monarch-initiative / monarch-disease-ontology-retired Goto Github PK

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.

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.

See README-editors

• disease2go.tsv
• disease2go.obo