Help:FileFormats
From WikiPathways
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__NOTOC__ <!-- Turn off Table of Contents --> | __NOTOC__ <!-- Turn off Table of Contents --> | ||
| - | <h2 class="frontPagePanel blueFg" style="width: | + | <h2 class="frontPagePanel blueFg" style="width:80%;margin:0em;">Supported File Formats</h2> |
| - | Below you can find a list of machine-readable | + | 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:80%;margin:0em;">Machine-readable formats</h2> | |
| - | <h2 class="frontPagePanel blueFg" style="width: | + | |
* '''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 | ||
| - | ** You can download all GPML files of | + | ** 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 [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: | + | <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) | ||
| - | ** You can download the monthly | + | ** 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: | + | <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. | ||
| - | |||
* '''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. | ||
| - | ** You can download all SVG files of | + | ** 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..
- 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.
