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Publication . Other literature type . Article . 2020

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Balaur, Irina; Roy, Ludovic; Mazein, Alexander; Karaca, S Gökberk; Dogrusoz, Ugur; Barillot, Emmanuel; Zinovyev, Andrei;
Open Access  
Published: 06 Jan 2020
Publisher: Oxford University Press (OUP)
Country: Turkey
Abstract
Motivation: 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 file format 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 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 (Noronha et al., 2019) and the complete Atlas of Cancer Signalling Network (Kuperstein et al., 2015), from the CellDesigner file format into SBGN-ML. Availability: 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).
Subjects by Vocabulary

Microsoft Academic Graph classification: Computer science Programming language computer.software_genre computer SBML Markup language Systems Biology Graphical Notation Set (abstract data type) Java computer.programming_language Interoperability Web service File format

ACM Computing Classification System: GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ComputingMilieux_MISCELLANEOUS

Subjects

Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability, celldesigner, sbgn, molecular maps

Funded by
EC| iPC
Project
iPC
individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology
  • Funder: European Commission (EC)
  • Project Code: 826121
  • Funding stream: H2020 | RIA
Validated by funder
,
TUBITAK| Kümelenmiş Ya Da Hiyerarşik Ilişkisel Bilginin Sorgulanması, Yerleşimi Ve Görselleştirmesi
Project
  • Funder: Türkiye Bilimsel ve Teknolojik Araştırma Kurumu (TUBITAK)
  • Project Code: 111E036
  • Funding stream: 1001 - Araştırma
,
EC| PrECISE
Project
PrECISE
PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION
  • Funder: European Commission (EC)
  • Project Code: 668858
  • Funding stream: H2020 | RIA