is a Ontology.
The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology.
biological systems, biomedical, health, phenotype
infores:efo
Unknown
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| efo.owl | EFO OWL | efo.owl (229.5 MB) | OntologyProduct | owl | The latest release of EFO in OWL format |
| efo.obo | EFO OBO | efo.obo (61.1 MB) | OntologyProduct | obo | The latest release of EFO in OBO format |
| efo.ols | EFO in OLS | efo | GraphicalInterface | http | Browse EFO with EBI's Ontology Lookup... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| ubkg.neo4j | UBKG Neo4j Docker Distribution | ubkg-downloads.xconsortia.org | GraphProduct | ❔ | Turnkey neo4j distributions that depl... |
| ubkg.csv | UBKG Ontology CSV Files | ubkg-downloads.xconsortia.org | GraphProduct | csv | Ontology CSV files that can be import... |
| clinicalkg.graph | CKG Graph Dump | 1 | GraphProduct | mixed | Neo4j database dump of the Clinical K... |
| clo.owl | clo.owl | clo.owl (2.0 MB) | OntologyProduct | owl | Cell Line Ontology in OWL format |
| microbiomekg.api | MicrobiomeKG Plover API | mbkp | ProgrammingInterface | http | TRAPI web API for querying MicrobiomeKG |
| epigraphdb.graph | EpiGraphDB Graph Database | graph-database | GraphProduct | neo4j | Integrated graph knowledge base combi... |
| cancer-genome-interpreter.clinicalkg.graph | CKG Graph Dump | 1 | GraphProduct | mixed | Neo4j database dump of the Clinical K... |
| ckg.graph | CKG Graph Database Dump | 1 | GraphProduct | neo4j | Graph database dump and additional re... |
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 most recently, 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).
EFO has undergone significant restructuring in version 3, particularly in the disease branch, to improve classification based on current medical understanding and alignment with existing domain ontologies. This was achieved through mapping the EFO disease and disease staging branches to the Monarch Disease Ontology (MONDO).
EFO is actively maintained with regular releases available through its GitHub repository. It is widely used in biomedical resources including:
Users can browse EFO through the EBI’s Ontology Lookup Service (OLS), submit new terms through GitHub issues, and download the latest release in various formats including OWL and OBO.
Created: June 04, 2025 | Last modified: February 18, 2026