Help:WikiPathways Portals

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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. The main advantages of portals include:
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{| class="wikitable sortable" style="float:right; margin-left: 100px;"
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* Simplifying drawing and databasing of your pathways  
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|-
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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.  
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For example, a portal could organize pathways for a particular species or research area.  
 +
 
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The main advantages of portals include:
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* Simplified drawing and collecting your pathways  
* Help to keep track of ‘works-in-progress’ with collaborators
* Help to keep track of ‘works-in-progress’ with collaborators
* Help attribute credit for pathway authors and curators
* Help attribute credit for pathway authors and curators
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* Help to define a community
* Help to define a community
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<p>WikiPathways currently has nine portals, highlighting pathway content contributed by specific communities:
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<br>Creating a portal is easy using existing templates available from WikiPathways.
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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.
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* [[Portal:GenMAPP|GenMAPP]] contributed pathways
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<br>WikiPathways has a growing list of portals:
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* [[Portal:Reactome|Reactome]] content periodically synced with the Reactome collection
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* [[Portal:Micronutrient|Micronutrient]] portal for the [http://www.nugo.org/micronutrient NuGO micronutrient project].
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* [[Portal:CIRM|CIRM]] portal for the [http://www.cirm.ca.gov/ California Institute for Regenerative Medicine].
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* [[Portal:NetPath|NetPath]] portal for the [http://www.netpath.org/ NetPath] signal transduction pathways.
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* [[Portal:WormBase|WormBase]] portal for the [http://www.wormbase.org/#01-23-6 WormBase] community
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* [[Portal:Plants|Plants]] portal for the plant research community, a collaboration with the [http://jaiswallab.cgrb.oregonstate.edu/ Jaiswal Lab] and [http://www.gramene.org/ Gramene].
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* [[Portal:ExRNA|ExRNA]] portal with pathway content relevant to the extracellular RNA research community
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<br>Creating a portal is easy using existing templates available from WikiPathways. If you are interested in creating a portal at WikiPathways, please [[Contact_Us|contact us!]].
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* [[Portal:AOP|Adverse Outcome Pathway]]
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</p>
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* [[Portal:IEM|Inherited Metabolic Disorders (IMDs), or Inborn Errors of Metabolism (IEM)]]
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* [[Portal:CIRM|California Institute for Regenerative Medicine, CIRM]]
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* [[Portal:Disease/COVIDPathways|COVID-19]]
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* [[Portal:CPTAC|Clinical Proteomic Tumor Analysis Consortium, CPTAC]]
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* [[Portal:Disease|Disease]]     
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* [[Portal:ExRNA|ExRNA]]
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* [[Portal:Lipids|Lipids]]
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* [[Portal:Micronutrient|Micronutrients]]
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* [[Portal:Nanomaterials|Nanomaterials]]
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* [[Portal:NetPath|NetPath]]
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* [[Portal:Plants|Plant Pathways]]
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* [[Portal:RareDisease|Rare Disease]]
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* [[Portal:RenalGenomics|Renal Genomics]]
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* [[Portal:Reactome|Reactome]]
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* [[Portal:SkeletalDysplasia|Skeletal Dysplasia]]
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* [[Portal:WormBase|WormBase]]
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<p>[[:Help:Contents|Return to Help Contents]]</p>
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[[Category:Portals]]
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<p>[[:Help:Databases|Continue to WikiPathways Databases]]</p>
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Current revision

Community Featured Pathways IEM

Cysteine and methionine catabolism (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/3/3b/WP4504_81315.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/3/3b/WP4504_81315.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), 'Cysteine and me...', 'https://classic...', 'Cysteine and me...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4504', '300', 'center', 'Cysteine and me...', 'pathway', 'Cysteine and me...')
  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

ACE2 inhibition leads to pulmonary fibrosis (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/4/49/WP5035_81315.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/4/49/WP5035_81315.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), 'ACE2 inhibition...', 'https://classic...', 'ACE2 inhibition...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP5035', '300', 'center', 'ACE2 inhibition...', 'pathway', 'ACE2 inhibition...')
  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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