Help:FileFormats

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Supported File Formats

Below you can find a list of machine-readable, gene list and image formats that WikiPathways pathways can be converted to. Some are available directly from the pathway page, others can be created using different converter tools.


Machine-readable formats

  • GPML: Graphical Pathway Markup Language for PathVisio (.gpml)
    • You can download the GPML file from each pathway page (Downloads button)
    • You can use the WikiPathways plugin in PathVisio to open a pathway in GPML format
    • You can download all GPML files of a specific monthly release from http://data.wikipathways.org.
  • BioPAX: Biological Pathway Exchange Format Level 3 (.owl)
    • Open a pathway in PathVisio, install the BioPAX plugin and export the pathway in Biopax format.
  • XGMML: eXtensible Graph Markup and Modeling Language for Cytoscape (.xgmml)
    • Open Cytoscape, install the WikiPathways app and open the pathway in pathway or network view. Then you can use the Cytoscape export function to save the pathway in XGMML format.
  • SBGN: Systems Biology Graphical Notation (.sbgn)
  • SBML: Systems Biology Markup Language (.sbml)


Gene lists

  • GMT: Gene Matrix Transposed file format for Gene Set Enrichment Analysis (.gmt)
  • Eu.Gene format (.txt)
    • Open a pathway in PathVisio and export the pathway in Eu.Gene format.


Image formats

  • PNG: Portable Network Graphics format (.png)
    • You can download the PNG file from each pathway page (Downloads button)
    • Open a pathway in PathVisio and export the pathway in PNG format.
    • You can download all PNG files of a specific monthly release from http://data.wikipathways.org.
  • SVG: Scalable Vector Graphics format (.svg)
    • You can download the SVG file from each pathway page (Downloads button)
    • Open a pathway in PathVisio and export the pathway in SVG format.
    • You can download all SVG files of a specific monthly release from http://data.wikipathways.org.
  • PDF: Portable Document Format (.pdf)
    • Open a pathway in PathVisio and export the pathway in PDF format.