{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,27]],"date-time":"2025-12-27T04:33:37Z","timestamp":1766810017556,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T00:00:00Z","timestamp":1606262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004410","name":"Scientific and Technological Research Council of Turkey","doi-asserted-by":"publisher","award":["118E131","5180088"],"award-info":[{"award-number":["118E131","5180088"]}],"id":[{"id":"10.13039\/501100004410","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Defense Advanced Research Projects Agency Communicating with Computers Program","award":["W911NF-15-1-0544"],"award-info":[{"award-number":["W911NF-15-1-0544"]}]},{"name":"Innovative Medicines Initiative Joint Undertaking","award":["IMI 115446"],"award-info":[{"award-number":["IMI 115446"]}]},{"name":"European Union\u2019s Seventh Framework Programme","award":["FP7\/2007\u20132013"],"award-info":[{"award-number":["FP7\/2007\u20132013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Visualization of cellular processes and pathways is a key recurring requirement for effective biological data analysis. There is a considerable need for sophisticated web-based pathway viewers and editors operating with widely accepted standard formats, using the latest visualization techniques and libraries.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a web-based tool named Newt for viewing, constructing and analyzing biological maps in standard formats such as SBGN, SBML and SIF.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Newt\u2019s source code is publicly available on GitHub and freely distributed under the GNU LGPL. Ample documentation on Newt can be found on http:\/\/newteditor.org and on YouTube.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa850","type":"journal-article","created":{"date-parts":[[2020,9,18]],"date-time":"2020-09-18T11:37:07Z","timestamp":1600429027000},"page":"1475-1477","source":"Crossref","is-referenced-by-count":40,"title":["Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps"],"prefix":"10.1093","volume":"37","author":[{"given":"Hasan","family":"Balci","sequence":"first","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"}]},{"given":"Metin Can","family":"Siper","sequence":"additional","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"},{"name":"Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University , Portland, OR 97239, USA"}]},{"given":"Nasim","family":"Saleh","sequence":"additional","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"}]},{"given":"Ilkin","family":"Safarli","sequence":"additional","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"},{"name":"University of Utah Visualization Design Lab, School of Computing, , Salt Lake City, UT 84112, USA"}]},{"given":"Ludovic","family":"Roy","sequence":"additional","affiliation":[{"name":"European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Universit\u00e9 de Lyon , 69007 Lyon, France"}]},{"given":"Merve","family":"Kilicarslan","sequence":"additional","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"}]},{"given":"Rumeysa","family":"Ozaydin","sequence":"additional","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7137-4171","authenticated-orcid":false,"given":"Alexander","family":"Mazein","sequence":"additional","affiliation":[{"name":"European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Universit\u00e9 de Lyon , 69007 Lyon, France"},{"name":"University of Luxembourg Luxembourg Centre for Systems Biomedicine, , L-4367 Belvaux, Luxembourg"}]},{"given":"Charles","family":"Auffray","sequence":"additional","affiliation":[{"name":"European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Universit\u00e9 de Lyon , 69007 Lyon, France"}]},{"given":"\u00d6zg\u00fcn","family":"Babur","sequence":"additional","affiliation":[{"name":"Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University , Portland, OR 97239, USA"},{"name":"University of Massachusetts Boston Computer Science Department, , Boston, MA 02125, USA"}]},{"given":"Emek","family":"Demir","sequence":"additional","affiliation":[{"name":"Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University , Portland, OR 97239, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7153-0784","authenticated-orcid":false,"given":"Ugur","family":"Dogrusoz","sequence":"additional","affiliation":[{"name":"Bilkent University i-Vis Research Lab, Computer Engineering Department, , Ankara 06800, Turkey"}]}],"member":"286","published-online":{"date-parts":[[2020,11,25]]},"reference":[{"key":"2023051709343084400_btaa850-B1","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1145\/1924421.1924439","article-title":"Design principles for visual communication","volume":"54","author":"Agrawala","year":"2011","journal-title":"Commun. ACM"},{"key":"2023051709343084400_btaa850-B2","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1186\/1471-2164-15-642","article-title":"Integrating biological pathways and genomic profiles with chibe 2","volume":"15","author":"Babur","year":"2014","journal-title":"BMC Genomics"},{"key":"2023051709343084400_btaa850-B3","doi-asserted-by":"crossref","first-page":"2620","DOI":"10.1093\/bioinformatics\/btz969","article-title":"cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats","volume":"36","author":"Balaur","year":"2020","journal-title":"Bioinformatics"},{"key":"2023051709343084400_btaa850-B4","doi-asserted-by":"crossref","first-page":"D691","DOI":"10.1093\/nar\/gkq1018","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","author":"Croft","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023051709343084400_btaa850-B5","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1093\/bioinformatics\/btq407","article-title":"Editing, validating and translating of SBGN maps","volume":"26","author":"Czauderna","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051709343084400_btaa850-B6","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"Biopax \u2013 a community standard for pathway data sharing","volume":"28","author":"Demir","year":"2010","journal-title":"Nat. Biotechnol"},{"key":"2023051709343084400_btaa850-B7","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1186\/1471-2105-10-376","article-title":"Algorithms for effective querying of compound graph-based pathway databases","volume":"10","author":"Dogrusoz","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051709343084400_btaa850-B8","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1016\/j.ins.2008.11.017","article-title":"A layout algorithm for undirected compound graphs","volume":"179","author":"Dogrusoz","year":"2009","journal-title":"Inf. Sci"},{"key":"2023051709343084400_btaa850-B9","doi-asserted-by":"crossref","first-page":"e0197238","DOI":"10.1371\/journal.pone.0197238","article-title":"Efficient methods and readily customizable libraries for managing complexity of large networks","volume":"13","author":"Dogrusoz","year":"2018","journal-title":"PLoS One"},{"key":"2023051709343084400_btaa850-B10","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene- regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"Biosilico"},{"key":"2023051709343084400_btaa850-B11","doi-asserted-by":"crossref","first-page":"4496","DOI":"10.1093\/bioinformatics\/btz286","article-title":"MINERVA API and plugins: opening molecular network analysis and visualization to the community","volume":"35","author":"Hoksza","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051709343084400_btaa850-B12","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023051709343084400_btaa850-B13","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/j.tibtech.2012.08.003","article-title":"Wiring diagrams in biology: towards the standardized representation of biological information","volume":"30","author":"Junker","year":"2012","journal-title":"Trends Biotechnol"},{"key":"2023051709343084400_btaa850-B14","doi-asserted-by":"crossref","first-page":"e1004321","DOI":"10.1371\/journal.pcbi.1004321","article-title":"Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways","volume":"11","author":"King","year":"2015","journal-title":"PLoS Comput. Biol"},{"key":"2023051709343084400_btaa850-B15","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nbt.1558","article-title":"The systems biology graphical notation","volume":"27","author":"Le Nov\u00e8re","year":"2009","journal-title":"Nat. Biotechnol"},{"key":"2023051709343084400_btaa850-B16","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cell.2014.09.019","article-title":"yCaMKII shuttles Ca2+\/CaM to the nucleus to trigger CREB phosphorylation and gene expression","volume":"159","author":"Ma","year":"2014","journal-title":"Cell"},{"key":"2023051709343084400_btaa850-B17","first-page":"D489","article-title":"Pathway Commons 2019 Update: integration, analysis and exploration of pathway data","volume":"48","author":"Rodchenkov","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023051709343084400_btaa850-B18","doi-asserted-by":"crossref","first-page":"e0128985","DOI":"10.1371\/journal.pone.0128985","article-title":"SBGNViz: a tool for visualization and complexity management of SBGN process description maps","volume":"10","author":"Sari","year":"2015","journal-title":"PLoS One"},{"key":"2023051709343084400_btaa850-B19","doi-asserted-by":"crossref","first-page":"D661","DOI":"10.1093\/nar\/gkx1064","article-title":"WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research","volume":"46","author":"Slenter","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023051709343084400_btaa850-B20","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1093\/bioinformatics\/bts270","article-title":"Software support for SBGN maps: SBGN-ML and LibSBGN","volume":"28","author":"van Iersel","year":"2012","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa850\/34542339\/btaa850.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/10\/1475\/50360989\/btaa850.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/10\/1475\/50360989\/btaa850.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T09:49:37Z","timestamp":1684316977000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/10\/1475\/5917629"}},"subtitle":[],"editor":[{"given":"Wren","family":"Jonathan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,11,25]]},"references-count":20,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2021,6,16]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa850","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,5,15]]},"published":{"date-parts":[[2020,11,25]]}}}