The onology lookup service, the backend behind rols has been updated. As a result, the rols package is being re-implemented and will undergo changes in its user interface. The current interface will be maintained for Bioconductor release 3.2 and will be discontinued afterwards. Please see the rols github page for the new release.

The Ontology Lookup Service

The Ontology Lookup Service (OLS), developed at the European Bioinformatics Institute (EBI), is a unified web interface to query multiple ontologies from a single location. The new version of the OLS uses a REST API.

The rols package uses functionality from the httr package to query the OLS directly from R.

Changes in version 1.99.0

See section Changes in rols 2.0 in the vignette.

The CVParam class

The CVParam S4 class allows to generate controlled vocabulary parameters for all 88 ontologies through the OLS, as used in the frame of the Proteomics Standards Initiative (PSI) effort.

Installation

rols is available from the Bioconductor repository. The package and its dependencies can be installed

source("http://www.bioconductor.org/biocLite.R")
biocLite("rols")

See also the rols Bioconductor page for on-line access to the vignette and the reference manual.

Help

• rols comes with plenty of documentation. Have a start with the vignette vignette("rols", package="rols").

• Please direct your questions to the Bioconductor support site.

• For feature requests and bug reports, use GitHub issues