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
Search for Pathways
The WikiPathways collection can be searched by gene symbol, pathway name or other keywords, either directly in the Search field at the top of each page and on the front page, or using the table view. For example, search for your favorite pathway by a word from the title (i.e. "Statin"), or your favorite gene either by symbol (i.e. "BRCA1").
The table view of the current collection offers a nice way to interactively explore pathways by searching for various parameters. The table displays all pathways, and entering for example keywords, WPIDs or other parameters in the search fields at the top of each column filters the table. For example:
- To see all pathways related to adipogenesis in humans, type adipogenesis in the search field at the top of the Pathway Title column, and type Homo sapiens in the search field at the top of the Organism column.
- To see all mouse pathways edited in 2022, type Mus musculus in the search field at the top of the Organism column and type 2022 in the search field at the top of the Last Edited column.
Browse Pathways
The browse page displays content in either gallery or list view, which can be filtered by a combination of parameters. For example:
- 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: Organism Community Annotation . 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.
Create Content
- Get started as a WikiPathways Contributor today!
- Learn everything about creating and editing pathways, from the basics to advanced topics at the WikiPathways Academy.
- For more detailed information on making pathway models, see Ten simple rules for creating reusable pathway models for computational analysis and visualization.
- Check out the PathVisio YouTube Channel for videos on how to use PathVisio for pathway editing.
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:
- 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 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:
- Uploading pathway content and making edits to pathways will require a WikiPathways account content, since content is wtill deposited to the classic site (https://www.wikipathways.org/). 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 (https://www.wikipathways.org/), 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 Curators. Once it is approved, it will be made available on the new site. This process typically takes 5-7 days right now.
FAQ
Have a question? See if the answer is in our collection of frequently asked questions.