cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

2020 Bioinformatics  
CellDesigner is a well-established biological map editor used in many large-scale scientific efforts (Funahashi et al., 2007). However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner's proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. We introduce a library named cd2sbgnml and an associated web service for bidirectional
more » ... nversion 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 (Noronha et al., 2019) and the complete Atlas of Cancer Signalling Network (Kuperstein et al., 2015), from the CellDesigner file format into SBGN-ML. 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 data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btz969 pmid:31904823 fatcat:je3bo324hneefe3pkyxjcn6sze