WikiPathways

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<h2 class="frontPagePanel blueFg">A Wiki for Biological Pathways</h2>
<h2 class="frontPagePanel blueFg">A Wiki for Biological Pathways</h2>
<font size=2>'''In the “tradition” of <span class=plainlinks>[http://wikipedia.org Wikipedia]</span> and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community.'''</font></div>
<font size=2>'''In the “tradition” of <span class=plainlinks>[http://wikipedia.org Wikipedia]</span> and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community.'''</font></div>
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<h2 class="frontPagePanel yellowFg">How To Find a Pathway</h2>
<h2 class="frontPagePanel yellowFg">How To Find a Pathway</h2>
:There are many ways to find your pathways of interest. You can search by:
:There are many ways to find your pathways of interest. You can search by:
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<h2 class="frontPagePanel redFg">''UNDER CONSTRUCTION''</h2>
<h2 class="frontPagePanel redFg">''UNDER CONSTRUCTION''</h2>
'''This site is undergoing rigorous beta testing through the end of May 2007.  We are still implementing critical features and making major changes to these pages. Nevertheless, feel free to use the site to find, edit and create pathway content.'''  
'''This site is undergoing rigorous beta testing through the end of May 2007.  We are still implementing critical features and making major changes to these pages. Nevertheless, feel free to use the site to find, edit and create pathway content.'''  
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<h2 class="frontPagePanel greenFg">Today's featured pathway</h2>
<h2 class="frontPagePanel greenFg">Today's featured pathway</h2>

Revision as of 00:13, 3 May 2007


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A Wiki for Biological Pathways

In the “tradition” of Wikipedia and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community.

How To Find a Pathway

There are many ways to find your pathways of interest. You can search by:
  • Name of the pathway
  • Browse by species
  • Browse by pathway categories
Coming soon:
  • Search by gene name
  • Advanced search options, limit by organism or category

Viewing Pathways

Image
Once you are on a Pathway Page you can click on the image of the pathway to view the SVG representation. The pathway image is available for download in SVG and PNG formats.
Text
Each Pathway Page has a text description, itemized gene list, references and relevant links.
Data
Each pathway is also available for download as a GPML data file (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. This format can be used with PathVisio.

Editing Pathways

In addition to editing the text fields on a given Pathway Page, this wiki also support the ability to edit the pathway itself! Click on "EDIT" and a webstart version of PathVisio will open with the current pathway loaded. You can then add, edit or delete content from the pathway. When you save, updated version of the images, controlled text, and data files are generated and are immediately available.
Try it out in the Sandbox pathway!
Also see the Help pages

UNDER CONSTRUCTION

This site is undergoing rigorous beta testing through the end of May 2007. We are still implementing critical features and making major changes to these pages. Nevertheless, feel free to use the site to find, edit and create pathway content.

If you have any questions or suggestions, you can add them to the Comments and Suggestions page, or email them directly to us:

Thomas Kelder: Thomas.Kelder[AT]BIGCAT.unimaas.nl
Alex Pico: apico[AT]gladstone.ucsf.edu

Also see the PathVisio bug tracker for WikiPathays and PathVisio related bugs.

Today's featured pathway


Proteasome Degradation (Rattus norvegicus)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/e/e0/WP302_5616.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/e/e0/WP302_5616.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), 'Proteasome Degr...', 'https://www.wik...', 'Proteasome Degr...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP302', '300', 'center', 'Proteasome Degr...', 'pathway', 'Proteasome Degr...')
  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), 'Tuesday 31 Marc...')
  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, 5616)
  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}


Contents


Overview of all human pathways

Overview of all mouse pathways

Overview of all rat pathways

Cellular Process category

Metabolic Process category

Physiological Process category

Molecular Function category

Statistics


  • There are 2817 pathways
  • Number of pathways (and unique genes) per species:
Anopheles gambiae: 23 (428)
Arabidopsis thaliana: 94 (956)
Bacillus subtilis: 3 (14)
Beta vulgaris: 1 (25)
Bos taurus: 275 (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: 1153 (8326)
Hordeum vulgare: 1 (9)
Mus musculus: 227 (4985)
Mycobacterium tuberculosis: 17 (148)
Oryza sativa: 69 (493)
Pan troglodytes: 116 (2937)
Populus trichocarpa: 5 (0)
Rattus norvegicus: 174 (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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