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


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nam##2200000uu#4500</leader>
  <datafield tag="041" ind1=" " ind2=" ">
    <subfield code="a">eng</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">celldesigner</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">sbgn</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">molecular maps</subfield>
  </datafield>
  <controlfield tag="005">20200120171822.0</controlfield>
  <datafield tag="500" ind1=" " ind2=" ">
    <subfield code="a">The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]</subfield>
  </datafield>
  <controlfield tag="001">3605509</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Curie</subfield>
    <subfield code="a">Ludovic Roy</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Luxembourg Centre for Systems Biomedicine</subfield>
    <subfield code="a">Alexander Mazein</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Bilkent University</subfield>
    <subfield code="a">S. Gökberk Karaca</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Bilkent University</subfield>
    <subfield code="a">Ugur Dogrusoz</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Curie</subfield>
    <subfield code="a">Emmanuel Barillot</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Curie</subfield>
    <subfield code="a">Andrei Zinovyev</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">510391</subfield>
    <subfield code="z">md5:7bc388c8d13b8caaa7a853b0a86d43fc</subfield>
    <subfield code="u">https://zenodo.org/record/3605509/files/Balaur2020Bioinformatics_AuthorVersion.pdf</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2020-01-06</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">openaire</subfield>
    <subfield code="p">user-ipc</subfield>
    <subfield code="o">oai:zenodo.org:3605509</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="4">
    <subfield code="p">Bioinformatics</subfield>
    <subfield code="n">btz969</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">European Institute for Systems Biology and Medicine</subfield>
    <subfield code="a">Irina Balaur</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-ipc</subfield>
  </datafield>
  <datafield tag="536" ind1=" " ind2=" ">
    <subfield code="c">826121</subfield>
    <subfield code="a">individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology</subfield>
  </datafield>
  <datafield tag="536" ind1=" " ind2=" ">
    <subfield code="c">668858</subfield>
    <subfield code="a">PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&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;</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.1093/bioinformatics/btz969</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">publication</subfield>
    <subfield code="b">article</subfield>
  </datafield>
</record>
274
238
views
downloads
Views 274
Downloads 238
Data volume 121.5 MB
Unique views 193
Unique downloads 224

Share

Cite as