Representing experimental variables with EFO

The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. 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. If you are new to ontologies, there is a short introduction on the subject available and a blog post by James Malone on what ontologies are for.

Browse

Browse EFO with EBI's OLS or The NCBO BioPortal (external). You can also search EFO using the search box, above. The EFO source ontology can be viewed on GitHub at https://github.com/EBISPOT/efo.

Submit

Submit new terms or report bugs using our GitHub issue tracker or if you prefer to e-mail us please contact efo-users [at] ebi.ac.uk. For EFO announcements and monthly updates please join the efo-users public mailing list efo-users public mailing list.

Download

Download the latest release of EFO in OWL format. There is an OBO format version and an inferred OWL view. Read the latest Release Notes.. You can also get previous releases by release day e.g. http://www.ebi.ac.uk/efo/releases/v2017-10-16/efo.owl

FAQ

Read more about EFO or see the Frequently Asked Questions. You can also read about ontologies in James Malone's blog. To cite EFO see the publication here.

Tools

We provide tools to support the development and use of EFO such as Webulous, a tools for creating new terms from Google Sheet, and Urigen, a URI creation manager, and Bubastis, an ontology diff tool, and the EBI RDF Platform See the complete list of tools from the SPOT team.

Contact

Please email the EFO user list with any questions or comments. EFO is released under the Apache 2.0 license and with the following terms of use.