January 6, 2020 Journal article Open Access

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

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    "title": "cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats", 
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      "molecular maps"
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    "publication_date": "2020-01-06", 
    "creators": [
      {
        "affiliation": "European Institute for Systems Biology and Medicine", 
        "name": "Irina Balaur"
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      {
        "affiliation": "Institut Curie", 
        "name": "Ludovic Roy"
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      {
        "affiliation": "Luxembourg Centre for Systems Biomedicine", 
        "name": "Alexander Mazein"
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      {
        "affiliation": "Bilkent University", 
        "name": "S. G\u00f6kberk Karaca"
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      {
        "affiliation": "Bilkent University", 
        "name": "Ugur Dogrusoz"
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      {
        "affiliation": "Institut Curie", 
        "name": "Emmanuel Barillot"
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      {
        "affiliation": "Institut Curie", 
        "name": "Andrei Zinovyev"
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    "notes": "The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]", 
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    "description": "<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>"
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