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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{
  "DOI": "10.1093/bioinformatics/btz969", 
  "container_title": "Bioinformatics", 
  "language": "eng", 
  "title": "cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats", 
  "issued": {
    "date-parts": [
      [
        2020, 
        1, 
        6
      ]
    ]
  }, 
  "abstract": "<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>\n\n<p><strong>Results:</strong> We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner&rsquo;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>\n\n<p><strong>Availability:</strong> The cd2sbgnml conversion library and the web service were developed in &nbsp;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>", 
  "author": [
    {
      "family": "Irina Balaur"
    }, 
    {
      "family": "Ludovic Roy"
    }, 
    {
      "family": "Alexander Mazein"
    }, 
    {
      "family": "S. G\u00f6kberk Karaca"
    }, 
    {
      "family": "Ugur Dogrusoz"
    }, 
    {
      "family": "Emmanuel Barillot"
    }, 
    {
      "family": "Andrei Zinovyev"
    }
  ], 
  "note": "The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]", 
  "version": "Author version", 
  "type": "article-journal", 
  "issue": "btz969", 
  "id": "3605509"
}
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