Information for WikiPathways Authors

We invite all interested researchers and authors to participate in the WikiPathways project! Here you'll find information about getting started as an author, requirements for pathway models, and our review process.

Requirements for Pathway Content

Pathway models published at WikiPathways must meet specific criteira for quality and completeness, to ensure that the content is useful, both for direct human consumption, and for computational analysis:

• All interactions between genes, proteins and other pathway objects must be connected
• >90% of datanodes (genes, proteins, metabolites etc.) must be annotated with external database references
• Each pathway must have a complete description, meaning a minimum of 2-3 sentences summarizing the process that the pathway describes
• Each pathway must have at least one literature reference
• Each pathway must have a minimum of one pathway ontology term
• Pathway titles must adhere to our pathway title guidelines

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Getting Started

1. Create a GitHub Account
   A free GitHub account is required to create or edit pathways at WikiPathways.
2. Create a WikiPathways account
   A free WikiPathways account is required to create or edit pathways at WikiPathways during our move from the classic WikiPathways site.
3. Install Tools and Resources
   To create and edit WikiPathways pathway models, you will need the pathway editor PathVisio with the WikiPathways plugin installed.
4. Learn!
   • Learn everything about creating and editing pathways, from the basics to advanced topics at the WikiPathways Academy.
   • Check out the PathVisio tutorial video by TogoTV (DOI: https://doi.org/10.7875/togotv.2023.078) and the PathVisio YouTube Channel to learn how to use PathVisio.
   • For in-depth information on pathway curation, see Ten simple rules for creating reusable pathway models for computational analysis and visualization.
5. Author: Create or Edit a Pathway Model
   

   Create a Pathway from Published Literature

   Browse our suggested pathway modeling tasks to find a published pathway of interest to you. Then create a pathway model and publish it at WikiPathways! The suggested pathways are selected based on novelty in terms of genes or disease focus.

   • Pathway modeling tasks
   • Step-by-step guide

   Improve an Existing Pathway

   Help improve WikiPathways by editing existing pathway models that are in need of improvement. These tasks include adding datanode identifiers, connecting interactions, updating labels, improving layout as well as larger tasks like completing an unfinished pathway.

   • High-priority tasks
   • Beginner tasks
6. Engage: Join the WikiPathways Community
   Join the public discussion on pathway authoring and other WikiPathways-related topics.

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Review Process

All new pathways and edits to existing pathways are subject to review by a combination of automated tests and human review. All new pathways will be reviewed by a reviewer from our "Reviewer of the week" group. If edits are needed, authors will be conatcted by the reviewer. Once an edit or new pathway is approved, it will be available on the new site. This process typically takes 5-7 days right now.

Our reviewers use our Quality Assurance Protocol to check 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.