Help:FileFormats

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<h2 class="frontPagePanel blueFg" style="width:100%;margin:0em;">Supported File Formats</h2>
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<h2 class="frontPagePanel blueFg" style="width:80%;margin:0em;">Supported File Formats</h2>
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.  
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.  
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<h2 class="frontPagePanel blueFg" style="width:100%;margin:0em;">Machine-readable formats</h2>
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<h2 class="frontPagePanel blueFg" style="width:80%;margin:0em;">Machine-readable formats</h2>
* '''GPML''': Graphical Pathway Markup Language for PathVisio (.gpml)
* '''GPML''': Graphical Pathway Markup Language for PathVisio (.gpml)
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<h2 class="frontPagePanel blueFg" style="width:100%;margin:0em;">Gene lists</h2>
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<h2 class="frontPagePanel blueFg" style="width:80%;margin:0em;">Gene lists</h2>
* '''GMT''': Gene Matrix Transposed file format for Gene Set Enrichment Analysis (.gmt)  
* '''GMT''': Gene Matrix Transposed file format for Gene Set Enrichment Analysis (.gmt)  
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<h2 class="frontPagePanel blueFg" style="width:100%;margin:0em;">Image formats</h2>
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<h2 class="frontPagePanel blueFg" style="width:80%;margin:0em;">Image formats</h2>
* '''PNG''': Portable Network Graphics format (.png)
* '''PNG''': Portable Network Graphics format (.png)

Revision as of 19:38, 12 October 2020

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.
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