Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz, Enabling semantic queries across federated bioinformatics databases, Database, Volume 2019, 2019, baz106, https://doi.org/10.1093/database/baz106
A repository for code and documentation of the BioQuery BETA system.
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The full set of Ontop mappings used to expose relational Bgee data as a virtual RDF graph is available in the Bgee_OBDA_mappings folder.
The Excel spreadsheet containing the 12 federated queries used to evaluate our system are available in the Queries folder. They can also be modified and executed in our template-based search interface at http://purl.org/bioquery .
The documentation for the GenEx semantic model, used to expose gene expression data from Bgee as a virtual RDF graph, is available at GenEx documentation draft and the raw files in the genex repository.
The documentation of the VoID extension describing the virtual links between the datasets considered in our work is available at VoIDext documentation draft and the Turtle files in the voidext repository by also including the metadata used in this project (i.e. voidext_bioquery.ttl file).
All supplementary material for the submission is available in the document in Supplementary.
The source code for the template-based search interface running on http://biosoda.expasy.org/build_biosodafrontend/ is available for reference in the biosoda_frontend folder.