From WikiPathways

Revision as of 01:02, 30 November 2018

Welcome to WikiPathways! This guide presents a quick overview of the most common use cases of WikiPathways.

Where do you want to start?

Browse pathway archives or find a specific pathway

1. To get an overview of the WikiPathways archives, select the Browse thumbnail on the main page. You can browse pathways by species, and fine-tune the results by Collection. Results can be viewed as thumbnail images or a list.
2. To find a specific pathway, search for it by name, data node name, data node identifier or keyword.

For details Search and Browse, see Finding Pathways.

Edit an existing pathway

1. Become part of the WikiPathways community by creating a user account.
2. Find a pathway to edit.
   To identify a pathway that is in need of editing, use the quality tag system. You can find lists of pathways organized by curation tag. For example, pathways tagged with the "Annotate nodes" tag or the "Fix interactions" tag can be greatly improved by relatively simple editing. You can also find a pathway through search or browse.
   

Graphical pathway representation

Once you decide on a pathway to edit, you can edit either the pathway diagram or the associated Pathway Page content:

1. 1. Open the Pathway Page for the pathway and click the Launch Editor link under the pathway image. This will open the pathway in the editor, where you can edit the pathway.
   2. When your edits are complete, click Plugins > WikiPathways > Update button to save your pathway to WikiPathways. The Pathway Page will be updated.

The content at WikiPathways is diverse in both style and content. While we don't enforce a particular drawing style, there are some guidelines for editing and graphical style. Our guidelines include general editing guidelines, a guide to the editor's palette, as well as a list of example pathways for your reference. There is also a specific process for including pathways into specific pathway collections at WikiPathways, read more about it here.

Additional fields of the pathway page

In addition to the graphical pathway representation, the Pathway Page has additional information fields that can be edited.

1. Add or remove relevant quality tags. For example, if you added database references to all unassigned DataNodes on the pathway, remove the "Annotate nodes" tag by clicking the Remove button next to the tag. Similarly, to add a quality tag, click the New tag button at the bottom of the Quality Tags section and select a tag from the drop-down menu. For example, if you consider the pathway incomplete, add the "Needs work" tag.
2. To edit the pathway description, click the Edit link in the Description section.
3. Add relevant ontology tags by searching for tags or by browsing the three ontologies.

Create a new pathway at WikiPathways

1. Become part of the WikiPathways community by creating a user account.
2. To create a pathway, you can either use the PathVisio webstart editor at WikiPathways, upload an existing gpml via the Upload File option, or create a pathway in PathVisio and upload it to WikiPathways via the WikiPathways plugin for PathVisio.

PathVisio webstart

1. To create a pathway in the WikiPathways editor, click the Create thumbnail on the main page or click the Create link in the left navigation panel.
2. On the Create new pathway page, enter a name for the pathway and then select which species the pathway is for from the drop-down menu.
3. Selecting the Make pathway private option hides your pathway from the rest of the community for 30 days. See the section on Private Pathways for details. Click the Create pathway button to continue.
4. Go to the newly created pathway page and click the Launch Editor" button. This starts the pathway editor where you can create your pathway.
5. Refer to the Guide for New Authors for pathway modeling tips.
6. When your pathway is complete, click Plugins > WikiPathways > Update button to save your pathway to WikiPathways. The Pathway Page for your newly created pathway will be updated.
7. Add information about your pathway by editing the text fields in the Pathway Page.

Upload gpml

1. You can also upload an existing gpml via the Upload File option on the Create new pathway page. Make sure the existing gpml contains a species designation.

PathVisio

You can also upload a local gpml directly from PathVisio by opening the pathway in PathVisio, and then selecting Plugins > WikiPathways > Upload New. Make sure the pathway contains a species designation.

Guide for New Authors

• Be sure to consult the Guide for New Authors for pathway modeling tips.