The WikiPathways App provides Cytoscape users with easy access to pathway content at WikiPathways.org. With the app installed, you can import GPML network files generated by WikiPathways or PathVisio. You can also query and import pathways via the *Import>Network>Public Databases...* interface provided by Cytoscape, or through the network search bar in the top of Network panel (starting in v.3.6) . Pathways can be loaded as either their native diagram format or as simplified network graphs to support either data visualization or network analysis and augmentation use cases.
Note: This app was formerly known as [http://apps.cytoscape.org/apps/gpmlplugin GPML-Plugin] for Cytoscape 2.8.
### Quick tutorial
1. Install the WikiPathways app.
1. In Cytoscape's menu bar, select File → Import → Network → Public Databases.
1. In the search text field at the top of the Network Panel, select Wikipathways from the pull down menu, then enter a term like *p53* or *apoptosis*. Press return.
1. Double-click on a pathway listed below to open the pathway.
### Importing from WikiPathways
The WikiPathways app supports two ways you can import a pathway into Cytoscape.
* **Pathway View** — The network in Cytoscape has complete graphical annotations of a pathway. This is ideal for visualizing your own molecular datasets (like gene expression profiles and protein abundance values) on top of pathways.
* **Network View** — The network in Cytoscape does not have graphical annotations of a pathway. The topology of the network reflects relationships in a pathway. This is ideal for performing algorithmic analysis of pathways and for merging several pathways together for a combined topology.
In the Public Databases dialog, you can select the import method by clicking the down arrow icon (▾) of the *Import* button on the lower-right corner.
### Cytoscape Commands
The WikiPathways app offers a Cytoscape command for scripting purposes.
**Importing GPML files**
* `gpml import-as-pathway file=<file-path>` — Import the GPML file at the given file path as a pathway view.
* `gpml import-as-network file=<file-path>` — Import the GPML file at the given file path as a network view.