Humans; Metabolic Networks and Pathways; Signal Transduction; Software; Systems Biology; Statistics and Probability; Biochemistry; Molecular Biology; Computer Science Applications; Computational Theory and Mathematics; Computational Mathematics
Abstract :
[en] [en] 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.
Disciplines :
Biotechnology
Author, co-author :
BALAUR, Irina-Afrodita ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France
Roy, Ludovic; Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France ; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France ; Institut Curie, PSL Research University, F-75005 Paris, France
MAZEIN, Alexander ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France ; Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Moscow Region, Pushchino 142290, Russia
Karaca, S Gökberk; Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
Dogrusoz, Ugur; Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
Barillot, Emmanuel; Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France ; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France ; Institut Curie, PSL Research University, F-75005 Paris, France
Zinovyev, Andrei; Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France ; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France ; Institut Curie, PSL Research University, F-75005 Paris, France
External co-authors :
yes
Language :
English
Title :
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.
European Union Horizon 2020 Scientific and Technological Research Council of Turkey
Funding text :
This work was supported by the European Union Horizon 2020 research and innovation programme PRECISE [668858 to L.R. and E.B.], iPC [826121 to A.Z. and E.B.]; and the Scientific and Technological Research Council of Turkey [111E036 to U.D.].
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