Process GPML changes

wikipathways · Aug 8, 2024 · 784e20b · 784e20b
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diff --git a/pathways/WP124/WP124.gpml b/pathways/WP124/WP124.gpml
diff --git a/pathways/WP2525/WP2525.gpml b/pathways/WP2525/WP2525.gpml
diff --git a/pathways/WP5055/WP5055.gpml b/pathways/WP5055/WP5055.gpml
diff --git a/pathways/WP5083/WP5083.gpml b/pathways/WP5083/WP5083.gpml
diff --git a/pathways/WP5094/WP5094.gpml b/pathways/WP5094/WP5094.gpml
diff --git a/pathways/WP5098/WP5098.gpml b/pathways/WP5098/WP5098.gpml
diff --git a/pathways/WP533/WP533.gpml b/pathways/WP533/WP533.gpml
@@ -1,9 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Lysine biosynthesis" Data-Source="WikiPathways" Version="WP533_r130617" Author="[M.Braymer, MaintBot, Ddigles, Egonw, Eweitz, Khanspers]" Last-Modified="20240529044202" Organism="Saccharomyces cerevisiae">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Lysine biosynthesis" Data-Source="WikiPathways" Version="WP533_r135187" Author="[M.Braymer, MaintBot, Ddigles, Egonw, Eweitz, Khanspers]" Last-Modified="20240807133705" Organism="Saccharomyces cerevisiae">
   <Comment Source="WikiPathways-description">S. cerevisiae synthesizes the essential amino acid L-lysine via the L-alpha-aminoadipic acid pathway instead of the diaminopmelate pathway (CITS: [10714900]).  Originally proposed to be characteristic of fungi, recent studies suggest prokaryotes also synthesize lysine via the alpha-aminoadipic acid pathway (CITS: [11029074]). Intermediates in this pathway are often incorporated into secondary metabolites.  For example, it has been well- studied that alpha-aminoadipate is required for penicillin production (CITS: [10714900]).    Regulation of the lysine biosynthetic pathway in S. cerevisiae is an interaction between general amino acid control (via Gcn4p) (CITS: [Hinnebusch]), feedback inhibition of homocitrate synthase activity by lysine (CITS: [10103047]), and induction of Lys14p by alpha-aminoadipate semialdehyde (CITS: [10975256]). 
 SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
   <BiopaxRef>nvb</BiopaxRef>
   <BiopaxRef>cfd</BiopaxRef>
+  <BiopaxRef>f0b</BiopaxRef>
+  <BiopaxRef>f64</BiopaxRef>
+  <BiopaxRef>d19</BiopaxRef>
   <Graphics BoardWidth="1084.9999999999911" BoardHeight="780.5168067226882" />
   <DataNode TextLabel="LYS12" GraphId="a04" Type="GeneProduct">
     <Attribute Key="org.pathvisio.model.BackpageHead" Value="LYS12" />
@@ -467,18 +470,6 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
   <Group GroupId="aaac2" GraphId="ea325" Style="Group" />
   <InfoBox CenterX="5.0" CenterY="578.3333333333334" />
   <Biopax>
-    <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">lysine biosynthetic 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:0000074</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="cfd">
-      <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">L-lysine biosynthesis IV</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://biocyc.org/pathway?orgid=META&amp;id=LYSINE-AMINOAD-PWY</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:YEAR>
-    </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="nvb">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10714900</bp:ID>
       <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
@@ -488,11 +479,54 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html</Comment>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zabriskie TM</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jackson MD</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="f64">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10103047</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">In Saccharomyces cerevisae, feedback inhibition of homocitrate synthase isoenzymes by lysine modulates the activation of LYS gene expression by Lys14p.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eur J Biochem</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1999</bp:YEAR>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Feller A</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ramos F</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Piérard A</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dubois E</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="d19">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10975256</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">Characterisation of a tripartite nuclear localisation sequence in the regulatory protein Lys14 of Saccharomyces cerevisiae.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Genet</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">El Alami M</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Feller A</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Piérard A</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dubois E</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">lysine biosynthetic 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:0000074</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">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: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="f0b">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11029074</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">What is characteristic of fungal lysine synthesis through the alpha-aminoadipate pathway?</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Mol Evol</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">Nishida H</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nishiyama M</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="cfd">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://biocyc.org/pathway?orgid=META&amp;id=LYSINE-AMINOAD-PWY</bp:ID>
+      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">URL</bp:DB>
+      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">L-lysine biosynthesis IV</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://biocyc.org/pathway?orgid=META&amp;id=LYSINE-AMINOAD-PWY</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:YEAR>
+    </bp:PublicationXref>
   </Biopax>
 </Pathway>