Download Pathways

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Contents

Pathways available for download have been explicitly marked with the Curated collection curation tag. This includes pathways that have been carefully curated and typically excludes draft or test pathways not intended for distribution. This is the recommended set for download.

A larger set of pathway which includes non-curated content is available here.

GPML

Click on one of the links below to download all pathways in GPML format. You can view and edit GPML files in PathVisio. You can also use GPML files for analysis in both PathVisio and Cytoscape using the WikiPathways app.

The pathways from the Human collection of Reactome are available through the Reactome portal at WikiPathways in the GPML format as well. Click here to download them.

BioPAX

Click on one of the links below to download all pathways in BioPAX level 3 format.

Eu.Gene

Click on one of the links below to download all pathways in the Eu.Gene format (pwf). Eu.Gene is a tool for microarray analysis in context of biological pathways (read more).

Plain text

Click on one of the links below to download all pathways in plain text format. This format contains a list of all datanodes, with the identifier in the first column, and the database system in the second column.

PDF

Click on one of the links below to download all pathways in Portable Document Format (PDF).

SVG

Click on one of the links below to download all pathways in SVG format. The SVG files can be used to create high quality images for publication purposes. You can edit and convert the SVG files using Inkscape.

PNG

Click on one of the links below to download all pathways in the Portable Network Graphics (png) format.

Flatfile

Click on one of the links below to download all pathways in either a tab-delimited or HTML table format. The output includes gene, protein and small molecule contents. You can choose between "original" and "mapped" versions, which refer to whether only the original identifiers are provided or if you want them mapped to all available identifier systems.


GMT Gene Sets

You can download the complete WikiPathways gene set collection here.

This file gets updated every day. We archive earlier versions of the collection here.

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