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. 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 *Data Source* menu at the top of the Public Databases dialog, choose *WikiPathways*.
1. In the search text field at the top, 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 the following Cytoscape commands for scripting purposes.
**Importing GPML files**
* `gpml import-as-network file=<file-path>` — Import the GPML file at the given file path as a network view.
* `gpml import-as-pathway file=<file-path>` — Import the GPML file at the given file path as a pathway view.
**Querying the WikiPathways website**
* `wikipathways get-species` — Return a list of species that WikiPathways supports.
* `wikipathways search query=<query> [species=<species>]` — Search the WikiPathways website for the given query. The species argument is optional. If the species argument is specified, this will only search for pathways under the given species. The species name must match what is returned by the `get-species` command.
* `wikipathways import-as-network id=<id>` — Import the given pathway specified by `ID` as a network view.
* `wikipathways import-as-pathway id=<id>` — Import the given pathway specified by `ID` as a pathway view.
