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

Metabolism of Spingolipids in ER and Golgi apparatus (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/6/6a/WP4142_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/6/6a/WP4142_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), 'Metabolism of S...', 'https://www.wik...', 'Metabolism of S...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4142', '300', 'center', 'Metabolism of S...', 'pathway', 'Metabolism of S...')
  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), 'Friday 30 Octob...', '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

Today
11b-HSD enzyme functions (5) by Denise Slenter
18 September 2020
WP4965 (1) by Denise Slenter
    more...

Forum

  Re: [wp-discuss] Removing the literature label number from pathway
Hi Alex, Thanks, I followed second option. On Mon, Sep 28, 2020, 10:22 PM 'Alex Pico' via wikipathways-discuss < wikipathwa...@googlegroups.com> wrote: > I may have replied too quickly! This pathway is perhaps too tall to > simply take a screenshot and the SVG export from WikiPathways does > [?]
  Re: [wp-discuss] Removing the literature label number from pathway
I may have replied too quickly! This pathway is perhaps too tall to simply take a screenshot and the SVG export from WikiPathways does include the citation numbers, so you have the same problem… Other options: 1. You could save the SVG export and then open it in Illustrator (or other SVG [?]
  Re: [wp-discuss] Removing the literature label number from pathway
Hi Alex, Thank you very much for your prompt reply with valuable suggestions. On Monday, September 28, 2020 at 9:27:37 PM UTC+3 alex.pico wrote: > Hi Firoz, > > The best way would be to upload the updated version back to WikiPathways. > The online version there does not currently show those [?]
  Re: [wp-discuss] Removing the literature label number from pathway
Hi Firoz, The best way would be to upload the updated version back to WikiPathways. The online version there does not currently show those numbers. Once uploaded, you then also have a URL you can cite and you share your improvements with others. https://www.wikipathways.org/index.php/Pathway:WP [?]
  Removing the literature label number from pathway
Dear All, I have modified a pathway in PathVisio 3.3, however, the literature reference was appeared on my figure. I want to remove it from my figure. Could you please help me how to disable these number from my figure. In this figure, 2, 3, 4, 5, 9 number associated with boxes/Nodes are the [?]
  Re: SPARQL property path for identifying downstream targets of a directed interaction
Ok I think there was a bug in the original query. Replace original with the following property path: " ?src (^wp:source/wp:target)+ ?tgt . " Which translates to: ("find ?directedInteraction that ?src is the source of" -> "find ?tgt that is the target of ?directedInteraction")+ Query 2: ``` PREFIX [?]
  SPARQL property path for identifying downstream targets of a directed interaction
Hi, First, I just want to say thanks for creating the wp RDF resource. I think you have done a really great job balancing the vocabulary of WP in terms of usability and level of detail! I am attempting to get all "(ancestor,descendent)" pairs where "ancestor" is a source and "descendent" is a [?]
  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 [?]
    Google group wikipathways-discuss
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