Irina Balaur
Ludovic Roy
Alexander Mazein
S. Gökberk Karaca
Ugur Dogrusoz
Emmanuel Barillot
Andrei Zinovyev
2020-01-06
<p><strong>Motivation:</strong> CellDesigner is a well-established biological map editor used in many large-scale scientific efforts <a href="https://www.zotero.org/google-docs/?ZGAm0o">(Funahashi </a><a href="https://www.zotero.org/google-docs/?ZGAm0o"><em>et al.</em></a><a href="https://www.zotero.org/google-docs/?ZGAm0o">, 2007)</a>. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner file format remains a challenge due to the proprietary extensions used in CellDesigner files.</p>
<p><strong>Results:</strong> We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary Systems Biology Markup Language (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 <a href="https://www.zotero.org/google-docs/?WP6wvI">(Noronha </a><a href="https://www.zotero.org/google-docs/?WP6wvI"><em>et al.</em></a><a href="https://www.zotero.org/google-docs/?WP6wvI">, 2019)</a> and the complete Atlas of Cancer Signalling Network <a href="https://www.zotero.org/google-docs/?mc4u5r">(Kuperstein </a><a href="https://www.zotero.org/google-docs/?mc4u5r"><em>et al.</em></a><a href="https://www.zotero.org/google-docs/?mc4u5r">, 2015)</a>, from the CellDesigner file format into SBGN-ML.</p>
<p><strong>Availability:</strong> 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).</p>
The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]
https://doi.org/10.1093/bioinformatics/btz969
oai:zenodo.org:3605509
eng
Zenodo
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https://zenodo.org/communities/eu
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
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Bioinformatics, btz969, (2020-01-06)
celldesigner
sbgn
molecular maps
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats
info:eu-repo/semantics/article