Irina Balaur1, Ludovic Roy2,3,4, Alexander Mazein1,5,6, S Gökberk Karaca7, Ugur Dogrusoz7, Emmanuel Barillot2,3,4, Andrei Zinovyev2,3,4. 1. European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France. 2. Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France. 3. MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France. 4. Institut Curie, PSL Research University, F-75005 Paris, France. 5. Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Moscow Region, Pushchino 142290, Russia. 6. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg. 7. Computer Engineering Department, Bilkent University, Ankara 06800, Turkey.
Abstract
MOTIVATION: CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner's proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. RESULTS: We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner's proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML. AVAILABILITY AND IMPLEMENTATION: The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner's proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. RESULTS: We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner's proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML. AVAILABILITY AND IMPLEMENTATION: The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Marek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Luis Cristóbal Monraz Gómez; Julia Somers; Matti Hoch; Shailendra Kumar Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G Yamada; Andreas Dräger; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Francesco Messina; Daniela Börnigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E Ackerman; Jason E Shoemaker; Jeremy Zucker; Kristie Oxford; Jeremy Teuton; Ebru Kocakaya; Gökçe Yağmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; Devasahayam Arokia Balaya Rex; Denise Slenter; Marvin Martens; Nhung Pham; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Varusai; Jean-Marie Ravel; Rupsha Fraser; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert W Overall; Dieter Maier; Angela Bauch; Benjamin M Gyori; John A Bachman; Carlos Vega; Valentin Grouès; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Peña-Chilet; Kinza Rian; Tomáš Helikar; Bhanwar Lal Puniya; Dezso Modos; Agatha Treveil; Marton Olbei; Bertrand De Meulder; Stephane Ballereau; Aurélien Dugourd; Aurélien Naldi; Vincent Noël; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C Freeman; Franck Augé; Jacques S Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon L Wilighagen; Alexander R Pico; Chris T Evelo; Marc E Gillespie; Lincoln D Stein; Henning Hermjakob; Peter D'Eustachio; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider Journal: Mol Syst Biol Date: 2021-10 Impact factor: 11.429