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Current Repository for the WikiPathways Web Site

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This repository contains the code and development history of the main web site for the WikiPathways project: wikipathways.org. Built upon MediaWiki, the site includes numerous custom extensions, javascript, skins and hacks.

How to Contribute

Installation

We do not recommend attempting to install this site code as-is. There are many parts and services required that are not included here. Contact one of the architects for more details.

If you do attempt to install, note instructions in the README.md files in each subdirectory of wpi/extensions/, e.g., GPMLConverter and Pathways.

Contributing Pathway Content

If you are interested in adding or editing pathway diagrams, check out these resources:

Old Repo: http://svn.bigcat.unimaas.nl/wikipathways/

WikiPathways's Projects

.github icon .github

A special repo for org templates and other goodies

academy icon academy

Organized training examples for new WikiPathways authors

academy-templates icon academy-templates

Repository containing all the pathway templates (starter pathways) used in the WikiPathways Academy

bioentities icon bioentities

Namespace encoding hierarchical relationships between proteins, protein families, and protein complexes.

cget icon cget

Robust streaming cache for HTTP requests

cord-19 icon cord-19

Pathway knowledge extracted from CORD-19 dataset for the fight against COVID-19

cxml icon cxml

Advanced schema-aware streaming XML parser

cxsd icon cxsd

Streaming XSD parser and XML parser generator with TypeScript output

data icon data

demo for a Markdown-based data download page.

famplex icon famplex

Resources for grounding protein families and complexes from text and describing their hierarchical relationships.

fdp icon fdp

Repository with the content of the WikiPathways FAIR Data Point.

go-classification icon go-classification

Uses GO-Elite to find over represented GO terms for a pathway based on the genes in the pathway.

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