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khansperskhanspers
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updated gpmls and images for pathway node
1 parent 1a63e9b commit 9ab0d50

17 files changed

Lines changed: 62 additions & 57 deletions

‎data/draw-unknown-node-start.gpml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="draw-unknown-node-start" Version="20241219" Organism="Homo sapiens">
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<Graphics BoardWidth="893.0" BoardHeight="530.5" />
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<Graphics BoardWidth="511.0" BoardHeight="403.5" />
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<DataNode TextLabel="ZFPM2" GraphId="d5fba" Type="GeneProduct" GroupRef="da39b">
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<Graphics CenterX="404.60504201680703" CenterY="100.25210084033614" Width="90.0" Height="25.0" ZOrder="32841" FontSize="12" Valign="Middle" />
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<Xref Database="Entrez Gene" ID="23414" />
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<Xref Database="Ensembl" ID="ENSG00000005513" />
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</DataNode>
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<DataNode TextLabel="Steroidigenesis" GraphId="edc15" Type="Pathway">
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<Graphics CenterX="426.0" CenterY="361.0" Width="110.0" Height="25.0" ZOrder="32870" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="426.0" CenterY="361.0" Width="110.0" Height="25.0" ZOrder="32870" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="" ID="" />
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</DataNode>
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<Interaction GraphId="ee947">
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<Label TextLabel="Leydig cell" GraphId="e7570">
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<Graphics CenterX="426.0" CenterY="234.0" Width="90.0" Height="25.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="12" Valign="Middle" Color="404040" />
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</Label>
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<Group GroupId="da39b" GraphId="d01c7" Style="Group" />
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<Group GroupId="f5201" GraphId="a9e98" Style="Group" />
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<Group GroupId="c7c44" GraphId="a6e0d" Style="Group" />
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<Group GroupId="f5201" GraphId="a9e98" Style="Group" />
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<Group GroupId="e6b72" GraphId="c9c00" Style="Group" />
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<Group GroupId="da39b" GraphId="d01c7" Style="Group" />
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<InfoBox CenterX="0.0" CenterY="0.0" />
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<Biopax />
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</Pathway>
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‎data/fig-met-1-fourth-start.gpml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="fig-met-1-third-solution" Version="20161128" Organism="Homo sapiens">
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<Comment Source="WikiPathways-description">Do not modify or delete. This pathway is part of the collection of content used by [https://wikipathways.github.io/academy/ WikiPathways Academy].</Comment>
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<Graphics BoardWidth="753.0" BoardHeight="527.8303695077044" />
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<Graphics BoardWidth="717.0" BoardHeight="507.8303695077044" />
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<DataNode TextLabel="Glucose" GraphId="ab04e" Type="Metabolite">
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<Graphics CenterX="297.72484141950963" CenterY="107.44111092062404" Width="90.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" Color="0000ff" />
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<Xref Database="HMDB" ID="HMDB00122" />
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<Xref Database="ChEBI" ID="CHEBI:18059" />
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</DataNode>
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<DataNode TextLabel="Pentose Phosphate Pathway" GraphId="e42e6" Type="Pathway">
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<Graphics CenterX="532.362420709755" CenterY="211.44111092062397" Width="183.27515858048992" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="532.362420709755" CenterY="211.44111092062397" Width="183.27515858048992" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="WikiPathways" ID="WP134" />
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</DataNode>
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<DataNode TextLabel="LDHA" GraphId="ee539" Type="GeneProduct">

‎images/cholesterol-full.png‎

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‎stages/draw-unknown-node/draw-unknown-node-solution.gpml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="draw-unknown-node-start" Version="20241219" Organism="Homo sapiens">
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<Graphics BoardWidth="893.0" BoardHeight="530.5" />
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<Graphics BoardWidth="511.0" BoardHeight="403.5" />
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<DataNode TextLabel="Leydig cell" GraphId="d8bb3">
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<Graphics CenterX="426.0" CenterY="236.0" Width="90.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" />
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<Xref Database="Wikidata" ID="Q636846" />
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<Xref Database="Ensembl" ID="ENSG00000005513" />
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</DataNode>
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<DataNode TextLabel="Steroidigenesis" GraphId="edc15" Type="Pathway">
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<Graphics CenterX="426.0" CenterY="361.0" Width="110.0" Height="25.0" ZOrder="32870" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="426.0" CenterY="361.0" Width="110.0" Height="25.0" ZOrder="32870" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="" ID="" />
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</DataNode>
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<Interaction GraphId="ee947">
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</Graphics>
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<Xref Database="" ID="" />
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</Interaction>
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<Group GroupId="da39b" GraphId="d01c7" Style="Group" />
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<Group GroupId="f5201" GraphId="a9e98" Style="Group" />
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<Group GroupId="c7c44" GraphId="a6e0d" Style="Group" />
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<Group GroupId="f5201" GraphId="a9e98" Style="Group" />
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<Group GroupId="e6b72" GraphId="c9c00" Style="Group" />
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<Group GroupId="da39b" GraphId="d01c7" Style="Group" />
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<InfoBox CenterX="0.0" CenterY="0.0" />
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<Biopax />
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</Pathway>
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‎stages/draw-unknown-node/draw-unknown-node-solution.png‎

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‎stages/fig-met-1-first/fig-met-1-first-solution.gpml‎

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<Xref Database="Ensembl" ID="ENSG00000156515" />
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</DataNode>
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<DataNode TextLabel="Pentose Phosphate Pathway" GraphId="e42e6" Type="Pathway">
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<Graphics CenterX="530.362420709755" CenterY="211.44111092062397" Width="179.27515858048992" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="530.362420709755" CenterY="211.44111092062397" Width="179.27515858048992" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="WikiPathways" ID="WP134" />
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</DataNode>
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<DataNode TextLabel="Glucose-6-phosphate" GraphId="fd5d5" Type="Metabolite">
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<InfoBox CenterX="0.0" CenterY="0.0" />
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<Biopax />
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</Pathway>
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‎stages/fig-met-1-first/index.html‎

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<li>Instead of searching for an ID, enter the id “WP134” in the <b>Identifier</b> field, and enter “WikiPathways”
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in the <b>Database field</b>.</li>
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<li>Type in “Pentose Phosphate Pathway” as the <b>Text label</b>. Click <b>OK</b>.</li>
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<li>A pathway node is by default of <b>Shape Type</b> "None". Update the <b>Shape Type</b> to "RoundedRectangle" for the “Pentose Phosphate Pathway” node.</li>
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<li>A pathway node is by default of <b>Shape Type</b> "None". Update the <b>Shape Type</b> to "RoundedRectangle" for the “Pentose Phosphate Pathway” node. This ensures that the pathway node is clickabile in WikiPathways.</li>
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<li>Draw the mim-conversion arrows between the glucose and glucose-6-phosphate nodes, and add an anchor to it.</li>
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<li>For the interaction between glucose-6-phosphate node and the pentose phosphate pathway node, add the default arrow interaction.</li>
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<li>Add the gene products that catalyze the conversion between glucose and glucose-6-phosphate, HK1. For the interaction between glucose-6-phosphate and the

‎stages/fig-met-1-fourth/fig-met-1-fourth-solution.gpml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="fig-met-1-fourth-solution" Version="20161128" Organism="Homo sapiens">
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<Comment Source="WikiPathways-description">Do not modify or delete. This pathway is part of the collection of content used by [https://wikipathways.github.io/academy/ WikiPathways Academy].</Comment>
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<Graphics BoardWidth="735.7531065267223" BoardHeight="802.3748341175058" />
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<Graphics BoardWidth="723.1396763996801" BoardHeight="802.3748341175058" />
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<DataNode TextLabel="OGDH" GraphId="a51ac" Type="GeneProduct">
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<Graphics CenterX="556.4200756737278" CenterY="624.7152922608363" Width="55.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" />
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<Xref Database="Ensembl" ID="ENSG00000105953" />
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<Xref Database="Ensembl" ID="ENSG00000169710" />
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</DataNode>
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<DataNode TextLabel="Pentose Phosphate Pathway" GraphId="e42e6" Type="Pathway">
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<Graphics CenterX="494.441368078176" CenterY="181.96742671009764" Width="181.11726384364795" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="494.441368078176" CenterY="181.96742671009764" Width="181.11726384364795" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="WikiPathways" ID="WP134" />
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</DataNode>
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<DataNode TextLabel="LDHA" GraphId="ee539" Type="GeneProduct">
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<InfoBox CenterX="0.0" CenterY="0.0" />
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<Biopax />
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</Pathway>
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‎stages/fig-met-1-last/fig-met-1-last-solution.gpml‎

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<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="fig-met-1-last-solution" Version="20161128" Organism="Homo sapiens">
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<Comment Source="WikiPathways-description">Do not modify or delete. This pathway is part of the collection of content used by [https://wikipathways.github.io/academy/ WikiPathways Academy].</Comment>
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<BiopaxRef>b84</BiopaxRef>
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<Graphics BoardWidth="758.7531065267223" BoardHeight="802.3748341175058" />
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<Graphics BoardWidth="723.1396763996801" BoardHeight="802.3748341175058" />
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<DataNode TextLabel="OGDH" GraphId="a51ac" Type="GeneProduct">
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<Graphics CenterX="556.4200756737278" CenterY="624.7152922608363" Width="55.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" />
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<Xref Database="Ensembl" ID="ENSG00000105953" />
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<Xref Database="Ensembl" ID="ENSG00000169710" />
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</DataNode>
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<DataNode TextLabel="Pentose Phosphate Pathway" GraphId="e42e6" Type="Pathway">
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<Graphics CenterX="494.441368078176" CenterY="181.96742671009764" Width="181.11726384364795" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="494.441368078176" CenterY="181.96742671009764" Width="181.11726384364795" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="WikiPathways" ID="WP134" />
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</DataNode>
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<DataNode TextLabel="ACO2" GraphId="e7735" Type="GeneProduct">

‎stages/fig-met-1-second/fig-met-1-second-solution.gpml‎

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<Xref Database="ChEBI" ID="CHEBI:15361" />
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</DataNode>
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<DataNode TextLabel="Pentose Phosphate Pathway" GraphId="e42e6" Type="Pathway">
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<Graphics CenterX="532.362420709755" CenterY="211.44111092062397" Width="183.27515858048992" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
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<Graphics CenterX="532.362420709755" CenterY="211.44111092062397" Width="183.27515858048992" Height="25.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="14961e" />
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<Xref Database="WikiPathways" ID="WP134" />
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</DataNode>
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<DataNode TextLabel="LDHA" GraphId="ee539" Type="GeneProduct">
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<InfoBox CenterX="0.0" CenterY="0.0" />
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<Biopax />
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</Pathway>
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