{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T21:59:59Z","timestamp":1774648799665,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,15]],"date-time":"2016-11-15T00:00:00Z","timestamp":1479168000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["12\/COEN\/18"],"award-info":[{"award-number":["12\/COEN\/18"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["13\/IA\/1881"],"award-info":[{"award-number":["13\/IA\/1881"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter, available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor (http:\/\/bioconductor.org\/packages\/miRNAmeConverter). The web interface is based on R Shiny and can be accessed under the URL http:\/\/www.systemsmedicineireland.ie\/tools\/mirna-name-converter\/. The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor (http:\/\/bioconductor.org\/packages\/miRBaseVersions.db). Minimum R version 3.3.0 is required.<\/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\/btw660","type":"journal-article","created":{"date-parts":[[2016,10,18]],"date-time":"2016-10-18T20:17:23Z","timestamp":1476821843000},"page":"592-593","source":"Crossref","is-referenced-by-count":55,"title":["miRNAmeConverter: an R\/bioconductor package for translating mature miRNA names to different miRBase versions"],"prefix":"10.1093","volume":"33","author":[{"given":"Stefan J","family":"Haunsberger","sequence":"first","affiliation":[{"name":"Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niamh M C","family":"Connolly","sequence":"additional","affiliation":[{"name":"Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jochen H M","family":"Prehn","sequence":"additional","affiliation":[{"name":"Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,11,15]]},"reference":[{"key":"2023020204431896400_btw660-B1","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1261\/rna.2183803","article-title":"A uniform system for microRNA annotation","volume":"9","author":"Ambros","year":"2003","journal-title":"RNA (New York, N.Y.)"},{"key":"2023020204431896400_btw660-B2","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2023020204431896400_btw660-B3","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1093\/nar\/gki200","article-title":"Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis","volume":"33","author":"Cheng","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020204431896400_btw660-B4","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkh023","article-title":"The microRNA Registry","volume":"32(Database issue)","author":"Griffiths-Jones","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020204431896400_btw660-B5","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1093\/nar\/gkt1266","article-title":"MiRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions","volume":"42","author":"Hsu","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204431896400_btw660-B6","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/nar\/gkt1181","article-title":"MiRBase: annotating high confidence microRNAs using deep sequencing data","volume":"42","author":"Kozomara","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204431896400_btw660-B7","doi-asserted-by":"crossref","first-page":"e42390","DOI":"10.1371\/journal.pone.0042390","article-title":"miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets","volume":"7","author":"Lu","year":"2012","journal-title":"PLoS One"},{"key":"2023020204431896400_btw660-B8","doi-asserted-by":"crossref","first-page":"btw008","DOI":"10.1093\/bioinformatics\/btw008","article-title":"EpimiRBase: a comprehensive database of microRNA-epilepsy associations","volume":"32","author":"Mooney","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020204431896400_btw660-B9","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1038\/ncb1373","article-title":"The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation","volume":"8","author":"Naguibneva","year":"2006","journal-title":"Nat. Cell Biol"},{"key":"2023020204431896400_btw660-B10","first-page":"1","article-title":"miRBase tracker: keeping track of microRNA annotation changes","volume":"2014","author":"Vandesompele","year":"2014","journal-title":"Database"},{"key":"2023020204431896400_btw660-B11","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s12935-015-0192-2","article-title":"MicroRNA-378-5p suppresses cell proliferation and induces apoptosis in colorectal cancer cells by targeting BRAF","volume":"15","author":"Wang","year":"2015","journal-title":"Cancer Cell Int"},{"key":"2023020204431896400_btw660-B12","article-title":"miRecords: an integrated resource for microRNA-target interactions","volume":"37(SUPPL. 1)","author":"Xiao","year":"2009","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/592\/49037955\/bioinformatics_33_4_592.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/592\/49037955\/bioinformatics_33_4_592.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:48:24Z","timestamp":1675313304000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/4\/592\/2606064"}},"subtitle":[],"editor":[{"given":"Cenk","family":"Sahinalp","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,11,15]]},"references-count":12,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw660","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,15]]},"published":{"date-parts":[[2016,11,15]]}}}