Training Example: WikiPathways – Review the Data, Give Your Score & Compare to the Real AI Evaluation

[H2] WikiPathways is an open science platform for biological pathways contributed, updated, and used by the research community.
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Video tour
Powered by:

[IMG: PathVisio]

&

[IMG: BridgeDB]

Interact with diagrams with clickable genes, drugs, and pathways.

[H1] Help Topics
Investigate
Video tour
Interactive viewer
Attributes
Participants
References
Editing

Navigate
Site
Search
Browse
Communities
Authors

Participate
Create
Review
Code
Analyze
Publish

[H1] Video Tour
Take a video tour of the new WikiPathways website!
TogoTV. Sep 21 2023, YouTube: https://youtu.be/oSyoDU2r4Q0, DOI: https://doi.org/10.7875/togotv.2023.
[H1] Interactive Pathway Viewer
Each pathway page 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.
See the WikiPathways Legend below to learn what the various objects in the pathway diagram represent:
[IMG: WikiPathways Reference Card]
[H1] 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
[H1] 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.
[H1] 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.
[H1] 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.
[H1] 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
[H1] Search for Pathways
The WikiPathways collection can be searched by gene symbol, pathway name or other keywords, in the Search field at the top of each page. By default, the first 40 results will appear on the search results page. To view all results, click the Show more button at the end of the results list. You can also include organism, ontology annotations, WPIDs, and even last-edited dates in your query. Multi-term queries are processed as AND queries. Here are some example queries:
Search for your favorite pathway by a word from the title, i.e. "Statin".
Search your favorite gene by symbol, i.e. "BRCA1".
Search for all human pathways that include ACE2 and aldosterone with the query "ace2 aldosterone human".
Search for all cancer pathways updated in 2023 with the query "cancer 2023".
Note that for searches with many results, adding search terms will update the results. However, the updating of results may not be evident without scrolling to see the full list.
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 offers search fields at the top of each column to filter the table. Additional sort options become available when the filtered set is fewer than 200 pathways. Example usage:
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.
[H1] 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.
[H1] 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.
[H1] 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 two gallery listing, one with of all the pathways edited by that author, and a second listing all pathways started by that 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.
[H1] 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!
[H1] 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.
[H1] Code New Features
Want to join the WikiPathways Development Community? Visit our GitHub repo to learn more.
[H1] 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.
[H1] Publish Pathway Figures
[H2] Citing WikiPathways
If you include WikiPathways in your publications, please review our How to Cite page for details on referencing the WikiPathways project.
[H2] 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://www.wikipathways.org/wikipathways-assets/pathways/{WPID}/{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://www.wikipathways.org/wikipathways-assets/pathways/{WPID}/{WPID}-bibliography.tsv
[H2] 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:

[IMG: Node Coloring Example Single]

[IMG: 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.
[H2] 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 ="https://pathway-viewer.toolforge.org/?id={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 LIPID MAPS 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:
[H2] Styling Pathways for Published Pathway Figures
WikiPathways models are "plain" by design, to allow for optimal data visualization. However, for published materials, it is sometimes preferred to display a pathway (without data, typically) in a more decorated style, more typical of how pathway figures are commonly represented. Starting with a pathway model at WikiPathways, you can apply custom pathway styling in Cytoscape to produce a pathway figure that is visually more comparable to typical published pathway figures. For more information see Styling WikiPathways Models.
[H1] Classic WikiPathways
The Classic WikiPathways site has now been retired and that includes the old web service. If you need help transitioning, please contact us.
[H1] FAQ
Have a question? See if the answer is in our collection of frequently asked questions.

[H1] Pathways by Community
The communities below represent pathway content specific to a research area or organism. These pages are designed to make it easier to explore pathway content, learn more about the community and to organize relevant pathway curation. To learn how to create or edit a community page, see our Communities Help.
Adverse Outcome Pathways
The Adverse Outcome Pathway Community is created to highlight the molecular basis of Adverse Outcome Pathways.
COVID-19
Molecular mechanisms of COVID-19
CPTAC
The CPTAC Community highlights pathway content relevant to the Clinical Proteomic Tumor Analysis Consortium (CPTAC).
Daphnia
The Daphnia Community is set up for collaboration on getting knowledge together about the biological processes in the Daphnia magna species.
Diseases
The Disease Community highlights WikiPathways content related to human disease, and is designed as a central organizing point for exploring, curating and expanding the collection of disease pathways.
ExRNA
The ExRNA Community highlights pathway content relevant to the extracellular RNA research community.
Inherited Metabolic Disorders (IMD) Pathways
The IMD Community is set up to give an overview of all Inherited Metabolic Disorders (IMDs), also known as Inborn Errors of Metabolism (IEM).
Lipids and LIPID MAPS
This community is set up to coordinate the development of lipid pathways and gather the community interested in interactive lipid pathways. Lipids serve several important biological purposes, such as providing membrane structure, and signalling.
Micronutrients
The Micronutrient Community highlights pathway content relevant to the micronutrient research community.
Mitochondrion
Nanomaterials Pathways
The Nanomaterials Community serves the interest of nano systems biology research by facilitating community-based annotation of biological pathways related to nanosafety.
ONTOX
The ONTOX Community lists molecular interaction pathways related to hepato-, nephro-, and neurodevelopmental toxicities.
PancCanNet
The PancCanNet Community highlights pathway content relevant to the pancreatic cancer research community.
Plants
In the interest of plant research and to facilitate community-based annotation of biological pathways (metabolic/biochemical, signaling, genetic and gene-interactions) in plants, we present to you a freely-available platform which allows you to add, edit and download known and novel published pathways from plants.
Rare Diseases
The Rare Disease Community highlights WikiPathways content related to rare genetic human diseases, and is designed as a central organizing point for exploring, curating and expanding the collection of rare disease pathways.
Reactome
The Reactome pathways can be found at https://github.com/wikipathways/reactome-gpml.
Renal Genomics Pathways
The Renal Genomics Community highlights WikiPathways content related to renal biology and disease
Skeletal Dysplasia
The Skeletal Dysplasia Community was initiated with the goal to create Wikipathways diagrams for all known skeletal dysplasia genes.
Serious Request 2024 - MetaKids
This community reflects the Serious Request 2024 action to raise funding for MetaKids.
WormBase
The WormBase Community highlights pathway content maintained by WormBase and the Worm Community. WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.

[H1] How to Cite
Depending on how you use WikiPathways, please consider citing one or more of the following articles:
[H2] Citing the WikiPathways project
We recommend citing our latest NAR database article:
Agrawal A, et al. (2024) WikiPathways 2024: next generation pathway database. NAR.
Potentially-relevant topics are highlighted in our other project articles:
Miller RA, et al. (2022) Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions. PLoS ONE.
Martens M, et al. (2021) WikiPathways: connecting communities. NAR
Slenter DN, et al. (2018) WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. NAR.
Kuhn T, et al. (2018) Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. 2018 IEEE 14th International Conference on e-Science (e-Science).
Kutmon M, et al. (2016) WikiPathways: capturing the full diversity of pathway knowledge. NAR.
Waagmeester A, et al. (2016) Using the semantic web for rapid integration of WikiPathways with other biological online data resources. PLoS Comput Biol.
Kelder T, et al. (2012) WikiPathways: building research communities on biological pathways. NAR
Kelder T, et al. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS One.
[H2] Citing individual pathways
To cite a specific pathway, use its permalink, for example: https://www.wikipathways.org/instance/WP254. The permalink for each pathway is available from the Share pathway icon under the pathway. When citing the live version of a pathway, attribution of individual authors is not necessary since it is continuously tracked and displayed on each pathway page.
The full citation, which includes the permanen link, is also available from the Share pathway icon under the pathway; for example "Zambon AC, Pico A, Kelder T, Coort S, Angelika A, Lawlor B, Iersel MV, Gillespie M, Hanspers K, Bouwman J, Riutta A, Nuno N, Willighagen E, Summer-Kutmon M, Kalafati M, Josip J, Anam A. Apoptosis (WP254) [Internet] Last edited: 2021-05-27. Available from: https://www.wikipathways.org/instance/WP254."
To cite a specific version of a pathway, we recommend downloading the pathway as PNG from the Download pathway as... icon under the pathway, and uploading it to Zenodo to generate a DOI that you can then reference in your paper. Alternatively, your can upload another image file or figure that you have made using WikPathways content. An example Zenodo record can be found here. Follow these steps:
Log in to Zenodo. Accounts are free.
Go to the WikiPathways community upload page.
Upload a PNG of the pathway you want to reference.
Complete the fields and click "Publish".

Once your paper is published, Add a citation to the corresponding pathway page(s):
To complete these steps, first make sure you are logged in to your GitHub account.
Find the corresponding pathway on WikiPathways, for example WP4629.
In the Cited In section, click the pencil icon to edit the list. This will open a new browser tab with the "citedin_lookup.yaml" file open in edit mode.
Click anywhere in the editable area and use Ctrl+F to search for the WPID, for example "WP4629".
If the PMCID or DOI for the publication has not already been added, add an entry under the relevant WPID in the following format: - link: PMC9603647.
Enter a commit message ("added citation for WP4629") and click "Commit changes".