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DO-KB SPARQL Sandbox

Select one of the provided SPARQL queries or paste in a novel query to retrieve bespoke ML-ready datasets. Searches may be performed against the DO's primary release file, doid.owl or the doid-merged.owl file for exploring annotations, e.g. ECO codes, and axiom relationships.
  • The DO's SPARQL endpoint (https://sparql.disease-ontology.org/) is available for building federated queries.
  • Visit our SPARQL Resources page to learn more about using the SPARQL Sandbox and endpoint.
  • Our SPARQL Sandbox and endpoint are currently in beta. If you discover any issues, please reach out and let us know!

Choose a Query:

  1. All diseases with their parents (identified by label)
  2. Count of diseases in each branch (diseases may be in multiple branches)
  3. Syndromes (branch search; returns IRI, ID and label)
  4. Sarcoma diseases with parents, identified as descendants of sarcoma (DOID:1115) or with 'sarcoma' in their label
  5. Diseases with MeSH cross-references
  6. Diseases with OMIM cross-references
  7. Complete mapping from MeSH disease to ICD10CM codes, using DO disease cross-references
  8. Diseases with PubMed sources (limited to first 10 results)
  9. Diseases in DO_infectious_disease_slim with their parents and branches
  10. Diseases with their definitions and count of logical axioms
  11. Diseases with their Evidence and Conclusion Ontology (ECO) reference types (queries the doid-merged.owl graph)
  12. Count of classes imported from other ontologies (queries the doid-merged.owl graph)
  13. All diseases with equivalent class axioms (axioms are formatted for readability and may not be displayed in full; queries the doid-merged.owl graph)
  14. Extract the disease and supporting import class hierarchies using subClassOf relationships (executes a CONSTRUCT query that returns RDF triples)
  15. Federated query (DO-PRO): Retrieve proteoforms associated with progression of cancer
  16. Common prefixes (not a full query)
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