Old README
Now KEGGScape supports all pathway data available in KGML format, including:
- Metabolic Pathways
- Global Map for Metabolic Pathways
- Overview Maps
- Signaling Pathways
- Organismal Systems
- Human Disease Pathways
We have tweaked custom Visual Style to present as mush information as possible out of the original KGML files. Directionality and type of reactions/relations are mapped to human understandable visual properties.
KEGG pathways have maplink nodes which point to other pathways. Cytoscape can automatically import those pathways by selecting a context menu:
- Select a maplink node and right-click to expand!
- Actual pathway data will be fetched dynamically from KEGG pathway database.
If you need complete information about compounds, genes, or pathways, you can view details in web browser by selecting right-click menu item.
From this version, KEGGScape supports network collection. You can organize your pathways based on the biological context.
By checking options in import window, you can add extra information from KEGG:
- KEGG Modules
- Diseases
- Pathway classes
Group information in KGML is now mapped to Cytoscape's CyGroup. This means intrnally, grouped nodes are handled as CyGroup, instead of set of nodes.
- Default representation (set of individdual nodes):
- Collapsed to a single group node:
Lots of bugs are fixed. Some of the missed edges in the last version are now correctly mapped in the view.
- Advanced example workflow written with cy-rest and IPython Notebook
- Automatic import from list of pathway IDs
- Import additional annotation on-demand:
- KEGG Modules
- Drug targets
- etc.
- Expanding pathways in existing network view