Bgee collaborations

This page provides current collaborations of the Bgee project (in alphabetical order).

BioSODA

BioSODA project aims at enabling sophisticated semantic queries across large, decentralized and heterogeneous databases via an intuitive interface. The system will enable scientists, without prior training, to perform powerful joint queries across resources in ways that cannot be anticipated and therefore goes far and above the query functionality of specialized knowledge bases. It is supported by NFP75 'Big Data'.

For this project, we created a sub-database of Bgee called 'Bgee Lite'. The MySQL dump is available on Bgee FTP. You can see the description of 'Bgee Lite' in Bgee pipeline documentation

BioSODA uses the 'Bgee Lite' relational database to expose a Bgee SPARQL endpoint reachable through the following URL: http://biosoda.expasy.org:8080/rdf4j-server/repositories/bgeelight. In the context of this project, the BioQuery web application provides a user-friendly interface to query 'Bgee Lite' database based on the SPARQL query language.

The SPARQL endpoint and 'Bgee Lite' are available and free to use for other projects or applications.

OMA

The OMA (Orthologous MAtrix) project is a method and database for the inference of orthologs among complete genomes.

As part of a scientific collaboration with OMA, we generated files containing gene expression in homologous anatomical entities. These files are available on Bgee FTP.

The homologous expression files are also available and free to use for other projects or applications.

OncoMX

OncoMX is a knowledgebase of unified cancer genomics data from integrated mutation, expression, literature, and biomarker databases, accessible through web portal. It is supported by NIH NCI.

For this project, we generated files containing a subset of calls of presence/absence of expression with expression level categories specific to OncoMX. Files are available on Bgee FTP. You can see the description of these files in Bgee pipeline documentation

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