Obtain the EFO and UBERON ontology

Lightweight wrapper around ontologyIndex::get_ontology to parse the Experimental Factor Ontology (EFO) or the Uber-anatomy ontology (UBERON) from OBO format into an R object.

getOntology(onto = c("efo", "uberon"), cache = TRUE)

Arguments

onto

character. Ontology to obtain. Should be either "efo" (default) to obtain the Experimental Factor Ontology (EFO) or "uberon" to obtain the Uber-anatomy ontology (UBERON).

cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

An object of class ontology_index as defined in the ontologyIndex package.

References

EFO: https://www.ebi.ac.uk/ols/ontologies/efo

UBERON: https://www.ebi.ac.uk/ols/ontologies/uberon

See also

get_ontology from the ontologyIndex package.

Examples

 uberon <- getOntology("uberon")
#> Using cached version from 2024-10-30 16:01:10