SBML
Domain-specific format for biological/biochemical models. Nodes are species, edges are reactions.
| Feature | Support | Notes |
|---|---|---|
| Attributes on Edges | ✅ | Kinetic laws, modifiers |
| Attributes on Graphs | ✅ | Model metadata |
| Attributes on Nodes | ✅ | Extensive annotations (RDF-based) |
| Directed Edges | ✅ | Reactions (reactants → products) |
| Edge Labels | ✅ | Via name attribute on reactions |
| Edges on Edges | ❌ | |
| Hyperedges | ✅ | Reactions with multiple reactants/products |
| Mixed-directionality Edges | ❌ | |
| Multiple Graphs per Document | ✅ | Via comp package (hierarchical model composition) |
| Nested Graphs in Edges | ❌ | |
| Nested Graphs in Graphs | ✅ | Via comp package |
| Nested Graphs in Nodes | ✅ | Compartments can be nested |
| Node Labels | ✅ | Via name attribute |
| Nodes | ✅ | Species in compartments |
| Typed Edges | ✅ | Implicit via reaction structure |
| Undirected Edges | ❌ | Reactions are directional |
Input Content
Input Format
Output Format
All Formats: Adjacency List (NetworkX)| BioGRID Tab 3.0| Chaco| Connected JSON| CytoScape JSON| DOT (GraphViz)| Edge List| GDF| GEXF| gJGF| GML| Graph6| GraphML| GXL| JGF| Matrix Market| Nested Network Format| Netdraw VNA| OCIF| Pajek| PSI-MI Tab 2.5| SBML| TGF| UCINET DL| VOSviewer JSON| XGMML