Limitations

These are some points you should keep in mind when translating maps. Not everything can be translated properly. But warnings or errors in the report should tell you when things were omitted or changed.

For both translations

Style

Gradients are not considered. Curved edges are not supported and changed to direct lines.

Misc

The converter was designed for one time translation. Do not use it to convert the same file several times as it will lead to unpredictable results or errors.

CellDesigner -> SBGN

Notes and annotations

Notes elements are taken from:

• model
• species
• celldesigner:species
• celldesigner:protein
• celldesigner:gene
• celldesigner:RNA
• celldesigner:AntisenseRNA
• reaction
• compartment

Annotations are taken from:

• model
• species
• reaction
• compartment

Misc

• Links pointing directly to other links are omitted (see re43 and re42 in CellDesigner sample file components44).
• The Unknown logic gate doesn't have any counterpart in SBGN. It is removed and the links associated to it point directly to the process the logic gate was previously pointing to.
• Truncation reactions are translated as dissociations.

SBGN -> CellDesigner

Shapes and glyph classes

• Some CellDesigner-specific shapes can only be properly translated from SBGN if a unit of information with adequate text content is provided. Letter case is ignored, meaning "rna", "Rna" and "RNA" will be properly recognized. The needed strings are the following:
  • Receptor: receptor
  • Ion channels: ion channel
  • Truncated protein: truncated
  • RNA: rna
  • Antisense RNA: asrna
  • If no unit of information is provided, it is assumed that a SBGN macromolecule is a CellDesigner generic protein and a SBGN nucleic acid feature is a CellDesigner gene.
• Perturbing agent glyphs are converted to phenotypes.
• Submaps are converted to phenotypes. The terminals inside the submaps are not translated, and the arcs pointing to each terminal are set to point to the replacing phenotype glyph. Those equivalence arcs are translated to POSITIVE_INFLUENCE.

Notes and annotations

• Any RDF annotation stored in elements that are included in a complex (no matter the nesting level) are lost during translation. CellDesigner doesn't allow annotations for elements in complexes (so called included species).
• Notes and annotations are taken from maps and glyphs only (not arcs). Process annotations will be used for <reaction>. Map annotations will be used for the <model> element. Glyph annotations will be put into the <species> elements.

Misc

• Infinite trees of logic gates are possible in SBGN, but not in CellDesigner. Only the logic gates directly linked to a process and glyphs directly linked to those logic gates can be translated and kept. Further connections to other glyphs are lost.
• There is no difference between brief view and usual view for complexes (aside from hidden content/border).
• Every SBGN glyph is associated to a different CellDesigner species with only one alias.