{"id":"https://openalex.org/W2536204818","doi":"https://doi.org/10.1093/bioinformatics/btw660","title":"miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions","display_name":"miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions","publication_year":2016,"publication_date":"2016-10-18","ids":{"openalex":"https://openalex.org/W2536204818","doi":"https://doi.org/10.1093/bioinformatics/btw660","mag":"2536204818","pmid":"https://pubmed.ncbi.nlm.nih.gov/27797767"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw660","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw660","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://figshare.com/articles/journal_contribution/miRNAmeConverter_an_R_bioconductor_package_for_translating_mature_miRNA_names_to_different_miRBase_versions_/10789313","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085864283","display_name":"Stefan J. Haunsberger","orcid":"https://orcid.org/0000-0002-4993-5654"},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Stefan J Haunsberger","raw_affiliation_strings":["Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006157798","display_name":"Niamh M. C. Connolly","orcid":"https://orcid.org/0000-0002-6005-1307"},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Niamh M C Connolly","raw_affiliation_strings":["Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075015717","display_name":"Jochen H.M. Prehn","orcid":"https://orcid.org/0000-0003-3479-7794"},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Jochen H M Prehn","raw_affiliation_strings":["Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5075015717"],"corresponding_institution_ids":["https://openalex.org/I142762351"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9925,"has_fulltext":false,"cited_by_count":64,"citation_normalized_percentile":{"value":0.85099026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"33","issue":"4","first_page":"592","last_page":"593"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9681000113487244,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9681000113487244,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","score":0.00279999990016222,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.0019000000320374966,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9953644871711731},{"id":"https://openalex.org/keywords/mirbase","display_name":"MiRBase","score":0.9396662712097168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7458814978599548},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5479356050491333},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5070173740386963},{"id":"https://openalex.org/keywords/eriophyidae","display_name":"Eriophyidae","score":0.4700768291950226},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.37659960985183716},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.33812111616134644},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2242443561553955},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18422725796699524},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.15547746419906616},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13781806826591492}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9953644871711731},{"id":"https://openalex.org/C49305753","wikidata":"https://www.wikidata.org/wiki/Q6826947","display_name":"MiRBase","level":4,"score":0.9396662712097168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7458814978599548},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5479356050491333},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5070173740386963},{"id":"https://openalex.org/C2779090125","wikidata":"https://www.wikidata.org/wiki/Q841786","display_name":"Eriophyidae","level":3,"score":0.4700768291950226},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37659960985183716},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.33812111616134644},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2242443561553955},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18422725796699524},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.15547746419906616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13781806826591492},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw660","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw660","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27797767","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27797767","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:epubs.rcsi.ie:physiolart-1135","is_oa":false,"landing_page_url":"https://epubs.rcsi.ie/physiolart/114","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Physiology and Medical Physics Articles","raw_type":"text"},{"id":"pmh:oai:figshare.com:article/10789313","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/miRNAmeConverter_an_R_bioconductor_package_for_translating_mature_miRNA_names_to_different_miRBase_versions_/10789313","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/10789313","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/miRNAmeConverter_an_R_bioconductor_package_for_translating_mature_miRNA_names_to_different_miRBase_versions_/10789313","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7287228899","display_name":"BCL-2 family proteins and cellular bioenergetics in the control of cell survival: Towards novel predictive and prognostic markers for disease progression and therapy responses in colorectal cancer patients","funder_award_id":"13/IA/1881","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G8247513913","display_name":"microRNA as novel therapeutic targets and disease biomarkers in Alzheimer's Disease, Frontotemporal dementia and Amyotrophic lateral sclerosis (NEURO-MIR)","funder_award_id":"12/COEN/18","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"}],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1993679825","https://openalex.org/W2003816656","https://openalex.org/W2016106370","https://openalex.org/W2062010389","https://openalex.org/W2075362596","https://openalex.org/W2077327925","https://openalex.org/W2098318517","https://openalex.org/W2123079914","https://openalex.org/W2134097555","https://openalex.org/W2134118500","https://openalex.org/W2137257434","https://openalex.org/W2261997464","https://openalex.org/W6680041271"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2183978128","https://openalex.org/W2011682793","https://openalex.org/W2003713452","https://openalex.org/W2891209917","https://openalex.org/W2952528394","https://openalex.org/W43224192","https://openalex.org/W2536204818","https://openalex.org/W90653389","https://openalex.org/W2162995709"],"abstract_inverted_index":{"Summary:":[0],"The":[1,89,107,138,158,175],"miRBase":[2,17,24,105],"database":[3,176],"is":[4,16,142,150,161,181,201],"the":[5,13,44,56,81,133,146,171,184],"central":[6],"and":[7,12,64,76,130,136,166,188],"official":[8],"repository":[9],"for":[10],"miRNAs":[11,43],"current":[14],"release":[15],"version":[18,32,199],"21.0.":[19],"Name":[20],"changes":[21],"in":[22,28,121,128],"different":[23],"releases":[25],"cause":[26],"inconsistencies":[27,61],"miRNA":[29,86,100,118],"names":[30,101,119],"from":[31,153,192],"to":[33,102,116],"version.":[34],"When":[35],"working":[36],"with":[37,51,84,114],"only":[38],"a":[39,72,124],"small":[40],"number":[41],"of":[42,54,59,97,123,132],"translation":[45,96],"can":[46,167,189],"be":[47,168,190],"done":[48],"manually.":[49],"However,":[50],"large":[52],"sets":[53],"miRNAs,":[55],"necessary":[57],"correction":[58],"such":[60],"becomes":[62],"burdensome":[63],"error-prone.":[65],"We":[66],"developed":[67],"miRNAmeConverter":[68,139,178],",":[69],"available":[70,152,210],"as":[71],"Bioconductor":[73,154,193],"R":[74,115,140,164,198],"package":[75,141,186],"web":[77,108,159],"interface":[78,109,160],"that":[79,177],"addresses":[80],"challenges":[82],"associated":[83],"mature":[85,99],"name":[87],"inconsistencies.":[88],"main":[90],"algorithm":[91],"implemented":[92],"enables":[93,110],"high-throughput":[94],"automatic":[95],"species-independent":[98],"user":[103],"selected":[104],"versions.":[106],"users":[111],"less":[112],"familiar":[113],"translate":[117],"given":[120],"form":[122],"list":[125],"or":[126],"embedded":[127],"text":[129],"download":[131],"results.":[134],"Availability":[135],"Implementation:":[137],"open":[143],"source":[144],"under":[145,170],"Artistic-2.0":[147],"license.":[148],"It":[149],"freely":[151],"(":[155,194],"http://bioconductor.org/packages/miRNAmeConverter":[156],").":[157,196],"based":[162],"on":[163,180],"Shiny":[165],"accessed":[169],"URL":[172],"http://www.systemsmedicineireland.ie/tools/mirna-name-converter/":[173],".":[174],"depends":[179],"provided":[182],"by":[183],"annotation":[185],"miRBaseVersions.db":[187],"downloaded":[191],"http://bioconductor.org/packages/miRBaseVersions.db":[195],"Minimum":[197],"3.3.0":[200],"required.":[202],"Contact:":[203],"stefanhaunsberger@rcsi.ie.":[204],"Supplementary":[205,207],"information:":[206],"data":[208],"are":[209],"at":[211],"Bioinformatics":[212],"online.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}