{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T09:12:34Z","timestamp":1786180354277,"version":"3.56.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,15]]},"abstract":"<jats:p>Summary: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported.<\/jats:p>\n               <jats:p>Availability and implementation: DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/DOSE.html).<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0gcyu@connect.hku.hk or tqyhe@jnu.edu.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu684","type":"journal-article","created":{"date-parts":[[2014,10,18]],"date-time":"2014-10-18T02:34:38Z","timestamp":1413599678000},"page":"608-609","source":"Crossref","is-referenced-by-count":1144,"title":["DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis"],"prefix":"10.1093","volume":"31","author":[{"given":"Guangchuang","family":"Yu","sequence":"first","affiliation":[{"name":"1 \u00a01State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, 2Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632 and 3Guangdong Information Center, Guangzhou 510031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Gen","family":"Wang","sequence":"additional","affiliation":[{"name":"1 \u00a01State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, 2Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632 and 3Guangdong Information Center, Guangzhou 510031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guang-Rong","family":"Yan","sequence":"additional","affiliation":[{"name":"1 \u00a01State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, 2Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632 and 3Guangdong Information Center, Guangzhou 510031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing-Yu","family":"He","sequence":"additional","affiliation":[{"name":"1 \u00a01State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, 2Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632 and 3Guangdong Information Center, Guangzhou 510031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,10,17]]},"reference":[{"key":"2023020108553180900_btu684-B1","first-page":"9008","article-title":"Semantic similarity based on corpus statistics and lexical taxonomy","volume-title":"International Conference Research on Computational Linguistics (ROCLING X), Taiwan","author":"Jiang","year":"1997"},{"key":"2023020108553180900_btu684-B2","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1186\/1471-2105-12-266","article-title":"DOSim: an R package for similarity between diseases based on disease ontology","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020108553180900_btu684-B3","first-page":"296","article-title":"An information-theoretic definition of similarity","volume-title":"Proceedings of the Fifteenth International Conference on Machine Learning","author":"Lin","year":"1998"},{"key":"2023020108553180900_btu684-B4","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2164-10-S1-S6","article-title":"Annotating the human genome with disease ontology","volume":"10","author":"Osborne","year":"2009","journal-title":"BMC Genomics"},{"key":"2023020108553180900_btu684-B5","doi-asserted-by":"crossref","first-page":"D553","DOI":"10.1093\/nar\/gks1244","article-title":"The disease and gene annotations (DGA): an annotation resource for human disease","volume":"41","author":"Peng","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020108553180900_btu684-B6","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. Artifical Intell. Res."},{"key":"2023020108553180900_btu684-B7","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1186\/1471-2105-7-302","article-title":"A new measure for functional similarity of gene products based on gene ontology","volume":"7","author":"Schlicker","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020108553180900_btu684-B8","doi-asserted-by":"crossref","first-page":"D940","DOI":"10.1093\/nar\/gkr972","article-title":"Disease Ontology: a backbone for disease semantic integration","volume":"40","author":"Schriml","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020108553180900_btu684-B9","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","article-title":"A new method to measure the semantic similarity of GO terms","volume":"23","author":"Wang","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020108553180900_btu684-B10","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":"2023020108553180900_btu684-B11","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS J. Integr. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/608\/49011315\/bioinformatics_31_4_608.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/608\/49011315\/bioinformatics_31_4_608.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:22:04Z","timestamp":1675282924000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/4\/608\/2748221"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,17]]},"references-count":11,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2015,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu684","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,17]]}}}