WikiPathways

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Revision as of 09:34, 19 February 2009


Welcome to WikiPathways BETA

In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. More about WikiPathways...

Finding Pathways

Search{{#googleCoop:}} Browse

Browse by species and category

You can search by:
  • Pathway name (Apoptosis)
  • Gene or protein name (p53)
  • Any page content (cancer)

Contributing New Pathways

Create

Create a new pathway page

Suggest

Add a pathway to the wish list

Sample Pathway Pages

Sandbox

Play with the editor tools

Check out the following pages:

For more information see the Help pages


Today's Featured Pathway

Signal Transduction of S1P Receptor (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/2/28/WP26_28620.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/2/28/WP26_28620.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Signal Transduc...', 'https://www.wik...', 'Signal Transduc...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP26', '300', 'center', 'Signal Transduc...', 'pathway', 'Signal Transduc...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Wednesday 3 Jun...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  19. 18 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('__NOEDITSECTION...')
  20. 19 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('__NOEDITSECTION...')
  21. 20 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('__NOEDITSECTION...', Object(Title), Object(ParserOptions), true, true, 28620)
  22. 21 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('__NOEDITSECTION...', Object(Title), true, true)
  23. 22 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('__NOEDITSECTION...', Object(Title), true)
  24. 23 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('__NOEDITSECTION...')
  25. 24 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  26. 25 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  27. 26 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  28. 27 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  29. 28 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  30. 29 {main}

Latest discussions

2 June 2020
Overlap with WP4861 (2) by Kristina Hanspers
31 May 2020
MLX and lipid droplets (1) by Egon Willighagen

New!

  • New species supported:
    • Arabidopsis thaliana
    • Oryza japonica
  • Private pathways (read more)
  • Stable Identifiers for all pathways (read more)

Community Interest

Portals within WikiPathways for communities with focused pathway interests:

Want to start your own Portal? Contact us!

Statistics

  • There are 2847 pathways
  • Number of pathways (and unique genes) per species:
Anopheles gambiae: 29 (428)
Arabidopsis thaliana: 93 (956)
Bacillus subtilis: 3 (14)
Beta vulgaris: 1 (25)
Bos taurus: 274 (3743)
Caenorhabditis elegans: 66 (882)
Canis familiaris: 112 (2820)
Danio rerio: 105 (2708)
Drosophila melanogaster: 35 (565)
Escherichia coli: 13 (28)
Equus caballus: 12 (200)
Gallus gallus: 100 (2106)
Glycine max: 1 (2)
Gibberella zeae: 2 (0)
Homo sapiens: 1179 (8442)
Hordeum vulgare: 1 (9)
Mus musculus: 229 (4985)
Mycobacterium tuberculosis: 16 (148)
Oryza sativa: 69 (493)
Pan troglodytes: 116 (2937)
Populus trichocarpa: 5 (0)
Rattus norvegicus: 173 (3623)
Saccharomyces cerevisiae: 135 (856)
Solanum lycopersicum: 7 (5)
Sus scrofa: 9 (65)
Vitis vinifera: 1 (0)
Zea mays: 58 (31)
Plasmodium falciparum: 1 (0)
Brassica napus: 2 (162)
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