cd2sbgnml

cd2sbgnml converts between CellDesigner's proprietary Systems Biology Markup Language (SBML) extension and Systems Biology Graphical Notation Markup Language (SBGN-ML) to enable interoperability of biological network representations.

Key Features:

• Bidirectional Conversion: Supports translation in both directions between CellDesigner's SBML extension and SBGN-ML.
• Comprehensive Translation Capabilities: Applied to large-scale networks such as the RECON Human Metabolic network and the Atlas of Cancer Signalling Network, demonstrating handling of complex diagrams.
• Development Language and Licensing: Implemented in Java and distributed under the GNU Lesser General Public License v3.0.
• Web Service: Provides a web service component alongside the conversion library.

Scientific Applications:

• Interoperability: Enables exchange of biological network maps between tools that use CellDesigner's SBML extensions and tools that consume SBGN-ML.
• Standardization and Reuse: Facilitates representation of maps in SBGN-ML to support standardized dissemination and reuse of network diagrams.
• Large-scale Network Analysis: Supports conversion of comprehensive datasets such as metabolic pathways and signalling networks for downstream analysis.

Methodology:

Implements an accurate translation mechanism between CellDesigner's SBML extensions and SBGN-ML that preserves relevant data and annotations during conversion.