This release is a beta version. Please be aware that the data will not be archived and should not yet be referenced in publications, expecting long-term retrieval. The SPARQL endpoint was not updated.

Bgee SPARQL endpoint

Bgee has a SPARQL endpoint which is based on the EasyBgee database (see documentation on Bgee pipeline github). EasyBgee is a view of the 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 for writing federated queries among UniProt, OMA and Bgee SPARQL endpoints.

Programmatic access to the latest version of the Bgee SPARQL endpoint

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

https://bgee.org/sparql/

For example, to retrieve all anatomic entities in Rattus norvegicus 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 .
?seq rdfs:label ?geneName .
?seq genex:isExpressedIn ?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 is possible to download the result of this query in JSON format or in XML format.

(Of note, as opposed to the example below to access an archived version, when accessing the endpoint for the latest version, it is important NOT to specify the name of a graph to target; otherwise, results will be incorrect)

Stable programmatic access to this version of the Bgee SPARQL endpoint

This version of the Bgee SPARQL endpoint is accessible in a stable manner by using your prefered programming language through the stable URL address below:

https://bgee.org/sparql14_2/

In the SELECT section of your query, it is essential to specify the URL of the graph you want to query (https://bgee.org/rdf_v14_2), otherwise you won't be using the data for this version. For example, to retrieve all anatomic entities in Rattus norvegicus 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 FROM <https://bgee.org/rdf_v14_2> {
?seq a orth:Gene .
?seq rdfs:label ?geneName .
?seq genex:isExpressedIn ?cond .
?cond genex:hasAnatomicalEntity ?anatEntity .
?anatEntity rdfs:label ?anatName .
?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> .
FILTER (LCASE(?geneName) = LCASE('APOC1'))
}

Again, it is essential to specify the name of the graph of the version to target (in the example above, https://bgee.org/rdf_v14_2); otherwise, results will be incorrect.

RDF serialisation and semantic models

The Bgee RDF data were created using an Ontology Based Data Access (OBDA) approach so-called Ontop. The RDF serialisation of the 'EasyBgee' database is based on the GenEx semantic model specification and the OBDA mappings defined in OBDA mappings. The mappings are defined using the Ontop mapping language. We also inferred all implicit information based on OWL 2 Web Ontology Language Profile QL reasoning over GenEx.

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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