A few contributions of the SIFR (Semantic Indexing of French biomedical Resources project) and how we reuse NCBO technology

Date: May 1, 2015

Speaker: Clement Jonquet, University of Montpellier, France

Abstract

In this talk I will quickly present the research and development contributions of the Semantic Indexing of French Biomedical Data Resources project (SIFR - www.lirmm.fr/sifr), mainly funded by the French ANR, which investigates the scientific and technical challenges of developing ontology-based services to leverage the use of biomedical ontologies and terminologies for indexing, mining and retrieval of French biomedical data. Within this project we extensively reuse and complement NCBO technology with the goals of:

• Designing and implementing a French version of the NCBO Annotator web service (the French Annotator) as well as implementing new features for the annotation workflows.
• Designing and implementing a multilingual version of BioPortal which can handle different kind of multilingual ontologies and alignments.
• Deploying a specific instance of the portal for the agronomic, plant and environment domain (the AgroPortal) in collaboration with IRD, CIRAD, INRA and Bioversity.

I will quickly demo our local developments and walk through the main research contributions of the project in terms of automatic term extraction, semantic annotation, multilingual representation, semantic distances, informal patient data analysis, semantic indexing of data.

References

• Soumia Melzi & Clement Jonquet. Scoring semantic annotations returned by the NCBO Annotator, In 7th International Semantic Web Applications and Tools for Life Sciences, SWAT4LS'14. Berlin, Germany, December 2014. CEUR Workshop Proceedings, Vol. 1320 pp. 15. CEUR-WS.org.
• Clement Jonquet, Vincent Emonet & Mark A. Musen . Roadmap for a multilingual BioPortal, In 4th Workshop on the Multilingual Semantic Web, MSW4. Portoroz, Slovenia, June 2015. (to come).
• Aravind Venkatesan, Pierre Larmande, Clement Jonquet, Manuel Ruiz & Patrick Valduriez. Facilitating efficient knowledge management and discovery in the Agronomic Sciences, In 4th Plenary Meeting of the Research Data Alliance. Amsterdam, The Netherlands, September 2014.
• Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche & Maguelonne Teisseire. Towards a mixed approach to extract biomedical terms from text corpus, Knowledge Discovery in Bioinformatics). 2014. Vol. 4 (1), pp. 15. IGI Global.

Bio

Dr. Clement Jonquet is assistant professor at University of Montpellier, France. He is a researcher at the Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM), on (biomedical)ontologies, semantic data indexing and annotation, semantic Web, text mining, knowledge representation. Dr. Jonquet obtained PhD in Informatics from the same university in 2006 (about multi-agent systems, grid and service-oriented computing), then he served as a postdoc for 3 years at the Stanford Center for Biomedical Informatics Research (BMIR) within Pr. Mark A. Musen’s group where he was working on semantic annotations of biomedical data using biomedical ontologies in the context of the National Center for Biomedical Ontology (NCBO) project. He contributed actively to the design, evolution and development of the NCBO BioPortal and won, with the NCBO team the 1st prize at ISWC Semantic Web Challenge. Since 2013, Dr Jonquet is the PI of the SIFR project (Semantic Indexing of French Biomedical Data Resources) mainly funded by the ANR Young Researcher program. Dr. Jonquet is the (co)author of 42 publications, cumulating 1200+ citations, including 10 international journals. He is a member of several workshop and conference program committees related to life sciences and informatics. He was local chair of ESWC 2013, program co-chair of S4BIODIV 2013 and TICE 2014.