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MonDO (Monarch Disease Ontology) is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.

The procedure is broken into the following steps:

  1. Pre-processing of ontologies -- see the src/ directory
  2. Gathering of loose ontology mappings, and translating these into weighted candidate axioms
  3. Estimation of the most likely Ontology using kBOOM
  4. Merging equivalence sets and post-processing.

See the Makefile in the src/ontology directory for the execution of these steps.


Each disease resource or ontology is pre-processed. In some cases, only a subset of the ontology is used

  • ORDO/Orphanet
  • DO
  • GARD -- aligned as post-processing step
  • OMIM -- note we only use labels from OMIM
  • MedGen -- not yet incorporated
  • NCIT -- aligned as post-processing step
  • OMIA -- Mendelian diseases in non-human animals
  • MESH -- We use MEDIC as our initial pre-processed set
  • DiseaseClusters -- Additional groupings of OMIM. Includes DECIPHER.

Translating mappings to weighted candidate axioms

We use mappings as an input, but not as an end-goal. Our end goal is a coherent merged ontology, with strictly defined relationships between them (next step). However, we make use of mappings to generate candidate weighted axioms.

We make use of some ready-made mappings. Additionally, we supplant these with our own using approaches such as entity matching.

MonDO Curators Instructions

See README-editors