Help:FileFormats

From WikiPathways

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..

• RDF: Resource Description Framework (.ttl)
  • 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).
  • 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.

• Nanopublications
  • Nanopublications describing complexes, interactions, and pathway participation can be downloaded from the decentralized nanopublication server network.

• 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)
  • Work in progress: Converter from PathVisio to Minerva and then export as SBGN (https://git-r3lab.uni.lu/minerva).

• SBML: Systems Biology Markup Language (.sbml)
  • Work in progress: Converter from PathVisio to Minerva and then export as SBML (https://git-r3lab.uni.lu/minerva).

Gene lists

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