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

Focal Adhesion (Mus musculus)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/b/b8/WP85_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/b/b8/WP85_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), 'Focal Adhesion', 'https://www.wik...', 'Focal Adhesion', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP85', '300', 'center', 'Focal Adhesion', 'pathway', 'Focal Adhesion')
  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), 'Thursday 20 Feb...', '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

29 January 2020
WP4767 (2) by Ritchie Lee
27 January 2020
«no subject» (46) by Denise Slenter
17 January 2020
Welcome to WikiPathways! (64) by Anders Riutta
    more...

Forum

  Re: [wp-discuss] Installing Pathvisio APPs
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 hopefully online again soon. For now, you can provide the needed jar files and install them locally (Plugins -> Install local plugins). For [?]
  Installing Pathvisio APPs
Hi there, I am using Wikipathways - Pathvisio quite heavily as a part of my PhD. I am trying to create a document/ tutorial on how I have used Pathvisio and to do this I need to show how to use the MAPP and Wikipathways Apps. I cannot access the Apps from the new Pathvisio website atm. Is there [?]
  NRNB Welcomes Mentors for Google Summer of Code 2020
Google Summer of Code 2020 is coming up and the National Resource for Network Biology (NRNB) will be applying as a mentoring organization for the joint efforts of WikiPathways and other network biology tools. If you have a WikiPathways related project you idea you would like to mentor, keep [?]
  Re: [wp-discuss] Can't install pathvisio
Dear Evgenii, Could you let me know which operating system and which Java version you are using? Do you receive an error message? Best regards, Tina On Wed, Dec 4, 2019 at 2:07 PM Evgenii Zorin wrote: > Hi, I am trying to install Pathvisio but either described methods [?]
  Can't install pathvisio
Hi, I am trying to install Pathvisio but either described methods doesn't work. I wonder if you could help me with this? Thank you, Evgenii [?]
  Re: [wp-discuss] Formal Representation of Post Translational Modifications
Hi Hannah, Attached is a list of WPIDs that have annotated phosphorylation sites. These are all human pathways except for the very last one, which is mouse. Regards, Kristina [?]
  Re: [wp-discuss] Formal Representation of Post Translational Modifications
Thanks for the feedback and suggestions! If you search each file for "ptm=p“ then you should find all the annotated phosphorylation events on our pathways so far. You’ll want to grab the other fields contained by the same “Comment” tag to get parent and position, etc. In fact, some of the [?]
  Re: [wp-discuss] Formal Representation of Post Translational Modifications
Hey Alex, I do not work with the GPML format so I cannot really speak to it. My plan was to parse each file manually by searching for a key term such as “phospho” and get the uniprot ID associated. The main information I am looking to extract is the Uniprot ID, the position of the modified [?]
  Re: [wp-discuss] Formal Representation of Post Translational Modifications
I can confirm that BioPax download is broken, but I don’t know that status on its fix… I can speak to the PTM information, however. This is still experimental and we are keen to know how you would use it. This would help us decide on the best approach to encode it and make it accessible. Our [?]
  Re: [wp-discuss] Homo Sapiens count of pathways discrepancy
You are doing it right. There are many ways to count pathways…. The monthly release via downloadPathwayArchive is the set of pathways that have been approved for use for pathway analysis, etc. This is the set that gets distributed to tools like Enrichr, WebGestalt and clusterProfiler. Via web [?]
  Formal Representation of Post Translational Modifications
Hello, Firstly, I am having problems with the BioPax download of the entirety of Homo Sapiens. Does anyone know when that will be fixed? Secondly, is there any formal representation of post-transnational modifications that I could access? I cannot seem to find a single official representation/ [?]
  Homo Sapiens count of pathways discrepancy
Hello, I am using R command: downloadPathwayArchive(date="current", organism="Homo Sapiens", format="gmt" ) and obtain 556 pathways. However listPathwayIds('Homo sapiens') shows 1136 pathways. Any ideas what I am doing wrong? Jonathan [?]
  Re: [wp-discuss] I kindly request to help me in importing and mapping ID
Dear Martina, Thank you so very much for being so generous, I am herewith forwarding the generated pgex.ex file for your kind perusal, I tried loading cell cycle, TCA cycle of zebra fish. (upon importing, three files are created, pgex.ex, pgex, xml of 0kb size) Thanking you Best Regards Ayesha [?]
  Re: [wp-discuss] I kindly request to help me in importing and mapping ID
Dear Ayesha, If all boxes are grey than the import was not successful. Did you download the appropriate identifier mapping database for Zebrafish (.bridge file)? Are you using the Zebrafish pathway collection? Could you send me the pgex.ex file? Best regards, Tina On Thu, Nov 14, 2019 at 11:25 [?]
  I kindly request to help me in importing and mapping ID
I am a Biologist, I could successfully install the Pathvisio, I prepared the input tab delimited data file of zebra fish, data is RNA seq, I would want to see the fold change values in pathways, but I am not able to understand what is happening. In input file, In first column I have Ensemble IDs [?]
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