What ontology is used for disease and phenotype terms?

The Open Targets Platform uses a customised version of the Experimental Factor Ontology (EFO) to describe diseases and phenotypes.

Our modified EFO ontology consists of a subset of EFO terms in addition to terms from other ontologies (e.g. Human Phenotype Ontology - HPO) for which an EFO term is not available.

The benefits of using EFO include:

  • It is an application ontology, therefore it can incorporate parts (or the whole) of other ontologies, such as the rare disease ontology ORDO
  • It is able to bring in additional (not disease only) ontologies
  • It can easily accommodate our requests for new ontology terms in addition to updates and changes, as Open Targets and the EFO team collaborate closely
  • It is the ontology of controlled vocabulary used by the GWAS catalog and the Expression Atlas. Therefore, no extra step was needed when incorporating those two data sources in our pipeline

When integrating evidence and disease/phenotype annotation data, we map terms provided by our data providers to our modified EFO ontology using OnToma.

For more information on ontologies in the Open Targets Platform, you can read our posts on the Open Targets Blog: on the migration from EFO2 to EFO3, and on the purpose of ontologies.