Help:New Contributor Quickstart

From WikiPathways

Revision as of 21:34, 27 January 2014

Welcome to WikiPathways! This guide let's you quickly get started with authoring pathways at WikiPathways, with step-by-step examples of the most common use cases.

Where do you want to start?

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.
   

1. Once you decide on a pathway to edit, open the Pathway Page for that pathway.
2. Click the Edit pathway link under the pathway image. This will open the pathway in the WikiPathways editor, where you can 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 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. Click the Create thumbnail on the main page or click the Create link in the left navigation panel.
3. 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. 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. PathVisio will open with a blank drawing board. Create your pathway in PathVisio.
   For information on editing guidelines, please review our genereal editing guidelines and our list of example pathways. For instructions on how to use PathVisio, please refer to PathVisio Help.
   
5. When your pathway is complete, click the "Close the editor" button to submit your pathway to WikiPathways. A new browser window will open with the Pathway Page for your newly created pathway at WikiPathways.
6. 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.

Transfer pathway from GenMAPP to WikiPathways

You can transfer a pathway that you have created in the GenMAPP program to WikiPathways using PathVisio. If you have the WikiPathways plugin installed in PathVisio, you can upload the pathway directly from PathVisio. Otherwise, you can save the pathway in gpml format and upload the pathway it to WikiPathways under Create new pathway.

1. Become part of the WikiPathways community by creating a user account.
2. Launch PathVisio. PathVisio will open with a blank drawing board. To access your existing GenMAPP pathway, go to File -> Import and select the appropriate .mapp file.
3. Make any necessary changes to the pathway in PathVisio.
   1. If you have the WikiPathways plugin installed in PathVisio, select Plugins -> WikiPathways -> Upload New. You will be asked to specify your login information and a description of the pathway.
   2. To upload the pathway without the plugin, click the Create thumbnail on the main page or click the Create link in the left navigation panel.
   3. 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. Click the Upload file button to continue.
   4. Select the gpml file using the file browser. There is also an option to make the pathway private, meaning it will be hidden from public view for 30 days. Click Upload pathway when done.
4. 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 in the lists of all pathways at WikiPathways.

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