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>
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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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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:80%;margin:0em;">Machine-readable formats</h2>
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<h2 class="frontPagePanel blueFg" style="width:100%;margin:0em;">Machine-readable formats</h2>
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* '''GPML''': Graphical Pathway Markup Language for PathVisio (.gpml)
* '''GPML''': Graphical Pathway Markup Language for PathVisio (.gpml)
** You can download the GPML file from each pathway page (Downloads button)
** 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 use the WikiPathways plugin in PathVisio to open a pathway in GPML format
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** You can download all GPML files of a specific monthly release from http://data.wikipathways.org.
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** You can download all GPML files of the latest monthly release from http://data.wikipathways.org/current/gpml or previous releases by browsing the releases at http://data.wikipathways.org..
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* '''RDF''': Resource Description Framework (.ttl)
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** You can query the pathway content using SPARQL at our SNORQL interface (http://sparql.wikipathways.org) or directly at our SPARQL endpoint (http://sparql.wikipathways.org/sparql).
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** You can download all pathways in RDF format in Turtle syntax (.ttl) of the latest monthly release from http://data.wikipathways.org/current/rdf or previous releases by browsing the releases at http://data.wikipathways.org.
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* '''Nanopublications'''
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** Nanopublications describing complexes, interactions, and pathway participation can be downloaded from the [http://app.tkuhn.eculture.labs.vu.nl/nanopub-monitor/ decentralized nanopublication server network].
* '''BioPAX''': Biological Pathway Exchange Format Level 3 (.owl)
* '''BioPAX''': Biological Pathway Exchange Format Level 3 (.owl)
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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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** You can download the monthly releases in GMT format from http://data.wikipathways.org.
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** You can download the latest monthly release in GMT format from http://data.wikipathways.org/current/gmt or previous releases by browsing the releases at http://data.wikipathways.org.
* '''Eu.Gene''' format (.txt)
* '''Eu.Gene''' format (.txt)
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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)
** You can download the PNG file from each pathway page (Downloads button)
** You can download the PNG file from each pathway page (Downloads button)
** Open a pathway in PathVisio and export the pathway in PNG format.
** Open a pathway in PathVisio and export the pathway in PNG format.
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** You can download all PNG files of a specific monthly release from http://data.wikipathways.org.
 
* '''SVG''': Scalable Vector Graphics format (.svg)
* '''SVG''': Scalable Vector Graphics format (.svg)
** You can download the SVG file from each pathway page (Downloads button)
** You can download the SVG file from each pathway page (Downloads button)
** Open a pathway in PathVisio and export the pathway in SVG format.
** Open a pathway in PathVisio and export the pathway in SVG format.
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** You can download all SVG files of a specific monthly release from http://data.wikipathways.org.
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** You can download all SVG files of the latest monthly release from http://data.wikipathways.org/current/svg or previous releases by browsing the releases at http://data.wikipathways.org..
* '''PDF''': Portable Document Format (.pdf)
* '''PDF''': Portable Document Format (.pdf)
** Open a pathway in PathVisio and export the pathway in PDF format.
** Open a pathway in PathVisio and export the pathway in PDF format.

Current revision

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 the latest monthly release from http://data.wikipathways.org/current/gpml or previous releases by browsing the releases at 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

  • 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.
  • SVG: Scalable Vector Graphics format (.svg)
  • PDF: Portable Document Format (.pdf)
    • Open a pathway in PathVisio and export the pathway in PDF format.
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