CytoscapeWikiPathwaysApp

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Revision as of 20:09, 14 May 2014

Contents

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.


Install WikiPathways App in Cytoscape 3

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


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):



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):


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.



Import pathway from local GPML file

Tutorial coming up soon.


Export network as GPML file

Under development

Retrieved from "https://classic.wikipathways.org/index.php/CytoscapeWikiPathwaysApp"
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