The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the NHGRI-EBI GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, Cell Ontology and the Monarch Disease Ontology (MONDO). The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets. EFO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We also add terms for external users when requested.
The latest version of the ontology can always be found attached to each EFO 3 release, found here: https://github.com/EBISPOT/efo/releases
You can explore EFO in the EMBL-EBI Ontology Lookup Service
Submit new terms or report bugs using our issue tracker, or join EFO mailing list for announcement and monthly update.
Editors of this ontology should use the edit version,
src/ontology/efo-edit.owl.
EFO is built using owlmake. To build the
release files, first install owlmake and make sure it is on your PATH. For
example, on an Apple silicon Mac:
mkdir -p ~/.local/bin
curl -fsSL https://github.com/EBISPOT/owlmake/releases/latest/download/om-macos-arm64 \
-o ~/.local/bin/om
chmod +x ~/.local/bin/omThen run om from the repository root to build the default targets, or run
om make gh_actions to execute the same build and QC target as EFO's GitHub
workflow.