From 205850e29968d994a7ea7bc76dae81acf71bf8a9 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 30 Sep 2024 02:59:13 +0000
Subject: [PATCH] Process GPML changes

---
 pathways/WP5323/WP5323.gpml | 178 +++++++++++++++++-------------------
 1 file changed, 83 insertions(+), 95 deletions(-)

diff --git a/pathways/WP5323/WP5323.gpml b/pathways/WP5323/WP5323.gpml
index dbaba3e3d..d64c03675 100644
--- a/pathways/WP5323/WP5323.gpml
+++ b/pathways/WP5323/WP5323.gpml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Fatty acids and lipoproteins transport in hepatocytes" Data-Source="WikiPathways" Version="WP5323_r135564" Author="[LLadeira, Mkutmon, Egonw, DeSl, Jmillanacosta, Eweitz]" Last-Modified="20240928020149" Organism="Homo sapiens">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Fatty acids and lipoproteins transport in hepatocytes" Data-Source="WikiPathways" Version="WP5323_r135566" Author="[LLadeira, Mkutmon, Egonw, DeSl, Jmillanacosta, Eweitz]" Last-Modified="20240929173110" Organism="Homo sapiens">
   <Comment Source="WikiPathways-description">This model was constructed integrating the Fatty acid transporters (Homo sapiens) metapathway (WP5061), the Cholesterol metabolism (Homo sapiens) (WP5304) and the KEGG Cholesterol metabolism pathway (map04979) as well as information from the literature.</Comment>
-  <Graphics BoardWidth="4745.0" BoardHeight="3200.745959378295" />
+  <Graphics BoardWidth="4428.0" BoardHeight="3200.745959378295" />
   <DataNode TextLabel="Mitochondrial Beta-Oxidation" GraphId="sa211" Type="Pathway">
     <Comment>A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).</Comment>
     <Graphics CenterX="1036.405063291139" CenterY="916.3670886075979" Width="230.0" Height="45.0" ZOrder="40" FillColor="cc99ff" FontSize="12" Valign="Middle" ShapeType="Hexagon" />
@@ -67,7 +67,7 @@
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa102" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2132.405063291139" CenterY="2659.402675796209" Width="110.0" Height="20.0" ZOrder="56" FontSize="12" Valign="Middle" Color="0000ff" />
+    <Graphics CenterX="2086.405063291139" CenterY="2659.402675796209" Width="110.0" Height="20.0" ZOrder="56" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17002" />
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa109" Type="Metabolite">
@@ -77,12 +77,12 @@
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa110" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="3502.405063291139" CenterY="2659.402675796209" Width="133.0" Height="26.0" ZOrder="58" FillColor="ccff66" FontSize="12" Valign="Middle" ShapeType="Oval" />
+    <Graphics CenterX="3464.405063291139" CenterY="2671.402675796209" Width="110.0" Height="20.0" ZOrder="58" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17002" />
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa111" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2693.405063291139" CenterY="2699.402675796209" Width="110.0" Height="20.0" ZOrder="59" FontSize="12" Valign="Middle" Color="0000ff" />
+    <Graphics CenterX="2665.405063291139" CenterY="2699.402675796209" Width="110.0" Height="20.0" ZOrder="59" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17002" />
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa173" Type="Metabolite">
@@ -122,12 +122,12 @@
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa84" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2722.405063291139" CenterY="1989.402675796209" Width="110.0" Height="20.0" ZOrder="68" FontSize="12" Valign="Middle" Color="0000ff" />
+    <Graphics CenterX="2440.405063291139" CenterY="1989.402675796209" Width="110.0" Height="20.0" ZOrder="68" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17002" />
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa93" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="1652.4050632911394" CenterY="2719.402675796209" Width="110.0" Height="20.0" ZOrder="69" FontSize="12" Valign="Middle" Color="0000ff" />
+    <Graphics CenterX="1634.4050632911394" CenterY="2673.402675796209" Width="110.0" Height="20.0" ZOrder="69" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17002" />
   </DataNode>
   <DataNode TextLabel="APOB" GraphId="sa100" Type="Protein">
@@ -142,22 +142,22 @@
   </DataNode>
   <DataNode TextLabel="APOE" GraphId="sa104" Type="Protein">
     <Comment></Comment>
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     <Xref Database="Ensembl" ID="ENSG00000130203" />
   </DataNode>
   <DataNode TextLabel="APOC1" GraphId="sa106" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1992.405063291139" CenterY="2709.402675796209" Width="60.0" Height="20.0" ZOrder="73" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="2023.405063291139" CenterY="2718.402675796209" Width="60.0" Height="20.0" ZOrder="73" FontSize="12" Valign="Middle" />
     <Xref Database="RefSeq" ID="NM_001321065" />
   </DataNode>
   <DataNode TextLabel="APOE" GraphId="sa107" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="2552.405063291139" CenterY="2711.7360091295423" Width="60.0" Height="20.0" ZOrder="74" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="2552.405063291139" CenterY="2681.7360091295423" Width="60.0" Height="20.0" ZOrder="74" FontSize="12" Valign="Middle" />
     <Xref Database="Ensembl" ID="ENSG00000130203" />
   </DataNode>
   <DataNode TextLabel="APOE" GraphId="sa113" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1992.405063291139" CenterY="2759.402675796209" Width="60.0" Height="20.0" ZOrder="75" FillColor="ccffcc" FontSize="12" Valign="Middle" />
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     <Xref Database="Ensembl" ID="ENSG00000130203" />
   </DataNode>
   <DataNode TextLabel="APOA1" GraphId="sa170" Type="Protein">
@@ -251,7 +251,7 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="APOB" GraphId="sa255" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1337.3723121994362" CenterY="3039.5991823464215" Width="60.0" Height="20.0" ZOrder="117" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="1337.3723121994362" CenterY="3039.5991823464215" Width="60.0" Height="20.0" ZOrder="117" FontSize="12" Valign="Middle" />
     <Xref Database="Entrez Gene" ID="338" />
   </DataNode>
   <DataNode TextLabel="APOE" GraphId="sa256" Type="Protein">
@@ -261,12 +261,12 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="ABCA1" GraphId="sa70" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1342.4050632911394" CenterY="2309.402675796209" Width="80.0" Height="40.0" ZOrder="133" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="1342.4050632911394" CenterY="2309.402675796209" Width="60.0" Height="20.0" ZOrder="133" FontSize="12" Valign="Middle" />
     <Xref Database="RefSeq" ID="NM_005502" />
   </DataNode>
   <DataNode TextLabel="SORT1" GraphId="sa73" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1982.405063291139" CenterY="2299.402675796209" Width="80.0" Height="40.0" ZOrder="134" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="1982.405063291139" CenterY="2299.402675796209" Width="60.0" Height="20.0" ZOrder="134" FontSize="12" Valign="Middle" />
     <Xref Database="Entrez Gene" ID="6272" />
   </DataNode>
   <DataNode TextLabel="APOA1" GraphId="sa78" Type="Protein">
@@ -281,13 +281,13 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="APOA1" GraphId="sa80" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1122.4050632911394" CenterY="2489.402675796209" Width="80.0" Height="40.0" ZOrder="137" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="1122.4050632911394" CenterY="2489.402675796209" Width="60.0" Height="20.0" ZOrder="137" FontSize="12" Valign="Middle" />
     <Xref Database="HGNC Accession number" ID="600" />
   </DataNode>
   <DataNode TextLabel="MTTP" GraphId="sa82" Type="Protein">
     <Comment></Comment>
     <BiopaxRef>ann1</BiopaxRef>
-    <Graphics CenterX="2222.405063291139" CenterY="2299.402675796209" Width="60.0" Height="20.0" ZOrder="138" FontSize="12" Valign="Middle" />
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     <Xref Database="HGNC Accession number" ID="7467" />
   </DataNode>
   <DataNode TextLabel="APOA4" GraphId="sa86" Type="Protein">
@@ -307,27 +307,27 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="APOA1" GraphId="sa90" Type="Protein">
     <Comment></Comment>
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     <Xref Database="HGNC Accession number" ID="600" />
   </DataNode>
   <DataNode TextLabel="LPA" GraphId="sa91" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="3387.405063291139" CenterY="2639.402675796209" Width="80.0" Height="40.0" ZOrder="144" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="3435.405063291139" CenterY="2631.402675796209" Width="60.0" Height="20.0" ZOrder="144" FontSize="12" Valign="Middle" />
     <Xref Database="Ensembl" ID="ENSG00000198670" />
   </DataNode>
   <DataNode TextLabel="APOB" GraphId="sa92" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="3387.405063291139" CenterY="2689.402675796209" Width="80.0" Height="40.0" ZOrder="145" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="3495.405063291139" CenterY="2631.402675796209" Width="60.0" Height="20.0" ZOrder="145" FontSize="12" Valign="Middle" />
     <Xref Database="Entrez Gene" ID="338" />
   </DataNode>
   <DataNode TextLabel="APOC1" GraphId="sa94" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1532.4050632911394" CenterY="2729.402675796209" Width="60.0" Height="20.0" ZOrder="146" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="1544.4050632911394" CenterY="2663.069342462876" Width="60.0" Height="20.0" ZOrder="146" FontSize="12" Valign="Middle" />
     <Xref Database="RefSeq" ID="NM_001321065" />
   </DataNode>
   <DataNode TextLabel="APOA2" GraphId="sa95" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1532.4050632911394" CenterY="2680.2360091295427" Width="60.0" Height="20.0" ZOrder="147" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="1544.4050632911394" CenterY="2643.069342462876" Width="60.0" Height="20.0" ZOrder="147" FontSize="12" Valign="Middle" />
     <Xref Database="HGNC Accession number" ID="601" />
   </DataNode>
   <DataNode TextLabel="APOC2" GraphId="sa96" Type="Protein">
@@ -342,7 +342,7 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="APOB" GraphId="sa98" Type="Protein">
     <Comment></Comment>
-    <Graphics CenterX="1992.405063291139" CenterY="2659.402675796209" Width="60.0" Height="20.0" ZOrder="150" FillColor="ccffcc" FontSize="12" Valign="Middle" />
+    <Graphics CenterX="2023.405063291139" CenterY="2698.402675796209" Width="60.0" Height="20.0" ZOrder="150" FontSize="12" Valign="Middle" />
     <Xref Database="Entrez Gene" ID="338" />
   </DataNode>
   <DataNode TextLabel="APOB" GraphId="sa99" Type="Protein">
@@ -352,12 +352,12 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="Triacylglycerol" GraphId="sa105" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2202.405063291139" CenterY="2699.402675796209" Width="100.0" Height="20.0" ZOrder="153" FontSize="12" Valign="Middle" Color="0000ff" />
+    <Graphics CenterX="2146.405063291139" CenterY="2699.402675796209" Width="100.0" Height="20.0" ZOrder="153" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17855" />
   </DataNode>
   <DataNode TextLabel="Triacylglycerol" GraphId="sa108" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2683.405063291139" CenterY="2661.7360091295423" Width="100.0" Height="20.0" ZOrder="154" FontSize="12" Valign="Middle" Color="0000ff" />
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     <Xref Database="ChEBI" ID="CHEBI:17855" />
   </DataNode>
   <DataNode TextLabel="Triacylglycerol" GraphId="sa179" Type="Metabolite">
@@ -377,12 +377,12 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="Triacylglycerol" GraphId="sa81" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2552.405063291139" CenterY="1979.402675796209" Width="90.0" Height="20.0" ZOrder="158" FontSize="12" Valign="Middle" Color="0000ff" />
+    <Graphics CenterX="2270.405063291139" CenterY="1979.402675796209" Width="90.0" Height="20.0" ZOrder="158" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17855" />
   </DataNode>
   <DataNode TextLabel="Triacylglycerol" GraphId="sa85" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="832.405063291139" CenterY="2749.402675796209" Width="100.0" Height="26.0" ZOrder="159" FillColor="ccff66" FontSize="12" Valign="Middle" ShapeType="Oval" />
+    <Graphics CenterX="832.405063291139" CenterY="2749.402675796209" Width="100.0" Height="26.0" ZOrder="159" FontSize="12" Valign="Middle" Color="0000ff" />
     <Xref Database="ChEBI" ID="CHEBI:17855" />
   </DataNode>
   <DataNode TextLabel="Secretion" GraphId="sa114" Type="Pathway">
@@ -452,7 +452,7 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="Phospholipids" GraphId="sa112" Type="Metabolite">
     <Comment></Comment>
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     <Xref Database="ChEBI" ID="CHEBI:16247" />
   </DataNode>
   <DataNode TextLabel="Phospholipid" GraphId="sa172" Type="Metabolite">
@@ -462,17 +462,17 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="Phospholipids" GraphId="sa77" Type="Metabolite">
     <Comment></Comment>
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     <Xref Database="ChEBI" ID="CHEBI:16247" />
   </DataNode>
   <DataNode TextLabel="Phospholipids" GraphId="sa83" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="2632.405063291139" CenterY="1929.402675796209" Width="85.0" Height="20.0" ZOrder="176" FontSize="12" Valign="Middle" Color="0000ff" />
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     <Xref Database="ChEBI" ID="CHEBI:16247" />
   </DataNode>
   <DataNode TextLabel="Phospholipids" GraphId="sa88" Type="Metabolite">
     <Comment></Comment>
-    <Graphics CenterX="1652.4050632911394" CenterY="2679.402675796209" Width="86.0" Height="20.0" ZOrder="177" FontSize="12" Valign="Middle" Color="0000ff" />
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     <Xref Database="ChEBI" ID="CHEBI:16247" />
   </DataNode>
   <DataNode TextLabel="Cholesterol ester" GraphId="sa212" Type="Metabolite">
@@ -497,17 +497,17 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
   </DataNode>
   <DataNode TextLabel="Cholesterol" GraphId="sa69" Type="Metabolite">
     <Comment></Comment>
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     <Xref Database="ChEBI" ID="CHEBI:16113" />
   </DataNode>
   <DataNode TextLabel="Cholesterol" GraphId="sa76" Type="Metabolite">
     <Comment></Comment>
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     <Xref Database="ChEBI" ID="CHEBI:16113" />
   </DataNode>
   <DataNode TextLabel="CoA" GraphId="sa202" Type="Metabolite">
     <Comment></Comment>
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   <DataNode TextLabel="LDLRAP1" GraphId="sa185" Type="Protein" GroupRef="csa45">
@@ -575,41 +575,36 @@ https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2690</Comment>
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   </DataNode>
-  <DataNode TextLabel="Long-chain fatty acid" GraphId="sa201" Type="Metabolite" GroupRef="f6ae3">
+  <DataNode TextLabel="Long-chain fatty acid" GraphId="sa201" Type="Metabolite" GroupRef="c3753">
     <Comment></Comment>
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     <Xref Database="ChEBI" ID="CHEBI:15904" />
   </DataNode>
-  <DataNode TextLabel="SLC27A2" GraphId="e513e" Type="Protein" GroupRef="f2b0e">
+  <DataNode TextLabel="SLC27A2" GraphId="e513e" Type="Protein" GroupRef="c3753">
     <Comment></Comment>
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   </DataNode>
-  <DataNode TextLabel="SLC27A4" GraphId="f64e0" Type="Protein" GroupRef="f2b0e">
+  <DataNode TextLabel="SLC27A4" GraphId="f64e0" Type="Protein" GroupRef="c3753">
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+      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">classic 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:0000002</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">hepatocyte</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">CL:0000182</bp:ID>