The editor exposes two GraphML outputs that look similar but serve different audiences.
| GraphML | Export yEd GraphML |
| Trigger | Auto-regenerated on every US save (Spec 2) | On-demand when you click the button (Spec 3-bis) |
| File | data/paradata/<site>/stratigraphy.graphml | data/exports/harris_yed/<site>-harris-yed.graphml |
| Schema | s3dgraphy clean — canonical EM nodes (StratigraphicNode) and edges (overlies, abuts, is_after, …) | yEd-flavored — y:TableNode + y:Rows for swimlanes, y:ShapeNode children with VocabProvider colors |
| Audience | EM Datacenter, 3D pipeline, Heriverse, programmatic consumers | Humans using yEd Desktop for review/printing |
| Round-trip | Yes (s3dgraphy reader) | No (one-way export for presentation) |
DOT / PNG
- DOT — Graphviz source, useful for batch rendering or version-controlling diagrams as text.
- PNG — Rasterized snapshot of the current Cytoscape view.
Quick reference
- Need to feed a 3D / EM pipeline → use GraphML.
- Need to open in yEd Desktop and tweak by hand → use Export yEd GraphML.
- Need a quick image for a report → use PNG.