WikiPathways Test: Metabolites and Metabolic Interactions (Homo sapiens)

From WikiPathways

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(Updated character in lit refs.)
Current revision (12:09, 16 August 2019) (view source)
(HMDB identifier normalization)
 
Line 94: Line 94:
   <DataNode TextLabel="Aspirin (HMDB old IDs)" GraphId="d973d" Type="Metabolite">
   <DataNode TextLabel="Aspirin (HMDB old IDs)" GraphId="d973d" Type="Metabolite">
     <Graphics CenterX="351.74074074074053" CenterY="194.17816017874011" Width="144.5" Height="20.0" ZOrder="32822" FontSize="10" Valign="Middle" Color="0000ff" />
     <Graphics CenterX="351.74074074074053" CenterY="194.17816017874011" Width="144.5" Height="20.0" ZOrder="32822" FontSize="10" Valign="Middle" Color="0000ff" />
-
     <Xref Database="HMDB" ID="HMDB01879" />
+
     <Xref Database="HMDB" ID="HMDB0001879" />
   </DataNode>
   </DataNode>
   <DataNode TextLabel="TG(15:0/i-15:0/i-21:0)&#xA;(HMDB new IDs, no sec.)" GraphId="cbe82" Type="Metabolite">
   <DataNode TextLabel="TG(15:0/i-15:0/i-21:0)&#xA;(HMDB new IDs, no sec.)" GraphId="cbe82" Type="Metabolite">
Line 299: Line 299:
   <InfoBox CenterX="0.0" CenterY="0.0" />
   <InfoBox CenterX="0.0" CenterY="0.0" />
   <Biopax>
   <Biopax>
 +
    <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="a97">
 +
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">23892182</bp:ID>
 +
      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
 +
      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.</bp:TITLE>
 +
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Drug Discov Today</bp:SOURCE>
 +
      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2014</bp:YEAR>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kell DB</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goodacre R</bp:AUTHORS>
 +
    </bp:PublicationXref>
     <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="ad9">
     <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="ad9">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">29136241</bp:ID>
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">29136241</bp:ID>
Line 327: Line 336:
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pico AR</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pico AR</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Willighagen EL</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Willighagen EL</bp:AUTHORS>
 +
    </bp:PublicationXref>
 +
    <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="e28">
 +
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">25110584</bp:ID>
 +
      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
 +
      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BridgeDb app: unifying identifier mapping services for Cytoscape.</bp:TITLE>
 +
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F1000Res</bp:SOURCE>
 +
      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2014</bp:YEAR>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gao J</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang C</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">van Iersel M</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang L</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xu D</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Schultz N</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">R Pico A</bp:AUTHORS>
     </bp:PublicationXref>
     </bp:PublicationXref>
     <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="ce7">
     <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="ce7">
Line 342: Line 365:
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Conklin BR</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Conklin BR</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Evelo CT</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Evelo CT</bp:AUTHORS>
-
    </bp:PublicationXref>
 
-
    <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="a97">
 
-
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">23892182</bp:ID>
 
-
      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
 
-
      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.</bp:TITLE>
 
-
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Drug Discov Today</bp:SOURCE>
 
-
      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2014</bp:YEAR>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kell DB</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goodacre R</bp:AUTHORS>
 
     </bp:PublicationXref>
     </bp:PublicationXref>
     <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="bb4">
     <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="bb4">
Line 359: Line 373:
       <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2016</bp:YEAR>
       <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2016</bp:YEAR>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wishart DS</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wishart DS</bp:AUTHORS>
-
    </bp:PublicationXref>
 
-
    <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="e28">
 
-
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">25110584</bp:ID>
 
-
      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
 
-
      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BridgeDb app: unifying identifier mapping services for Cytoscape.</bp:TITLE>
 
-
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F1000Res</bp:SOURCE>
 
-
      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2014</bp:YEAR>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gao J</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang C</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">van Iersel M</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang L</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xu D</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Schultz N</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">R Pico A</bp:AUTHORS>
 
     </bp:PublicationXref>
     </bp:PublicationXref>
   </Biopax>
   </Biopax>
</Pathway>
</Pathway>

Current revision

Error rendering pathway page

This revision of the pathway probably contains invalid GPML code. If this happens to the most recent revision, try reverting the pathway using the pathway history displayed below or contact the site administrators (see WikiPathways:About) to resolve this problem.

Pathway history

View all...
CompareRevisionActionTimeUserComment
106200view12:09, 16 August 2019MaintBotHMDB identifier normalization
104196view14:07, 9 May 2019DeSlUpdated character in lit refs.
104195view14:02, 9 May 2019DeSlUpdated DrugBank identifier.
103428view12:29, 28 February 2019DeSlUpdated layout
103426view12:26, 28 February 2019DeSlAdded new test for metabolic interaction mapping files.
103058view11:53, 7 February 2019DeSlEnterobacterin is part of HMDB now, changed note in DataNode on this.
103050view10:52, 7 February 2019DeSlAdded name for IUPHAR database manually (waiting for new release of bridgeDb).
103049view10:51, 7 February 2019DeSlAdded checks for ChEMBL, Drugbank and IUPHAR.
102473view09:21, 24 December 2018DeSlAdded latest WPs paper as reference
102472view09:17, 24 December 2018DeSlAdded 2 new tests, changed layout
98035view10:57, 5 July 2018DeSlAdded new testcase for recently added LIPID Maps IDs to wikidata
98034view09:54, 5 July 2018DeSlAdded correct ID for latest testcase.
98033view09:46, 5 July 2018DeSlAdded lit. ref to BridgeDb paper and BridgeDb Cytoscape app paper.
98032view09:43, 5 July 2018DeSlChanged version number.
98031view09:41, 5 July 2018DeSlAdded more testcases
95851view14:52, 26 January 2018DeSlAdded node to check mapping to old and new HMDB IDs.
92873view08:07, 12 July 2017EgonwAdded an EPA CompTox test case.
90665view19:33, 4 December 2016AlexanderPicoModified title
85438view09:46, 15 May 2016EgonwAdded two review papers about metabolomics.
85430view09:30, 15 May 2016EgonwAdded quotes around "Glucose".
85429view09:27, 15 May 2016EgonwSome tweaks, and "released" as version 4.
85428view09:27, 15 May 2016EgonwRemoved redundant new lines.
85427view09:21, 15 May 2016EgonwAdded MOM test cases.
85076view06:33, 12 April 2016EgonwAdded a KNApSAcK test.
84782view10:07, 20 March 2016EgonwReverted to version '20:28, 17 July 2015' by Egonw
84480view20:41, 25 February 2016AlexanderPicoReverted to version '13:36, 25 February 2016' by AlexanderPico
84479view20:41, 25 February 2016AlexanderPico
84478view20:36, 25 February 2016AlexanderPicoQuick edit to datanode annotation or property
81054view20:28, 17 July 2015EgonwHacked in the InChIKey DataSource via the GPML.
81053view20:27, 17 July 2015EgonwAn InChIKey node.
81052view20:14, 17 July 2015EgonwHacked in the Wikidata DataSource via the GPML.
81051view20:12, 17 July 2015EgonwAdded a Wikidata node (for future testing).
80972view13:53, 6 July 2015EgonwModified description
72071view18:10, 24 October 2013EgonwModified description
72070view18:09, 24 October 2013EgonwNew pathway

Error details

exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/5/57/WP2582_prev.svg:
<BR>Status:1
<BR>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)

<BR>Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/5/57/WP2582_prev.svg" 2>&1<BR>' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255
Stack trace:
#0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
#1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
#2 /var/www/wikipathways/wpi/extensions/Pathways/PathwayPage.php(21): Pathway->updateCache('svg')
#3 [internal function]: renderPathwayPage(Object(Parser), '<?xml version="...', Object(StripState))
#4 /var/www/wikipathways/includes/Hooks.php(125): call_user_func_array('renderPathwayPa...', Array)
#5 /var/www/wikipathways/includes/parser/Parser.php(318): wfRunHooks('ParserBeforeStr...', Array)
#6 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('<?xml version="...', Object(Title), Object(ParserOptions), true, true, 106200)
#7 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('<?xml version="...', Object(Title), true, true)
#8 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('<?xml version="...', Object(Title), true)
#9 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('<?xml version="...')
#10 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
#11 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
#12 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
#13 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
#14 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
#15 {main}
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