Help:WikiPathways Portals

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Current revision (13:11, 13 April 2022) (view source)
 
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{| class="wikitable sortable" style="float:right; margin-left: 10px;"
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{| class="wikitable sortable" style="float:right; margin-left: 100px;"
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|-
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| Portals within WikiPathways serve as organizing points for communities with focused pathway interests.  
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|<h2 class="frontPagePanel blueFg">Community Featured Pathways IEM</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:IEM | true}}
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|-
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|<h2 class="frontPagePanel blueFg">Community Featured Pathways COVID-19</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:COVID19 | true}}
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|}
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Portals within WikiPathways serve as organizing points for communities with focused pathway interests.  
For example, a portal could organize pathways for a particular species or research area.  
For example, a portal could organize pathways for a particular species or research area.  
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If you are interested, please [https://docs.google.com/document/d/176BshTLE97V-gjzWrt0cgZEpQwnGUI86NdTaatETeSU/edit?pli=1#heading=h.b85xd25jlcie consult the portal maintenance guide] and [[Contact_Us|contact us]] for assistance.
If you are interested, please [https://docs.google.com/document/d/176BshTLE97V-gjzWrt0cgZEpQwnGUI86NdTaatETeSU/edit?pli=1#heading=h.b85xd25jlcie consult the portal maintenance guide] and [[Contact_Us|contact us]] for assistance.
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|| <h2 class="frontPagePanel blueFg">Community Featured Pathways Blau</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:Blau | true}}
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|-
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<br>WikiPathways has a growing list of portals:
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|<br>WikiPathways has a growing list of portals:
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* [[Portal:AOP|Adverse Outcome Pathway]]
* [[Portal:AOP|Adverse Outcome Pathway]]
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* [[Portal:Blau|Blau (Inborn Errors of Metabolism)]]
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* [[Portal:IEM|Inherited Metabolic Disorders (IMDs), or Inborn Errors of Metabolism (IEM)]]
* [[Portal:CIRM|California Institute for Regenerative Medicine, CIRM]]
* [[Portal:CIRM|California Institute for Regenerative Medicine, CIRM]]
* [[Portal:Disease/COVIDPathways|COVID-19]]
* [[Portal:Disease/COVIDPathways|COVID-19]]
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* [[Portal:SkeletalDysplasia|Skeletal Dysplasia]]
* [[Portal:SkeletalDysplasia|Skeletal Dysplasia]]
* [[Portal:WormBase|WormBase]]  
* [[Portal:WormBase|WormBase]]  
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|| <h2 class="frontPagePanel blueFg">Community Featured Pathways COVID-19</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:COVID19 | true}}
 
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|}
 
[[Category:Portals]]
[[Category:Portals]]

Current revision

Community Featured Pathways IEM

Glycosylation and related congenital defects (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/0/08/WP4521_111711.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/0/08/WP4521_111711.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), 'Glycosylation a...', 'https://classic...', 'Glycosylation a...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4521', '300', 'center', 'Glycosylation a...', 'pathway', 'Glycosylation a...')
  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 6 May 20...', 'Curation:IEM', '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('{| class="wikit...')
  20. 19 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{| class="wikit...')
  21. 20 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{| class="wikit...', Object(Title), Object(ParserOptions), true, true, 122535)
  22. 21 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{| class="wikit...', Object(Title), true, true)
  23. 22 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{| class="wikit...', Object(Title), true)
  24. 23 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{| class="wikit...')
  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}

Community Featured Pathways COVID-19

FOXP3 in COVID-19 (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/c/c0/WP5063_111711.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/c/c0/WP5063_111711.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), 'FOXP3 in COVID-...', 'https://classic...', 'FOXP3 in COVID-...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP5063', '300', 'center', 'FOXP3 in COVID-...', 'pathway', 'FOXP3 in COVID-...')
  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 6 May 20...', 'Curation:COVID1...', '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('{| class="wikit...')
  20. 19 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{| class="wikit...')
  21. 20 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{| class="wikit...', Object(Title), Object(ParserOptions), true, true, 122535)
  22. 21 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{| class="wikit...', Object(Title), true, true)
  23. 22 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{| class="wikit...', Object(Title), true)
  24. 23 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{| class="wikit...')
  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}

Portals within WikiPathways serve as organizing points for communities with focused pathway interests. For example, a portal could organize pathways for a particular species or research area.

The main advantages of portals include:

  • Simplified drawing and collecting your pathways
  • Help to keep track of ‘works-in-progress’ with collaborators
  • Help attribute credit for pathway authors and curators
  • Attract new collaborators
  • Help to define a community


Creating a portal is easy using existing templates available from WikiPathways.

If you are interested, please consult the portal maintenance guide and contact us for assistance.


WikiPathways has a growing list of portals:

Retrieved from "https://classic.wikipathways.org/index.php/Help:WikiPathways_Portals"
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