SBGN-ED

SBGN-ED is a desktop editor and add-on for the VANTED network-analysis framework that lets users create, edit, validate, and translate diagrams drawn in the Systems Biology Graphical Notation (SBGN). It was developed by Tobias Czauderna, Christian Klukas, and Falk Schreiber at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben and Martin Luther University of Halle-Wittenberg, and introduced in a 2010 Bioinformatics paper. As a VANTED add-on it inherits the host system's Java Swing graph editor plus its facilities for mapping high-throughput experimental data onto networks, layout, and analysis, adding SBGN-specific glyphs, rules, and importers on top.

The tool supports all three SBGN sublanguages: Process Description (PD), which captures the temporal sequence of biochemical interactions; Entity Relationship (ER), which expresses relationships independent of ordering; and Activity Flow (AF), which abstracts influence between activities. Maps are drawn from a palette of standardized glyphs, and SBGN-ED performs both syntactic and semantic validation, checking that connections respect the incidence rules of the relevant SBGN specification and graphically flagging offending elements so the user can correct them.

A distinguishing capability is automatic translation of existing non-SBGN networks into SBGN. It can convert pathways from the KGML exports of the KEGG database (see KEGG) and from the plant-metabolism MetaCrop resource into SBGN Process Description maps, and translate SBML models into PD as well, though the authors note that some layout and semantic details may need manual adjustment after translation. Related translators in this space include KEGGtranslator and SBFC.

For interchange and publication, SBGN-ED reads and writes the standardized SBGN-ML XML exchange format (the same format underlying libSBGN and consumed by editors such as Newt and Cytoscape), and exports to graph formats including GML and GraphML plus image formats PDF, SVG, PNG, JPG, and clickable PNG/HTML image maps. This makes it a bridge between curated pathway databases and standards-based diagram exchange.

Its main limitations follow from its heritage: it is a heavyweight Java desktop application tied to a specific VANTED release rather than a web or scriptable library, development has been largely maintenance-only in recent years, and the ER and AF editors are less mature than PD. For programmatic SBGN handling or lightweight web editing, libraries and newer editors are often preferred, but SBGN-ED remains notable for combining rule-based validation with database-to-SBGN translation in one package.