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. 2020 Apr 15;36(8):2620-2622.
doi: 10.1093/bioinformatics/btz969.

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Irina Balaur  1 , Ludovic Roy  2   3   4 , Alexander Mazein  1   5   6 , S Gökberk Karaca  7 , Ugur Dogrusoz  7 , Emmanuel Barillot  2   3   4 , Andrei Zinovyev  2   3   4
Affiliations

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Irina Balaur et al. Bioinformatics. .

Erratum in

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.

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