{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T20:59:15Z","timestamp":1772830755153,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1928,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms.<\/jats:p>\n               <jats:p>We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those.<\/jats:p>\n               <jats:p>Availability: KEGGtranslator is freely available as a Java\u2122 Web Start application and for download at http:\/\/www.cogsys.cs.uni-tuebingen.de\/software\/KEGGtranslator\/. KGML files can be downloaded from within the application.<\/jats:p>\n               <jats:p>Contact: \u00a0clemens.wrzodek@uni-tuebingen.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr377","type":"journal-article","created":{"date-parts":[[2011,6,24]],"date-time":"2011-06-24T01:56:40Z","timestamp":1308880600000},"page":"2314-2315","source":"Crossref","is-referenced-by-count":59,"title":["KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats"],"prefix":"10.1093","volume":"27","author":[{"given":"Clemens","family":"Wrzodek","sequence":"first","affiliation":[{"name":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Zell","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,23]]},"reference":[{"key":"2023012511511995500_B1","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btr361","article-title":"JSBML: a flexible and entirely Java-based library for working with SBML","author":"Dr\u00e4ger","year":"2011","journal-title":"Bioinformatics."},{"key":"2023012511511995500_B2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1752-0509-2-39","article-title":"SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks","volume":"2","author":"Dr\u00e4ger","year":"2008","journal-title":"BMC Syst. Biol."},{"key":"2023012511511995500_B3","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1093\/bioinformatics\/btp170","article-title":"SBML2LaTeX: conversion of SBML files into human-readable reports","volume":"25","author":"Dr\u00e4ger","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511511995500_B4","article-title":"Converting KEGG pathway database to SBML","volume-title":"8th Annual International Conference on Research in Computational Molecular Biology.","author":"Funahashi","year":"2004"},{"key":"2023012511511995500_B5","volume-title":"The Regulation of Cellular Systems","author":"Heinrich","year":"2006","edition":"2"},{"key":"2023012511511995500_B6","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012511511995500_B7","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1186\/1471-2105-10-324","article-title":"KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG pathways database","volume":"10","author":"Moutselos","year":"2009","journal-title":"BMC Bioinf."},{"key":"2023012511511995500_B8","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1038\/nbt1156","article-title":"Minimum information requested in the annotation of biochemical models (MIRIAM)","volume":"23","author":"Nov\u00e8re","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023012511511995500_B9","first-page":"453","article-title":"yFiles: visualization and automatic layout of graphs","author":"Wiese","year":"2001","journal-title":"Proceedings of the 9th International Symposium on Graph Drawing (GD 2001)."},{"key":"2023012511511995500_B10","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1093\/bioinformatics\/btp167","article-title":"KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor","volume":"25","author":"Zhang","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/16\/2314\/48862131\/bioinformatics_27_16_2314.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/16\/2314\/48862131\/bioinformatics_27_16_2314.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:54:11Z","timestamp":1674647651000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/16\/2314\/255063"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,23]]},"references-count":10,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2011,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr377","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,8,15]]},"published":{"date-parts":[[2011,6,23]]}}}