WikiPathways

WikiPathways web service client and GPML file format importer
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 &rarr; Import &rarr; Network &rarr; 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** &mdash; 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** &mdash; 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 (&#x25be;) 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>` &mdash; Import the GPML file at the given file path as a network view. * `gpml import-as-pathway file=<file-path>` &mdash; Import the GPML file at the given file path as a pathway view. **Querying the WikiPathways website** * `wikipathways get-species` &mdash; Return a list of species that WikiPathways supports. * `wikipathways search query=<query> [species=<species>]` &mdash; 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>` &mdash; Import the given pathway specified by `ID` as a network view. * `wikipathways import-as-pathway id=<id>` &mdash; Import the given pathway specified by `ID` as a pathway view.

3.2.1

Works with Cytoscape 3.1

Release Notes

* Updated to use new wikipathways web services for improved performance and stability

3.2.0

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Apps that depend on this release

Release Notes

New features: * Users can preview pathways before importing them in the *Import Network from Web Service* dialog. * Data nodes that link to other pathways can be imported by right-clicking on the node and choosing *Apps* > *WikiPathways* > *Open Linked Pathway*. * Z order of pathway elements are drawn correctly (Cytoscape 3.2+ only). Bug fixes: * The app uses the proxy settings to connect to WikiPathways. * Pathways should load more consistently in Cytoscape 3.2. * The `wikipathways import-as-pathway` command is now fixed in Cytoscape 3.2. * Retrieval of species is now cached. Known issues: * Cytoscape 3.2.0 does not always take nodes' Z order into account when the user tries to select a node.

3.1.2

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Apps that depend on this release

Release Notes

Fixed library dependency issues.

3.1.1

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Apps that depend on this release

Release Notes

Bug fix: networks created by WikiPathways &mdash; either by Public Database Import or by GPML file import &mdash; will now correctly appear in Cytoscape's Control Panel.

3.1

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Release Notes

New features: * New Cytoscape commands for importing GPML files and for querying the WikiPathways web service. In Cytoscape, select the *Tools* menu and choose *Command Line Dialog*. * To learn how to import GPML files, enter `help gpml`. * To learn how to query the WikiPathways web service, enter `help wikipathways`. * New API for importing GPML files in the service `GpmlReaderFactory`. * `GpmlReaderFactory` allows separating the creation of a GPML network from its network view. * `GpmlReaderFactory` allows users to pass in their own `CyNetwork`s and `CyNetworkView`s. Bug fixes: * The user no longer sees an error after canceling a task. * Clicking on the *View* menu without a network view will now work.

3.0

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Release Notes

* In version 1.0, the appearance of all pathway elements was specified by bypass values. In version 2.0, it was specified by mappings. Now in 3.0, we strike a balance between bypass values and mappings to ease data visualization with pathways: * Visual appearance of pathway data nodes are mapped. * Visual appearance of non-data nodes are set by bypass values. * Pathway shapes often obscure many nodes, making it difficult to select nodes. Shape nodes can be hidden by choosing in the menu bar *View &rarr; Toggle Pathway Shapes*. * The IDs of pathways on WikiPathways are now shown in the WikiPathways Web Client dialog. The ID of a pathway can be entered in the search field. * A pathway's web page in WikiPathways can be opened from the WikiPathways Web Client dialog

2.0

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Release Notes

* Pathway appearance can be modified by the visual style and/or node attributes. * New API for querying the WikiPathways REST service. * Several bug fixes with opening GPML files

1.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 3.2.1

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Released 26 May 2016

Works with Cytoscape 3.1

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