Help:Editing Pathways

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The main editor for WikiPathways is a webstart version of PathVisio.

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. 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 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.

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.

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.

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 and an interface for adding ontology tags. To add ontology tags, click the Add Ontology tags link, which will open two tools for finding and adding ontology tags: a search interface and browsable trees for the supported ontologies. To search for a term, simply begin typing in the Search field. Pick a term from the results and click the Add button (green check mark) to add the term. Alternatively, find a term from the browsable ontology trees, select it and click the Add button. You can delete any ontology term from the pathway by selecting it and clicking the Remove button (red x). To learn more about a particular term, click the View more info on BioPortal button (blue i).

Editing Guidelines

Best practices

  • Our comprehensive Instructions for Authors outlines how to author pathways from a beginner's perspective and includes recommendations for best practices for authoring pathways.
  • The Editor Palette guide describes the recommended utilization of the most commonly used elements of the WikiPathways editor palette. Examples are taken directly from the WikiPathways archives.

General Guidelines

  • Complete pathway authoring guidelines are available here.

Creating a new pathway

To create a pathway, you can either:

  • Use the PathVisio webstart editor at WikiPathways.
  • Upload an existing gpml via the Upload File option.
  • Create a pathway in PathVisio and upload it to WikiPathways via the WikiPathways plugin for PathVisio.

For details on how to create a new pathway, refer to the New Contributor Quickstart guide.

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