KEGGscape is a Cytoscape 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.
- Install KEGGscape with Cytoscape app manager.
- Get a kgml file. For example, to get the kgml of E.coli TCA cycle pathway (eco00020), open https://www.genome.jp/kegg-bin/show_pathway?eco00020 with web browser and click the KGML link
. - Click the "Import Network from File System" icon in Cytoscape, select the eco00020.xml file, and click the open button.
That's all. Now you should see 
Cytoscape is a de-facto standard bioinformatics software platform for integrating, analyzing, and visualizing biological network data. KEGGscape is a Cytoscape App to import KEGG Pathway data to Cytoscape. KEGGscape 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 source of pathway data.
- Full support for KEGG Pathway, including signaling pathways.
On-demand access to KEGG RESTful API to add extra annotations for the pathways.(Due to the restriction of KEGG API, we stopped supporting KEGG API. For more information, please check https://www.kegg.jp/kegg/rest/#main:~:text=Restriction .)Annotation by KEGG MEDICUS database(Due to the restriction of KEGG API, we stopped supporting KEGG API. For more information, please check https://www.kegg.jp/kegg/rest/#main:~:text=Restriction .)- Merging multiple pathways in a same network view.
- Kozo Nishida (Riken, Japan)
- Keiichiro Ono (Cytoscape Consortium / UC, San Diego, USA)
Please send them to cytoscape-helpdesk.