Download Pathways

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(June update)
Current revision (18:06, 10 July 2019) (view source)
(updating for july)
 
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<font size=4>'''Current version: [http://data.wikipathways.org/20190610/ 20190610 (10 June 2019)]'''</font>
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<font size=4>'''Current version: [http://data.wikipathways.org/20190710/ 20190710 (10 July 2019)]'''</font>
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Bos_taurus.zip Bos taurus]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Bos_taurus.zip Bos taurus]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Canis_familiaris.zip Canis familiaris]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Canis_familiaris.zip Canis familiaris]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Danio_rerio.zip Danio rerio]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Danio_rerio.zip Danio rerio]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Equus_caballus.zip Equus caballus]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Equus_caballus.zip Equus caballus]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Gallus_gallus.zip Gallus gallus]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Gallus_gallus.zip Gallus gallus]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Homo_sapiens.zip Homo sapiens]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Homo_sapiens.zip Homo sapiens]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Mus_musculus.zip Mus musculus]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Mus_musculus.zip Mus musculus]
  |-
  |-
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  |align="center"|{{#imgLink:Bos_taurus.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Bos_taurus.zip|Bos taurus}}
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  |align="center"|{{#imgLink:Bos_taurus.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Bos_taurus.zip|Bos taurus}}
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  |align="center"|{{#imgLink:Canis_familiaris.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Canis_familiaris.zip|Canis familiaris}}
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  |align="center"|{{#imgLink:Canis_familiaris.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Canis_familiaris.zip|Canis familiaris}}
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  |align="center"|{{#imgLink:Danio_rerio.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Danio_rerio.zip|Danio rerio}}
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  |align="center"|{{#imgLink:Danio_rerio.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Danio_rerio.zip|Danio rerio}}
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  |align="center"|{{#imgLink:Equus_caballus.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Equus_caballus.zip|Equus caballus}}
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  |align="center"|{{#imgLink:Equus_caballus.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Equus_caballus.zip|Equus caballus}}
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  |align="center"|{{#imgLink:Gallus_gallus.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Gallus_gallus.zip|Gallus gallus}}
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  |align="center"|{{#imgLink:Gallus_gallus.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Gallus_gallus.zip|Gallus gallus}}
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  |align="center"|{{#imgLink:Human_baby.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Homo_sapiens.zip|Homo sapiens}}
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  |align="center"|{{#imgLink:Human_baby.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Homo_sapiens.zip|Homo sapiens}}
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  |align="center"|{{#imgLink:House_Mouse.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Mus_musculus.zip|Mus musculus}}
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  |align="center"|{{#imgLink:House_Mouse.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Mus_musculus.zip|Mus musculus}}
|}
|}
{|class="prettytable"
{|class="prettytable"
  |-
  |-
-
  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Pan_troglodytes.zip Pan troglodytes]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Pan_troglodytes.zip Pan troglodytes]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Rattus_norvegicus.zip Rattus norvegicus]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Rattus_norvegicus.zip Rattus norvegicus]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Sus_scrofa.zip Sus scrofa]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Sus_scrofa.zip Sus scrofa]
  |-
  |-
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  |align="center"|{{#imgLink:Pan_Troglodytes.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Pan_troglodytes.zip|Pan troglodytes}}
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  |align="center"|{{#imgLink:Pan_Troglodytes.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Pan_troglodytes.zip|Pan troglodytes}}
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  |align="center"|{{#imgLink:Rat.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Rattus_norvegicus.zip |Rattus norvegicus}}
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  |align="center"|{{#imgLink:Rat.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Rattus_norvegicus.zip |Rattus norvegicus}}
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  |align="center"|{{#imgLink:Sus_scrofa.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Sus_scrofa.zip|Sus scrofa}}
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  |align="center"|{{#imgLink:Sus_scrofa.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Sus_scrofa.zip|Sus scrofa}}
|}
|}
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Anopheles_gambiae.zip Anopheles gambiae]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Anopheles_gambiae.zip Anopheles gambiae]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Caenorhabditis_elegans.zip Caenorhabditis elegans]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Caenorhabditis_elegans.zip Caenorhabditis elegans]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Drosophila_melanogaster.zip Drosophila melanogaster]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Drosophila_melanogaster.zip Drosophila melanogaster]
  |-
  |-
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  |align="center"|{{#imgLink:Anopheles_gambiae.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Anopheles_gambiae.zip|Anopheles gambiae}}
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  |align="center"|{{#imgLink:Anopheles_gambiae.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Anopheles_gambiae.zip|Anopheles gambiae}}
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  |align="center"|{{#imgLink:Celegans.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Caenorhabditis_elegans.zip|Caenorhabditis elegans}}
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  |align="center"|{{#imgLink:Celegans.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Caenorhabditis_elegans.zip|Caenorhabditis elegans}}
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  |align="center"|{{#imgLink:Drosophila-melanogaster.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Drosophila_melanogaster.zip|Drosophila melanogaster}}
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  |align="center"|{{#imgLink:Drosophila-melanogaster.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Drosophila_melanogaster.zip|Drosophila melanogaster}}
|}
|}
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
-
  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Arabidopsis_thaliana.zip Arabidopsis thaliana]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Arabidopsis_thaliana.zip Arabidopsis thaliana]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Hordeum_vulgare.zip Hordeum vulgare]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Hordeum_vulgare.zip Hordeum vulgare]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Oryza_sativa.zip Oryza sativa]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Oryza_sativa.zip Oryza sativa]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Populus_trichocarpa.zip Populus trichocarpa]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Populus_trichocarpa.zip Populus trichocarpa]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Solanum_lycopersicum.zip Solanum lycopersicum]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Solanum_lycopersicum.zip Solanum lycopersicum]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Zea_mays.zip Zea mays]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Zea_mays.zip Zea mays]
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  <!-- ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Beta_vulgaris.zip Beta vulgaris] -->
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  <!-- ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Beta_vulgaris.zip Beta vulgaris] -->
  |-
  |-
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  |align="center"|{{#imgLink:Arabidopsis_thaliana.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Arabidopsis_thaliana.zip|Arabidopsis thaliana}}
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  |align="center"|{{#imgLink:Arabidopsis_thaliana.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Arabidopsis_thaliana.zip|Arabidopsis thaliana}}
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  |align="center"|{{#imgLink:Hordeum_vulgare.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Hordeum_vulgare.zip|Hordeum vulgare}}
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  |align="center"|{{#imgLink:Hordeum_vulgare.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Hordeum_vulgare.zip|Hordeum vulgare}}
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  |align="center"|{{#imgLink:Oryza_sativa.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Oryza_sativa.zip|Oryza sativa}}
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  |align="center"|{{#imgLink:Oryza_sativa.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Oryza_sativa.zip|Oryza sativa}}
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  |align="center"|{{#imgLink:Populus_trichocarpa.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Populus_trichocarpa.zip|Populus trichocarpa}}
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  |align="center"|{{#imgLink:Populus_trichocarpa.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Populus_trichocarpa.zip|Populus trichocarpa}}
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  |align="center"|{{#imgLink:Solanum_lycopersicum.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Solanum_lycopersicum.zip|Solanum lycopersicum}}
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  |align="center"|{{#imgLink:Solanum_lycopersicum.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Solanum_lycopersicum.zip|Solanum lycopersicum}}
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  |align="center"|{{#imgLink:Zea_mays.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Zea_mays.zip|Zea mays}}
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  |align="center"|{{#imgLink:Zea_mays.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Zea_mays.zip|Zea mays}}
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  <!-- |align="center"|{{#imgLink:Beta_vulgaris.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Beta_vulgaris.zip|Beta vulgaris}} -->
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  <!-- |align="center"|{{#imgLink:Beta_vulgaris.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Beta_vulgaris.zip|Beta vulgaris}} -->
|}
|}
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Gibberella_zeae.zip Gibberella zeae]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Gibberella_zeae.zip Gibberella zeae]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Saccharomyces_cerevisiae.zip Saccharomyces cerevisiae]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Saccharomyces_cerevisiae.zip Saccharomyces cerevisiae]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Plasmodium_falciparum.zip Plasmodium falciparum]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Plasmodium_falciparum.zip Plasmodium falciparum]
  |-
  |-
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  |align="center"|{{#imgLink:Giberella_zeae.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Gibberella_zeae.zip|Gibberella zeae}}
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  |align="center"|{{#imgLink:Giberella_zeae.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Gibberella_zeae.zip|Gibberella zeae}}
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  |align="center"|{{#imgLink:Yeast.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Saccharomyces_cerevisiae.zip|Saccharomyces cerevisiae}}
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  |align="center"|{{#imgLink:Yeast.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Saccharomyces_cerevisiae.zip|Saccharomyces cerevisiae}}
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  |align="center"|{{#imgLink:Plasmodium_falciparum.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Plasmodium_falciparum.zip|Plasmodium falciparum}}
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  |align="center"|{{#imgLink:Plasmodium_falciparum.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Plasmodium_falciparum.zip|Plasmodium falciparum}}
|}
|}
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Bacillus_subtilis.zip Bacillus subtilis]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Bacillus_subtilis.zip Bacillus subtilis]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Escherichia_coli.zip E.coli]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Escherichia_coli.zip E.coli]
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  ![http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Mycobacterium_tuberculosis.zip Mycobacterium tuberculosis]
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  ![http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Mycobacterium_tuberculosis.zip Mycobacterium tuberculosis]
  |-
  |-
-
  |align="center"|{{#imgLink:Bacillus_subtilis.jpeg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Bacillus_subtilis.zip|Bacillus subtilis}}
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  |align="center"|{{#imgLink:Bacillus_subtilis.jpeg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Bacillus_subtilis.zip|Bacillus subtilis}}
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  |align="center"|{{#imgLink:Ecoli.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Escherichia_coli.zip|E.coli}}
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  |align="center"|{{#imgLink:Ecoli.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Escherichia_coli.zip|E.coli}}
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  |align="center"|{{#imgLink:MycobacteriumTuberculosis.jpg|120|center||external|http://data.wikipathways.org/20190610/gpml/wikipathways-20190610-gpml-Mycobacterium_tuberculosis.zip|Mycobacterium tuberculosis}}
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  |align="center"|{{#imgLink:MycobacteriumTuberculosis.jpg|120|center||external|http://data.wikipathways.org/20190710/gpml/wikipathways-20190710-gpml-Mycobacterium_tuberculosis.zip|Mycobacterium tuberculosis}}
|}
|}

Current revision

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: 20190710 (10 July 2019)


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

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

Personal tools