KEGGscape is a Cytoscape 3.* app for importing KGML(KEGG pathway XML).
KEGGscape is formerly known as KGMLReader
If you use KEGGscape in your research, please cite:
- KEGGscape: a Cytoscape app for pathway data integration. Nishida K, Ono K, Kanaya S, Takahashi K. F1000Res. 2014 Jul 1;3:144. doi: 10.12688/f1000research.4524.1. eCollection 2014.
Cytoscape is a de-facto standard bioinformatics software platform for integrating, analyzing, and visualizing biological network data. KEGGscape is a Cytoscape App to provide comprehensive support for KEGG Pathway database and other resources available in KEGG. KEGGscape uses only basic data structures in Cytoscape core, and users can use powerful Cytoscape core features to visualize additional (experimental) data sets on top of KEGG pathways.
KEGG Pathway database is one of the most comprehensive databases of human-curated biological pathways. KGML (KEGG Markup Language) is the file format to represent KEGG Pathway data files in XML. KEGGscape uses those KGML files as its primary source of pathway data.
You can install KEGGscape with Cytoscape app manager.
- Full support for KEGG Pathway, including signaling pathways.
- On-demand access to KEGG RESTful API to add extra annotations for the pathways.
- Annotation by KEGG MEDICUS database
- Merging multiple pathways in a same network view
(Available soon...)
Basic support for KEGG metabolic pathways.
This is a major version up and has lots of new features!
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
- Kozo Nishida (Riken, Japan)
- Keiichiro Ono (Cytoscape Consortium / UC, San Diego, USA)
Please send them to cytoscape-helpdesk.