Semantic Indexing of French Biomedical Data Resources (SIFR) project

 

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Project Objectives

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.

Executive Summary

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. Biomedical data integration and semantic interoperability is necessary to enable new scientific discoveries that could be made by merging different available data. A key aspect to address those issues is the use of terminologies and ontologies as a common denominator to structure biomedical data and make them interoperable.

Scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of French biomedical data.

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. 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, coordinates the project and capitalize on a strong experience in the field acquired after a 3 year postdoc at Stanford. He is accompanied by 2 young researchers (HDR): Dr. Sandra Bringay and Dr. Mathieu Roche both expert in biomedical data/text mining. In addition, highly qualified and experienced partners are 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)°The TETIS group, a joint applied research unit (AgroParisTech, Irstea, Cirad) specialized in geographic information, environment and agriculture. (iii)°the Computational Biology Institute (IBC) of Montpellier.

Build an ontology-based indexing workflow (i.e., French Annotator) similar to what exists for English resources but dedicated and specialized for French.

Researchers have called for the need of automated annotation methods and for leveraging natural language processing tools in the curation process. Still, even if the issue is being currently addressed for English, French is not in the same situation: there is little readily available technology (i.e.,“off-the-shelf” technology) that allows the use of ontologies uniformly in various annotation and curation pipelines with minimal effort.

Within SIFR, we build an ontology-based indexing workflow (i.e., French Annotator) similar to what exists for English resources but dedicated and specialized for French. This service is available within a portal of ~10 French biomedical ontologies/terminologies which reuse the BioPortal technology, developed at Stanford University. Ontologies has been offered by the CISMEF group from Rouen University Hospital, or taken from the UMLS, or directly uploaded by users. The SIFR BioPortal has been released in June 2015: http://bioportal.lirmm.fr

Within the project, we work on several research questions from semantic indexing, text mining, terminology extraction, ontology enrichment, disambiguation, multilingualism in ontologies and semantic annotation in order to offer the community with services and applications capable of leveraging the use of biomedical ontologies in their data workflows. For instance, in order to extract specialized terminology from free texts in French, our approaches are based on new ranking functions that combine statistical and linguistic methods for highlighting relevant terms. Then we offer a complete methodology to identify (non)polysomic terms and choose the appropriate attachment in an already existing ontology. As another example, we develop a new agent-centered graph-based knowledge representation approach that enables to merge formal data representation (e.g. from the semantic Web) with informal users’ contributions (from the social Web) and reveal relevant semantic paths between resources.

We plan to capitalize upon the work already accomplished in the last 16 years in France, however, SIFR enables the emergence of new research domains and applications at LIRMM and materialize an important international collaboration with 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. In addition, the results of the project are not limited to French (also include English, Spanish) and we are also transferring our results in the agronomic domain in the context of the new AgroPortal project (http://agroportal.lirmm.fr). The project will put France in a key position to lead future European projects related to multilingual data issues in biomedicine and other domains.

Main results

People

Young researchers Advisors Students Staff Close collaborators

Clement Jonquet
Mathieu Roche
Sandra Bringay

Stefano A. Cerri
Maguelonne Teisseire
Pascal Poncelet
Zohra Bellahsene

Juan Antonio Lossio Ventura
Guillaume Surroca
Amina Annane
Mike Tapi-Nzali
~4 MSc students / year

Vincent Emonet
Philippe Lemoisson (TETIS)
Pierre Larmande (IRD / IBC)
Mark Musen (BMIR)
John Graybeal (NCBO)
Stefan Darmoni (CISMEF)
Sebastien Harispe (LGI2P)

Available Positions

[Master research inter - 5 months] Annotation sémantique de dossiers patients électroniques [PDF]

[Master Devlopment Intern - 3-6 months] Développement d’un Web service parseur de documents structurés en Java [PDF]

[Master Devlopment Intern - 3-6 months] Développement d’une application web d’extraction et prédiction de métadonnées pour des ontologies [PDF]

[Research engineer - 12 months] Research engineer position: Web architect – JEE, Ruby/RoR – Semantic web technologies [PDF]

Closed Positions

Collaboration

Project support

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

Contact

Clement Jonquet (LIRMM) - jonquet@lirmm.fr