Help:Editing Pathways

From WikiPathways

Revision as of 19:18, 15 May 2008

In addition to editing the text fields on a given Pathway Page, this wiki also supports the ability to edit the pathway itself! Click on Edit pathway on any Pathway Page and a version of the PathVisio program will open with the current pathway loaded. You can then add, edit or delete content from the pathway. When you save, updated versions of the images, controlled text, and data files are generated and are immediately available. Try it out in the Sandbox pathway!

Editing the pathway image

Pathway editing for WikiPathways is done in an embedded version of the PathVisio program. PathVisio supports a number of common drawing tools, as well as an interface for linking objects on pathways to an underlying gene database. For detailed instructions on how to use the PathVisio program please refer to PathVisio Help and PathVisio FAQ. In addition to the drawing features described for the PathVisio webstart program, the WikiPathways embedded editor has some additional features.

Save to WikiPathways.org

You can save your pathway directly to WikiPathways by clicking the "Save to pathway to WikiPathways.org" button in the toolbar.

Right-click menu

Right-clicking anywhere on the drawing board or on an object will bring up the right-click menu. The menu options depend on the type of object you clicked:

• Drawing Board:

* Delete: Deletes the selected object
* Select all: Selects all objects in the pathway
* Select all DataNode objects: Selects all gene objects in the pathway
* Order>Bring to front: Brings the selected object to the front
* Order>Send to back: Sends the selected object to the back
* Order>Bring forward: Brings the selected object forward one layer
* Order>Send backward: Sends the selected object backward one layer
* Add literature reference: Literature references can be added for any object by entering a PMID or by manually entering information on authors, journal etc.

• Data node:

* Delete: Deletes the selected object
* Select all: Selects all objects in the pathway
* Select all DataNode objects: Selects all gene objects in the pathway
* Order>Bring to front: Brings the selected object to the front
* Order>Send to back: Sends the selected object to the back
* Order>Bring forward: Brings the selected object forward one layer
* Order>Send backward: Sends the selected object backward one layer
* Add literature reference: Literature references can be added for any object by entering a PMID or by manually entering information on authors, journal etc.
* Properties: Comments, Literature and Annotation for objects can be viewed and edited through the Properties window. 

• Line object:

* Delete: Deletes the selected object
* Select all: Selects all objects in the pathway
* Select all DataNode objects: Selects all gene objects in the pathway
* Add A
* Order>Bring to front: Brings the selected object to the front
* Order>Send to back: Sends the selected object to the back
* Order>Bring forward: Brings the selected object forward one layer
* Order>Send backward: Sends the selected object backward one layer
* Add literature reference: Literature references can be added for any object by entering a PMID or by manually entering information on authors, journal etc.
* Properties: Comments, Literature and Annotation for objects can be viewed and edited through the Properties window. 

• Order>Send to back: Sends the selected object to the back
• Add literature reference: Literature references can be added for any object by entering a PMID or by manually entering information on authors, journal etc.
• Edit literature reference: Any existing literature references can be edited
• Properties: Comments, Literature and Annotation for objects can be viewed and edited through the Properties window. Comments and Literature can also be added and modified at the pathway-level, by accessing the Properties window from any blank space on the drawing board.

Editing text fields

Text fields on Pathway Page is edited like any other text on a wiki. Please refer to the WikiMedia website for details on formatting.

Description

Each Pathway Page includes a Description section, which contains information about the biological process described in the pathway. The Description can be edited by clicking the Edit link to the right of the Description section.

Bibliography

Each Pathway Page includes a Bibliography section, designed to hold reference information relevant to the pathway. When editing a pathway in the editor, any references to publications, textbooks and websites can be added to this section by right-clicking anywhere on the drawing board and selecting Add or Edit from the Literature menu. Details on how to incorporate literature references can be found here.

Categories

Categories Each pathway is categorized into one or several categories, listed under Categories. The category assignment can be edited or new categories added to the pathway by clicking the Edit link to the right of the Categories section.

Creating a new pathway

You can create a new pathway at WikiPathways by clicking the Create new pathway link in the navigation panel on the left side of each page. For details on how to create a new pathway, refer to the New Contributor Quickstart guide.

Deleting a pathway

A Pathway Page can only be deleted by an administrator. If you want to delete a pathway you have created, contact the Help Desk.

Return to Help Contents

Continue to Watching Pathways