CytoscapeWikiPathwaysApp - Revision history

Mkutmon at 20:28, 14 May 2014

2014-05-14T20:28:59Z

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Mkutmon at 20:09, 14 May 2014

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Mkutmon at 20:09, 14 May 2014

2014-05-14T20:09:26Z

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Mkutmon at 20:09, 14 May 2014

2014-05-14T20:09:18Z

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Mkutmon at 20:08, 14 May 2014

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Mkutmon: /* Install WikiPathways App in Cytoscape 3 */

2014-05-09T20:37:31Z

Install WikiPathways App in Cytoscape 3

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Mkutmon: /* Import pathway from local GPML file */

2014-05-09T20:17:30Z

Import pathway from local GPML file

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	=== Import pathway from local GPML file ===		=== Import pathway from local GPML file ===
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		+	Tutorial coming up soon.

Mkutmon at 20:17, 9 May 2014

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	The WikiPathways App for Cytoscape version 3 (http://apps.cytoscape.org/apps/wikipathways) provides Cytoscape users with easy access to pathway content at WikiPathways.org and pathways created with PathVisio in GPML format.		The WikiPathways App for Cytoscape version 3 (http://apps.cytoscape.org/apps/wikipathways) provides Cytoscape users with easy access to pathway content at WikiPathways.org and pathways created with PathVisio in GPML format.

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	=== Install WikiPathways App in Cytoscape 3 ===		=== Install WikiPathways App in Cytoscape 3 ===

Mkutmon: New page: == Connecting WikiPathways and PathVisio to Cytoscape == The WikiPathways App for Cytoscape version 3 (http://apps.cytoscape.org/apps/wikipathways) provides Cytoscape users with easy acce...

2014-05-09T20:13:15Z

New page: == Connecting WikiPathways and PathVisio to Cytoscape == The WikiPathways App for Cytoscape version 3 (http://apps.cytoscape.org/apps/wikipathways) provides Cytoscape users with easy acce...

New page

== Connecting WikiPathways and PathVisio to Cytoscape ==

The WikiPathways App for Cytoscape version 3 (http://apps.cytoscape.org/apps/wikipathways) provides Cytoscape users with easy access to pathway content at WikiPathways.org and pathways created with PathVisio in GPML format.

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=== Install WikiPathways App in Cytoscape 3 ===

* Go to Apps -> App Manager
* Select WikiPathways in 'Install Apps' and click on 'Install'

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=== Curated diagram view vs. basic node-and-edge network view ===

The '''curated diagram''' view ('pathway' import) shows the pathway with the same layout and graphical elements and shapes as on drawn in GPML. This view is intended for data visualization.

The figure blow shows the human ACE Inhibitor pathway from WikiPathways and opened in Cytoscape using the "Pathway" import ([http://wikipathways.org/index.php/Pathway:WP554 http://wikipathways.org/index.php/Pathway:WP554]):

[[Image:Cywpapp-1.png | 1000px]]

The '''Basic node-edge network''' view ('network' import) shows a reduced view of the pathway. All graphical elements are removed and nodes that are present multiple times in the pathways are merged into one. Therefore the layout is changed, a forced-directed layout is applied. This view is intended for network analysis.

The figure below shows the human ACE Inhibitor pathway from WikiPathways and opened in Cytoscape using the "Network" import ([http://wikipathways.org/index.php/Pathway:WP554 http://wikipathways.org/index.php/Pathway:WP554]):

[[Image:Cywpapp-2.png | 900px]]
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=== Import pathways through WikiPathways webservice ===

WikiPathways is available through the 'Public Database' interface of Cytoscape.

* Go to File -> Import -> Network -> Public Databases.
* In the DataSources drop down box, select WikiPathways.
* Type in a search word, pathway name or pathway identifier. You can select to search in a specific organism or all.
* Specify if you want to import the pathway as a pathway or network at the bottom right of the dialog.

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=== Import pathway from local GPML file ===

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=== Export network as GPML file ===

Under development