Process GPML changes

wikipathways · Dec 3, 2024 · 68298e8 · 68298e8
1 parent 1aae38e
commit 68298e8
Show file tree

Hide file tree

Showing 9 changed files with 880 additions and 849 deletions.
diff --git a/pathways/WP121/WP121.gpml b/pathways/WP121/WP121.gpml
diff --git a/pathways/WP132/WP132.gpml b/pathways/WP132/WP132.gpml
diff --git a/pathways/WP256/WP256.gpml b/pathways/WP256/WP256.gpml
diff --git a/pathways/WP275/WP275.gpml b/pathways/WP275/WP275.gpml
diff --git a/pathways/WP432/WP432.gpml b/pathways/WP432/WP432.gpml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Asparagine degradation" Data-Source="WikiPathways" Version="WP432_r135498" Author="[J.Heckman, MaintBot, Mkutmon, Christine Chichester, Khanspers]" Last-Modified="20240920161537" Organism="Saccharomyces cerevisiae">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Asparagine degradation" Data-Source="WikiPathways" Version="WP432_r135938" Author="[J.Heckman, MaintBot, Mkutmon, Christine Chichester, Khanspers]" Last-Modified="20241203021324" Organism="Saccharomyces cerevisiae">
   <Comment Source="WikiPathways-description">Like many other amino acids, asparagine may be utilized by S. cerevisiae as a sole source of nitrogen. Catabolism of asparagine for nitrogen involves the action of asparaginases, which hydrolyze the amide group in the side chain of asparagine. This converts asparagine to aspartate and releases an assimilable molecule of ammonia (NH3). Further nitrogen can be derived from the newly generated aspartate molecule via its reversible conversion to glutamate by aspartate aminotransferases. Glutamate, whose amino group can be hydrolyzed to release ammonia, represents one of the major sources of nitrogen for biosynthetic reactions in S. cerevisiae.
 
 SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
@@ -86,7 +86,7 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
   <Interaction GraphId="id67eb511">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="174.0" Y="184.75" GraphRef="f5f" RelX="1.0" RelY="0.0" />
-      <Point X="409.75" Y="184.75" GraphRef="c4e23" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="409.75" Y="184.75" GraphRef="c4e23" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.4" Shape="None" GraphId="fe7bb" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -101,7 +101,7 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
   <Interaction GraphId="idb6e0f93b">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="499.75" Y="184.75" GraphRef="c4e23" RelX="1.0" RelY="0.0" />
-      <Point X="727.6666666666667" Y="184.75" GraphRef="dd8" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="727.6666666666667" Y="184.75" GraphRef="dd8" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.4" Shape="None" GraphId="f4a6d" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -131,6 +131,16 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
   <Group GroupId="a6e9e" GraphId="fcacb" Style="Group" />
   <InfoBox CenterX="601.6666666666666" CenterY="221.66666666666666" />
   <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="djh">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10640599</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">The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FEMS Microbiol Rev</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2000</bp:YEAR>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ter Schure EG</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">van Riel NA</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Verrips 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="f5d">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&amp;object=ASPARAGINE-DEG2-PWY</bp:ID>
       <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">URL</bp:DB>
@@ -143,16 +153,6 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
       <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0001083</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="djh">
-      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10640599</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">The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae.</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FEMS Microbiol Rev</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2000</bp:YEAR>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ter Schure EG</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">van Riel NA</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Verrips CT</bp:AUTHORS>
-    </bp:PublicationXref>
   </Biopax>
 </Pathway>
 
diff --git a/pathways/WP479/WP479.gpml b/pathways/WP479/WP479.gpml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Chorismate biosynthesis" Data-Source="WikiPathways" Version="WP479_r135465" Author="[J.Heckman, MaintBot, Ddigles, Egonw, DeSl, Khanspers, Eweitz]" Last-Modified="20240910202154" Organism="Saccharomyces cerevisiae">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Chorismate biosynthesis" Data-Source="WikiPathways" Version="WP479_r135940" Author="[J.Heckman, MaintBot, Ddigles, Egonw, DeSl, Khanspers, Eweitz]" Last-Modified="20241203022106" Organism="Saccharomyces cerevisiae">
   <Comment Source="WikiPathways-description">Chorismate, an intermediate in the synthesis of the aromatic amino acids and the vitamins, p-aminobenzoate and p-hydroxybenzoate, is synthesized by the shikimate pathway. The shikimate pathway has been found to be common to all eukaryotes and prokaryotes studied thus far (as reported in.  In Saccharomyces cerevisiae the initial step is catalyzed by two deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase isoenzymes, one of which (ARO3) is feedback inhibited by phenylalanine, and the other (ARO4) by tyrosine.  Both DAHP isoenzymes are derepressed by amino acid starvation (general control of amino acid biosynthesis). The 5 subsequent reactions are catalyzed by the pentafunctional arom enzyme, Aro1p.  Aro1p is a mosaic of five monofunctional domains, each of which corresponds to one of five separate monofunctional E. coli enzymes.  The last step of chorismate biosynthesis, before the pathway branches to synthesize different terminal products, is catalyzed by Aro2p. 
 
 Description from YeastPathways.</Comment>
@@ -94,7 +94,7 @@ Description from YeastPathways.</Comment>
   </DataNode>
   <DataNode TextLabel="ARO1" GraphId="fb6" Type="GeneProduct">
     <Attribute Key="org.pathvisio.model.BackpageHead" Value="ARO1" />
-    <Graphics CenterX="466.66666666666663" CenterY="198.0" Width="40.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
+    <Graphics CenterX="465.66666666666663" CenterY="197.0" Width="40.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
     <Xref Database="SGD" ID="S000002534" />
   </DataNode>
   <DataNode TextLabel="ARO1" GraphId="fe4" Type="GeneProduct">
@@ -111,15 +111,15 @@ Description from YeastPathways.</Comment>
   </DataNode>
   <Interaction GraphId="id1037a0e9">
     <Graphics ZOrder="12288" LineThickness="1.0">
-      <Point X="486.66666666666663" Y="198.0" GraphRef="fb6" RelX="1.0" RelY="0.0" />
+      <Point X="485.66666666666663" Y="197.0" GraphRef="fb6" RelX="1.0" RelY="0.0" />
       <Point X="565.3333333333333" Y="197.03637713437269" GraphRef="fc864" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis" />
     </Graphics>
     <Xref Database="" ID="" />
   </Interaction>
   <Interaction GraphId="id1084bf5c">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="565.3333333333334" Y="110.83333333333331" GraphRef="faa" RelX="0.0" RelY="1.0" />
-      <Point X="565.3333333333333" Y="257.1666666666667" GraphRef="a23" RelX="0.0" RelY="-1.0" ArrowHead="Arrow" />
+      <Point X="565.3333333333333" Y="257.1666666666667" GraphRef="a23" RelX="0.0" RelY="-1.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.5890868596881961" Shape="None" GraphId="fc864" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -154,9 +154,9 @@ Description from YeastPathways.</Comment>
   </Interaction>
   <Interaction GraphId="id2fc7b6a8">
     <Graphics ConnectorType="Elbow" ZOrder="12288" LineThickness="1.0">
-      <Point X="446.66666666666663" Y="198.0" GraphRef="fb6" RelX="-1.0" RelY="0.0" />
-      <Point X="426.66666666666663" Y="198.0" />
-      <Point X="318.66666666666663" Y="198.0" />
+      <Point X="445.66666666666663" Y="197.0" GraphRef="fb6" RelX="-1.0" RelY="0.0" />
+      <Point X="426.66666666666663" Y="197.5" />
+      <Point X="323.5" Y="198.0" />
       <Point X="220.33333333333334" Y="267.08683473389357" GraphRef="c9ece" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -178,15 +178,15 @@ Description from YeastPathways.</Comment>
   <Interaction GraphId="id5a83e55">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="179.66666666666669" Y="101.33333333333331" GraphRef="b0d" RelX="1.0" RelY="0.0" />
-      <Point X="415.33333333333337" Y="101.33333333333331" GraphRef="faa" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="415.33333333333337" Y="101.33333333333331" GraphRef="faa" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.4" Shape="None" GraphId="e8313" />
     </Graphics>
     <Xref Database="" ID="" />
   </Interaction>
   <Interaction GraphId="id62b1ba9a">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="495.16666666666663" Y="266.6666666666667" GraphRef="a23" RelX="-1.0" RelY="0.0" />
-      <Point X="423.3333333333333" Y="266.6666666666667" GraphRef="cb5" RelX="1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="423.3333333333333" Y="266.6666666666667" GraphRef="cb5" RelX="1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.4" Shape="None" GraphId="a4171" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -200,7 +200,7 @@ Description from YeastPathways.</Comment>
   </Interaction>
   <Interaction GraphId="id74f88a41">
     <Graphics ZOrder="12288" LineThickness="1.0">
-      <Point X="466.66666666666663" Y="208.0" GraphRef="fb6" RelX="0.0" RelY="1.0" />
+      <Point X="465.66666666666663" Y="207.0" GraphRef="fb6" RelX="0.0" RelY="1.0" />
       <Point X="466.4333333333333" Y="266.6666666666667" GraphRef="a4171" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -229,31 +229,31 @@ Description from YeastPathways.</Comment>
   <Interaction GraphId="id990e6693">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="283.3333333333333" Y="266.6666666666667" GraphRef="cb5" RelX="-1.0" RelY="0.0" />
-      <Point X="125.83333333333336" Y="267.7170868347339" GraphRef="d76" RelX="1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="125.83333333333336" Y="267.7170868347339" GraphRef="d76" RelX="1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.4" Shape="None" GraphId="c9ece" />
     </Graphics>
     <Xref Database="" ID="" />
   </Interaction>
   <Interaction GraphId="idaa3d7ddc">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="86.66666666666669" Y="277.2170868347339" GraphRef="d76" RelX="0.0" RelY="1.0" />
-      <Point X="86.66666666666669" Y="454.8837535014005" GraphRef="b86" RelX="0.0" RelY="-1.0" ArrowHead="Arrow" />
+      <Point X="86.66666666666669" Y="454.8837535014005" GraphRef="b86" RelX="0.0" RelY="-1.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.5562851782363978" Shape="None" GraphId="a7c9e" />
     </Graphics>
     <Xref Database="" ID="" />
   </Interaction>
   <Interaction GraphId="idb1300b84">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="544.0" Y="464.3837535014005" GraphRef="ed5" RelX="1.0" RelY="0.0" />
-      <Point X="690.5" Y="464.3837535014005" GraphRef="bbb" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="690.5" Y="464.3837535014005" GraphRef="bbb" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.4" Shape="None" GraphId="fb39c" />
     </Graphics>
     <Xref Database="" ID="" />
   </Interaction>
   <Interaction GraphId="idbd38b42e">
     <Graphics ZOrder="12288" LineThickness="1.0">
       <Point X="161.66666666666669" Y="464.3837535014005" GraphRef="b86" RelX="1.0" RelY="0.0" />
-      <Point X="314.0" Y="464.3837535014005" GraphRef="ed5" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
+      <Point X="314.0" Y="464.3837535014005" GraphRef="ed5" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" />
       <Anchor Position="0.5076765970028364" Shape="None" GraphId="d2096" />
     </Graphics>
     <Xref Database="" ID="" />
@@ -297,14 +297,6 @@ Description from YeastPathways.</Comment>
   <Group GroupId="b00ba" GraphId="b6a3e" Style="Group" />
   <InfoBox CenterX="648.3333333333334" CenterY="8.333333333333334" />
   <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="ium">
-      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1943992</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">Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway.</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Microbiol Rev</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1991</bp:YEAR>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Braus GH</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="d6e">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&amp;object=ARO-PWY-1</bp:ID>
       <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">URL</bp:DB>
@@ -322,6 +314,14 @@ Description from YeastPathways.</Comment>
       <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: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="ium">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1943992</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">Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Microbiol Rev</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1991</bp:YEAR>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Braus GH</bp:AUTHORS>
+    </bp:PublicationXref>
   </Biopax>
 </Pathway>