cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats

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buir.contributor.authorKaraca, S. Gökberk
buir.contributor.authorDoğrusöz, Uğur
dc.citation.epage2622en_US
dc.citation.issueNumber8en_US
dc.citation.spage2620en_US
dc.citation.volumeNumber36en_US
dc.contributor.authorBalaur, I.en_US
dc.contributor.authorRoy, L.en_US
dc.contributor.authorMazein, A.en_US
dc.contributor.authorKaraca, S. Gökberken_US
dc.contributor.authorDoğrusöz, Uğuren_US
dc.contributor.authorBarillot, E.en_US
dc.contributor.authorZinovyev, A.en_US
dc.date.accessioned2021-02-25T13:17:07Z
dc.date.available2021-02-25T13:17:07Z
dc.date.issued2020-01
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractMotivation: CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGNML) and the CellDesigner’s proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. Results: We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary 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 and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML. Availability and implementation: The cd2sbgnml conversion library and the web service were developed in 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). Supplementary information: Supplementary data are available at Bioinformatics online.en_US
dc.identifier.doi10.1093/bioinformatics/btz969en_US
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11693/75596
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttps://dx.doi.org/10.1093/bioinformatics/btz969en_US
dc.source.titleBioinformaticsen_US
dc.titlecd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formatsen_US
dc.typeArticleen_US
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