Portal:Lipids

From WikiPathways

Revision as of 15:10, 24 October 2019 by DeSl (Talk | contribs)
Jump to: navigation, search

edit  

Welcome to the Lipids Pathways Portal on WikiPathways

http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=gpml&tag=Curation:Lipids


http://www.wikipathways.org//wpi/batchDownload.php?species=Mus%20musculus&fileType=gpml&tag=Curation:Lipids

This portal is set up to coordinate the development of lipid pathways and get together the community interested in interactive lipid pathways.

Lipids serve several important biological purposes, such as providing membrane structure, and signalling.

Thanks to the LIPID MAPS team for sharing their pathway knowledge through WikiPathways!

For more details on the LipidMaps pathways, please read the following paper: "A Mouse Macrophage Lipidome" Edward A. Dennis et.al. J Biol Chem. 2010 Dec 17; 285(51): 39976-39985.[1]

This portal is also featured in the latest NAR Database Issue on WikiPathways.

edit  

Download

RDF API
Data can be obtained using
SPARQL queries. An example to obtain all
Proteins from the Lipids Community:
The WikiPathways Webservice (API)
allows for automated retrieval
of Pathway content (in several
formats, e.g. json, XML, html, GPML).
Example SPARQL Query API Call Lipids Community

edit  

Pathways

Existing pathways

Pathways which have been approved for data analysis can be found on the Featured pathway page. We have split these up in 7 groups (Sphingolipids, Eicosanoids, Glycerolipids and Glycerophospholipids, Phosphatidylglycerides, Fatty Acids, Cholesterol, General Pathways related to Lipids).

Extend existing (approved) pathways with new literature

Update existing (not yet approved) pathways

Sphingolipid Metabolism (integrated pathway) (mouse)
Elongation of (very) long chain fatty acids (mouse)

Create new pathways

Start a new pathway!

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  

Featured Pathway

Lipid Metabolism Pathway (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/8/8f/WP3965_111872.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/8/8f/WP3965_111872.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), 'Lipid Metabolis...', 'https://www.wik...', 'Lipid Metabolis...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP3965', '300', 'center', 'Lipid Metabolis...', 'pathway', 'Lipid Metabolis...')
  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), 'Thursday 3 Dece...', 'Portal:Lipids/F...')
  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/Article.php(3406): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107623)
  32. 31 /var/www/wikipathways/includes/Article.php(875): Article->outputWikiText('{{{{FULLPAGENAM...', false)
  33. 32 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  34. 33 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  35. 34 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  36. 35 {main}
View all Featured Pathways for this Portal

edit  

News

2020-10-13 - The EpiLipidNET project has started. See Twitter and the COST action info page.

2020-10-01 - A brand new pathway on Phosphoinositides metabolism (WP4971) is now available (Human).

2019-10-23 - All Mouse pathways (originally from LipidMaps) have been converted to Human! See WP4718 - WP4726 .

2019-08-21 - Pathway:WP4350 and Pathway:WP4351 on Omega 3 & 6 FA synthesis and Omega 9 and saturated FA synthesis (mouse) have been updated!

2019-08-19 - Pathway:WP4344 and Pathway:WP4690 on Sphingolipids (general overview) and Sphingolipids (integrated pathway) have been updated!

2019-08-16 - Pathway:WP4345 on Glycerolipids and Glycerophospholipids has been updated!

2019-01-29 - Pathway:WP4348 and Pathway:WP4349 on Eicosanoid metabolism by LOX and CYP (mouse) have been updated!

2019-01-25 - Pathway:WP4347 on Eicosanoid metabolism by COX (mouse) has been updated!

2019-01-21 - Pathway:WP4346 on Cholesterol metabolism (mouse) has been updated!

2019-01-11 - More pathways were added to the featured pathway list.

2018-10-11 - This portal was created.


Personal tools