Help Topics

Interactive Pathway Viewer

Each pathway has a dedicated page that includes an interactive view. Zoom in and out by scrollwheel, pan by click-n-drag, and click on genes, proteins and metabolites to open external pages in Scholia dedicated to each molecule. Here's an example:

Pro-tip: Click on the "options" button in the lower-right to download the pathway in one of a variety of formats, or to view the pathway in its own window to help you explore the details. This is also where you'll find a permalink for the page that you can cite and embed code so you can include this interactive viewer in your own web site.

Pathway Attributes

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

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

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 "options" button in the lower-right to download the complete table which includes mappings to many common identifiers. This button also includes functionality to query 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 also be downloaded as a table (see the "options" button).

How to Edit

To edit the pathway diagram and properties such as title, description, and participants, you should use our PathVisio drawing tool. See the Create section below. In addition to the pathway model, you can also edit the "Cited In" 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 menu icon . The menu provides quick links to common pages. At the bottom of every page is a footer with packed 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

Curate Changes

To maintain WikiPathways as a high-quality pathway resource, a weekly rotation of community editors work 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?
  • Are all pathways tagged with appropriate ontology tags, and does each pathway have a useful description?

Anyone is welcome to join as a Community Editor. 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 in the options drop-down under 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://assets.wikipathways.org/pathways/{WPID}/{WPID}.png.
  • SVG: The link to the SVG version of a pathway image has the URL pattern https://assets.wikipathways.org/pathways/{WPID}/{WPID}.svg
  • GPML: Using the option Dowbload GPML will downloaded the GPML code for the pathway. The URL pattern to access this file is https://gitcdn.link/cdn/wikipathways/wikipathways-database/main/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

If you want to include data visualizations of pathway figures in your publication, 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.

You can also achieve a simpler visualization with just a few nodes highlighted, you can use our interactive pathway viewer. Nodes can matched by label("label") or external reference("xref") and colors("colors") can be specified by name or hexadecimal code. Some data mapping is possible when specifying nodes by xref.

  • Highlight nodes by label and color: Nodes specified by node label; https://pathway-viewer.toolforge.org/?id=WP528&lightgreen=PEMT" width="600px" height="300px" style="overflow:hidden;.
  • Highlight multiple nodes by label and color: Multilpe nodes specified; https://pathway-viewer.toolforge.org/?id=WP528&lightgreen=PEMT&pink=Choline&lightblue=CHKA" width="600px" height="300px" style="overflow:hidden;.
  • Highlight node by xref and color: Nodes specified by the external reference identifier assigned to them; https://pathway-viewer.toolforge.org/?id=WP528&lightgreen=Entrez_Gene_10400&pink=CAS_62-49-7&lightblue=Entrez_Gene_1119.
  • Highlight node by xref and color: Nodes specified using Ensembl identifiers, while the pathway uses NCBI Gene identifiers for nodes; https://pathway-viewer.toolforge.org/?id=WP528&yellow=Ensembl_ENSG00000110721,Ensembl_ENSG00000161217.

  • To embed either of these as an iframe, simply add the iframe tag and parameters like so:
    <iframe src ="https://pathway-viewer.toolforge.org/?id=WP528&yellow=Ensembl_ENSG00000110721,Ensembl_ENSG00000161217" 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 classi WikiPathways site, and during this time some aspects of the site will work differently:


FAQ

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