{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:32Z","timestamp":1753875812981,"version":"3.41.2"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,11,7]],"date-time":"2023-11-07T00:00:00Z","timestamp":1699315200000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Ministry of Education and Research","award":["031L0164A"],"award-info":[{"award-number":["031L0164A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resources, often providing the data in simple tab-delimited formats that differ between the databases. There is no standardized data format that can capture the nature of all these different interactions in detail.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Here, we propose the RNA interaction format (RIF) for the detailed representation of RNA\u2013RNA and RNA\u2013Protein interactions and provide reference implementations in C\/C++, Python, and JavaScript. RIF is released under licence GNU General Public License version 3 (GNU GPLv3) and is available on https:\/\/github.com\/RNABioInfo\/rna-interaction-format.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad665","type":"journal-article","created":{"date-parts":[[2023,11,9]],"date-time":"2023-11-09T20:50:20Z","timestamp":1699563020000},"source":"Crossref","is-referenced-by-count":0,"title":["RNA interaction format: a general data format for RNA interactions"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9938-1920","authenticated-orcid":false,"given":"Richard A","family":"Sch\u00e4fer","sequence":"first","affiliation":[{"name":"RNA-Biology and Bioinformatics, Institute of Biomedical Genetics, University of Stuttgart , Allmandring 31 , 70569 Stuttgart, Germany"}]},{"given":"Dominik","family":"Rabsch","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Georges-K\u00f6hler-Allee 106 , 79110 Freiburg, Germany"}]},{"given":"Guillaume E","family":"Scholz","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig , H\u00e4rtelstr. 16-18 , 04107 Leipzig, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter F","family":"Stadler","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig , H\u00e4rtelstr. 16-18 , 04107 Leipzig, Germany"}]},{"given":"Wolfgang R","family":"Hess","sequence":"additional","affiliation":[{"name":"Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg , Sch\u00e4nzlestr. 1 , 79104 Freiburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Georges-K\u00f6hler-Allee 106 , 79110 Freiburg, Germany"}]},{"given":"J\u00f6rg","family":"Fallmann","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig , H\u00e4rtelstr. 16-18 , 04107 Leipzig, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5377-2800","authenticated-orcid":false,"given":"Bj\u00f6rn","family":"Vo\u00df","sequence":"additional","affiliation":[{"name":"RNA-Biology and Bioinformatics, Institute of Biomedical Genetics, University of Stuttgart , Allmandring 31 , 70569 Stuttgart, Germany"}]}],"member":"286","published-online":{"date-parts":[[2023,11,7]]},"reference":[{"key":"2023111203123794500_btad665-B1","doi-asserted-by":"crossref","first-page":"167530","DOI":"10.1016\/j.jmb.2022.167530","article-title":"PEPPI: whole-proteome protein-protein interaction prediction through structure and sequence similarity, functional association, and machine learning","volume":"434","author":"Bell","year":"2022","journal-title":"J Mol Biol"},{"key":"2023111203123794500_btad665-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1748-7188-1-3","article-title":"Partition function and base pairing probabilities of RNA heterodimers","volume":"1","author":"Bernhart","year":"2006","journal-title":"Algorithms Mol Biol"},{"key":"2023111203123794500_btad665-B3","doi-asserted-by":"crossref","first-page":"D220","DOI":"10.1093\/nar\/gkz884","article-title":"snoDB: an interactive database of human snoRNA sequences, abundance and interactions","volume":"48","author":"Bouchard-Bourelle","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023111203123794500_btad665-B4","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1007\/3-540-45848-4_59","volume-title":"Graph Drawing","author":"Brandes","year":"2002"},{"year":"2018.","author":"Bray","key":"2023111203123794500_btad665-B5"},{"key":"2023111203123794500_btad665-B6","doi-asserted-by":"crossref","first-page":"btad172","DOI":"10.1093\/bioinformatics\/btad172","article-title":"sInterBase: a comprehensive database of Escherichia coli sRNA\u2013mRNA interactions","volume":"39","author":"Cohen","year":"2023","journal-title":"Bioinformatics"},{"key":"2023111203123794500_btad665-B7","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"The BioPAX community standard for pathway data sharing","volume":"28","author":"Demir","year":"2010","journal-title":"Nat Biotechnol"},{"key":"2023111203123794500_btad665-B8","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2005-6-5-r44","article-title":"The sequence ontology: a tool for the unification of genome annotations","volume":"6","author":"Eilbeck","year":"2005","journal-title":"Genome Biol"},{"key":"2023111203123794500_btad665-B9","doi-asserted-by":"crossref","first-page":"D194","DOI":"10.1093\/nar\/gkx864","article-title":"RISE: a database of RNA interactome from sequencing experiments","volume":"46","author":"Gong","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023111203123794500_btad665-B10","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nbt926","article-title":"The HUPO PSI\u2019s molecular interaction format\u2014a community standard for the representation of protein interaction data","volume":"22","author":"Hermjakob","year":"2004","journal-title":"Nat Biotechnol"},{"key":"2023111203123794500_btad665-B11","first-page":"D148","article-title":"miRTarBase 2020: updates to the experimentally validated microRNA\u2013target interaction database","volume":"48","author":"Huang","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023111203123794500_btad665-B12","first-page":"2","article-title":"The systems biology markup language (SBML): language specification for level 3 version 2 core","volume":"15","author":"Hucka","year":"2018","journal-title":"J Integr Bioinform"},{"key":"2023111203123794500_btad665-B13","doi-asserted-by":"crossref","first-page":"R17","DOI":"10.1186\/gb-2014-15-1-r17","article-title":"GraphProt: modeling binding preferences of RNA-binding proteins","volume":"15","author":"Maticzka","year":"2014","journal-title":"Genome Biol"},{"key":"2023111203123794500_btad665-B14","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1039\/b008780g","article-title":"Development of chemical markup language (CML) as a system for handling complex chemical content","volume":"25","author":"Murray-Rust","year":"2001","journal-title":"New J Chem"},{"key":"2023111203123794500_btad665-B15","doi-asserted-by":"crossref","first-page":"5493","DOI":"10.1093\/nar\/gkab340","article-title":"RNAnue: efficient data analysis for RNA\u2013RNA interactomics","volume":"49","author":"Sch\u00e4fer","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023111203123794500_btad665-B16","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"first-page":"850024","year":"2021","author":"Uhl","key":"2023111203123794500_btad665-B17"},{"key":"2023111203123794500_btad665-B18","doi-asserted-by":"crossref","first-page":"D248","DOI":"10.1093\/nar\/gkv1127","article-title":"sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria","volume":"44","author":"Wang","year":"2016","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad665\/53000531\/btad665.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/11\/btad665\/53287121\/btad665.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/11\/btad665\/53287121\/btad665.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,12]],"date-time":"2023-11-12T03:13:02Z","timestamp":1699758782000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad665\/7379667"}},"subtitle":[],"editor":[{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,11,1]]},"references-count":18,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad665","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,11,1]]},"published":{"date-parts":[[2023,11,1]]},"article-number":"btad665"}}