Disease knowledge bases
Mondo Disease Ontology
Unified disease ontology
"The reference vocabulary for cross-database disease integration."
About the resource
Mondo is the Monarch Initiative's unified disease ontology, built by merging and harmonising terms from DO, Orphanet (ORDO), OMIM, ICD-10/11, MeSH, NCIt, MedGen, EFO, GARD and others. Where these sources have overlapping terms with subtly different scopes, Mondo decides on a single canonical entity and records the equivalences explicitly — solving the longstanding problem that 'congenital heart disease' in OMIM, Orphanet and ICD don't quite line up.
Mondo is now adopted by GA4GH, Open Targets, the European Joint Programme on Rare Diseases, the NIH N3C COVID cohort, and most major rare-disease databases. Monthly releases ship on GitHub with full provenance and tracked rationale for every merge. CC BY 4.0.
What you'd use it for
- 01Use as the single disease vocabulary across a federated dataset
- 02Reconcile ICD, OMIM, Orphanet and MeSH terms that nearly — but not quite — match
- 03Annotate variants, cohorts and trials with stable cross-database identifiers
- 04Trace any merge or alignment back to its source via provenance metadata
How you access it
OWLOBOJSONRobot/ODK pipelineGitHub
Recent updates
- 22 Apr 2026Monthly release with cleaner cancer-subtype alignment to NCIt and 240 new ORDO equivalences.