Help:Editing Pathways
From WikiPathways
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!
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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.
Adding, selecting, sizing, moving and grouping objects
For instructions on basic editing features please refer to PathVisio Help.
Adding connectors between objects
Creating curved lines and composite lines
Right-click menu
Right-clicking anywhere on the drawing board or on an object will bring up the right-click menu. Some menu options are universal, and some depend ong the type of object you click.
- 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 anchor: Adds an anchor point to a line, for connecting to other objects.
- Line type>Curved: Creates a curved line, which can be customized in shape by connecting the end points to objects and by dragging the way points on the line. Way points appear as blue diamond shapes on the curved line.
- Line type>Elbow: Creates an elbow line, which can be customized in shape by connecting the end points to objects and by dragging the way points on the line. Way points appear as blue diamond shapes on the curved line.
- Line type>Straight: Creates a straight line.
- 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.
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.
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.
