Help:Editing Pathways
From WikiPathways
The main editor for WikiPathways is a webstart version of PathVisio. You can also edit data node annotation and style directly at WikiPathways using the Quick Edit feature.
Editing in PathVisio Webstart
Each pathway page at WikiPathways has an Launch Editor button, which launches PathVisio webstart with the pathway in question loaded. This utilizes the WikiPathways Client plugin.
- Click the Launch Editor button on any Pathway Page to open the PathVisio program with the current pathway loaded. You can add, edit or delete content from the pathway and when you save, updated versions of the images, controlled text, and data files are generated and are immediately available.
PathVisio supports a number of common drawing tools, as well as an interface for linking objects on pathways to an underlying gene database. For instructions on basic editing features please refer to PathVisio documentation.
- Save your pathway by clicking Plugins > WikiPathways > Update. You will be asked to describe your edits.
Editing using Quick Edit
We have a new, quick way to edit data node annotations and styles. When logged in, the Quick Edit button is located at the bottom center of the pathway view. Clicking the Quick Edit button opens the editor:
Editing data node annotation
- Open Quick Edit.
- Select any data node to display its current annotation in the annotation tab.
- To search for a new identifier, type in a gene name or label in the Search by name field and click the green Search button. Results are displayed in a separate results panel. Select an identifier from the list of results to assign it to the node.
- To change only the data node type or data source, simply select from the drop-down lists.
- To manually change the label or identifier, simply type directly in the corresponding field.
- Click the Save & Close button to save and exit Quick Edit.
Editing data node style
- Open Quick Edit.
- Select a data node and click the Properties tab in Quick Edit.
- Use the color chooser to change the border and label color of the node, or use the buttons to set the label text to bold and italic.
- Click the Save & Close button to save and exit Quick Edit.
Editing Pathway Page 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.
Quality Tags
Quality tags can be added to a pathway to notify the author and community about the state of the pathway. For example, you could tag a pathway that isn't annotated properly or tag your own pathway as work in progress. Quality Tags can be added by clicking the green plus sign icon in the Quality Tags section. Choose the type of Quality Tag from the drop-down list and enter a comment if appropriate.
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 on any object in the pathway and selecting Add or Edit from the Literature menu. Details on how to incorporate literature references can be found here.
Ontology Tags
The Ontology Tags section contains any ontology tags added to the pathway. The interface for adding and editing ontology tags is currently disabled. A new version will be available in the future.
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.
