Tyrosine Metabolism (Homo sapiens)

From WikiPathways

(Difference between revisions)
Jump to: navigation, search
(Added Rhea identifiers and CheBi identifiers)
(HMDB identifier normalization)
Line 89: Line 89:
   <DataNode TextLabel="4-fumarylacetoacetate(2-)" GraphId="a243b" Type="Metabolite">
   <DataNode TextLabel="4-fumarylacetoacetate(2-)" GraphId="a243b" Type="Metabolite">
     <Graphics CenterX="645.5" CenterY="534.0" Width="179.0" Height="25.0" ZOrder="32819" FontSize="12" Valign="Middle" Color="0000ff" />
     <Graphics CenterX="645.5" CenterY="534.0" Width="179.0" Height="25.0" ZOrder="32819" FontSize="12" Valign="Middle" Color="0000ff" />
-
     <Xref Database="HMDB" ID="HMDB62563" />
+
     <Xref Database="HMDB" ID="HMDB0062563" />
   </DataNode>
   </DataNode>
   <DataNode TextLabel="Porphobilinogen" GraphId="bbfe8" Type="Metabolite">
   <DataNode TextLabel="Porphobilinogen" GraphId="bbfe8" Type="Metabolite">
Line 377: Line 377:
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bodamer OA</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bodamer OA</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="ac8">
 +
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></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">Physician's Guidee to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</bp:TITLE>
 +
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></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">Blau, Nenad</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Duran, Marinus</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gibson, K. Michael</bp:AUTHORS>
 +
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dionisi-Vici, Carlo</bp:AUTHORS>
 +
    </bp:PublicationXref>
 +
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 +
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tyrosine degradation pathway</bp:TERM>
 +
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0001284</bp:ID>
 +
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
 +
    </bp:openControlledVocabulary>
 +
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 +
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inherited metabolic disorder</bp:TERM>
 +
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:655</bp:ID>
 +
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disease</bp:Ontology>
 +
    </bp:openControlledVocabulary>
 +
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 +
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alkaptonuria</bp:TERM>
 +
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:9270</bp:ID>
 +
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disease</bp:Ontology>
 +
    </bp:openControlledVocabulary>
 +
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 +
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alkaptonuria pathway</bp:TERM>
 +
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0002277</bp:ID>
 +
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
 +
    </bp:openControlledVocabulary>
     <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="c54">
     <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="c54">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">20677779</bp:ID>
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">20677779</bp:ID>
Line 413: Line 444:
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Moran GR</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Moran GR</bp:AUTHORS>
     </bp:PublicationXref>
     </bp:PublicationXref>
-
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 
-
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alkaptonuria</bp:TERM>
 
-
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:9270</bp:ID>
 
-
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disease</bp:Ontology>
 
-
    </bp:openControlledVocabulary>
 
-
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 
-
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inherited metabolic disorder</bp:TERM>
 
-
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:655</bp:ID>
 
-
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disease</bp:Ontology>
 
-
    </bp:openControlledVocabulary>
 
     <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
     <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
       <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tyrosine metabolic pathway</bp:TERM>
       <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tyrosine metabolic pathway</bp:TERM>
       <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000052</bp:ID>
       <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000052</bp:ID>
-
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
 
-
    </bp:openControlledVocabulary>
 
-
    <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="ac8">
 
-
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></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">Physician's Guidee to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</bp:TITLE>
 
-
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></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">Blau, Nenad</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Duran, Marinus</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gibson, K. Michael</bp:AUTHORS>
 
-
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dionisi-Vici, Carlo</bp:AUTHORS>
 
-
    </bp:PublicationXref>
 
-
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 
-
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tyrosine degradation pathway</bp:TERM>
 
-
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0001284</bp:ID>
 
-
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
 
-
    </bp:openControlledVocabulary>
 
-
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
 
-
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alkaptonuria pathway</bp:TERM>
 
-
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0002277</bp:ID>
 
       <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
       <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
     </bp:openControlledVocabulary>
     </bp:openControlledVocabulary>
   </Biopax>
   </Biopax>
</Pathway>
</Pathway>

Revision as of 12:09, 16 August 2019

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
108293view17:08, 4 December 2019AgustinGVfix width and realign Succinylacetone
108292view17:07, 4 December 2019AgustinGV
108076view11:46, 28 November 2019FehrhartOntology Term : 'disease pathway' added !
106201view12:09, 16 August 2019MaintBotHMDB identifier normalization
104393view13:59, 23 May 2019GMKeulenAdded Rhea identifiers and CheBi identifiers
104019view17:35, 25 April 2019IreneHemelModified description
102787view13:24, 24 January 2019EgonwReplaced secondary ChEBI IDs with primary IDs.
102783view10:23, 24 January 2019DeSlOntology Term : 'alkaptonuria pathway' added !
102782view10:23, 24 January 2019DeSlOntology Term : 'alkaptonuria' added !
102781view10:22, 24 January 2019DeSlCreated unique ref for Pubmed 20677779
102780view10:18, 24 January 2019DeSlAdded lit. ref for reaction to Hawkinsin.
102779view10:04, 24 January 2019DeSlAdded side reaction to Hawkinsin.
102777view09:25, 24 January 2019DeSlChanged layout, added last disease, converted lines to disease node to graphical lines.
102759view12:50, 23 January 2019L DupuisModified description
102758view12:47, 23 January 2019L DupuisFramed diagnostically important metabolites
102757view12:42, 23 January 2019L DupuisAdded reference
102756view12:36, 23 January 2019L DupuisLinked omim ids to the disorders
102755view12:24, 23 January 2019L DupuisConverted interaction lines to graphical interface lines to indicate a point where pathology could occur
102754view11:56, 23 January 2019L DupuisConnected unconnected lines
102753view10:06, 23 January 2019L DupuisOntology Term : 'inherited metabolic disorder' added !
102752view10:04, 23 January 2019L DupuisOntology Term : 'tyrosine metabolic pathway' added !
102751view10:03, 23 January 2019L DupuisOntology Term : 'tyrosine degradation pathway' added !
102750view09:58, 23 January 2019L DupuisNew pathway

Error details

exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/a/a3/WP4506_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/a/a3/WP4506_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, 106201)
#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}
Personal tools