Download Pathways

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== GPML ==
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__NOEDITSECTION__ <!-- Turn off section editing -->
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Click on one of the links below to download all pathways in GPML format. You can view and edit GPML files in [http://pathvisio.org PathVisio]. From [http://pathvisio.org PathVisio] you can also export these files to the [www.genmapp.org GenMAPP] mapp format and [http://en.wikipedia.org/wiki/Portable_Document_Format PDF].
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{| align="right"
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  | __NOTOC__
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  |}
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<batchDownload filetype="gpml"></batchDownload>
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=== Versioned Releases ===
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Each month we release an updated set of pathways in various data and image formats. These pathways have been reviewed and tagged as approved, and are considered ready for analysis and data overlays.
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== SVG ==
 
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Click on one of the links below to download all pathways in [http://www.w3.org/Graphics/SVG/ SVG] format. The [http://www.w3.org/Graphics/SVG/ SVG] files can be used to create high quality images for publication purposes. You can convert the SVG files to any image format using [http://www.inkscape.org Inkscape].
 
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<batchDownload filetype="svg"></batchDownload>
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<font size=4>'''Current version: [http://data.wikipathways.org/20240410/ 20240410 (10 April 2024)]'''</font>
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<!-- doesn't work yet
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== PNG ==
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=== Vertebrates ===
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<batchDownload filetype="png"></batchDownload>
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-->
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Bos_taurus.zip Bos taurus]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Canis_familiaris.zip Canis familiaris]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Danio_rerio.zip Danio rerio]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Equus_caballus.zip Equus caballus]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Gallus_gallus.zip Gallus gallus]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Homo_sapiens.zip Homo sapiens]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Mus_musculus.zip Mus musculus]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Pan_troglodytes.zip Pan troglodytes]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Rattus_norvegicus.zip Rattus norvegicus]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Sus_scrofa.zip Sus scrofa]'''
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=== Invertebrates ===
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Anopheles_gambiae.zip Anopheles gambiae]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Caenorhabditis_elegans.zip Caenorhabditis elegans]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Drosophila_melanogaster.zip Drosophila melanogaster]'''
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=== Plants ===
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Arabidopsis_thaliana.zip Arabidopsis thaliana]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Hordeum_vulgare.zip Hordeum vulgare]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Oryza_sativa.zip Oryza sativa]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Populus_trichocarpa.zip Populus trichocarpa]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Solanum_lycopersicum.zip Solanum lycopersicum]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Zea_mays.zip Zea mays]'''
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<!-- * '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Beta_vulgaris.zip Beta vulgaris]''' -->
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=== Eukaryotic microorganisms ===
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Gibberella_zeae.zip Gibberella zeae]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Saccharomyces_cerevisiae.zip Saccharomyces cerevisiae]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Plasmodium_falciparum.zip Plasmodium falciparum]'''
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=== Bacteria ===
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Bacillus_subtilis.zip Bacillus subtilis]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Escherichia_coli.zip E.coli]'''
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* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Mycobacterium_tuberculosis.zip Mycobacterium tuberculosis]'''
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== Programmatic Access ==
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The archive of current and past collections of pathways in various formats at data.wikipathways.org is accessible programmatically as well. Depending on your preferences, there are many ways to identify and download the collection you need.
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''Note: Our files contain the date of creation in their names so that you can be sure which collection your are using and to avoid overwriting local copies of these files.''
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# '''[https://github.com/wikipathways/rwikipathways rWikiPathways]''' is an R package that provides an helper function called ''downloadPathwayArchive'' that will retrieve the latest file for you per species and format, e.g.,  <pre>downloadPathwayArchive(organism="Mus musculus”, format=‘gmt’)</pre>
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# '''Filename pattern''' allows you to infer the filename of the latest collection given the current date. For example, since we always release our archive collections on the 10th of each month, you know that the latest filename is the nearest prior date matching that pattern, e.g., 20180910 would be the current file from Sep 10 to Oct 10, 2018. ''Caution: this might break if for some unforeseen reason we are unable to produce the archive on schedule.''
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# '''Bash scripting''' allows you to scrape the currently available filenames and guarantee that you are getting the latest file no matter what the name might be.  Here is an example of a one-liner to get a list of all the current GMT files: <pre>echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">(.*gmt)<" | sed -E 's/(<|>)//g'</pre> And here is a version that would return the latest GMT for mouse: <pre>echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">.*Mus_musculus.gmt<" | sed -E 's/(<|>)//g'</pre>
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== Other Collections ==
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<font size=3>
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* [http://data.wikipathways.org Prior monthly releases]
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* [[Daily_Download|Daily curated releases]]
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* [http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=gpml&tag=Curation:Reactome_Approved  Reactome Human Collection]
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* [http://data.wikipathways.org/current/gmt Gene lists per pathway (GMT)]
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* [http://data.wikipathways.org/current/svg Pathway image files (SVG)]
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* [http://data.wikipathways.org/current/rdf Linked data files (RDF)]
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* [http://data.wikipathways.org/current/index Database index files (index)]
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* [[Help:FileFormats|Other file formats]]
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</font>

Revision as of 14:50, 11 April 2024

Versioned Releases

Each month we release an updated set of pathways in various data and image formats. These pathways have been reviewed and tagged as approved, and are considered ready for analysis and data overlays.


Current version: 20240410 (10 April 2024)


Vertebrates

Invertebrates

Plants

Eukaryotic microorganisms

Bacteria


Programmatic Access

The archive of current and past collections of pathways in various formats at data.wikipathways.org is accessible programmatically as well. Depending on your preferences, there are many ways to identify and download the collection you need.

Note: Our files contain the date of creation in their names so that you can be sure which collection your are using and to avoid overwriting local copies of these files.

  1. rWikiPathways is an R package that provides an helper function called downloadPathwayArchive that will retrieve the latest file for you per species and format, e.g., 
    downloadPathwayArchive(organism="Mus musculus”, format=‘gmt’)
  2. Filename pattern allows you to infer the filename of the latest collection given the current date. For example, since we always release our archive collections on the 10th of each month, you know that the latest filename is the nearest prior date matching that pattern, e.g., 20180910 would be the current file from Sep 10 to Oct 10, 2018. Caution: this might break if for some unforeseen reason we are unable to produce the archive on schedule.
  3. Bash scripting allows you to scrape the currently available filenames and guarantee that you are getting the latest file no matter what the name might be. Here is an example of a one-liner to get a list of all the current GMT files: 
    echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">(.*gmt)<" | sed -E 's/(<|>)//g'
    And here is a version that would return the latest GMT for mouse: 
    echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">.*Mus_musculus.gmt<" | sed -E 's/(<|>)//g'


Other Collections

Retrieved from "https://classic.wikipathways.org/index.php/Download_Pathways"
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