title: ontologyX: a suite of R packages for working with ontological data.
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.
  
  
  
  ontologyIndex , ontologyPlot and ontologySimilarity are all available on the Comprehensive R Archive Network website under https://cran.r-project.org/web/packages/ .
  
  
  
  Daniel Greene dg333@cam.ac.uk.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge CB2 0SR, UK.|Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Greene
authors.affiliation: MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge CB2 0SR, UK.
authors.forename: Sylvia
authors.initials: S
authors.lastname: Richardson
authors.affiliation: MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge CB2 0SR, UK.|Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, UK.
authors.forename: Ernest
authors.initials: E
authors.lastname: Turro
mesh_terms: D064229:Biological Ontologies; D012984:Software