Help:Frequently Asked Questions
From WikiPathways
General
Who, What and Why is WikiPathways?
See About WikiPathways.
Where does the pathway content at WikiPathways come from?
At the start of WikiPathways, the pathway content mirrored that of GenMAPP.org, which was originally contributed by the GenMAPP user community. The content has since grown by contributions from the community.
How many pathways are part of WikiPathways?
Pathway statistics per species are published on our Home page.
Does WikiPathways check the content of contributed pathways for quality and accuracy?
No, WikiPathways does not review pathway content, except to look for vandalism and obvious problems.
How is WikiPathways different from KEGG, Reactome, BioCarta, Pathway Commons and other online pathway resources?
In addition to viewing and distributing pathways, WikiPathways content is also fully editable directly on the website. This is possible since WikiPathways is based on a wiki platform, similar to Wikipedia.
What is GPML?
GPML is the file format used to store pathway content at WikiPathways. GPML is short for GenMAPP Pathway Markup Language and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio.
Using WikiPathways
How can I use the pathway content from WikiPathways?
In addition to browsing and editing the content online, WikiPathways content can be downloaded in multiple formats for a variety of purposes:
- Pathways in GPML format can be used in the PathVisio program for editing.
- Pathways at WikiPathways can be opened in the Cytoscape program for network analysis purposes.
- Pathways in SVG, PNG and PDF graphical formats can be directly incorporated into presentations and publications.
- Pathways in MAPP format can be exported from the WikiPathways editor and used in GenMAPP program for integrating pathway information with data and for data over-representation analysis on collections of pathways. Note: MAPP export currently works only under the Windows operating system.
- Pathways can be downloaded in PWF format for use with the Eu.Gene tool.
How can I download all pathways at WikiPathways?
Batch download of pathways in gpml and svg format is available here: Batch Download
I created a pathway and made a mistake in it, how can I correct it?
You can revert the changes to your pathways under the History section of the Pathway page.
I want to delete a pathway, but there is no option for deleting.
Deleting a pathway is only possible with an Administrator account, contact the Help Desk for help.
I want to use one of the pathways in GenMAPP, but since I am not on a PC, the download MAPP option doesn't work. How can I get a pathway in GenMAPP format?
On the Pathway Page, click the Edit pathway link. When the pathway opens in PathVisio, go to File>Export to save the pathway in .mapp format.
It's difficult to view large pathways in the editor window. Is there a way to increase the size of the editor window?
In the editor, click the Switch to full-screen mode button in the tool bar. This will open a separate editor window that can be resized to fit the whole pathway.
Where can I report bugs?
Please report any bugs you encounter and submit any general comments to our Google group. You can also report bugs directly to our bug tracker. Also check our known problems to see if your problem is a known issue.
