Journal article Open Access

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Irina Balaur; Ludovic Roy; Alexander Mazein; S. Gökberk Karaca; Ugur Dogrusoz; Emmanuel Barillot; Andrei Zinovyev


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  <dc:creator>Irina Balaur</dc:creator>
  <dc:creator>Ludovic Roy</dc:creator>
  <dc:creator>Alexander Mazein</dc:creator>
  <dc:creator>S. Gökberk Karaca</dc:creator>
  <dc:creator>Ugur Dogrusoz</dc:creator>
  <dc:creator>Emmanuel Barillot</dc:creator>
  <dc:creator>Andrei Zinovyev</dc:creator>
  <dc:date>2020-01-06</dc:date>
  <dc:description>Motivation: CellDesigner is a well-established biological map editor used in many large-scale scientific efforts (Funahashi et al., 2007). 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.

Results: 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 (Noronha et al., 2019) and the complete Atlas of Cancer Signalling Network (Kuperstein et al., 2015), from the CellDesigner file format into SBGN-ML.

Availability: 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).</dc:description>
  <dc:description>The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]</dc:description>
  <dc:identifier>https://zenodo.org/record/3605509</dc:identifier>
  <dc:identifier>10.1093/bioinformatics/btz969</dc:identifier>
  <dc:identifier>oai:zenodo.org:3605509</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>info:eu-repo/grantAgreement/EC/H2020/826121/</dc:relation>
  <dc:relation>info:eu-repo/grantAgreement/EC/H2020/668858/</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/ipc</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:source>Bioinformatics btz969</dc:source>
  <dc:subject>celldesigner</dc:subject>
  <dc:subject>sbgn</dc:subject>
  <dc:subject>molecular maps</dc:subject>
  <dc:title>cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats</dc:title>
  <dc:type>info:eu-repo/semantics/article</dc:type>
  <dc:type>publication-article</dc:type>
</oai_dc:dc>
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