Bgee SPARQL endpoint

Bgee has a SPARQL endpoint which is based on the 'Bgee Lite' database. 'Bgee Lite' is a lighter version of Bgee database, that contains most useful, and explicit information.

Web interface to query the Bgee SPARQL endpoint

Bgee SPARQL queries can be run using the web interface Bio-Query search created for the BioSODA project. Bgee specific queries are present under the category Bgee database queries. It is possible to see the SPARQL queries and edit them by clicking on the Show SPARQL Query Editor button. Moreover, Bio-Query allows to do federated queries between UniProt, OMA and Bgee SPARQL endpoints.

Programmatic access to the Bgee SPARQL endpoint

The Bgee SPARQL endpoint is accessible by using your prefered programming language through the URL address below:

http://biosoda.expasy.org:8080/rdf4j-server/repositories/bgeelight

For example, to retrieve all anatomic entities in human where the APOC1 gene is expressed, the query is:

PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT DISTINCT ?anatEntity ?anatName {
?seq a orth:Gene .
?expr genex:hasSequenceUnit ?seq .
?seq rdfs:label ?geneName .
?expr genex:hasExpressionCondition ?cond .
?cond genex:hasAnatomicalEntity ?anatEntity .
?anatEntity rdfs:label ?anatName .
?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> .
FILTER (LCASE(?geneName) = LCASE('APOC1'))
}
It's possible to download result of this query in JSON format or in XML format.

Virtual RDF serialisation and semantic models

The Bgee SPARQL endpoint was created using an Ontology Based Data Access (OBDA) approach allowing to create a virtual RDF serialisation without exporting data from the original relational database. It queries data stored in the 'Bgee Lite' relational database. The virtual RDF serialisation of the 'Bgee Lite' is based on the GenEx semantic model specification and the OBDA mappings defined in OBDA mappings. The mappings are defined with the Ontop mapping language.

To cross-reference other resources, this SPARQL endpoint contains annotation property assertions defined by a first draft of the life-sciences cross-reference (LSCR) ontology that is available to download at the Quest for Orthologs GitHub repository here.

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