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wikipathways · Oct 24, 2023 · ce194f2 · ce194f2
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diff --git a/pathways/WP4255/WP4255.gpml b/pathways/WP4255/WP4255.gpml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Non-small cell lung cancer" Data-Source="WikiPathways" Version="WP4255_r127490" Author="[Khanspers, AlexanderPico, Egonw, Fehrhart, Finterly]" Last-Modified="20231011171327" Organism="Homo sapiens">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Non-small cell lung cancer" Data-Source="WikiPathways" Version="WP4255_r127573" Author="[Khanspers, AlexanderPico, Egonw, Fehrhart, Finterly]" Last-Modified="20231023172551" Organism="Homo sapiens">
   <Comment Source="WikiPathways-description">Non-small cell lung cancer (NSCLC) represents 85% of lung cancer and is defined as any type of epithelial lung cancer that is NOT small cell carcinoma, including squamous cell (SCC), adeno (AC) and large-cell carcinoma. 
 Mutations in NSCLC:
 
@@ -8,7 +8,9 @@ Mutations in NSCLC:
 * The abnormal fusion of EML4-ALK (~5% of NSCLC patients) leads to constitutive ALK activation, which causes cell proliferation, invasion, and inhibition of apoptosis. 
 * Inactivating mutation of p53 (~50% of NSCLC patients) leads to reduced apoptosis and proliferation. 
 * The protein encoded by the p16INK4a, CDKN2A, inhibits formation of CDK-cyclin-D complexes by competitive binding of CDK4 and CDK6. p16INK4a is mutated in ~12% of NSCLC patients, which leads to a loss of this inhibitory effect.
-* RARB is a nuclear retinoic acid receptor whose function is often lost in NSCLC, leading to a loss of cell growth control. Phosphorylation sites were added based on information from PhosphoSitePlus (R), www.phosphosite.org.</Comment>
+* RARB is a nuclear retinoic acid receptor whose function is often lost in NSCLC, leading to a loss of cell growth control. 
+
+This pathway was developed based on https://www.kegg.jp/dbget-bin/www_bget?pathway+map05223. Phosphorylation sites were added based on information from PhosphoSitePlus (R), www.phosphosite.org.</Comment>
   <BiopaxRef>f51</BiopaxRef>
   <BiopaxRef>ea7</BiopaxRef>
   <BiopaxRef>e17</BiopaxRef>
@@ -1056,17 +1058,7 @@ Mutations in NSCLC:
   <Group GroupId="d46b2" GraphId="facf9" Style="Group" />
   <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">lung cancer</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">DOID:1324</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">Disease</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">disease 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:0000013</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="d76">
+    <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="d67">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">17328863</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">Induction of apoptosis by tumor suppressor FHIT via death receptor signaling pathway in human lung cancer cells.</bp:TITLE>
@@ -1083,24 +1075,20 @@ Mutations in NSCLC:
       <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000703</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">cancer 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:0000605</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">bronchial epithelial 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:0002328</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="ea7">
-      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">28572459</bp:ID>
+    <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="e17">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">25514926</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">AACR Project GENIE: Powering Precision Medicine through an International Consortium.</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Discov</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2017</bp:YEAR>
+      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nucleic Acids Res</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2015</bp:YEAR>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hornbeck PV</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang B</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Murray B</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kornhauser JM</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Latham V</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Skrzypek 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="d67">
+    <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="d76">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">17328863</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">Induction of apoptosis by tumor suppressor FHIT via death receptor signaling pathway in human lung cancer cells.</bp:TITLE>
@@ -1112,6 +1100,28 @@ Mutations in NSCLC:
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Roth JA</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ji L</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="ea7">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">28572459</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">AACR Project GENIE: Powering Precision Medicine through an International Consortium.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Discov</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2017</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="b72">
+      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">23322901</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">Molecular pathways: current role and future directions of the retinoic acid pathway in cancer prevention and treatment.</bp:TITLE>
+      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Clin Cancer Res</bp:SOURCE>
+      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2013</bp:YEAR>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Connolly RM</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nguyen NK</bp:AUTHORS>
+      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sukumar S</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">disease 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:0000013</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="ff3">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">20418096</bp:ID>
       <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
@@ -1130,29 +1140,21 @@ Mutations in NSCLC:
       <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://www.kegg.jp/dbget-bin/www_bget?pathway+map05223</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="e17">
-      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">25514926</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">PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nucleic Acids Res</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2015</bp:YEAR>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hornbeck PV</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang B</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Murray B</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kornhauser JM</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Latham V</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Skrzypek 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="b72">
-      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">23322901</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">Molecular pathways: current role and future directions of the retinoic acid pathway in cancer prevention and treatment.</bp:TITLE>
-      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Clin Cancer Res</bp:SOURCE>
-      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2013</bp:YEAR>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Connolly RM</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nguyen NK</bp:AUTHORS>
-      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sukumar S</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">lung cancer</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">DOID:1324</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">Disease</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">cancer 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:0000605</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">bronchial epithelial 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:0002328</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>
   </Biopax>
 </Pathway>