{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T03:03:02Z","timestamp":1783738982161,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,1,6]],"date-time":"2017-01-06T00:00:00Z","timestamp":1483660800000},"content-version":"vor","delay-in-days":7,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","award":["RG65966"],"award-info":[{"award-number":["RG65966"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UP_ 0801\/1"],"award-info":[{"award-number":["MC_UP_ 0801\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>ontologyIndex, ontologyPlot and ontologySimilarity are all available on the Comprehensive R Archive Network website under https:\/\/cran.r-project.org\/web\/packages\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw763","type":"journal-article","created":{"date-parts":[[2016,11,29]],"date-time":"2016-11-29T12:06:33Z","timestamp":1480421193000},"page":"1104-1106","source":"Crossref","is-referenced-by-count":162,"title":["ontologyX: a suite of R packages for working with ontological data"],"prefix":"10.1093","volume":"33","author":[{"given":"Daniel","family":"Greene","sequence":"first","affiliation":[{"name":"MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge, UK"},{"name":"Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Institute for Medical Research, Wellcome Trust\/MRC Building, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvia","family":"Richardson","sequence":"additional","affiliation":[{"name":"MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernest","family":"Turro","sequence":"additional","affiliation":[{"name":"MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge, UK"},{"name":"Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Institute for Medical Research, Wellcome Trust\/MRC Building, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,12,30]]},"reference":[{"key":"2023020205003540800_btw763-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-218","article-title":"OntoCAT\u2013simple ontology search and integration in Java, R and REST\/JavaScript","volume":"12","author":"Adamusiak","year":"2011","journal-title":"BMC Bioinf"},{"key":"2023020205003540800_btw763-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v040.i08","article-title":"Rcpp: Seamless R and C\u2009++ integration","volume":"40","author":"Eddelbuettel","year":"2011","journal-title":"J. Stat. Softw"},{"key":"2023020205003540800_btw763-B3","doi-asserted-by":"crossref","first-page":"1.","DOI":"10.1186\/1471-2105-8-166","article-title":"GOSim\u2013an R-package for computation of information theoretic GO similarities between terms and gene products","volume":"8","author":"Fr\u00f6hlich","year":"2007","journal-title":"BMC Bioinf"},{"key":"2023020205003540800_btw763-B4","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1002\/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N","article-title":"An open graph visualization system and its applications to software engineering","volume":"30","author":"Gansner","year":"2000","journal-title":"Softw. Pract. Exp"},{"key":"2023020205003540800_btw763-B5","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene ontology consortium: going forward","volume":"43","author":"Gene Ontology Consortium","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020205003540800_btw763-B6","author":"Gentleman","year":"2016"},{"key":"2023020205003540800_btw763-B7","author":"Greene","year":"2016"},{"key":"2023020205003540800_btw763-B8","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1016\/j.ajhg.2016.01.008","article-title":"Phenotype similarity regression for identifying the genetic determinants of rare diseases","volume":"98","author":"Greene","year":"2016","journal-title":"Am. J. Hum. Genet"},{"key":"2023020205003540800_btw763-B9","author":"Hansen","year":"2016"},{"key":"2023020205003540800_btw763-B10","doi-asserted-by":"crossref","first-page":"D966","DOI":"10.1093\/nar\/gkt1026","article-title":"The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data","volume":"42","author":"K\u00f6hler","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020205003540800_btw763-B11","author":"Lin","year":"1998"},{"key":"2023020205003540800_btw763-B12","author":"Overton","year":"2015"},{"key":"2023020205003540800_btw763-B13","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1613\/jair.514","article-title":"Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language","volume":"11","author":"Resnik","year":"1999","journal-title":"J. Artif. Intell. Res. (JAIR)"},{"key":"2023020205003540800_btw763-B14","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt1346","article-title":"The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration","volume":"25","author":"Smith","year":"2007","journal-title":"Nat. Biotechnol"},{"key":"2023020205003540800_btw763-B15","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci"},{"key":"2023020205003540800_btw763-B16","doi-asserted-by":"crossref","first-page":"1.","DOI":"10.1186\/s13073-015-0151-5","article-title":"Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders","volume":"7","author":"Westbury","year":"2015","journal-title":"Genome Med"},{"key":"2023020205003540800_btw763-B17","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1093\/bioinformatics\/btq064","article-title":"GOSemSim: an R package for measuring semantic similarity among GO terms and gene products","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020205003540800_btw763-B18","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btu684","article-title":"DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/7\/1104\/49038303\/bioinformatics_33_7_1104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/7\/1104\/49038303\/bioinformatics_33_7_1104.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:01:10Z","timestamp":1675314070000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/7\/1104\/2843897"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,12,30]]},"references-count":18,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2017,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw763","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,4,1]]},"published":{"date-parts":[[2016,12,30]]}}}