Enabling semantic queries across federated bioinformatics databases

By A. Sima, Tarcisio Mendes de Farias, E. Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz. 2019

40 citations recorded by the source corpus.

Motivation Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. Results We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: 1) Bgee, a gene expression relational database; 2) OMA, a Hierarchical Data Format 5 (HDF5) orthology data store, and 3) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialised RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface. Project URL http://biosoda.expasy.org, https://github.com/biosoda/bioquery

Subfields: Artificial Intelligence, Molecular Biology

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In Artificial Intelligence

  1. Christophe Dessimoz

In Molecular Biology

  1. Christophe Dessimoz
  2. Natasha M. Glover
  3. David Moi
  4. Adrian M. Altenhoff
  5. Alex Warwick Vesztrocy
  6. Clément-Marie Train
  7. Tarcisio Mendes de Farias

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