Process GPML changes

wikipathways · Sep 21, 2024 · 3dfb592 · 3dfb592
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diff --git a/pathways/WP178/WP178.gpml b/pathways/WP178/WP178.gpml
diff --git a/pathways/WP23/WP23.gpml b/pathways/WP23/WP23.gpml
diff --git a/pathways/WP266/WP266.gpml b/pathways/WP266/WP266.gpml
diff --git a/pathways/WP432/WP432.gpml b/pathways/WP432/WP432.gpml
@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Asparagine degradation" Data-Source="WikiPathways" Version="WP432_r135491" Author="[J.Heckman, MaintBot, Mkutmon, Christine Chichester, Khanspers]" Last-Modified="20240920005423" Organism="Saccharomyces cerevisiae">
- <Comment Source="WikiPathways-description">ter Schure, E.G. et al suggest that in yeast, degradation of nitrogen sources yields either ammonia or glutamate. 
+<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">
+ <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>
  <BiopaxRef>djh</BiopaxRef>
  <BiopaxRef>f5d</BiopaxRef>

diff --git a/pathways/WP503/WP503.gpml b/pathways/WP503/WP503.gpml
@@ -1,7 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Glutamate degradation III" Data-Source="WikiPathways" Version="WP503_r134374" Author="[J.Heckman, MaintBot, Christine Chichester, Egonw, Maxvanson, Khanspers, Eweitz]" Last-Modified="20240721153146" Organism="Saccharomyces cerevisiae">
- <Comment Source="WikiPathways-description">Based on BioCyc.</Comment>
- <BiopaxRef>a90</BiopaxRef>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Glutamate degradation IX" Data-Source="WikiPathways" Version="WP503_r135505" Author="[J.Heckman, MaintBot, Christine Chichester, Egonw, Maxvanson, Khanspers, Eweitz]" Last-Modified="20240920172700" Organism="Saccharomyces cerevisiae">
+ <Comment Source="WikiPathways-description">In S. cerevisiae cells, the amino group of glutamate and the amide group of glutamine are the source of nitrogen for all other macromolecules. In order to provide ammonia for the synthesis of glutamine during growth on glutamate-yielding nitrogen sources, cells degrade glutamate into ammonia. The main pathway for S. cerevisiae glutamate degradation is catalyzed by the NAD dependent glutamate dehydrogenase (GDH2). 
+
+Description adapted from on https://pathway.yeastgenome.org/.</Comment>
+ <BiopaxRef>d60</BiopaxRef>
  <Graphics BoardWidth="385.7333333333333" BoardHeight="252.5" />
  <DataNode TextLabel="2-Oxoglutarate" GraphId="ff34b" Type="Metabolite">
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@@ -72,17 +74,22 @@
  <InfoBox CenterX="0.0" CenterY="0.0" />
  <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">glutamate degradation pathway III</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:0001382</bp:ID>
+ <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="a90">
- <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">glutamate degradation to 2-oxoglutarate</bp:TITLE>
- <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://biocyc.org/pathway?orgid=YEAST&amp;id=GLUTAMATE-DEG1-PWY</bp:SOURCE>
+ <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="d60">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&amp;object=PWY-3322</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">glutamate degradation IX</bp:TITLE>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yeast Pathways</bp:SOURCE>
  <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:YEAR>
  </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">glutamate degradation pathway IX</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:0001389</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>
  </Biopax>
 </Pathway>
 
diff --git a/pathways/WP5489/WP5489.gpml b/pathways/WP5489/WP5489.gpml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Regulation of cytotoxic T cell responses by Malat1 - miR-15/16 circuit " Data-Source="WikiPathways" Version="WP5489_r135486" Author="[Khanspers, Eweitz]" Last-Modified="20240919235504" Organism="Homo sapiens">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Regulation of cytotoxic T cell responses by Malat1 - miR-15/16 circuit " Data-Source="WikiPathways" Version="WP5489_r135496" Author="[Khanspers, Eweitz]" Last-Modified="20240920161253" Organism="Homo sapiens">
  <Comment Source="WikiPathways-description">Regulation of activation and differentiation of cytotoxic T cells by long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16.
 
 This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10735224/ Wheeler et al).</Comment>
@@ -50,11 +50,11 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  <Xref Database="HGNC" ID="CD3D" />
  </DataNode>
  <DataNode TextLabel="CD27" GraphId="e0b2c" Type="GeneProduct">
- <Graphics CenterX="42.0" CenterY="287.0" Width="60.0" Height="20.0" ZOrder="32790" FontSize="12" Valign="Middle" />
+ <Graphics CenterX="39.0" CenterY="270.0" Width="60.0" Height="20.0" ZOrder="32790" FontSize="12" Valign="Middle" />
  <Xref Database="HGNC" ID="CD27" />
  </DataNode>
  <DataNode TextLabel="CD43" GraphId="aaece" Type="GeneProduct">
- <Graphics CenterX="42.0" CenterY="267.0" Width="60.0" Height="20.0" ZOrder="32792" FontSize="12" Valign="Middle" />
+ <Graphics CenterX="39.0" CenterY="250.0" Width="60.0" Height="20.0" ZOrder="32792" FontSize="12" Valign="Middle" />
  <Xref Database="HGNC" ID="SPN" />
  </DataNode>
  <DataNode TextLabel="MIR15B" GraphId="e2e51" Type="Rna" GroupRef="cf5fd">
@@ -90,9 +90,9 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  <Xref Database="" ID="" />
  </Interaction>
  <Interaction GraphId="id6883b40b">
- <Graphics ZOrder="12290" LineThickness="1.0">
- <Point X="321.0" Y="317.0" GraphRef="dbddc" RelX="0.0" RelY="1.0" />
- <Point X="168.0" Y="277.0" GraphRef="bc3d7" RelX="0.0" RelY="1.0" ArrowHead="Arrow" />
+ <Graphics ConnectorType="Elbow" ZOrder="12290" LineThickness="1.0">
+ <Point X="291.0" Y="307.0" GraphRef="dbddc" RelX="-1.0" RelY="0.0" />
+ <Point X="119.0" Y="276.0" GraphRef="bc3d7" RelX="0.0" RelY="1.0" ArrowHead="Arrow" />
  </Graphics>
  <Xref Database="" ID="" />
  </Interaction>
@@ -105,7 +105,7 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  </Interaction>
  <Interaction GraphId="ideb0d774c">
  <Graphics ZOrder="12294" LineThickness="1.0">
- <Point X="340.0" Y="202.0" GraphRef="d0fa5" RelX="0.0" RelY="1.0" />
+ <Point X="359.0" Y="202.0" GraphRef="d0fa5" RelX="0.5" RelY="1.0" />
  <Point X="500.0" Y="254.0" GraphRef="a76e9" RelX="-1.0" RelY="0.0" ArrowHead="mim-inhibition" />
  </Graphics>
  <Xref Database="" ID="" />
@@ -142,7 +142,7 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  <Interaction GraphId="b944f">
  <Graphics ZOrder="32802" LineThickness="1.0">
  <Point X="500.0" Y="259.0" GraphRef="a76e9" RelX="-1.0" RelY="0.5" />
- <Point X="225.0" Y="259.75" GraphRef="bc3d7" RelX="1.0" RelY="0.0" ArrowHead="Arrow" />
+ <Point X="176.0" Y="258.75" GraphRef="bc3d7" RelX="1.0" RelY="0.0" ArrowHead="Arrow" />
  </Graphics>
  <Xref Database="" ID="" />
  </Interaction>
@@ -157,7 +157,7 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  <Graphics CenterX="762.5" CenterY="156.0" Width="60.0" Height="20.0" ZOrder="28672" FillColor="ffffff" FontSize="12" Valign="Middle" ShapeType="Rectangle" />
  </Label>
  <Label TextLabel="Memory Cell &#xA;Persistance" GraphId="bc3d7">
- <Graphics CenterX="168.0" CenterY="259.75" Width="114.0" Height="34.5" ZOrder="28674" FillColor="ffffff" FontWeight="Bold" FontSize="12" Valign="Middle" />
+ <Graphics CenterX="119.0" CenterY="258.75" Width="114.0" Height="34.5" ZOrder="28674" FillColor="ffffff" FontWeight="Bold" FontSize="12" Valign="Middle" />
  </Label>
  <Shape TextLabel="Cytotoxic T cell" GraphId="c523a">
  <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
@@ -191,6 +191,17 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL:0000813</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">Cell Type</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="d89">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9199340</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">CD28 mediates transcriptional upregulation of the interleukin-2 (IL-2) promoter through a composite element containing the CD28RE and NF-IL-2B AP-1 sites.</bp:TITLE>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol</bp:SOURCE>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1997</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shapiro VS</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Truitt KE</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Imboden JB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiss A</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">adaptive immune response 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:0000235</bp:ID>
@@ -214,17 +225,6 @@ This pathway model is developed based on Figure 8 in (https://www.ncbi.nlm.nih.g
  <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Marson A</bp:AUTHORS>
  <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ansel KM</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="d89">
- <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9199340</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">CD28 mediates transcriptional upregulation of the interleukin-2 (IL-2) promoter through a composite element containing the CD28RE and NF-IL-2B AP-1 sites.</bp:TITLE>
- <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol</bp:SOURCE>
- <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1997</bp:YEAR>
- <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shapiro VS</bp:AUTHORS>
- <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Truitt KE</bp:AUTHORS>
- <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Imboden JB</bp:AUTHORS>
- <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiss A</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">cytotoxic T cell</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:0000910</bp:ID>