Table 1.
Summary depicting purpose, online availability and capabilities of different tools
| Purpose | Tool | Browser tool | Online tool | Collaborative | Linkable | Annotation | Layout aware | SBML SBGN |
|---|---|---|---|---|---|---|---|---|
| General text annotation | tagtog (22) | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ |
| brat (31) | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | |
| WebAnno (32) | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | |
| FLAT (33) | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | |
| Biomedical text annotation | MyMiner (21) | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ |
| BioQRator (19) | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | |
| ezTag (20) | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | |
| Diagram editor | CellDesigner (23) | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ |
| Newt (8) | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | |
| Visual repository | WikiPathways (6) | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ |
| KEGG (5) | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | |
| Reactome (4) | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | |
| CellCollective (28) | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | |
| Visualization platform | Cytoscape (24) | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ |
| NaviCell (26) | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | |
| MINERVA (25) | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | |
| BioUML (27) | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ |
Some browser-based tools are not available online, and this distinction is shown in the first two columns. ‘Collaborative’ column states which tools allow multi-user simultaneous operation. ‘Linkable’ criterion refers to the ability to share and use the tool output as annotable content via uniform resource identifier-like links. Conversely, the ‘Annotation’ criterion indicates if a tool is able to produce annotations on the content.