Outline


Installation

If you have a pre-release version of the plugin installed, please uninstall the plugin through the plugin manager and restart PathVisio before you install the new version.

  1. Download and start PathVisio
  2. Open the Plugin Manager: Plugins » Plugin Manager
  3. Click the Install button for WikiPathways Plugin
  4. On success the plugin will be displayed in “installed plugins”. If some error happens a message is displayed.
  5. You can now use the plugin. Check out the description or the tutorials to get started.
  6. If you have problems installing this plugin, please contact us.

Functionality of the plugin

  1. Search by text, optional species selection (Keyword Search)
  2. Search for pathways by identifier/title (Pathway Search)
  3. Search for pathways containing specific gene or metabolite (Identifier Search)
  4. Search for pathways citing a specific publication (Literature Search)


Browse pathways in WikiPathways

  1. Browse by Organism
    WikiPathways currently supports more than 25 species.
  2. Browse by Collection
    WikiPathways adds pathways to different collections and portals when the quality and content of the pathways fit specific criteria, e.g. curated collection, WormBase collection or featured collection.
  3. Browse by Curation Tag
    WikiPathways tags pathways if they e.g. need more work, contain missing annotations or unconnected lines. They are used in curation events to improve the quality of the pathways.


Upload / update pathways to WikiPathways

Both features require a WikiPathways username with special permission rights. The permissions can be requested through the developers mailing list.

  1. Upload pathway
    This feature allows users to draw pathways offline in PathVisio and upload the pathway directly to WikiPathways when it is ready.
  2. Update pathway
    If a pathway has been opened through the plugin by searching or browsing, the pathway can be adapted in PathVisio and then updated on WikiPathways. Closing PathVisio or opening a new pathway will result in loosing the changes and a later upload is not possible.


Right click menu for pathway elements

  1. Pathway datanode
    Right click on an annotated pathway node allows the user to open the pathway directly from WikiPathways.
  2. Other datanodes
    Right click on an annotated pathway element (not pathway node) allows the user to find pathways containing the same element (identifier mapping is enabled).