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Call to Action
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Revision as of 14:35, 11 September 2020


Welcome to the COVID-19 Pathways Portal on WikiPathways

This special subset of disease pathways is being highlighted during the current COVID-19 crisis. This content is released under a CC0 waiver to be freely used, re-used and distributed. Let us know if you add a new pathway or want to recommend one for this collection.


Covered Pathways

Pathway Collection

All pathways tagged with "Curation: COVID-19" will be linked to this overview table, to help keep track of the relevant pathways.

Download all human COVID19 pathways

Contact us

Send questions about WikiPathways to the wikipathways-discuss mailing list.

How to add a pathway to the portal

The list of Featured Pathways is not static and can be updated at any time. If you know of a pathway that should be added, please contact the administrator.


Call to Action

We are helping to coordinate an international effort to build and curate pathway models relevant to the COVID-19 pandemic. Review the resources below to see how you can get involved.

IMPORTANT: WikiPathways is dedicated to FAIR standards. All content at WikiPathways is freely available for use and reuse by a CC0 waiver.


There are curation tests being done, that check a number of drawing patterns, e.g. as agreed with the COVID-19 Disease Maps project. The reports can be found in this repository.



  • 28 Oct. 2020 A longer paper from the whole COVID Disease Pathways community is available on bioRxiv
  • 09 Sept. 2020 This portal was created with content from the Disease portal created in March
  • 02 Sept. 2020 COVID19 tag created and added to relevant pathways
  • 05 May 2020 The COVID-19 Disease Maps project paper was published
  • 23 March 2020 As part of the Disease portal, a collection of COVID-19 disease pathways was started


Featured Pathway

SARS-CoV-1 Infection (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/9/9b/WP5020_111952.svg:
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/WP5020_111952.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), 'SARS-CoV-1 Infe...', 'https://www.wik...', 'SARS-CoV-1 Infe...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP5020', '300', 'center', 'SARS-CoV-1 Infe...', 'pathway', 'SARS-CoV-1 Infe...')
  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 4 Marc...', 'Portal:COVID-19...')
  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(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('
  30. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  31. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  32. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  33. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  34. 39 {main}
View all Featured Pathways for this Portal




The current list of authors and contributors of content of this portal (in alphabetical order): Matthew Conroy, Rex D A B, Jordi Doijen, Lauren Dupuis, Friederike Ehrhart, Chris Evelo, Kristina Hanspers, Amber Koning, Martina Kutmon, Marvin Martens, Penny Nymark, Alex Pico, Denise Slenter, Caroline Thorn, the Reactome project, and many more.


  • A paper about this project was published in Scientific Data: Ostaszewski, et al. "COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms." Scientific data 7.1 (2020): 1-4.
  • A more recent, longer paper from the whole community is available on bioRxiv: Ostaszewski, et al. "COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms." bioRxiv 2020.10.26.356014
  • This portal is also featured in the latest NAR Database Issue on WikiPathways.

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