WikiPathways

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* Want to add your ORCID id to your WikiPathways account? [http://wikipathways.org/index.php/Template:User_ORCID Learn how]
* Want to add your ORCID id to your WikiPathways account? [http://wikipathways.org/index.php/Template:User_ORCID Learn how]
<h2 class="frontPagePanel blueFg">Discussions</h2><recentChanges class="blueBg" style="border:none" namespace='90' limit='3'></recentChanges>&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Discussions|more...]]
<h2 class="frontPagePanel blueFg">Discussions</h2><recentChanges class="blueBg" style="border:none" namespace='90' limit='3'></recentChanges>&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Discussions|more...]]
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<h2 class="frontPagePanel blueFg">Forum</h2><rss max=3>https://groups.google.com/group/wikipathways-discuss/feed/rss_v2_0_msgs.xml</rss>&nbsp;&nbsp;&nbsp;&nbsp;[http://groups.google.com/group/wikipathways-discuss Google group wikipathways-discuss]
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<h2 class="frontPagePanel blueFg">Forum</h2><rss max="3" item-max-length="10">https://groups.google.com/group/wikipathways-discuss/feed/rss_v2_0_msgs.xml</rss>&nbsp;&nbsp;&nbsp;&nbsp;[http://groups.google.com/group/wikipathways-discuss Google group wikipathways-discuss]
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Revision as of 22:28, 26 June 2017


We made the switch to CC0 for the most unrestricted access possible. Read all about it...

Welcome to WikiPathways BETA

WikiPathways is a database of biological pathways maintained by and for the scientific community.

Find Pathways

Search

Browse

Browse by species and category

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

Get Pathways

Download

Multiple formats and methods

Growth

New pathways added each month

Edit Pathways

Sandbox

Play with the editor tools

Check out the following pages:

For more information see our Help topics


Today's Featured Pathway

Biogenic Amine Synthesis (Mus musculus)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/f/fe/WP522_92636.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/f/fe/WP522_92636.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), 'Biogenic Amine ...', 'https://www.wik...', 'Biogenic Amine ...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP522', '300', 'center', 'Biogenic Amine ...', 'pathway', 'Biogenic Amine ...')
  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), 'Sunday 29 March...', 'Curation:Featur...', 'true')
  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, 92637)
  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}

Updates

  • June 2017 Release: 124 edits by 21 contributors, and 6 new pathways this month
  • April 2017 Release: 80 edits by 8 contributors this month
  • March 2017 Release: 54 edits by 10 contributors this month
  • February 2017 Release: 56 edits by 8 contributors this month
  • February 2: Rett syndrome pathway is now live at Wikipedia
  • January 2017 Release: 25 new human pathways with 181 new genes
  • December 22: Blog post about our translation of mouse pathways
  • December 2016 Release: 201 edits by 15 contributors this month
  • November 11: Enrichment analysis of single-cell dataset on differentiation
  • November 2016 Release: 143 new human genes added to pathways
  • October 2016 Release: 12 new human pathways contributed
  • Sept 30: New pathways featured in blog post
  • September 2016 Release: 42 new human genes added
  • August 2016 Release: 60 genes and 10 new human pathways added
  • Want to add your ORCID id to your WikiPathways account? Learn how

Discussions

26 March 2020
Pathway is very simplified (2) by Chris Evelo
22 March 2020
Pathway is very simplified (1) by Matthew Conroy
23 February 2020
Welcome new user (6) by Susan Coort
    more...

Forum

  Call to Action: COVID-19 -- New Pathway Authors
It has been inspiring to see a lot of inquiries from new pathway authors about how they can get involved and specifically contribute to modeling COVID-related pathways. We have updated our introductory help page for new authors, including a simplified Getting Started section and a special Call [?]
  Re: [wp-discuss] request access to wikipathways plugin
Hi, Is this about installing the plugin in PathVisio or receiving permissions for the webservice? Regarding the installation: the plugin repository is back online since this morning. So you can simply install plugins through the plugin manager in PathVisio. If you want to have access for the [?]
  request access to wikipathways plugin
tried to do this via https://pathvisio.github.io/plugin/wikipathways-plugin/ but page returned This page isn’t working plugins.pathvisio.org didn’t send any data. ERR_EMPTY_RESPONSE [?]
  Re: [wp-discuss] KEGG converter
Hi Thomas, You can find the simple KEGG2GPML parser here: https://github.com/mkutmon/KEGG2GPML/releases/tag/1.0.0. It's a simple Java script so hopefully it will be easy to run. You have to select the species and output directory. Please let me know if you run into any problems or have any [?]
  Re: [wp-discuss] KEGG converter
Dear Tina: It would be great if you could share the converter for generating the gene lists. And we will also start to play with Cytoscape. Thanks again. Thomas Martina Summer-Kutmon schrieb: For pathway statistics, I can provide a converter that creates gene lists in GPML for KEGG pathways. [?]
  Re: [wp-discuss] KEGG converter
For pathway statistics, I can provide a converter that creates gene lists in GPML for KEGG pathways. Then they can simply be combined in the analysis. This will not work for data visualization, but for that you could probably use a Cytoscape apps for KEGG pathways. I have no experience for that [?]
  Re: [wp-discuss] KEGG converter
Dear Tina: Thanks for your reply. We would be mainly interested in pathway statistics but data/pathway visualizations would be also of interest at a later stage. Do you have another idea how we could do this comparing WikiPathways and KEGG? Thanks. Thomas Martina Summer-Kutmon schrieb: Dear [?]
  Re: [wp-discuss] KEGG converter
Dear Thomas, The code is very old and hasn't been updated in a long time. I feel like there will not be a fast and straight-forward solution. Can I ask what you want to do with the pathways? Do you want to perform pathway statistics or create certain data visualizations? Best, Tina On Mon, Mar [?]
  Re: [wp-discuss] KEGG converter
Dear Alex and all: Thanls for you reply. And yes. This is the idea to adapt it to locally provided KEGG pathway files. However, I am not sure what to take as starting point. Where should I take the code from and is there anyone who could point me to where the changes have to be made? Thanks. [?]
  Re: [wp-discuss] KEGG converter
I suspect we haven’t been able to run that script this KEGG licensed their content and started charging for access. Our tool does not get around that barrier. Do you own your own copy of KEGG content? Perhaps the tool could be adapted to run from that... - Alex On Mar 6, 2020, at 9:31 AM, [?]
  KEGG converter
Dear WikiPathways community: We would like to compare the WikiPathways with KEGG using PathVisio. However, the converter for the KEGG files is unfortunately not available right now (probably due to the shutdown of the Maastricht servers as a result of a hacking). Is there a way to access the [?]
  Re: [wp-discuss] Installing Pathvisio APPs
Thanks a lot, Sorry for the late reply but this was very helpful. On Monday, 17 February 2020 14:42:08 UTC, Martina Kutmon wrote: > > Dear Krutik, > > At this moment, it is not possible to install the plugins from the > repository. We are moving the repository to a new location so it will > [?]
  Re: [wp-discuss] Installing Pathvisio APPs
Can you provide more information about the error you get? Which operating system / Java version do you use? Best regards, Tina On Tue, Feb 25, 2020 at 9:54 AM Aisya Gany wrote: > My bat. file doesnt want to open. what do i do? > > Thanks > > On Mon, 24 Feb 2020 at 19:01, Alex [?]
  Re: [wp-discuss] Installing Pathvisio APPs
My bat. file doesnt want to open. what do i do? Thanks On Mon, 24 Feb 2020 at 19:01, Alex Pico wrote: > https://pathvisio.github.io/pages/download > > > - Current version: PathVisio 3.3.0 > - Download the file and unzip it. > - On Windows: start PathVisio by [?]
  Re: [wp-discuss] Installing Pathvisio APPs
https://pathvisio.github.io/pages/download - Current version: PathVisio 3.3.0 - Download the file and unzip it. - On Windows: start PathVisio by double-clicking the pathvisio.bat file - On MacOSX / Linux: start PathVisio by running pathvisio.sh or double-click the pathvisio.jar [?]
    Google group wikipathways-discuss
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