The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It 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.

A key feature of Mondo is that it goes beyond loose database cross-references (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 Online Mendelian Inheritance in Man (OMIM), Orphanet, Experimental Factor Ontology (EFO), Disease Ontology (DOID) and the neoplasm branch of National Cancer Institute Thesaurus (NCIt).

These precise mappings are available in three ways depending on the format:

  • the mondo-with-equivalent 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 primary release versions (mondo.owl, mondo.obo) are simpler, lacking owl equivalence axioms from Mondo classes to terms from other databases; instead, xrefs are used for linking these terms. If the ID is one of Orphanet, OMIM, DOID or EFO then the xref precisely shadows the equivalence axiom.
  • The mondo-with-equivalents json edition has all owl equivalencies as well as all xrefs to other disease sources.

Tracker

  • https://github.com/monarch-initiative/mondo/issues

Products

mondo.owl Main OWL edition Complete ontology. Uses MONDO IDs. Imports merged. The original mondo.owl without merged imports and with equivalence axioms can now be obtained from the release pages and is called mondo-with-equivalents.
mondo.obo obo-format edition As OWL. xrefs can be used as proxy for equivalence. Uses Mondo IDs.
mondo.json json edition Equivalent to the OWL edition.

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