Portal:COVID-19

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<big>Welcome to the COVID-19 Pathways Portal on WikiPathways</big>   
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Call to Action
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<br/><big><font color="#407F7F" size="5">Welcome to the COVID-19 Pathway Collection</font></big><br/><br/>
 
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<p>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, reused and distributed. Let us know if you add a new pathway or want to recommend one for this collection.</p>
 
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<p>The current list of authors and contributors of content of this portal: [[User:Fehrhart|Friederike Ehrhart]], [[User:AlexanderPico|Alex Pico]], [[User:Khanspers|Kristina Hanspers]], [[User:Amber|Amber Koning]], [[User:Rex_D_A_B|Rex D A B]], [[User:Penny|Penny Nymark]], [[User:DeSl|Denise Slenter]], [[User:C.F.Thorn|Caroline Thorn]], the Reactome project, [[User:Evelo|Chris Evelo]], [[User:L Dupuis|Lauren Dupuis]], [[User:Conroy_lipids|Matthew Conroy]], [[User:Mkutmon|Martina Kutmon]], [[User:Marvin M2|Marvin Martens]], and many more.</p>
 
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<p>We also thank the authors of all the cited articles (recursively).</p>
 
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{{#section:Help:Authors|covid-help}}
 
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|{{#imgLink:Page1-601px-COVID19-Disease-Map-project-icon.pdf.jpg|230|right|Part of the <a href="https://covid.pages.uni.lu/">COVID-19 Disease Map</a> project<p>A paper about this project was published in <a href="http://dx.doi.org/10.1038/s41597-020-0477-8">Scientific Data</a>. </p>|external|https://covid.pages.uni.lu/|COVID19 Disease Map}}
 
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== SARS-CoV-2 Pathways ==
 
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{| style="margin: 10px; background-color:#AFDCDE"
 
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|width=100px; cell padding=50px|{{#pwImage:Pathway:WP4846|250px||SARS-CoV-2 and COVID-19 Pathway}}
 
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Collaborative project for curation of biological processes involved in the COVID-19 disease after SARS-Cov-2 infection.
 
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|width=100px|{{#pwImage:Pathway:WP4860|250px||Hijack of Ubiquitination by SARS-CoV-2}}
 
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SARS-CoV-2 includes a novel Orf10 that interacts with muliple members of the Cullin 2 ubiquitin ligase complex.
 
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|width=100px|{{#pwImage:Pathway:WP4868|250px||Type I Interferon Induction and Signaling During SARS-CoV-2 Infection}}
 
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The induction and signaling of type I interferon with specific SARS-CoV-2 protein and relevant drug.
 
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|width=100px|{{#pwImage:Pathway:WP4927|250px||COVID-19, thrombosis and anticoagulation}}
 
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|width=100px|{{#pwImage:Pathway:WP4876|250px||Activation of NLRP3 Inflammasome by SARS-CoV-2}}
 
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Orf3a from SARS-CoV has been shown to bind TRAF3 and activate the NLRP3 inflammasome.
 
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|width=100px|{{#pwImage:Pathway:WP4883|250px||SARS-CoV-2 and Angiotensin-converting enzyme 2 (ACE2) receptor : Molecular mechanisms and potential therapeutic target}}
 
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|width=100px|{{#pwImage:Pathway:WP4891|250px||COVID-19 AOP}}
 
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Experimental pathway to investigate overlap of virus-host interaction and adverse outcome pathways
 
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|width=100px|{{#pwImage:Pathway:WP4884|250px||nsp9/nsp10-mediated SARS-CoV-2 pathogenesis}}
 
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Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis
 
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|width=100px|{{#pwImage:Pathway:WP4904|250px||LDLRAD4 pathway in COVID-19}}
 
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|width=100px|{{#pwImage:Pathway:WP4936|250px||Overview of perturbations to host-cell autophagy, induced by distinct proteins of SARS-CoV-2 (Homo sapiens)}}
 
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== Other coronaviruses: MERS, SARS-CoV, etc ==
 
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|width=100px|{{#pwImage:Pathway:WP4853|250px||Coronavirus lipid metabolism}}
 
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Lipid metabolism alternations that are related to infection by the corona virus.
 
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|width=100px|{{#pwImage:Pathway:WP4863|250px||Host-pathogen interaction of human corona viruses - autophagy}}
 
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|width=100px|{{#pwImage:Pathway:WP4864|250px||Host-pathogen interaction of human corona viruses - apoptosis}}
 
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|width=100px|{{#pwImage:Pathway:WP4912|250px||SARS coronavirus and innate immunity}}
 
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|width=100px|{{#pwImage:Pathway:WP4861|250px||ER stress response in Coronavirus infection}}
 
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|width=100px|{{#pwImage:Pathway:WP4799|250px||Downregulation of ACE2 expression by SARS-CoV infection and SARS-CoV Spike protein}}
 
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|width=100px|{{#pwImage:Pathway:WP4877|250px||Host-pathogen interaction of human corona viruses - MAPK signaling}}
 
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|width=100px|{{#pwImage:Pathway:WP4880|250px||Host-pathogen interaction of human corona viruses - Interferon induction}}
 
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== More about ACE2 ==
 
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|width=100px|{{#pwImage:Pathway:WP554|250px||ACE Inhibitor Pathway}}
 
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|width=100px|{{#pwImage:Pathway:WP2729|250px||Metabolism of Angiotensinogen to Angiotensins (Reactome)}}
 
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[[Category:Portals]]
[[Category:Portals]]

Current revision

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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.


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Collaborators

Authors

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.

Publications

  • 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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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.

Curation

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.


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Featured Pathway

Linoleic acid metabolism known to be affected by coronavirus infection (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/3/3f/WP4853_111831.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/3/3f/WP4853_111831.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), 'Linoleic acid m...', 'https://www.wik...', 'Linoleic acid m...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4853', '300', 'center', 'Linoleic acid m...', 'pathway', 'Linoleic acid m...')
  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), 'Sunday 17 Janua...', '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('
    internalParse('
    parse('
    addWikiTextTitle('
    addWikiTextTitleTidy('
    addWikiTextTidy('
    renderNewRevision()
  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


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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.


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News

  • 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


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