Portal:COVID-19

From WikiPathways

(Difference between revisions)
Jump to: navigation, search
(Added proper covid-19 portal)
Line 1: Line 1:
-
 
{{{{FULLPAGENAME}}/box-title
{{{{FULLPAGENAME}}/box-title
|<!-- TITLE OF BOX -->
|<!-- TITLE OF BOX -->
Line 70: Line 69:
}}
}}
-->
-->
-
 
-
 
-
{|style="margin: 10px;"
 
-
|width=800px|
 
-
<br/><big><font color="#407F7F" size="5">Welcome to the COVID-19 Pathway Collection</font></big><br/><br/>
 
-
<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>
 
-
<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>
 
-
 
-
<p>We also thank the authors of all the cited articles (recursively).</p>
 
-
{{#section:Help:Authors|covid-help}}
 
-
 
-
|{{#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}}
 
-
|}
 
-
 
-
== SARS-CoV-2 Pathways ==
 
-
 
-
{| style="margin: 10px; background-color:#AFDCDE"
 
-
|width=100px; cell padding=50px|{{#pwImage:Pathway:WP4846|250px||SARS-CoV-2 and COVID-19 Pathway}}
 
-
Collaborative project for curation of biological processes involved in the COVID-19 disease after SARS-Cov-2 infection.
 
-
|width=100px|{{#pwImage:Pathway:WP4860|250px||Hijack of Ubiquitination by SARS-CoV-2}}
 
-
SARS-CoV-2 includes a novel Orf10 that interacts with muliple members of the Cullin 2 ubiquitin ligase complex.
 
-
|width=100px|{{#pwImage:Pathway:WP4868|250px||Type I Interferon Induction and Signaling During SARS-CoV-2 Infection}}
 
-
The induction and signaling of type I interferon with specific SARS-CoV-2 protein and relevant drug.
 
-
|width=100px|{{#pwImage:Pathway:WP4927|250px||COVID-19, thrombosis and anticoagulation}}
 
-
|-
 
-
|}
 
-
{| style="margin: 10px; background-color:#AFDCDE"
 
-
|width=100px|{{#pwImage:Pathway:WP4876|250px||Activation of NLRP3 Inflammasome by SARS-CoV-2}}
 
-
Orf3a from SARS-CoV has been shown to bind TRAF3 and activate the NLRP3 inflammasome.
 
-
|width=100px|{{#pwImage:Pathway:WP4883|250px||SARS-CoV-2 and Angiotensin-converting enzyme 2 (ACE2) receptor : Molecular mechanisms and potential therapeutic target}}
 
-
|width=100px|{{#pwImage:Pathway:WP4891|250px||COVID-19 AOP}}
 
-
Experimental pathway to investigate overlap of virus-host interaction and adverse outcome pathways
 
-
|width=100px|{{#pwImage:Pathway:WP4884|250px||nsp9/nsp10-mediated SARS-CoV-2 pathogenesis}}
 
-
Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis
 
-
|-
 
-
|}
 
-
{| style="margin: 10px; background-color:#AFDCDE"
 
-
|width=100px|{{#pwImage:Pathway:WP4904|250px||LDLRAD4 pathway in COVID-19}}
 
-
|width=100px|{{#pwImage:Pathway:WP4936|250px||Overview of perturbations to host-cell autophagy, induced by distinct proteins of SARS-CoV-2 (Homo sapiens)}}
 
-
|-
 
-
|}
 
-
 
-
== Other coronaviruses: MERS, SARS-CoV, etc ==
 
-
 
-
{| style="margin: 10px; background-color:#AFDCDE"
 
-
|width=100px|{{#pwImage:Pathway:WP4853|250px||Coronavirus lipid metabolism}}
 
-
Lipid metabolism alternations that are related to infection by the corona virus.
 
-
|width=100px|{{#pwImage:Pathway:WP4863|250px||Host-pathogen interaction of human corona viruses - autophagy}}
 
-
|width=100px|{{#pwImage:Pathway:WP4864|250px||Host-pathogen interaction of human corona viruses - apoptosis}}
 
-
|width=100px|{{#pwImage:Pathway:WP4912|250px||SARS coronavirus and innate immunity}}
 
-
|-
 
-
|}
 
-
{| style="margin: 10px; background-color:#AFDCDE"
 
-
|width=100px|{{#pwImage:Pathway:WP4861|250px||ER stress response in Coronavirus infection}}
 
-
|width=100px|{{#pwImage:Pathway:WP4799|250px||Downregulation of ACE2 expression by SARS-CoV infection and SARS-CoV Spike protein}}
 
-
|width=100px|{{#pwImage:Pathway:WP4877|250px||Host-pathogen interaction of human corona viruses - MAPK signaling}}
 
-
|width=100px|{{#pwImage:Pathway:WP4880|250px||Host-pathogen interaction of human corona viruses - Interferon induction}}
 
-
|-
 
-
|}
 
-
 
-
== More about ACE2 ==
 
-
 
-
{| style="margin: 10px; background-color:#AFDCDE"
 
-
|width=100px|{{#pwImage:Pathway:WP554|250px||ACE Inhibitor Pathway}}
 
-
|width=100px|{{#pwImage:Pathway:WP2729|250px||Metabolism of Angiotensinogen to Angiotensins (Reactome)}}
 
-
|-
 
-
|}
 
[[Category:Portals]]
[[Category:Portals]]

Revision as of 11:18, 9 September 2020

edit  

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.


edit  

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.


edit  

Contribute

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.


edit  

Featured Pathway

Type I Interferon Induction and Signaling During SARS-CoV-2 Infection (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/f/f5/WP4868_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/f/f5/WP4868_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), 'Type I Interfer...', 'https://www.wik...', 'Type I Interfer...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4868', '300', 'center', 'Type I Interfer...', 'pathway', 'Type I Interfer...')
  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('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 111833)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
View all Featured Pathways for this Portal


edit  

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


Personal tools