Title: BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery

Authors: Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Emmanuel Bresso, Amedeo Napoli, Malika Smail-Tabbone

Addresses: LORIA UMR 7503, CNRS, INRIA Nancy Grand-Est, Nancy-Universite, 615, rue du Jardin Botanique, 54600 Villers-les-Nancy, France. ' LORIA UMR 7503, CNRS, INRIA Nancy Grand-Est, Nancy-Universite, 615, rue du Jardin Botanique, 54600 Villers-les-Nancy, France. ' LORIA UMR 7503, CNRS, INRIA Nancy Grand-Est, Nancy-Universite, 615, rue du Jardin Botanique, 54600 Villers-les-Nancy, France. ' LORIA UMR 7503, CNRS, INRIA Nancy Grand-Est, Nancy-Universite, 615, rue du Jardin Botanique, 54600 Villers-les-Nancy, France. ' LORIA UMR 7503, CNRS, INRIA Nancy Grand-Est, Nancy-Universite, 615, rue du Jardin Botanique, 54600 Villers-les-Nancy, France. ' LORIA UMR 7503, CNRS, INRIA Nancy Grand-Est, Nancy-Universite, 615, rue du Jardin Botanique, 54600 Villers-les-Nancy, France

Abstract: The need for a well-maintained searchable directory is an important issue with regard to the numerous biological databases produced by genomic and post-genomic research. The BioRegistry repository aims to associate content metadata belonging to a biomedical thesaurus with biological databases in view of retrieval or discovery. It is automatically generated from a publicly available list of biological databases. The querying modalities include a search by semantic similarity. The system performance is evaluated in terms of precision and recall on a collection test. A classification method is proposed for browsing and discovering databases through the BioRegistry.

Keywords: resource discovery; biological databases; metadata extraction; FCA; formal concept analysis; information retrieval; semantic similarity; biomedical thesaurus; semantics; classification; information retrieval; biological data sources; bioinformatics.

DOI: 10.1504/IJMSO.2010.034043

International Journal of Metadata, Semantics and Ontologies, 2010 Vol.5 No.3, pp.184 - 193

Available online: 06 Jul 2010 *

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