau, MSc thesis (mémoire de DEA), Université Montpellier 2, Montpellier, France, June 2003. [LIRMM's web site] [UM2's web site] [pdf - 1536 Kb]

Research Reports & Miscellaneous

Clement Jonquet, Mark A. Musen, Nigam H. Shah, Help will be provided for this task: Ontology-Based Annotator Web Service, Research Report BMIR-2008-1317, BMIR, Stanford University, USA, May 2008. [BMIR's web site] [pdf - 306Kb]

Nigam H. Shah, Clement Jonquet, Mark A. Musen, Ontrez project report, Research Report BMIR-2007-1289, BMIR, Stanford University, USA, November 2007. [BMIR's web site] [pdf - 1.51Mb]

Clement Jonquet, Pascal Dugenie, Stefano A. Cerri, Intégration orientée service des modèles Grid et multi-agents, Rapport de Recherche, RR06036, LIRMM, CNRS & Université Montpellier 2, Montpellier, France, June 2006. [LIRMM's web site] [pdf - 1389 Kb]

Clement Jonquet, Pascal Dugenie, Stefano A. Cerri, Service based integration of Grid and Multi-Agent Systems models, Rapport de Recherche, RR06012, LIRMM, CNRS & Université Montpellier 2, Montpellier, France, February 2006. [LIRMM's web site] [pdf - 780 Kb]

Clement Jonquet, Stefano A. Cerri, Characterization of the Dynamic Service Generation Concept, Rapport de Recherche, RR06007, LIRMM, CNRS & Université Montpellier 2, Montpellier, France, February 2006. [LIRMM's web site] [pdf - 586 Kb]

Clement Jonquet, A framework and ontology for Semantic Grid Services: An integrated view of WSMF and WSRF, Unpublished draft research report, LIRMM, CNRS & Université Montpellier 2, Montpellier, France and KMi, Open University, Milton Keynes, UK, May 2005. [LIRMM's web site] [KMi's web site] [pdf - 123 Kb]

Poster, Presentation & Demonstration

Clement Jonquet, Nigam H. Shah, Cherie H. Youn, Chris Callendar, Margaret-Anne Storey, and Mark A. Musen. NCBO Annotator: Semantic Annotation of Biomedical Data. Poster & Demonstration Session, 8th International Semantic Web Conference, ISWC’09, Washington DC, USA, November 2009. [Conference's web site] [abstract - pdf - 205Kb] [poster - pdf - 1.33Mb]

Patricia L. Whetzel, Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Daniel L. Rubin, Cherie H. Youn, Mark A. Musen, BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse, 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB'09) and the 8th European Conference on Computational Biology (ECCB'09), Poster session, Stockholm, Sweden, July 2009. [Conference's web site]

Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Cherie H. Youn, Adrien Coulet, Chris Callendar, Daniel L. Rubin, Barry Smith, Margaret-Anne Storey, Christopher G. Chute, Mark A. Musen, BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse, Bio-Ontologies: Knowledge in Biology, SIG, Poster session, ISMBECCB 2009, Stockholm, Sweden, July 2009. [SIG's web site] [proceedings]

Patricia L. Whetzel, Natasha F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Cherie H. Youn, Michael J. Montegut, Daniel L. Rubin, Margaret-Anne Storey, Chris G. Chute, Mark A. Musen, BioPortal: A Web Repository for Biomedical Ontologies and Data Resources, 3rd International Biocuration Conference, Poster presentations, p. 97, Berlin, Germany, April 2009. [conference's web site] [abstract proceedings]

Simon Twigger, Jennifer Smith, Rajni Nigam, Clement Jonquet, Mark A. Musen, Billion Data Points Trapped in International Data Repository - Daring rescue Planned!, 3rd International Biocuration Conference, Poster presentations, p. 34, Berlin, Germany, April 2009. [conference's web site] [abstract proceedings]

Patricia L. Whetzel, Natasha F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Michael J. Montegut, Daniel L. Rubin, Cherie H. Youn, Mark A. Musen, BioPortal: A Web Repository for Biomedical Ontologies and Ontology-indexed Data Resources, Pacific Symposium on Biocomputing, Poster presentations, p. 90, Hawaii, USA, January 2009. [conference's web site] [abstract proceedings]

Mark A. Musen, Nigam H. Shah, Natasha F. Noy, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, James Buntrock, Clement Jonquet, Michael J. Montegut, Daniel L. Rubin, BioPortal: Ontologies and Data Resources with the Click of a Mouse, AMIA 2008 Annual Symposium, Demonstrations, p.1223-1224, Washington DC, USA, November 2008 [conference's web site]

Natasha F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Michael J. Montegut, Daniel L. Rubin, Cherie H. Youn, Mark A. Musen, BioPortal: A Web Repository for Biomedical Ontologies and Data Resources, Poster & Demonstration Session at the 7th International Semantic Web Conference, ISWC'08, Karlsruhe, Germany, November 2008 [conference's web site] [pdf - 115 Kb]

Clement Jonquet, Nigam H. Shah, Mark A. Musen, Using Biomedical Ontologies for Annotations of Biomedical Data, National Centers for Biomedical Computing All Hands Meeting, August 2008. [meeting's web site] [pdf - 1.71 Mb]

Mark A. Musen, Daniel L. Rubin, Nigam H. Shah, Clement Jonquet, Benjamin Dai, Michael Montegut, Ida Sim, Christopher G. Chute, Margaret-Anne Storey, Barry Smith, The National Center for Biomedical Ontology, National Centers for Biomedical Computing All Hands Meeting, August 2008. [meeting's web site] [pdf - 544 Kb]