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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 version 2.0 branch 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. It also provides Simple Object Access Protocol (SOAP) webservice for programmatic access.

The rols R package

The rols package uses functionality from the SSOAP and XMLSchema packages to query the OLS directly from R. It also uses some functionality from the Biobase package.

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.

The code on github is for sharing, testing, issue tracking and forking/pulling purposes. The official source code is available from the Bioconductor svn server. Get is with

svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rols

(user name: readonly, password: readonly)

Help

rols comes with plenty of documentation. Have a start with the vignette vignette("rols", package="rols"). Do not hesitate to contact me for questions/comments/suggestions.

Building from source

Some of the functions in rols are documented with the roxygen2 (CRAN package). The respective Rd pages have been created with

R --vanilla -e "library(roxygen2); roxygenize('"$(PKG)"', roclets=\"rd\")";

Note that only the rd roclet has been used, i.e. only roxygen's Rd-generation functionality. roxygen can also generate the NAMESPACE (namespace roclet) and parts of (?) the DESCRIPTION (previous and collate roclet) files, which is not used here. If all roclets are used, some original data will be overwritten.