Complete Solution for KEGG Dataset Support in Cytoscape

Cytoscape is a widely used bioinformatics software platform for integrating, analyzing, and visualizing biological network data sets. This is a plugin for importing KGML files to Cytoscape.

About KEGG

KEGG Pathway database is one of the most comprehensive databases of human-curated biological pathways.

This is one of the Google Summer of Code 2010 projects. The proposal is here.

Quick Start Guide for Users

KGMLReader plugin is compatible with Cytoscape 2.7.0.

1. download KGMLReader.jar from Featured downloads link
2. Copy KGMLReader.jar to plugins folder under Cytoscape home directory.
3. run Cytoscape
4. import kgml from menubar (File -> Import -> Network (Multiple File Types) -> select the kgml you want to import)

KGMLReader automatically import KEGG fields not in KGML in background. If you want to stop the background process, please check off Automatic Annotation Import from TogoWS from menubar Plugins -> KEGG Browser -> Options

You can import maplink pathway without downloading the pathway kgml by yourself. To import the maplink pathway, please right-click the maplink node and click import maplink pathway: maplink pathwayID and set as NNF from KEGG Options

This import also sets Nested Network to the maplink node. Once import the maplink pathway, you can go to the maplink pathway by clicking Go to Nested Network from right-click menu Nested Network.

Data Files

KGML is a XML version of KEGG pathway data set. You can download them from their FTP site. We will provide some more nicer interface to access these existing files in the future. For now, please download them from here.

KGMLReader plugin is compatible with KGML version 0.7.1.

Examples and QandA

• UseCase
• MappingChartOnPathway
• QandA

Status

• ReleaseNote
• ToDo

Slides and Poster

• Cytoscape retreat 2010 plugin demonstrations