Submitting a pathway to WikiPathways

Prerequisites

These instructions require two things:

• A complete pathway in .mapp format, created in GenMAPP, OR a pathway in gpml format, created in PathVisio.
• Your computer needs to have Java Web Start installed.

If your pathway is in gpml format already, proceed to Uploading the pathway at WikiPathways.org below.

If your pathway is in GenMAPP format, continue with Converting the pathway to gpml below.

Converting the pathway to gpml

WikiPathways is an open, public platform dedicated to the curation of biological pathways. To contribute your completed pathway to WikiPathways without re-drawing it, the pathway must first be converted to the gpml format, which is the main pathway format used by WikiPathways. This can be done in the PathVisio program.

Download PathVisio databases

1. Go to www.pathvisio.org and click the Download link. On the download page, under Step 3, click the download link for the Gene Database for the relevant species. 
2. During download, you will be asked for an application to open the file with. Select Java Web Start, which should be the default.
3. Save the database to the suggested default location.

Running PathVisio

1. Go to www.pathvisio.org and click the Download link. On the download page, click the link to download PathVisio for Windows.
2. During download, you will be asked for an application to open the file with. Select Java Web Start, which should be the default.
3. In PathVisio, select Data>Select Gene Database and browse to load the appropriate database.
4. Under File>Import select the .mapp file containing your pathway.
5. When the pathway has loaded in PathVisio, double-check that all layout is intact and make any necessary changes. For detailed instructions on how to use PathVisio, see PathVisio Help.
6. Select File>Save As to save the pathway as gpml.
7. Quit PathVisio.

Converting .mapp to gpml using PathVisio

Uploading the pathway at WikiPathways

1. Go to www.wikipathways.org and register as a new user, or login if you already have an account.
2. On the main page, click Create.
3. Type in a name for the pathway and specify for which species it is relevant using the drop-down menu. Click Create pathway to continue.
4. A blank pathway page will open, with the pathway in edit mode. In the editor, select the Import pathway button from the Toolbar.
5. In the Import pathway file browser, find the gpml-formatted file saved in PathVisio. Click Import to continue.
6. Your pathway will be displayed in the editor window. Save the pathway by clicking the Save the pathway to WikiPathways.org button in the Toolbar. After saving is complete your pathway will appear on the pathway page.
7. Add a description to your pathway by clicking the Edit button in the Description section of the pathway page. In the applet that appears, enter your description and click the Save pathway and close editor button.
8. Add categories to your pathway by clicking the Edit button in the Categories section of the pathway page. In the applet that appears, select one or more categories using the check boxes and click the Save pathway and close editor button.

Uploading a pathway to WikiPathways

Do you have comments or questions about this tutorial? Contact GenMAPP Support.