SBGNML

SBGNML, also written SBGN-ML, is the XML-based markup language used to encode diagrams that conform to the Systems Biology Graphical Notation (SBGN). It provides a machine-readable format that enables interchange, archiving, and reproducibility of SBGN diagrams across software tools. By encoding glyphs, arcs, and layout information in a structured document, SBGNML supports the faithful representation of molecular interactions and processes depicted by SBGN.

SBGNML covers the three SBGN languages: Process Description, Entity Relationship, and Activity Flow. A diagram is composed of a map containing glyph elements that correspond to SBGN glyphs (such as macromolecules, simple chemicals, complexes, processes, and compartments) and arc elements that express relationships between glyphs (production, consumption, catalysis, modulation, and others). Each element includes identifiers, class attributes, and optional metadata, as well as layout attributes such as coordinates, size, and port connections, to support automatic rendering.

The format is defined by the SBGN community as an open standard and is implemented by libraries and tools for reading and writing SBGN-ML, enabling round-tripping between editors and simulators. It is commonly used to exchange diagrams between software tools, convert between formats, and annotate diagrams with provenance information. SBGNML complements other standards such as SBML by focusing on graphical representation rather than mathematical encoding, though it can accompany SBML models in a workflow.

Adoption and tooling: LibSBGN libraries, diagram editors, and visualization tools support SBGN-ML import/export; ongoing efforts aim to standardize cross-tool interoperability and to provide reliable rendering and layout.