Retrieving Information from the EBI Ontology Lookup Service (OLS) • OLSr

The Ontology Lookup Service (OLS) is a repository of biomedical ontologies provided by the European Bioinformatics Institute (‘EMBL-EBI’). OLSr provides an interface to this service, allowing discovery of ontologies, terms, and relations. Results are presented in a ‘tidy’ framework, so that manipulation tasks are easily accomplished with verbs such as ‘filter()’, ‘select()’, and ‘mutate()’. An effort is made to integrate with other packages useful for more comprehensive biological and ontological analysis.

Installation

Install the development version of OLSr with

if (!"remotes" in rownames(installed.packages()))
    install.packages("remotes", repos = "https://cran.r-project.org")
devtools::install_github("mtmorgan/OLSr")

Attach the installed package to your R session with

library(OLSr)

Use

The introductory vignette outlines common use cases, including

Discovering ontologies available in the OLS.
Retrieving terms within an ontology
Retrieving relatives (parents, ancestors, children, descendents) of terms.

The CELLxGENE case study vignette outlines ontology representation as graphs, and manipulation and visualization using igraph, visNetwork and other R packages.

OLSr uses a cache to minimize the number of calls to the OLS; the introductory vignette includes a short section discussing cache management.

Next steps

See the introductory vignette for next steps.