Help:New Contributor Quickstart

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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 curation tag system. You can find lists of pathways organized by curation tag. For example, pathways tagged with the "Missing gene/protein database references" (MissingXRef) tag or the "Unconnected lines" (NoInteractions) tag can be greatly improved by relatively simple editing. You can also find a pathway through search or browse.

Graphical pathway representation

  1. Once you decide on a pathway to edit, you have two options for editing the pathway:
    1. Open the Pathway Page for the pathway and click the Edit pathway link under the pathway image. This will open the pathway in the WikiPathways editor, where you can edit the pathway.
    2. Use the WikiPathways plugin for PathVisio to edit the pathway.
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.
When you are done editing, save the pathway in PathVisio by clicking the "Close the editor" button and then return to the Pathway Page. Click the Refresh button in your browser to view your recent changes.

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 curation tags. For example, if you added database references to all unassigned DataNodes on the pathway, remove the "Missing gene/protein database references" tag by clicking the Remove button next to the tag. Similarly, to add a curation tag, click the New tag button at the bottom of the Curation 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 editor at WikiPathways (see below), upload an existing gpml via the Upload File option (see below), or create a pathway in PathVisio and upload it to WikiPathways via the WikiPathways plugin for PathVisio.
  3. 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.
  4. 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.
  5. Alternatively, 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.
  6. 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.
  7. The WikiPathways editor contains a full set of drawing tools for pathway creation. See Editing Pathways for details.

For information on editing guidelines, please review our general editing guidelines and our list of example pathways.

  1. When your pathway is complete, click the Close the editor button to save your pathway to WikiPathways. The Pathway Page for your newly created pathway will be displayed.
  2. Add information about your pathway by editing the text fields in the Pathway Page. Remember to assign a category to your pathway so that the pathway will appear on the browse page listing all categorized pathways at WikiPathways.

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