{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:53:06Z","timestamp":1753887186771,"version":"3.41.2"},"reference-count":16,"publisher":"Walter de Gruyter GmbH","issue":"4","license":[{"start":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T00:00:00Z","timestamp":1669852800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.<\/jats:p>","DOI":"10.1515\/jib-2022-0030","type":"journal-article","created":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T22:14:23Z","timestamp":1671833663000},"source":"Crossref","is-referenced-by-count":1,"title":["GraphML-SBGN bidirectional converter for metabolic networks"],"prefix":"10.1515","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3671-895X","authenticated-orcid":false,"given":"Irina","family":"Balaur","sequence":"first","affiliation":[{"name":"European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Universit\u00e9 de Lyon , 50 Avenue Tony Garnier, 69007 Lyon , France"},{"name":"Luxembourg Centre for Systems Biomedicine , University of Luxembourg , 6 Avenue du Swing, L-4367 Belvaux , Luxembourg"}]},{"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 , 50 Avenue Tony Garnier, 69007 Lyon , France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4639-4431","authenticated-orcid":false,"given":"Vasundra","family":"Tour\u00e9","sequence":"additional","affiliation":[{"name":"European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Universit\u00e9 de Lyon , 50 Avenue Tony Garnier, 69007 Lyon , France"},{"name":"Department of Biology , Norwegian University of Science and Technology (NTNU) , H\u00f8gskoleringen 5, Realfagbygget, 7491 Trondheim , Norway"}]},{"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 , 50 Avenue Tony Garnier, 69007 Lyon , France"},{"name":"Luxembourg Centre for Systems Biomedicine , University of Luxembourg , 6 Avenue du Swing, L-4367 Belvaux , Luxembourg"},{"name":"Russian Academy of Sciences , Institute of Cell Biophysics , 3 Institutskaya Street , Pushchino , Moscow Region , 142290 , Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2226-7411","authenticated-orcid":false,"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 , 50 Avenue Tony Garnier, 69007 Lyon , France"}]}],"member":"374","published-online":{"date-parts":[[2022,12,26]]},"reference":[{"key":"2024010601153682743_j_jib-2022-0030_ref_001","doi-asserted-by":"crossref","unstructured":"Hucka, M, Nickerson, DP, Bader, GD, Bergmann, FT, Cooper, J, Demir, E, et al.. 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