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>http://groups.google.com/group/wikipathways-discuss/feed/rss_v2_0_msgs.xml|short|max=3</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>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 22:27, 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

Glycerophospholipid Biosynthetic Pathway (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/9/9b/WP2533_92554.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/9/9b/WP2533_92554.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), 'Glycerophosphol...', 'https://www.wik...', 'Glycerophosphol...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP2533', '300', 'center', 'Glycerophosphol...', 'pathway', 'Glycerophosphol...')
  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), 'Monday 21 Septe...', '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, 92636)
  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

18 September 2020
WP4965 (1) by Denise Slenter
25 August 2020
Welcome new user (7) by Susan Coort
    more...

Forum

  Re: [wp-discuss] Suggestions to automate downloading the most current gmt files
Hi Tina, Thank you for the suggestion, I will try this. The mouse pathway is WP449 and the human pathway is WP558. Now that I compare them, they are slightly different. Best wishes, Krutik Patel PhD Student Newcastle University On Tuesday, 15 September 2020 at 16:09:17 UTC+1 Martina Kutmon [?]
  Re: [wp-discuss] Suggestions to automate downloading the most current gmt files
Dear Krutik, You mention that you use the rWikiPathways package, right? You can use this function: wp.hs.gmt <- rWikiPathways::downloadPathwayArchive(organism="Homo sapiens", format = "gmt") It always downloads the latest GMT file in the working directory. I will check the mouse pathway that [?]
  Suggestions to automate downloading the most current gmt files
Hello Wikipathways forum, This query is a bit specific so I will give a short preamble. I have developed an R package (TimiRGeN -- final stages of bioconductor review) that utilises wikipathways to identify microRNAs that may be effecting signalling pathways. This package uses rWikipathways [?]
  Re: [wp-discuss] Issues downloading all pathways
Gotcha, that makes sense. Thanks for your help! On Sunday, September 6, 2020 at 11:36:35 AM UTC-6 alex.pico wrote: > Good question. Sorry for the confusion! > > WikiPathways hosts around 600 Reactome pathways for human. So, the total > count at WikiPathways.org is correct. Our monthly data [?]
  Re: [wp-discuss] Issues downloading all pathways
Good question. Sorry for the confusion! WikiPathways hosts around 600 Reactome pathways for human. So, the total count at WikiPathways.org is correct. Our monthly data release, however, excludes these since Reactome has its own distribution effort for third party analysis tools, etc. So, the [?]
  Issues downloading all pathways
Hello, I want to download all the pathway files for Homo sapiens. According to the WikiPathways statistics page, there are currently 1200 pathways for Homo sapiens. However, when I download the Homo sapiens zip file from the downloads page, it only contains information for 621 pathways. Am I [?]
  Re: [wp-discuss] Mapping database
Hello Kristina My query has been resolved. Somehow the data was not loaded earlier but when I tried again, it was a success. Pathvisio in my laptop is working smoothly now. Thanks, Ipsa On Wednesday, August 26, 2020 at 1:03:05 AM UTC+5:30 kristina...@gladstone.ucsf.edu wrote: > Hi Ipsa, > > [?]
  Re: [wp-discuss] Mapping database
Hi Ipsa, I'm not sure if this was resolved or not (hard to tell from time stamps on the email thread), but if you are still having trouble go to "Data>Identifier mapping setup...". If you can send a screenshot of this interface, that would be great. Thanks, Kristina On Thu, Aug 20, 2020 at [?]
  Re: [wp-discuss] Wikipathway Widget xref recognition
Hi Ondrej, We have another version of the viewer in development. It maps gene product identifiers to all of the following: Ensembl, Entrez (NCBI) Gene, HGNC and Wikidata. For example, if you'd like to specify just Ensembl identifiers, you can use link (note the underscores): https://pathway-vie [?]
  Re: [wp-discuss] Wikipathway Widget xref recognition
Dear Egon, I would like to use GPML pathways with the normalized identifiers. Is there a way how to convert all xrefs in the GPML file into HMDB for offline use? Or would it be possible to update the repository with normalized identifiers? The ecosystem of identifiers is so complex that some kind [?]
  Re: [wp-discuss] Mapping database
Here is the screenshot. I am not able to search for any RNA, metabolite or gene. On Wednesday, August 19, 2020 at 11:31:35 AM UTC+5:30 egon.wil...@gmail.com wrote: > > For RNA/Gene ID mapping, you only need the Hs_derby_ensemble_91.bridge > file. > > I am not sure what you mean with "Everytime [?]
  Re: X/cross in some boxes in pathway diagrams
This will be changed in a future release. It just indicates that data can not be visualized on those data nodes. But it is misleading indeed. Best, Tina On Thursday, August 20, 2020 at 12:03:29 AM UTC+2 Grandezza Aburido wrote: > What does the X mean in some of these boxes? e.g. TCA cycle is [?]
  X/cross in some boxes in pathway diagrams
What does the X mean in some of these boxes? e.g. TCA cycle is crossed out, etc. (Sorry if I am being dumb hahaha) [image: glyco.png] [?]
  Re: [wp-discuss] Mapping database
For RNA/Gene ID mapping, you only need the Hs_derby_ensemble_91.bridge file. I am not sure what you mean with "Everytime it shows No identifier mapping database loaded". Can you plz share a screenshot? Egon On Tue, Aug 18, 2020 at 11:51 AM wrote: > Hello > I have downloade [?]
  Re: [wp-discuss] Mapping database
Hello I have downloaded the databases according to the tutorial but still I am not able to search the information for a RNA or a Gene. Everytime it shows No identifier mapping database loaded. Can you tell me what are the essential databases which should be downloaded I have already downloaded [?]
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