Download and Access

GPML: Graphical Pathway Markup Language

• Download an organism-specific GPML archive of pathways.
• Download individual pathways in GPML format from each pathway page by accessing the Download pathway as... icon under the pathway graphic.
• Access pathways via the WikiPathways plugin in PathVisio to open a pathway in GPML format.

GMT: Gene Matrix Transposed

• Download the latest organism-specific GMT file for Gene Set Enrichment Analysis.

RDF: Resource Description Framework

• Read about the WikiPathways RDF model.
• Query the WikiPathways content in RDF format.
• Download all pathways in Turtle syntax.
• Download Reactome pathways in gpml and RDF format from the Reactome gpml repo.

SVG: Scalable Vector Graphics

• Download individual pathways in SVG format from each pathway page by accessing the Download pathway as... icon under the pathway graphic.
• Download all SVG files of the latest monthly release.

PNG: Portable Network Graphics

• Download individual pathways in PNG format from each pathway page by accessing the Download pathway as... icon under the pathway graphic.

Archive

• Access all monthly releases of the WikiPathways content.
• Access citeable DOIs for any GMT or GPML release of WikiPathways content via Zenodo.

Programmatic Access

The archive of current and past collections of pathways in various formats is accessible programmatically. Depending on your preferences, there are many ways to identify and access a collection of pathways or individual pathways:

• rWikiPathways is an R package that provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions. For example, a helper function called downloadPathwayArchive will retrieve the latest file for you per species and format, e.g.:
  downloadPathwayArchive(organism="Mus musculus”, format=‘gmt’)
• pywikipathways is a Python package for the WikiPathways API and provides the same functions as the rWikiPathways package.
• Bash scripting allows you to scrape the currently available filenames and guarantee that you are getting the latest file no matter what the name might be. Here is an example of a one-liner to get a list of all the current GMT files:
  echo "cat //html/body/div/table/tbody/tr/td/a" | xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">(.*gmt)<" | sed -E 's/(<|>)//g'
  And here is a version that would return the latest GMT for mouse:
  echo "cat //html/body/div/table/tbody/tr/td/a" | xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">.*Mus_musculus.gmt<" | sed -E 's/(<|>)//g'