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This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010

Open Access Research

User centered and ontology based information retrieval system for life sciences

Mohameth-François Sy1, Sylvie Ranwez1*, Jacky Montmain1, Armelle Regnault2, Michel Crampes1 and Vincent Ranwez3

Author Affiliations

1 LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035 Nîmes cedex 1, France

2 Inserm/Institut Multi-Organismes, Immunologie, Hématologie et Pneumologie (ITMO IHP), 175, rue du Chevaleret, 75013 Paris, France

3 Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS Université Montpellier II, place E. Bataillon, CC 064, 34 095 Montpellier cedex 05, France

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BMC Bioinformatics 2012, 13(Suppl 1):S4  doi:10.1186/1471-2105-13-S1-S4

Published: 25 January 2012



Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations.


This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway.


The ontology based information retrieval system described in this paper (OBIRS) is freely available at: webcite. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help.