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Data Integration in the Life Sciences

Volume 5109 of the series Lecture Notes in Computer Science pp 124-131

Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species

  • Frederic BastianAffiliated withDepartment of Ecology and Evolution, University of Lausanne, quartier UNIL-SorgeSwiss institute of bioinformatics
  • , Gilles ParmentierAffiliated withDepartment of Ecology and Evolution, University of Lausanne, quartier UNIL-SorgeSwiss institute of bioinformatics
  • , Julien RouxAffiliated withDepartment of Ecology and Evolution, University of Lausanne, quartier UNIL-SorgeSwiss institute of bioinformatics
  • , Sebastien MorettiAffiliated withDepartment of Ecology and Evolution, University of Lausanne, quartier UNIL-SorgeSwiss institute of bioinformatics
  • , Vincent LaudetAffiliated withInstitut Fédératif, Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, ENS Lyon, Université Lyon 1, CNRS, INRA
  • , Marc Robinson-RechaviAffiliated withDepartment of Ecology and Evolution, University of Lausanne, quartier UNIL-SorgeSwiss institute of bioinformatics

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Abstract

Gene expression patterns are a key feature in understanding gene function, notably in development. Comparing gene expression patterns between animals is a major step in the study of gene function as well as of animal evolution. It also provides a link between genes and phenotypes. Thus we have developed Bgee, a database designed to compare expression patterns between animals, by implementing ontologies describing anatomies and developmental stages of species, and then designing homology relationships between anatomies and comparison criteria between developmental stages. To define homology relationships between anatomical features we have developed the software Homolonto, which uses a modified ontology alignment approach to propose homology relationships between ontologies. Bgee then uses these aligned ontologies, onto which heterogeneous expression data types are mapped. These already include microarrays and ESTs. Bgee is available at http://bgee.unil.ch/

Keywords

gene expression pattern homology ontology data integration