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

• DOI: 10.1093/bioinformatics/btw763
• Publication Date: 2016-11-29T12:06:33Z
• Authors: Daniel Greene; Sylvia Richardson; Ernest Turro
• Keywords: Representation

Abstract Summary Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple consistent tools has made exploratory systematic analysis such data unnecessarily difficult. Here we present three packages which aim to simplify procedures. The ontologyIndex package enables arbitrary ontologies be read into R, supports representation ontological objects by native R types, provides a parsimonius set performant functions querying ontologies. ontologySimilarity ontologyPlot extend with functionality straightforward visualization semantic similarity calculations, including statistical routines. Availability Implementation ontologyIndex, all available on Comprehensive Archive Network website under https://cran.r-project.org/web/packages/. Supplementary information at Bioinformatics online.