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.

Browse Pathways

The Filters page displays content in either gallery or list view, which can be filtered by multiple categories. Additional sort options become available when the filtered set is fewer than 200 pathways. Example usage:

• To see all human pathways cancer pathways sorted by newest pathway, select Homo sapiens from Organism, disease of cellular proliferation from Disease Ontology and click the Date button at the top.
• To see all yeast classic metabolic pathways sorted by title, select Saccharomyces cerevisiae from Organism, classic metabolic pathway from Pathway Ontology, then click the Title button at the top.

The WikiPathways collection can be browsed by shared attributes: Organisms Communities Annotations , as well as by Authors or by whether they are New or recently Updated.

Join a Community

WikiPathways Communities organize pathways specific to a research area or organism. Community pages are designed to make it easier to explore relevant pathway content, learn more about the community and to organize pathway curation.

• To contribute pathway content to a community, refer to each community page for details on how to contribute.
• To learn how to create or edit a community page, see our Communities Help.

Get Recognition

Each of the authors who has contributed to WikiPathways has their own profile page. In addtion to a standard biographicial field and professional linkouts, these pages provide a gallery listing of all the pathways edited by a given author. Click on the pencil icons next to your name to edit your user profile. See the sections below to learn more about how to contribute to WikiPathways while enabling your own research.

Pro-tip: Your profile picture comes directly from your associated GitHub account. Update your avatar on your GitHub settings page to update the picture shown in your WikiPathways author profile.

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 reviewers 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:

• Learn how to use WikiPathways in enrichment analysis, data visualization in PathVisio and Cytoscape, and querying the WikiPathways RDF.
• See a listing of all tools supporting WikiPathways.

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 https://www.wikipathways.org/instance/{WPID}.
• Embed code: The code to embed a pathway image into webpage has the pattern <iframe src ="https://pathway-viewer.toolforge.org/?id={WPID}`" width="600px" height="300px" style="overflow:hidden;"></iframe>.
• Full size image: The link to a full size pathway image has the URL pattern https://pathway-viewer.toolforge.org/?id={WPID}
• PNG: The link to the PNG version of a pathway image has the URL pattern https://www.wikipathways.org/wikipathways-assets/pathways/{WPID}/{WPID}.png.
• SVG: The link to the SVG version of a pathway image has the URL pattern https://www.wikipathways.org/wikipathways-assets/pathways/{WPID}/{WPID}.svg
• JSON: The link to the JSON version of a pathway has the URL pattern https://www.wikipathways.org/wikipathways-assets/pathways/{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 https://www.wikipathways.org/wikipathways-assets/pathways/{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 https://gitcdn.link/cdn/wikipathways/wikipathways.github.io/main/_data/{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 https://gitcdn.link/cdn/wikipathways/wikipathways.github.io/main/_data/{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: https://pathway-viewer.toolforge.org/embed/WP554?red=ACE.
• Highlight multiple nodes by label and color: https://pathway-viewer.toolforge.org/embed/WP554?red=ACE&lightgreen=AGT.
• Highlight node by xref and color: https://pathway-viewer.toolforge.org/embed/WP554?red=Ensembl_ENSG00000159640.
• Highlight nodes by label using multiple colors per node: https://pathway-viewer.toolforge.org/embed/WP554?yellow=ACE&lightgreen=AGT,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:

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:

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 ="https://pathway-viewer.toolforge.org/embed/WP554?red=ACE&lightgreen=AGT" width="600px" height="300px" style="overflow:hidden;"></iframe>
This code will produce the following iframe: