SBGN

SBGN facilitates accurate translation between GraphML (used by yEd) and SBGN-ML Process Description formats to enable interoperable representation of biochemical networks.

Key Features:

• Bidirectional conversion: Accurate bidirectional translation between GraphML (yEd) and SBGN-ML Process Description file formats.
• SBGN-ML v0.3 support: Implements SBGN-ML v0.3 features including attributes for metadata, support for multiple maps and sub-maps, and color and annotation support.
• Interoperability: Compatibility with BioPAX and SBML and with tools and converters such as CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA.
• Representation scope: Enables precise representation of biochemical interactions including gene regulation, metabolism, and cellular signaling using the SBGN Process Description language.

Scientific Applications:

• Metabolic network integration: Enables integration and interoperability of metabolic network diagrams between GraphML/yEd and SBGN-ML.
• Cross-format data exchange: Facilitates data exchange and reuse across BioPAX, SBML, and SBGN-compatible tools and converters.
• Structured system representation: Supports representation of complex biological systems through multiple maps and sub-maps for hierarchical or modular network depiction.

Methodology:

Performs bidirectional translation between GraphML (yEd) and SBGN-ML Process Description formats and supports SBGN-ML v0.3 features such as metadata attributes, multiple maps/sub-maps, and color/annotation.