MonDO (Monarch Disease Ontology) is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. Original versions of MonDO were constructed entirely automatically and used the IDs of source databases and ontologies. Later, additional manually curated cross-ontology axioms were added, and a native MONDO ID system was used to avoid confusion with source databases.

One feature of MONDO is that it goes beyond loose xrefs. It curated precise 1:1 equivalence axioms connecting to other resources, validated by OWL reasoning. This means it is safe to propagate across these from OMIM, Orphanet, EFO, DOID (soon NCIT).

These precise mappings are available in two ways depending on the format

  • the .owl edition uses OWL equivalence axioms directly in the ontology. Note this makes it harder to browse in some portals, but this edition may be preferable for computational use. The owl edition also includes axiomatization using CL, Uberon, GO, HP, RO, NCBITaxon.
  • the .obo versions are simpler, lacks inter-ontology axiomatization, and lack equivalence axioms to other databases; instead xrefs are used as the linking mechanism. If the ID is one of Orphanet, OMIM, DOID or EFO then the xref precisely shadows the equivalence axiom.


  • - original tracker, primarily for examining kboom output and for feeding back changes to sources
  • - new tracker primarily for curating the grouped classes


mondo.owl Main OWL edition Complete ontology, plus inter-ontology equivalence axioms. Uses MONDO IDs.
mondo.obo obo-format edition As OWL, but omits equivalence axioms. xrefs can be used as proxy for equivalence. Uses MONDO IDs
mondo.json json edition Equivalent to the OWL edition
mondo/subsets/mondo-minimal.owl Minimal OWL edition. Complete logical axioms, no textual definitions, subsets
mondo/subsets/mondo-minimal.obo Minimal OBO edition. Identical to Minimal OWL edition, in OBO Format
mondo/subsets/mondo-minimal.json Minimal JSON edition. Identical to Minimal OWL edition, in OBO Graph JSON Format

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