User centered and ontology based information retrieval system for life sciences

Abstract

Background: 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.

Results: 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.

Conclusions: The ontology based information retrieval system described in this paper (OBIRS) is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help.

Figure 1

Exploration of gene ontology concepts hierarchy in OBIRS. OBIRS allows navigating within the concepts hierarchy to assist the query formulation. The user can be aware that "sequence-specific DNA-binding" is a specialisation of "DNA binding" and that "erythrocyte homeostasis" is a generalisation of "erythrocyte development".

Figure 2

Interpolated precision-recall curve. Impact of IC based semantic similarity measures on precision. Five information retrieval approaches are compared using the MuchMore benchmark. Three rely on OBIRS 3-step strategy based on different concept-concept semantic proximities (Lin, Resnik and Jaccard) and the two others are Boolean search based on AND/OR operators.

Figure 3

OBIRS querying interface. A. Input with auto-completion functionality. B. Visualisation of query concepts' position within the Gene ontology. C. Parameters panel setting.

Figure 4

OBIRS result interface. Genes returned by OBIRS while querying with {"erythrocyte development", "regulation of transcription, DNA-dependent", "DNA binding"} are displayed on a semantic map according to their relevance (4-A). When selecting a gene on this map (here HOXB6) detailed information are provided (4-B). The user can move cursors to adjust concept weights for query reformulation (4-C).