Cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats

Irina Balaur; Ludovic Roy; Ludovic Roy; Ludovic Roy; Alexander Mazein; Alexander Mazein; Alexander Mazein; S. Gökberk Karaca; Ugur Dogrusoz; Emmanuel Barillot; Emmanuel Barillot; Emmanuel Barillot; Andrei Zinovyev; Andrei Zinovyev; Andrei Zinovyev

doi:10.1093/bioinformatics/btz969

Cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats

Irina Balaur^*, Ludovic Roy, Ludovic Roy, Ludovic Roy, Alexander Mazein^*, Alexander Mazein^*, Alexander Mazein^*, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Emmanuel Barillot, Emmanuel Barillot, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev

^*Corresponding author for this work

Research output: Contribution to journal › Article › Research › peer-review

6 Citations (Scopus)

Abstract

Motivation: 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 (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. 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.

Original language	English
Pages (from-to)	2620-2622
Number of pages	3
Journal	Bioinformatics
Volume	36
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btz969
Publication status	Published - 15 Apr 2020
Externally published	Yes

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10.1093/bioinformatics/btz969

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title = "Cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats",

abstract = "Motivation: 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 (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. 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.",

author = "Irina Balaur and Ludovic Roy and Ludovic Roy and Ludovic Roy and Alexander Mazein and Alexander Mazein and Alexander Mazein and Karaca, {S. G{\"o}kberk} and Ugur Dogrusoz and Emmanuel Barillot and Emmanuel Barillot and Emmanuel Barillot and Andrei Zinovyev and Andrei Zinovyev and Andrei Zinovyev",

year = "2020",

month = apr,

day = "15",

doi = "10.1093/bioinformatics/btz969",

language = "English",

volume = "36",

pages = "2620--2622",

journal = "Bioinformatics",

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publisher = "Oxford University Press",

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TY - JOUR

T1 - Cd2sbgnml

T2 - Bidirectional conversion between CellDesigner and SBGN formats

AU - Balaur, Irina

AU - Roy, Ludovic

AU - Mazein, Alexander

AU - Karaca, S. Gökberk

AU - Dogrusoz, Ugur

AU - Barillot, Emmanuel

AU - Zinovyev, Andrei

PY - 2020/4/15

Y1 - 2020/4/15

N2 - Motivation: 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 (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. 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.

AB - Motivation: 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 (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. 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.

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DO - 10.1093/bioinformatics/btz969

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SP - 2620

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JO - Bioinformatics

JF - Bioinformatics

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ER -

Cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats

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