The SIFR project proposes to investigate the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of French biomedical data.
Obj1: Design, development and deployment of the French Annotator.
Obj2: Obtain new research results to exploit and enhance ontology-based indexing services.
Obj3: Valorization of indexing services.
The volume of data in biomedicine is constantly increasing. Despite a large adoption of English in science, a significant quantity of these data uses the French language. Usually, the content of the resources is indexed to enable querying with keywords. However, there are obvious limits to keyword-based indexing: use of synonyms, polysemy, lack of domain knowledge. Biomedical data integration and semantic interoperability is necessary to enable new scientific discoveries that could be made by merging different available data (i.e., translational research). A key aspect in addressing semantic interoperability for life sciences is the use of terminologies and ontologies as a common denominator to structure biomedical data and make them interoperable. Especially, the community has turned toward ontologies to design semantic indexes of data that leverage the medical knowledge for better information mining and retrieval. However, besides the existence of various English tools, there are considerably less ontologies available in French and there is a strong lack of related tools and services to exploit them. This lack does not match the huge amount of biomedical data produced in French, especially in the clinical world (e.g., electronic health records).
The Semantic Indexing of French Biomedical Data Resources (SIFR) project proposes to investigate the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of French biomedical data. We will build an ontology-based indexing workflow (i.e., French Annotator) similar to what exists for English resources but dedicated and specialized for French. This will prepare the creation (in a future research project), of an index allowing semantic and multilingual search and mining of biomedical data resources. Within SIFR, we will follow the translational bioinformatics and semantic Web visions to discover new knowledge by recombining already existing knowledge. Our main goal is to enable straightforward use of ontologies freeing health researchers to deal with knowledge engineering issues and to concentrate on the biological and medical challenges.
The SIFR project brings together several young researchers at LIRMM to achieve this objective. Dr. Clement Jonquet, assistant professor at University of Montpellier since 2010, will coordinate the project and capitalize on a strong experience in the field acquired after a 3 year postdoc at Stanford. He will be accompanied by 3 young assistant professors: Dr. Francois Scharffe (semantic Web), Dr. Sandra Bringay (data mining) and Dr. Mathieu Roche (NLP). In addition, highly qualified and experienced partners will be associated to the project: (i)°Stanford BMIR, a worldwide leader providing (English-)ontology-based services to assist health professionals and researchers in the use of ontologies to design biomedical knowledge-based systems; (ii)°CISMeF group, which is the national leader to provide French health terminology-based services. Furthermore, other academic and industrial partners have been also identified (e.g., Ontologos Corp, CNRS-INIST) and will collaborate to illustrate concrete valorization of the project outcomes in terms of scientific and economic impact.
We plan to capitalize upon the work already accomplished in the last 16 years in France, especially by the CISMeF group. However, SIFR will enable the emergence of new research domain and applications at LIRMM and will set up a strong collaboration with an international leader lab such as Stanford BMIR. SIFR will offer the French biomedical community (e.g., clinicians, health professionals, researchers) highly valuable ontology-based indexing services that will enhance their data production and consumption workflows. The project will put France in a key position to lead future European projects related to multilingual data issues in biomedicine and other domains..
[Intern - stage] Conception d’un prototype d’annotateur sémantique biomédical francophone. [PDF]
[Projet - TER] Conception et implémentation d’une application web et d’un web service pour des distances sémantiques [PDF]
[Intern - stage] Construction d’une application web pour la navigation et la recherche d’information au sein d’un graphe de connaissances communautaires [PDF]
[Intern - stage] Expérimentation du calcul hétérogène dans l'approche VIEWPOINTS [PDF]
[Projet - TER] Formalisation et extraction de points de vue de à partir de multiples ressources du Web [PDF]
The SIFR project is mainly funded by the French ANR organization wityhin the Young Researcher (JCJC) program 2012.
The project is also supported by the CNRS and University Montpellier 2 and the Computational Biology Institute of Montpellier project
Clement Jonquet (LIRMM) - email@example.com