Help:FileFormats

From WikiPathways

Revision as of 19:10, 12 October 2020 (view source) Mkutmon (Talk | contribs) (New page: # Supported file formats) ← Previous diff		Revision as of 19:29, 12 October 2020 (view source) Mkutmon (Talk | contribs) Next diff →
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-	# Supported file formats	+	<h2 class="frontPagePanel blueFg" style="width:660px;margin:1em;">Machine-readable formats</h2>
		+
		+	* '''GPML''': Graphical Pathway Markup Language for PathVisio (.gpml)
		+	** You can download the GPML file from each pathway page (Downloads)
		+	** 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)
		+	** ''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).
		+
		+
		+	<h2 class="frontPagePanel blueFg" style="width:660px;margin:1em;">Gene lists</h2>
		+
		+	* GMT: Gene Matrix Transposed file format (.gmt)
		+	* Eu Gene list (.txt)
		+
		+	<h2 class="frontPagePanel blueFg" style="width:660px;margin:1em;">Image formats</h2>
		+
		+	* PNG: Portable Network Graphics format (.png)
		+	* SVG: Scalable Vector Graphics format (.svg)
		+	* PDF: Portable Document Format (.pdf)

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Revision as of 19:29, 12 October 2020

Machine-readable formats

• GPML: Graphical Pathway Markup Language for PathVisio (.gpml)
  • You can download the GPML file from each pathway page (Downloads)
  • 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)
  • 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 (.gmt)
• Eu Gene list (.txt)

Image formats

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