Download Pathways

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Pathways available for download have been explicitly marked with the '''Curated collection''' curation tag. This includes pathways that have been carefully curated and typically excludes draft or test pathways not intended for distribution. '''This is the recommended set for download'''.
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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 curated, and are considered ready for analysis and data overlays.  
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A larger set of pathway which includes non-curated content is available [[:Download_All_Pathways | here]].
 
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== GPML ==
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<font size=4>'''Current version: [http://data.wikipathways.org/20161010/ 20161010 (10 October 2016)]'''</font>
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The pathways from the Human collection of Reactome are available through the Reactome portal at WikiPathways. Click [http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=gpml&tag=Curation:Reactome_Approved  here] to download them.
 
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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]. You can also use GPML files for analysis in both PathVisio and [http://cytoscape.org Cytoscape] using the [http://apps.cytoscape.org/apps/wikipathways WikiPathways app].
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=== Vertebrates ===
{|class="prettytable"
{|class="prettytable"
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  |-
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  |<batchDownload filetype="gpml" tag="Curation:AnalysisCollection"></batchDownload>
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Bos_taurus.zip Bos taurus]
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  |}
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Canis_familiaris.zip Canis familiaris]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Danio_rerio.zip Danio rerio]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Equus_caballus.zip Equus caballus]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Gallus_gallus.zip Gallus gallus]
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== BioPAX ==
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Homo_sapiens.zip Homo sapiens]
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Click on one of the links below to download all pathways in [http://www.biopax.org BioPAX] level 3 format.
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Mus_musculus.zip Mus musculus]
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|-
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|align="center"|{{#imgLink:Bos_taurus.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Bos_taurus.zip|Bos taurus}}
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  |align="center"|{{#imgLink:Canis_familiaris.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Canis_familiaris.zip|Canis familiaris}}
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|align="center"|{{#imgLink:Danio_rerio.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Danio_rerio.zip|Danio rerio}}
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|align="center"|{{#imgLink:Equus_caballus.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Equus_caballus.zip|Equus caballus}}
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  |align="center"|{{#imgLink:Gallus_gallus.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Gallus_gallus.zip|Gallus gallus}}
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|align="center"|{{#imgLink:Human_baby.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Homo_sapiens.zip|Homo sapiens}}
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|align="center"|{{#imgLink:House_Mouse.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Mus_musculus.zip|Mus musculus}}
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|}
{|class="prettytable"
{|class="prettytable"
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  |-
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  |<batchDownload filetype="owl" tag="Curation:AnalysisCollection"></batchDownload>
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Pan_troglodytes.zip Pan troglodytes]
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|}
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Rattus_norvegicus.zip Rattus norvegicus]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Sus_scrofa.zip Sus scrofa]
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|-
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|align="center"|{{#imgLink:Pan_Troglodytes.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Pan_troglodytes.zip|Pan troglodytes}}
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  |align="center"|{{#imgLink:Rat.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Rattus_norvegicus.zip |Rattus norvegicus}}
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|align="center"|{{#imgLink:Sus_scrofa.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Sus_scrofa.zip|Sus scrofa}}
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|}
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=== Invertebrates ===
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== Eu.Gene ==
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Click on one of the links below to download all pathways in the [http://www.duccioknights.org/?page_id=169 Eu.Gene] format (pwf). Eu.Gene is a tool for microarray analysis in context of biological pathways ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=17599938&dopt=AbstractPlus read more]).
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{|class="prettytable"
{|class="prettytable"
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  |-
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  |<batchDownload filetype="pwf" tag="Curation:AnalysisCollection"></batchDownload>
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Anopheles_gambiae.zip Anopheles gambiae]
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|}
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Caenorhabditis_elegans.zip Caenorhabditis elegans]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Drosophila_melanogaster.zip Drosophila melanogaster]
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== Plain text ==
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|-
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Click on one of the links below to download all pathways in plain text format. This format contains a list of all datanodes, with the identifier in the first
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|align="center"|{{#imgLink:Anopheles_gambiae.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Anopheles_gambiae.zip|Anopheles gambiae}}
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column, and the database system in the second column.
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  |align="center"|{{#imgLink:Celegans.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Caenorhabditis_elegans.zip|Caenorhabditis elegans}}
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|align="center"|{{#imgLink:Drosophila-melanogaster.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Drosophila_melanogaster.zip|Drosophila melanogaster}}
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|}
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=== Plants ===
{|class="prettytable"
{|class="prettytable"
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  |<batchDownload filetype="txt" tag="Curation:AnalysisCollection"></batchDownload>
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Arabidopsis_thaliana.zip Arabidopsis thaliana]
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  |}
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Hordeum_vulgare.zip Hordeum vulgare]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Oryza_sativa.zip Oryza sativa]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Populus_trichocarpa.zip Populus trichocarpa]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Solanum_lycopersicum.zip Solanum lycopersicum]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Zea_mays.zip Zea mays]
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|-
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|align="center"|{{#imgLink:Arabidopsis_thaliana.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Arabidopsis_thaliana.zip|Arabidopsis thaliana}}
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  |align="center"|{{#imgLink:Hordeum_vulgare.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Hordeum_vulgare.zip|Hordeum vulgare}}
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|align="center"|{{#imgLink:Oryza_sativa.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Oryza_sativa.zip|Oryza sativa}}
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|align="center"|{{#imgLink:Populus_trichocarpa.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Populus_trichocarpa.zip|Populus trichocarpa}}
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  |align="center"|{{#imgLink:Solanum_lycopersicum.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Solanum_lycopersicum.zip|Solanum lycopersicum}}
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|align="center"|{{#imgLink:Zea_mays.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Zea_mays.zip|Zea mays}}
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|}
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== PDF ==
 
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Click on one of the links below to download all pathways in Portable Document Format (PDF).
 
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{|class="prettytable"
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=== Eukaryotic microorganisms ===
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|- valign="top"
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|<batchDownload filetype="pdf" tag="Curation:AnalysisCollection"></batchDownload>
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|}
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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 edit and convert the SVG files using [http://www.inkscape.org Inkscape].
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{|class="prettytable"
{|class="prettytable"
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  |-
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  |<batchDownload filetype="svg" tag="Curation:AnalysisCollection"></batchDownload>
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Gibberella_zeae.zip Gibberella zeae]
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|}
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Saccharomyces_cerevisiae.zip Saccharomyces cerevisiae]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Plasmodium_falciparum.zip Plasmodium falciparum]
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|-
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|align="center"|{{#imgLink:Giberella_zeae.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Gibberella_zeae.zip|Gibberella zeae}}
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  |align="center"|{{#imgLink:Yeast.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Saccharomyces_cerevisiae.zip|Saccharomyces cerevisiae}}
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|align="center"|{{#imgLink:Plasmodium_falciparum.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Plasmodium_falciparum.zip|Plasmodium falciparum}}
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|}
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== PNG ==
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=== Bacteria ===
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Click on one of the links below to download all pathways in the Portable Network Graphics (png) format.
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{|class="prettytable"
{|class="prettytable"
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  |-
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  |<batchDownload filetype="png" tag="Curation:AnalysisCollection"></batchDownload>
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Bacillus_subtilis.zip Bacillus subtilis]
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  |}
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Escherichia_coli.zip E.coli]
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![http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Mycobacterium_tuberculosis.zip Mycobacterium tuberculosis]
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|-
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|align="center"|{{#imgLink:Bacillus_subtilis.jpeg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Bacillus_subtilis.zip|Bacillus subtilis}}
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  |align="center"|{{#imgLink:Ecoli.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Escherichia_coli.zip|E.coli}}
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  |align="center"|{{#imgLink:MycobacteriumTuberculosis.jpg|120|center||external|http://data.wikipathways.org/20161010/gpml/wikipathways-20161010-gpml-Mycobacterium_tuberculosis.zip|Mycobacterium tuberculosis}}
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|}
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== GMT Gene Sets ==
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== Other Collections ==
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You can download the species-specific WikiPathways gene set collections [http://www.pathvisio.org/data/bots/gmt/current/ here].
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<font size=3>
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This file gets updated every day.
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* [http://data.wikipathways.org Prior monthly releases]
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* [[Daily_Download|Daily curated releases]]
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* [[:Download_All_Pathways | Daily release of all pathways]] (warning: includes non-curated content!)
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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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</font>

Revision as of 20:35, 19 October 2016

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 curated, and are considered ready for analysis and data overlays.


Current version: 20161010 (10 October 2016)


Vertebrates

Bos taurus Canis familiaris Danio rerio Equus caballus Gallus gallus Homo sapiens Mus musculus
Pan troglodytes Rattus norvegicus Sus scrofa

Invertebrates

Anopheles gambiae Caenorhabditis elegans Drosophila melanogaster

Plants

Arabidopsis thaliana Hordeum vulgare Oryza sativa Populus trichocarpa Solanum lycopersicum Zea mays


Eukaryotic microorganisms

Gibberella zeae Saccharomyces cerevisiae Plasmodium falciparum

Bacteria

Bacillus subtilis E.coli Mycobacterium tuberculosis

Other Collections

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