Revision as of 12:06, 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

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Revision	Action	Time	User	Comment
107574	view	05:05, 23 October 2019	Khanspers	Modified description
107573	view	05:01, 23 October 2019	Khanspers	Modified description
107115	view	14:19, 17 September 2019	MaintBot	ChEBI identifier normalization
106171	view	12:06, 16 August 2019	MaintBot	HMDB identifier normalization
105875	view	04:49, 16 August 2019	Khanspers	Modified description
105436	view	04:36, 8 August 2019	Khanspers	Modified description
105119	view	22:00, 8 July 2019	Khanspers	Modified description
102414	view	09:50, 23 December 2018	Egonw	Replaced a deleted CAS number with the active one.
94196	view	14:39, 25 August 2017	Mkutmon	added missing metabolite identifier
92993	view	18:20, 21 July 2017	Khanspers	fixed unconnected
92992	view	18:17, 21 July 2017	Khanspers	Modified description
92991	view	18:17, 21 July 2017	Khanspers	removed GenMAPP notes
92892	view	18:57, 14 July 2017	Egonw	Added a missing metabolite ID.
92891	view	18:51, 14 July 2017	Egonw	Replace a CAS number for a totally different compound with the ChEBI ID for L-alanine.
92890	view	18:51, 14 July 2017	Egonw	Added a missing metabolite ID.
91240	view	20:15, 21 January 2017	AlexanderPico	Quick edit to datanode annotation or property
89638	view	06:26, 22 September 2016	Egonw	Connected a line (the 2nd was too hard).
74147	view	11:26, 1 April 2014	Egonw	Replaced an InChI with a more traditional identifier.
71277	view	22:57, 16 October 2013	MaintBot	Updated UniProt/TrEMBL data source
67036	view	09:57, 26 June 2013	Christine Chichester	Ontology Term : 'alanine, aspartate and glutamate metabolic pathway' added !
63140	view	19:17, 8 May 2013	MaintBot	Updating GPML version
54702	view	13:23, 7 December 2012	Andra	RDF Tidy
53476	view	23:01, 7 November 2012	Andra
45055	view	19:43, 6 October 2011	AlexanderPico	added db refs for metabolites
45039	view	18:57, 6 October 2011	AlexanderPico	added EC number refs
44946	view	12:32, 6 October 2011	MartijnVanIersel	Ontology Term : 'amino acid metabolic pathway' added !
41117	view	23:37, 1 March 2011	MaintBot	Removed redundant pathway information and comments
38938	view	22:12, 24 September 2010	Khanspers	overhaul of metabolites, pathway links and connectors
38933	view	21:50, 24 September 2010	Khanspers	Periodical save, work in progress
38931	view	21:40, 24 September 2010	Khanspers	Periodical save, work in progress
38925	view	21:30, 24 September 2010	Khanspers	Periodical save, work in progress
38922	view	21:19, 24 September 2010	Khanspers	Periodical save, work in progress
38921	view	21:09, 24 September 2010	Khanspers
38826	view	10:24, 24 September 2010	MartijnVanIersel	linked pathway
38640	view	11:36, 23 September 2010	MartijnVanIersel	pathway link
35516	view	13:51, 12 February 2010	Michiel	Added ref
35424	view	10:53, 12 February 2010	Andra	Added reference
34472	view	18:34, 10 December 2009	MaintBot	Automatic update of empty xrefs
32205	view	12:40, 15 August 2009	MaintBot	Fixed text labels
31692	view	11:47, 14 August 2009	MaintBot	Fixed group labels
20905	view	11:30, 14 November 2008	MaintBot	[[Pathway:Homo sapiens:Alanine and aspartate metabolism KEGG]] moved to [[Pathway:WP106]]: Moved to stable identifier
14689	view	19:24, 23 May 2008	Khanspers	Periodical save, work in progress
14686	view	19:14, 23 May 2008	Khanspers	Periodical save, work in progress
14684	view	19:02, 23 May 2008	Khanspers	connectors
14682	view	18:57, 23 May 2008	Khanspers	connectors
14679	view	18:47, 23 May 2008	Khanspers	Periodical save, work in progress
14677	view	18:37, 23 May 2008	Khanspers	connectors
14675	view	18:27, 23 May 2008	Khanspers	Connectors
14672	view	18:17, 23 May 2008	Khanspers	Periodical save, work in progress
14670	view	18:07, 23 May 2008	Khanspers	test

Error details

exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/2/20/WP106_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/2/20/WP106_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, 106171)
#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}

Alanine and aspartate metabolism (Homo sapiens)

From WikiPathways

Revision as of 12:06, 16 August 2019

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@@ Line 7: / Line 7: @@
    <BiopaxRef>e65</BiopaxRef>
    <BiopaxRef>f1b</BiopaxRef>
-   <Graphics BoardWidth="1336.6666666666667" BoardHeight="1243.0"/>
+   <Graphics BoardWidth="1336.6666666666667" BoardHeight="1243.0" />
    <DataNode TextLabel="Fatty acid metabolism" GraphId="d5a97" Type="Pathway">
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-     <Xref Database="WikiPathways" ID="WP143"/>
+     <Xref Database="WikiPathways" ID="WP143" />
    </DataNode>
    <DataNode TextLabel="Pyruvate" GraphId="a3720" Type="Metabolite">
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-     <Xref Database="ChEBI" ID="32816"/>
+     <Xref Database="ChEBI" ID="32816" />
    </DataNode>
    <DataNode TextLabel="3.5.1.3" GraphId="a3a" Type="GeneProduct">
-     <Graphics CenterX="421.3333333333333" CenterY="1020.6666666666666" Width="46.666666666666664" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle"/>
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-     <Xref Database="Enzyme Nomenclature" ID="3.5.1.3"/>
+     <Xref Database="Enzyme Nomenclature" ID="3.5.1.3" />
    </DataNode>
    <DataNode TextLabel="GOT2" GraphId="a43" Type="GeneProduct" GroupRef="b134d">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="GOT2 | glutamic-oxaloacetic transaminase 2 mit..."/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="GOT2 | glutamic-oxaloacetic transaminase 2 mit..." />
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-     <Xref Database="Entrez Gene" ID="2806"/>
+     <Xref Database="Entrez Gene" ID="2806" />
    </DataNode>
    <DataNode TextLabel="3.4.13.3" GraphId="a77" Type="GeneProduct">
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-     <Xref Database="Enzyme Nomenclature" ID="3.4.13.3"/>
+     <Xref Database="Enzyme Nomenclature" ID="3.4.13.3" />
    </DataNode>
    <DataNode TextLabel="L-Alanine" GraphId="ab0" Type="Metabolite">
-     <Graphics CenterX="936.0" CenterY="235.66666666666666" Width="58.333333333333336" Height="15.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff"/>
+     <Graphics CenterX="936.0" CenterY="235.66666666666666" Width="58.333333333333336" Height="15.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
-     <Xref Database="ChEBI" ID="CHEBI:16977"/>
+     <Xref Database="ChEBI" ID="CHEBI:16977" />
    </DataNode>
    <DataNode TextLabel="ASL" GraphId="ac6" Type="GeneProduct">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ASL | argininosuccinate lyase"/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ASL | argininosuccinate lyase" />
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+     <Graphics CenterX="1136.6666666666667" CenterY="911.0" Width="46.666666666666664" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
-     <Xref Database="Entrez Gene" ID="435"/>
+     <Xref Database="Entrez Gene" ID="435" />
    </DataNode>
    <DataNode TextLabel="Lysine biosynthesis" GraphId="ac9a7" Type="Pathway">
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-     <Xref Database="" ID=""/>
+     <Xref Database="" ID="" />
    </DataNode>
    <DataNode TextLabel="ABAT" GraphId="aca" Type="GeneProduct" GroupRef="ba4cb">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ABAT | 4-aminobutyrate aminotransferase"/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ABAT | 4-aminobutyrate aminotransferase" />
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-     <Xref Database="Entrez Gene" ID="18"/>
+     <Xref Database="Entrez Gene" ID="18" />
    </DataNode>
    <DataNode TextLabel="4.1.1.11" GraphId="adf" Type="GeneProduct" GroupRef="a9af5">
-     <Graphics CenterX="867.0" CenterY="397.6666971842448" Width="55.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle"/>
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-     <Xref Database="Enzyme Nomenclature" ID="4.1.1.11"/>
+     <Xref Database="Enzyme Nomenclature" ID="4.1.1.11" />
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    <DataNode TextLabel="1.4.3.2" GraphId="ae1" Type="GeneProduct" GroupRef="dfc9e">
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-     <Xref Database="Enzyme Nomenclature" ID="1.4.3.2"/>
+     <Xref Database="Enzyme Nomenclature" ID="1.4.3.2" />
    </DataNode>
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-     <Xref Database="Enzyme Nomenclature" ID="4.1.1.12"/>
+     <Xref Database="Enzyme Nomenclature" ID="4.1.1.12" />
    </DataNode>
    <DataNode TextLabel="DARS" GraphId="aff" Type="GeneProduct">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="DARS | aspartyl-tRNA synthetase"/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="DARS | aspartyl-tRNA synthetase" />
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-     <Xref Database="Entrez Gene" ID="1615"/>
+     <Xref Database="Entrez Gene" ID="1615" />
    </DataNode>
    <DataNode TextLabel="ASPA" GraphId="b10" Type="GeneProduct">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ASPA | aspartoacylase (aminoacylase 2 Canavan ..."/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ASPA | aspartoacylase (aminoacylase 2 Canavan ..." />
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-     <Xref Database="Entrez Gene" ID="443"/>
+     <Xref Database="Entrez Gene" ID="443" />
    </DataNode>
    <DataNode TextLabel="N-Carbamoyl-L-aspartate" GraphId="b174e" Type="Metabolite">
-     <Graphics CenterX="652.0" CenterY="710.0" Width="128.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff"/>
+     <Graphics CenterX="652.0" CenterY="710.0" Width="128.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
-     <Xref Database="ChEBI" ID="15859"/>
+     <Xref Database="ChEBI" ID="15859" />
    </DataNode>
    <DataNode TextLabel="D-Alanine" GraphId="b23" Type="Metabolite">
      <Comment Source="GenMAPP remarks">D-Alanine</Comment>
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-     <Xref Database="CAS" ID="338-69-2"/>
+     <Xref Database="CAS" ID="338-69-2" />
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    <DataNode TextLabel="5.1.1.1" GraphId="b27" Type="GeneProduct">
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-     <Xref Database="Enzyme Nomenclature" ID="5.1.1.1"/>
+     <Xref Database="Enzyme Nomenclature" ID="5.1.1.1" />
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-     <Xref Database="Enzyme Nomenclature" ID="2.6.1.12"/>
+     <Xref Database="Enzyme Nomenclature" ID="2.6.1.12" />
    </DataNode>
    <DataNode TextLabel="b-Alanine" GraphId="b94" Type="Metabolite">
      <Comment Source="GenMAPP remarks">beta-alanine</Comment>
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-     <Xref Database="CAS" ID="6912-68-1"/>
+     <Xref Database="CAS" ID="6912-68-1" />
    </DataNode>
    <DataNode TextLabel="DARS" GraphId="ba3" Type="GeneProduct">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="DARS | aspartyl-tRNA synthetase"/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="DARS | aspartyl-tRNA synthetase" />
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-     <Xref Database="Entrez Gene" ID="1615"/>
+     <Xref Database="Entrez Gene" ID="1615" />
    </DataNode>
    <DataNode TextLabel="AGXT" GraphId="bcc" Type="GeneProduct">
-     <Attribute Key="org.pathvisio.model.BackpageHead" Value="AGXT | alanine-glyoxylate aminotransferase (oxa..."/>
+     <Attribute Key="org.pathvisio.model.BackpageHead" Value="AGXT | alanine-glyoxylate aminotransferase (oxa..." />
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-     <Xref Database="Entrez Gene" ID="189"/>
+     <Xref Database="Entrez Gene" ID="189" />
    </DataNode>
    <DataNode TextLabel="Glycine, serine and threonine metabolism" GraphId="bd17e" Type="Pathway">
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-     <Xref Database="" ID=""/>
+     <Xref Database="" ID="" />
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    <DataNode TextLabel="L-Asparagine acid" GraphId="be00d" Type="Metabolite" GroupRef="b758d">
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-     <Xref Database="CAS" ID="70-47-3"/>
+     <Xref Database="CAS" ID="70-47-3" />
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    <DataNode TextLabel="6.3.1.1" GraphId="c02" Type="GeneProduct">
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-     <Xref Database="Enzyme Nomenclature" ID="6.3.1.1"/>
+     <Xref Database="Enzyme Nomenclature" ID="6.3.1.1" />
    </DataNode>
    <DataNode TextLabel="1.2.1.18" GraphId="c1a" Type="GeneProduct">
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+     <Graphics CenterX="576.6666666666666" CenterY="616.6666666666666" Width="55.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
-     <Xref Database="Enzyme Nomenclature" ID="1.2.1.18"/>
+     <Xref Database="Enzyme Nomenclature" ID="1.2.1.18" />
    </DataNode>
    <DataNode TextLabel="Acetyl-CoA" GraphId="c39" Type="Metabolite">
      <Comment Source="GenMAPP remarks">Acetyl-CoA</Comment>
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-     <Xref Database="CAS" ID="72-89-9"/>
+     <Xref Database="CAS" ID="72-89-9" />
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      <Comment Source="GenMAPP remarks">Protein</Comment>
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    <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="e65">
-      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9687539</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">Intestinal mucosal amino acid catabolism.</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Nutr</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1998</bp:YEAR>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu G</bp:AUTHORS>
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@@ Line 1,105: / Line 1,097: @@
        <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>
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+      <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">Intestinal mucosal amino acid catabolism.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Nutr</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1998</bp:YEAR>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu G</bp:AUTHORS>
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