Greene Daniel, Richardson Sylvia, Turro Ernest
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.
Bioinformatics. 2017 Apr 1;33(7):1104-1106. doi: 10.1093/bioinformatics/btw763.
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.
本体是用于编码和分析生物医学数据的广泛使用的结构，但缺乏简单且一致的工具使得对此类数据的探索性和系统性分析变得不必要地困难。在此，我们展示了三个旨在简化此类程序的软件包。ontologyIndex软件包能够将任意本体读入R，支持通过原生R类型表示本体对象，并提供一组简洁高效的查询本体的功能。ontologySimilarity和ontologyPlot通过直接可视化和语义相似性计算功能（包括统计例程）扩展了ontologyIndex。
ontologyIndex、ontologyPlot和ontologySimilarity均可在综合R存档网络网站（https://cran.r-project.org/web/packages/ ）上获取。
Daniel Greene，dg333@cam.ac.uk。
补充数据可在《生物信息学》在线获取。
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