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SPARQL Resources

The DO-KB's SPARQL Sandbox provides programmatic access to the DO-KB Knowledgebase for exploring DO diseases, disease features, cross references and mechanisms, and exploring disease-data connections to other SPARQL endpoints. The "SPARQL Protocol and RDF Query Language" (SPARQL) enables semantic queries of the Disease Ontology database and data retrieval of customized datasets. The DO-KB SPARQL Sandbox provides an access point for receiving and processing SPARQL protocol requests, a HTTP-based protocol, that is used to perform SELECT and CONSTRUCT operations.
  • Select one of the provided SPARQL queries or paste in a novel query to retrieve bespoke ML-ready datasets.
  • Searches may be performed against:
    • doid.owl (may be specified, queried by default): The DO's primary release file. This includes imported classes but excludes annotations on those classes.
      • Graph: http://purl.obolibrary.org/obo/doid.owl
    • doid-merged.owl (must be specified): Includes DO and all imported classes, e.g. ECO codes and classes used in logical relationships. Query this file when information about imported classes is desired, such as labels or imported hierarchical relationships.
      • Graph: http://purl.obolibrary.org/obo/doid/doid-merged.owl
  • Additional queries will be periodically added to this site. If you would like to have your favorite query added here, please submit a request.
    Request New SPARQL Queries

SPARQL Federation

Remote endpoints can be reached using the SERVICE keyword as part of a federated query. The DO's SPARQL endpoint is https://sparql.disease-ontology.org/ (trailing slash must be included).

Select Federated Endpoints of Interest

Additional SPARQL Resources

W3C logo Documentation

Additional SPARQL queries can be found in the HumanDiseaseOntology data repository.

A tutorial is also now available on the tutorials page.