Help:FileFormats

From WikiPathways

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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 (.gmt)
  • Eu Gene list (.txt)

Image formats

  • PNG: Portable Network Graphics format (.png)
  • SVG: Scalable Vector Graphics format (.svg)
  • PDF: Portable Document Format (.pdf)
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