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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  <identifier identifierType="URL">https://zenodo.org/record/3605509</identifier>
  <creators>
    <creator>
      <creatorName>Irina Balaur</creatorName>
      <affiliation>European Institute for Systems Biology and Medicine</affiliation>
    </creator>
    <creator>
      <creatorName>Ludovic Roy</creatorName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Alexander Mazein</creatorName>
      <affiliation>Luxembourg Centre for Systems Biomedicine</affiliation>
    </creator>
    <creator>
      <creatorName>S. Gökberk Karaca</creatorName>
      <affiliation>Bilkent University</affiliation>
    </creator>
    <creator>
      <creatorName>Ugur Dogrusoz</creatorName>
      <affiliation>Bilkent University</affiliation>
    </creator>
    <creator>
      <creatorName>Emmanuel Barillot</creatorName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Andrei Zinovyev</creatorName>
      <affiliation>Institut Curie</affiliation>
    </creator>
  </creators>
  <titles>
    <title>cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>celldesigner</subject>
    <subject>sbgn</subject>
    <subject>molecular maps</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-01-06</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="JournalArticle"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3605509</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1093/bioinformatics/btz969</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/ipc</relatedIdentifier>
  </relatedIdentifiers>
  <version>Author version</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Motivation:&lt;/strong&gt; CellDesigner is a well-established biological map editor used in many large-scale scientific efforts &lt;a href="https://www.zotero.org/google-docs/?ZGAm0o"&gt;(Funahashi &lt;/a&gt;&lt;a href="https://www.zotero.org/google-docs/?ZGAm0o"&gt;&lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt;&lt;a href="https://www.zotero.org/google-docs/?ZGAm0o"&gt;, 2007)&lt;/a&gt;. 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.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Results:&lt;/strong&gt; We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner&amp;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 &lt;a href="https://www.zotero.org/google-docs/?WP6wvI"&gt;(Noronha &lt;/a&gt;&lt;a href="https://www.zotero.org/google-docs/?WP6wvI"&gt;&lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt;&lt;a href="https://www.zotero.org/google-docs/?WP6wvI"&gt;, 2019)&lt;/a&gt; and the complete Atlas of Cancer Signalling Network &lt;a href="https://www.zotero.org/google-docs/?mc4u5r"&gt;(Kuperstein &lt;/a&gt;&lt;a href="https://www.zotero.org/google-docs/?mc4u5r"&gt;&lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt;&lt;a href="https://www.zotero.org/google-docs/?mc4u5r"&gt;, 2015)&lt;/a&gt;, from the CellDesigner file format into SBGN-ML.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Availability:&lt;/strong&gt; The cd2sbgnml conversion library and the web service were developed in &amp;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).&lt;/p&gt;</description>
    <description descriptionType="Other">The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/826121/">826121</awardNumber>
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    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/668858/">668858</awardNumber>
      <awardTitle>PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION</awardTitle>
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