From WikiPathways

Revision as of 10:38, 14 September 2020 by DeSl (Talk | contribs)
(diff) ←Older revision | Current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search


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.




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 Molecular Systems Biology: Ostaszewski, et al. "COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms." Mol Syst Biol (2021) 17:e10387
  • This portal is also featured in the latest NAR Database Issue on WikiPathways.


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.


Featured Pathway

Pathogenesis of SARS-CoV-2 mediated by nsp9-nsp10 complex (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/7/77/WP4884_111990.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/7/77/WP4884_111990.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), 'Pathogenesis of...', 'https://classic...', 'Pathogenesis of...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4884', '300', 'center', 'Pathogenesis of...', 'pathway', 'Pathogenesis of...')
  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 24 June ...', '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. 33 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  31. 34 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  32. 35 {main}
View all Featured Pathways for this Portal


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.



  • 26 Nov. 2021 A hackathon led to three new COVID-19 pathways
  • 22 Jan. 2021 An index was added to the list of curation reports
  • 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

Personal tools