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How to cite this work

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,


A repository for code and documentation of the BioQuery BETA system.

Hint for users of the frontend

Some of the queries only work if you install a CORS plugin in your browser (e.g. Moesif CORS) to allow Cross-Origin Resource Sharing

Use and License

Here data and code-source are licensed under the CC0 1.0 Universal (CC0 1.0). A human-readable version and explanation is available at the Creative Commons website. For information about how to properly credit data use, please review the Creative Commons FAQ or contact us.

Relational-to-RDF (OBDA) mappings

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.

Federated Queries Catalog

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 .

GenEx documentation

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.

VoID extension documentation

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).

Supplementary material

All supplementary material for the submission is available in the document in Supplementary.

Source code for template-based search interface

The source code for the template-based search interface running on is available for reference in the biosoda_frontend folder.


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