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Video Tour

Take a video tour of the new WikiPathways website!

TogoTV. Sep 21 2023, YouTube:, DOI:

Interactive Pathway Viewer

Each pathway offers a dedicated page for interactive viewing. Click on the open icon or anywhere on the image to open the interactive in a new tab. Zoom in and out by scrollwheel, pan by click-n-drag, and click on genes, proteins and metabolites to open links to external resources dedicated to each molecule. Here's a mini example:

Pro-tip: Use the orange icons on a pathway page to download the pathway in one of a variety of formats, or to share the pathway as a citation, permalink, or via social media. You can also get embed code so you can include this interactive viewer in your own web site.

Pathway Attributes

In addition to the title and organism at the top of each pathway page, you'll also find (in order):

  • pathway description
  • all the authors that have contributed to the pathway over the years
  • the status of the pathway, including last-edited date, whether new edits are under review and if it passes all curation checks
  • links open issues and discussions about the pathway
  • links to any publications citing the pathway
  • Organism represented by the pathway
  • Communities that are interested in the pathway
  • Annotation from Pathway, Disease and Cell Type ontologies

Participants in a Pathway

A table of participants lists the names, types, and sources for every identified gene, protein and small molecule in a given pathway.

Pro-tip: Click on the Download as TSV icon at the top of the table to download the complete table which includes mappings to many common identifiers. The Query options icon allows for querying external services, like Drugst.One, using the list of participants as the query input.

Literature References

As authors construct a pathway or make new additions, they add literature references to the bibliography of a given pathway. The reference list also includes links to PubMed, Europe PMC and Scholia. The references can be downloaded as a table via the Download as TSV icon.

How to Edit

To edit the pathway diagram and properties such as title, description, and participants, use our PathVisio drawing tool. See the Create section below. In addition to the pathway model, you can also edit the Cited By and Communities sections directly on the site. Click on the pencil icons near the section headers on each pathway page.

Navigating the Website

At the top of every page is a clickable logo that will take you to the home page, a search bar (see below), and a set of quick links to common pages. At the bottom of every page is a footer with information and links, including:

  • the status of the overall site and when it was last updated
  • a declaration of our CC0 waiver on all pathway content
  • a column of external links for our code repository, social media, and public forum
  • a few columns of common resource links related to using WikiPathways

Create Content

You can contribute to WikiPathways by creating new pathway models or by improving existing models. Learn everything you need to know about getting started as a WikiPathways author today!

Review Changes

To maintain WikiPathways as a high-quality pathway resource, a weekly rotation of reviwers from the community help to ensure the quality of new content and edits to existing content. Our Quality Assurance Protocol checks for the following things:

  • Do pathway nodes have valid database identifiers?
  • Are interactions properly connected to nodes?
  • Do pathway titles conform to guidelines?
  • Do pathways have appropriate ontology tags, and does each pathway have a useful description?

Anyone is welcome to join the Reviewer Roster. Please contact us if you are interested.

Code New Features

Want to join the WikiPathways Development Community? Visit our GitHub repo to learn more.

Analyze Your Data

WikiPathways models can be used for data visualization and analysis in many tools:

Publish Pathway Figures

Citing WikiPathways

If you include WikiPathways in your publications, please review our How to Cite page for details on referencing the WikiPathways project.

Downloading and Accessing Individual Pathways

On each pathway page, a set of options for download and links is a available via the icons under the pathway image, the Participants table and the References list. Each of these options can also be accessed directly by using the below URL patterns:

  • Permalink: The permanent link to a specific pathway has the pattern{WPID}.
  • Embed code: The code to embed a pathway image into webpage has the pattern <iframe src ="{WPID}`" width="600px" height="300px" style="overflow:hidden;"></iframe>.
  • Full size image: The link to a full size pathway image has the URL pattern{WPID}
  • PNG: The link to the PNG version of a pathway image has the URL pattern{WPID}/{WPID}.png.
  • SVG: The link to the SVG version of a pathway image has the URL pattern{WPID}/{WPID}.svg
  • JSON: The link to the JSON version of a pathway has the URL pattern{WPID}/{WPID}.json
  • GPML: Using the option Dowbload GPML will downloaded the GPML code for the pathway. The URL pattern to access this file is{WPID}/{WPID}.gpml
  • Participants: Using the option Download TSV option will downloaded a TSV-formatted table of the data nodes for the pathway. The URL pattern to access this file is{WPID}-datanodes.tsv
  • References: Using the option Download TSV will downloaded a TSV-formatted table of the literature for the pathway. The URL pattern to access this file is{WPID}-bibliography.tsv

Visualizing Data on Pathways

You can achieve quick and easy pathway visualizations highlighting multiple nodes with mulitple colors in a single pathway using our interactive pathway viewer.

Pro-tip: Click the View full size button in the upper-left corner of the pathway viewer on the pathway page. This will open a new browser tab where you can immediately add node names and colors to the url as paramaters according to the following patterns:

  • Highlight nodes by label and color:
  • Highlight multiple nodes by label and color:
  • Highlight node by xref and color:
  • Highlight nodes by label using multiple colors per node:,ACE,ACE2&orange=AGT,KNG1,CMA1,ACE.

The images below correspond to the first and last example in the list; nodes highlighted by label with one color; and nodes highlighted by label with multiple colors per node:

Node Coloring Example Single Node Coloring Example Multiple

If you want even more control over your pathway visualizations, like editing and adding objects, then refer to our tutorial describing data visualization on pathways in Cytoscape. From this workflow, you can get high-resolution images to include in manuscript, posters and other publications.

Embedding Pathway Visualizations in Web Pages

You can easily embed a simple pathway diagram in any web page using the embed code that is available in via the Share icon under the pathway image. This code has the following pattern:

<iframe src ="{WPID}`" width="600px" height="300px" style="overflow:hidden;"></iframe>.

An example of embedding of a WikiPathways pathway diagram in a website can be found on the LIPIDMAPS website.

It is also possible to embed a pathway with node visualization (described above) in a similar way, simply by adding the iframe tag and parameters like so:
<iframe src ="" width="600px" height="300px" style="overflow:hidden;"></iframe>
This code will produce the following iframe:

Move from classic WikiPathways

We are still in the process of moving from the classic WikiPathways site, and during this time some aspects of the site will work differently:

  • Uploading pathway content and making edits to pathways will require a WikiPathways account, since content is still being deposited to the classic site ( Once the move is complete, a GitHub account will be sufficient to upload/edit pathways at WikiPathways.
  • This website contains only approved pathways that have undergone review. Consequently, newly uploaded pathways will be immediately available on the classic site (, but will not be visible on this site until they are completed and approved. Once a pathway is uploaded to WikiPathways classic, the process of including them on the new site is as follows:
    • Pathways under construction: If your pathway is still under construction, keep the "Under Construction" tag. You can keep working on the pathway and it will stay on the classic site.
    • Completed pathways: If your pathway is complete, remove the "Under Construction" tag. The pathway will be reviewed by our Reviewers. Once it is approved, it will be made available on the new site. This process typically takes 5-7 days right now.


Have a question? See if the answer is in our collection of frequently asked questions.