Help:FileFormats
From WikiPathways
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| - | + | <h2 class="frontPagePanel blueFg" style="width:660px;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. | 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. | ||
| - | <h2 class="frontPagePanel blueFg" style="width:660px;margin: | + | <h2 class="frontPagePanel blueFg" style="width:660px;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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** ''Work in progress:'' Converter from PathVisio to Minerva and then export as SBML (https://git-r3lab.uni.lu/minerva). | ** ''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: | + | <h2 class="frontPagePanel blueFg" style="width:660px;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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** Open a pathway in PathVisio and export the pathway in Eu.Gene format. | ** Open a pathway in PathVisio and export the pathway in Eu.Gene format. | ||
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* '''PNG''': Portable Network Graphics format (.png) | * '''PNG''': Portable Network Graphics format (.png) | ||
Revision as of 19:37, 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)
- 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 monthly releases in GMT format from 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.
- 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.
