Repository logo
 

ontologyX: a suite of R packages for working with ontological data

Published version
Peer-reviewed

Change log

Authors

Greene, D 
Turro, E 

Abstract

Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three packages which aim to simplify such procedures. The ontologyIndex package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies. ontologySimilarity and ontologyPlot extend ontologyIndex with functionality for straightforward visualization and semantic similarity calculations, including statistical routines.

AVAILABILITY AND IMPLEMENTATION: ontologyIndex, ontologyPlot and ontologySimilarity are all available on the Comprehensive R Archive Network website under https://cran.r-project.org/web/packages

Description

Keywords

Biological Ontologies, Software

Journal Title

Bioinformatics

Conference Name

Journal ISSN

1367-4803
1367-4811

Volume Title

2017

Publisher

Oxford University Press
Sponsorship
Cambridge University Hospitals NHS Foundation Trust (CUH) (BRC 2012-2017)
This work was supported by National Institute for Health Research award RG65966 (D.G. and E.T.) and the Medical Research Council programme grant MC_UP_ 0801/1 (D.G. and S.R.).