{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T15:43:39Z","timestamp":1774539819881,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,22]],"date-time":"2018-01-22T00:00:00Z","timestamp":1516579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61502125"],"award-info":[{"award-number":["61502125"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2016M590291"],"award-info":[{"award-number":["2016M590291"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>DincRNA aims to provide a comprehensive web-based bioinformatics toolkit to elucidate the entangled relationships among diseases and non-coding RNAs (ncRNAs) from the perspective of disease similarity. The quantitative way to illustrate relationships of pair-wise diseases always depends on their molecular mechanisms, and structures of the directed acyclic graph of Disease Ontology (DO). Corresponding methods for calculating similarity of pair-wise diseases involve Resnik\u2019s, Lin\u2019s, Wang\u2019s, PSB and SemFunSim methods. Recently, disease similarity was validated suitable for calculating functional similarities of ncRNAs and prioritizing ncRNA\u2013disease pairs, and it has been widely applied for predicting the ncRNA function due to the limited biological knowledge from wet lab experiments of these RNAs. For this purpose, a large number of algorithms and priori knowledge need to be integrated. e.g. \u2018pair-wise best, pairs-average\u2019 (PBPA) and \u2018pair-wise all, pairs-maximum\u2019 (PAPM) methods for calculating functional similarities of ncRNAs, and random walk with restart (RWR) method for prioritizing ncRNA\u2013disease pairs. To facilitate the exploration of disease associations and ncRNA function, DincRNA implemented all of the above eight algorithms based on DO and disease-related genes. Currently, it provides the function to query disease similarity scores, miRNA and lncRNA functional similarity scores, and the prioritization scores of lncRNA\u2013disease and miRNA\u2013disease pairs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/bio-annotation.cn:18080\/DincRNAClient\/<\/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\/bty002","type":"journal-article","created":{"date-parts":[[2018,1,19]],"date-time":"2018-01-19T14:01:56Z","timestamp":1516370516000},"page":"1953-1956","source":"Crossref","is-referenced-by-count":215,"title":["DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6665-6710","authenticated-orcid":false,"given":"Liang","family":"Cheng","sequence":"first","affiliation":[{"name":"Department of College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Sheng, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4508-5365","authenticated-orcid":false,"given":"Yang","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang Sheng, China"}]},{"given":"Jie","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Sheng, China"}]},{"given":"Meng","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Sheng, China"}]},{"given":"Qinghua","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang Sheng, China"}]}],"member":"286","published-online":{"date-parts":[[2018,1,22]]},"reference":[{"key":"2023012713560243600_bty002-B1","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1002\/humu.21466","article-title":"A new face and new challenges for Online Mendelian Inheritance in Man (OMIM\u00ae)","volume":"32","author":"Amberger","year":"2011","journal-title":"Hum. Mutat"},{"key":"2023012713560243600_bty002-B2","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/ng0504-431","article-title":"The genetic association database","volume":"36","author":"Becker","year":"2004","journal-title":"Nat. Genet"},{"key":"2023012713560243600_bty002-B3","doi-asserted-by":"crossref","first-page":"D262","DOI":"10.1093\/nar\/gkh021","article-title":"The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology","volume":"32","author":"Camon","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023012713560243600_bty002-B4","doi-asserted-by":"crossref","first-page":"D983","DOI":"10.1093\/nar\/gks1099","article-title":"LncRNADisease: a database for long-non-coding RNA-associated diseases","volume":"41","author":"Chen","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012713560243600_bty002-B5","doi-asserted-by":"crossref","first-page":"11338.","DOI":"10.1038\/srep11338","article-title":"Constructing lncRNA functional similarity network based on lncRNA\u2013disease associations and disease semantic similarity","volume":"5","author":"Chen","year":"2015","journal-title":"Sci. Rep"},{"key":"2023012713560243600_bty002-B6","doi-asserted-by":"crossref","first-page":"e99415","DOI":"10.1371\/journal.pone.0099415","article-title":"SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association","volume":"9","author":"Cheng","year":"2014","journal-title":"PLoS One"},{"key":"2023012713560243600_bty002-B7","doi-asserted-by":"crossref","first-page":"e75504.","DOI":"10.1371\/journal.pone.0075504","article-title":"SIDD: a semantically integrated database towards a global view of human disease","volume":"8","author":"Cheng","year":"2013","journal-title":"PLoS One"},{"key":"2023012713560243600_bty002-B8","doi-asserted-by":"crossref","first-page":"D1104","DOI":"10.1093\/nar\/gks994","article-title":"The comparative toxicogenomics database: update 2013","volume":"41","author":"Davis","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012713560243600_bty002-B9","doi-asserted-by":"crossref","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","article-title":"Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data","volume":"43","author":"Kibbe","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012713560243600_bty002-B10","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1101\/gr.118992.110","article-title":"Prioritizing candidate disease genes by network-based boosting of genome-wide association data","volume":"21","author":"Lee","year":"2011","journal-title":"Genome Res"},{"key":"2023012713560243600_bty002-B11","doi-asserted-by":"crossref","first-page":"D1070","DOI":"10.1093\/nar\/gkt1023","article-title":"HMDD v2.0: a database for experimentally supported human microRNA and disease associations","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023012713560243600_bty002-B12","first-page":"296","article-title":"An information-theoretic definition of similarity","author":"Lin","year":"1998","journal-title":"ICML"},{"key":"2023012713560243600_bty002-B13","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.jbi.2011.11.017","article-title":"Finding disease similarity based on implicit semantic similarity","volume":"45","author":"Mathur","year":"2012","journal-title":"J. Biomed. Inf"},{"key":"2023012713560243600_bty002-B14","first-page":"460","author":"Mitchell","year":"2003"},{"key":"2023012713560243600_bty002-B15","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkv1094","article-title":"Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers","volume":"44","author":"Ning","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012713560243600_bty002-B16","doi-asserted-by":"crossref","first-page":"e1000443.","DOI":"10.1371\/journal.pcbi.1000443","article-title":"Semantic similarity in biomedical ontologies","volume":"5","author":"Pesquita","year":"2009","journal-title":"PLoS Comput. Biol"},{"key":"2023012713560243600_bty002-B17","author":"Resnik","year":"1995"},{"key":"2023012713560243600_bty002-B18","first-page":"170","author":"Sqalli","year":"2012"},{"key":"2023012713560243600_bty002-B19","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1039\/C3MB70608G","article-title":"Inferring novel lncRNA\u2013disease associations based on a random walk model of a lncRNA functional similarity network","volume":"10","author":"Sun","year":"2014","journal-title":"Mol. bioSystems"},{"key":"2023012713560243600_bty002-B20","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1093\/bioinformatics\/btq241","article-title":"Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases","volume":"26","author":"Wang","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012713560243600_bty002-B21","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1953\/48937701\/bioinformatics_34_11_1953.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1953\/48937701\/bioinformatics_34_11_1953.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:27:29Z","timestamp":1674829649000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/11\/1953\/4820333"}},"subtitle":[],"editor":[{"given":"Cenk","family":"Sahinalp","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,1,22]]},"references-count":21,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty002","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,6,1]]},"published":{"date-parts":[[2018,1,22]]}}}