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.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| efo.owl | EFO OWL | efo.owl (229.5 MB) | Ontology | owl | The latest release of EFO in OWL format |
| efo.obo | EFO OBO | efo.obo (61.1 MB) | Ontology | obo | The latest release of EFO in OBO format |
| efo.ols | EFO in OLS | efo | Graphical Interface | http | Browse EFO with EBI's Ontology Lookup... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| ubkg.neo4j | UBKG Neo4j Docker Distribution | ubkg-downloads.xconsortia.org | Graph | neo4j | had primary source | Turnkey neo4j distributions that depl... |
| ubkg.csv | UBKG Ontology CSV Files | ubkg-downloads.xconsortia.org | Graph | csv | had primary source | Ontology CSV files that can be import... |
| clinicalkg.graph | CKG Graph Dump | 1 | Graph | mixed | had primary source | Neo4j database dump of the Clinical K... |
| microbiomekg.api | MicrobiomeKG Plover TRAPI API | mbkp | Programming Interface | http | had primary source | Plover-hosted TRAPI web API for query... |
| epigraphdb.graph | EpiGraphDB Graph Database | graph-database | Graph | neo4j | had primary source | Integrated graph knowledge base combi... |
| cancer-genome-interpreter.clinicalkg.graph | CKG Graph Dump | 1 | Graph | mixed | had primary source | Neo4j database dump of the Clinical K... |
| pharmebinet.json | PharMeBINet JSON Release | content (3.4 GB) | Graph | json | was derived from | PharMeBINet V3 JSON release (Zenodo v... |
| pharmebinet.tsv | PharMeBINet TSV Release | content (3.5 GB) | Graph | tsv | was derived from | PharMeBINet V3 TSV release (Zenodo ve... |
| pharmebinet.graphml | PharMeBINet GraphML Release | content (3.8 GB) | Graph | mixed | was derived from | PharMeBINet V3 GraphML release (Zenod... |
| pharmebinet.neo4j | PharMeBINet Neo4j Database | content (7.7 GB) | Graph | neo4j | was derived from | PharMeBINet V3 Neo4j database release... |
| pharmebinet.neo4j.dump | PharMeBINet Neo4j Dump | content (7.5 GB) | Graph | neo4j | was derived from | PharMeBINet V3 Neo4j dump release (Ze... |
| biobtree.api | BioBTree REST API | api | Programming Interface | http | had primary source | REST API for searching identifiers an... |
| genecards.web.interface | GeneCards Web Interface | www.genecards.org | Graphical Interface | http | had primary source | Web-based interface for searching and... |
| biobtree.graph.human-subgraph | BioBTree Knowledge Graph - Human Subgraph (KGX) | 20816742 | Graph | kgx | had primary source | Human-scoped, Neo4j-ready subgraph of... |
| genomickb.graph | GenomicKB Graph Dump | genomickb-a-knowledgebase-for-the-human-genome | Graph | http | had primary source | GenomicKB 1.0 Neo4j Database Dump (Re... |
| babel.compendia | Babel Compendia | compendia | Product | json | had primary source | Babel compendia, one file per Biolink... |
| pride-cv.obo | pride_cv.obo | pride_cv.obo (219.4 KB) | Ontology | obo | used | PRIDE Controlled Vocabulary in OBO fo... |
| pride-cv.owl | pride_cv.owl | pride_cv.owl (1.0 MB) | Ontology | owl | used | PRIDE Controlled Vocabulary in OWL fo... |
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: September 23, 2026