getOntology: Obtain the EFO and UBERON ontology

In waldronlab/bugsigdbr: R-side access to published microbial signatures from BugSigDB

Obtain the EFO and UBERON ontology

Description

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.

Usage

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")

waldronlab/bugsigdbr documentation built on Oct. 31, 2024, 3:43 a.m.