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


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://zenodo.org/record/3605509">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/3605509</dct:identifier>
    <foaf:page rdf:resource="https://zenodo.org/record/3605509"/>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Irina Balaur</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>European Institute for Systems Biology and Medicine</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Ludovic Roy</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Institut Curie</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Alexander Mazein</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Luxembourg Centre for Systems Biomedicine</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>S. Gökberk Karaca</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Bilkent University</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Ugur Dogrusoz</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Bilkent University</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Emmanuel Barillot</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Institut Curie</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Andrei Zinovyev</foaf:name>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Institut Curie</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2020</dct:issued>
    <dcat:keyword>celldesigner</dcat:keyword>
    <dcat:keyword>sbgn</dcat:keyword>
    <dcat:keyword>molecular maps</dcat:keyword>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/826121/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/668858/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-01-06</dct:issued>
    <dct:language rdf:resource="http://publications.europa.eu/resource/authority/language/ENG"/>
    <owl:sameAs rdf:resource="https://zenodo.org/record/3605509"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/3605509</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <owl:sameAs rdf:resource="https://doi.org/10.1093/bioinformatics/btz969"/>
    <dct:isPartOf rdf:resource="https://zenodo.org/communities/ipc"/>
    <owl:versionInfo>Author version</owl:versionInfo>
    <dct:description>&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;</dct:description>
    <dct:description>The paper is supported by Scientific and Technological Research Council of Turkey [111E036 to U.D.]</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.1093/bioinformatics/btz969"/>
        <dcat:byteSize>510391</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/3605509/files/Balaur2020Bioinformatics_AuthorVersion.pdf"/>
        <dcat:mediaType>application/pdf</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/826121/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">826121</dct:identifier>
    <dct:title>individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/668858/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">668858</dct:identifier>
    <dct:title>PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
</rdf:RDF>
274
238
views
downloads
Views 274
Downloads 238
Data volume 121.5 MB
Unique views 193
Unique downloads 224

Share

Cite as