Update JSON, SVG, PNG, TSV and GPML files

pathways/WP1021/WP1021-bibliography.tsv

@@ -1,2 +1,2 @@
 ID	Database	Citation
-978-0-07-138914-3	ISBN	"Watkins JB, Klaassen CD. Casarett and Doull’s essentials of toxicology [Internet]. New York: McGraw-Hill Medical Pub. Division; 2003. 533 p. Available from: https://openlibrary.org/books/OL17085521M/Casarett_and_Doull’s_essentials_of_toxicology <a href=""https://openlibrary.org/search?isbn=978-0-07-138914-3"" target=""_blank"" class=""external"" rel=""nofollow"">OpenLibrary</a> <a href=""https://www.worldcat.org/search?qt=wikipathways&q=isbn%3A978-0-07-138914-3"" target=""_blank"" class=""external"" rel=""nofollow"">Worldcat</a>"
+978-0-07-138914-3	ISBN	"Casarett & Doull’s Essentials of Toxicology [Internet]. Klaassen C, Watkins JB III. McGraw-Hill Professional; 2003. 548 p. Available from: https://books.google.com/books/about/Casarett_Doull_s_Essentials_of_Toxicolog.html?hl=&id=pj5iQgAACAAJ <a href=""https://openlibrary.org/search?isbn=978-0-07-138914-3"" target=""_blank"" class=""external"" rel=""nofollow"">OpenLibrary</a> <a href=""https://www.worldcat.org/search?qt=wikipathways&q=isbn%3A978-0-07-138914-3"" target=""_blank"" class=""external"" rel=""nofollow"">Worldcat</a>"

pathways/WP1021/WP1021-datanodes.tsv

@@ -1,17 +1,17 @@
 Label	Type	Identifier	Comment	Ensembl	NCBI gene	HGNC	UniProt	Wikidata	ChEBI	InChI
-thio esters	Metabolite	chebi:51277						wikidata:Q422794	chebi:51277;chebi:51277	
-Phosphoric acid esters	Metabolite	chebi:37734						wikidata:Q411097	chebi:37734;chebi:37734	
-thio esters	Metabolite	chebi:51277						wikidata:Q422794	chebi:51277;chebi:51277	
-carboxylic acid esters	Metabolite	chebi:33308						wikidata:Q355518	chebi:33308;chebi:33308	
-amides	Metabolite	chebi:32988						wikidata:Q188777	chebi:32988;chebi:32988	
-carboxylic acid esters	Metabolite	chebi:33308						wikidata:Q355518	chebi:33308;chebi:33308	
-Phosphoric acid esters	Metabolite	chebi:37734						wikidata:Q411097	chebi:37734;chebi:37734	
-amides	Metabolite	chebi:32988						wikidata:Q188777	chebi:32988;chebi:32988	
-CES5A	GeneProduct	ensembl:ENSBTAG00000011164	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000159398	ensembl:ENSBTAG00000011164	ncbigene:513992		uniprot:E1BN79			
-ESD	GeneProduct	ensembl:ENSBTAG00000003415	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000139684	ensembl:ENSBTAG00000003415	ncbigene:535653		uniprot:A0A3Q1MAU7;uniprot:Q08E20			
-LIPA	GeneProduct	ensembl:ENSBTAG00000003636	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000107798	ensembl:ENSBTAG00000003636	ncbigene:100125267		uniprot:A0A3Q1M1X5;uniprot:A6H713			
-PON3	GeneProduct	ensembl:ENSBTAG00000034645	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000105852	ensembl:ENSBTAG00000034645	ncbigene:510953		uniprot:Q1JQD3			
-CES2	GeneProduct	ensembl:ENSBTAG00000005093	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000172831	ensembl:ENSBTAG00000005093	ncbigene:505928		uniprot:F1MU22			
-PON2	GeneProduct	ensembl:ENSBTAG00000008361	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000105854	ensembl:ENSBTAG00000008361	ncbigene:281417		uniprot:Q58DS7;uniprot:A0A3Q1M1W2			
-CES1	GeneProduct	ensembl:ENSBTAG00000011021	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000198848	ensembl:ENSBTAG00000011021	ncbigene:512098		uniprot:A0A3S5ZPA1;uniprot:A0A3Q1LYA7;uniprot:A0A3Q1MQJ1			
-PON1	GeneProduct	ensembl:ENSBTAG00000015654	Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000005421	ensembl:ENSBTAG00000015654	ncbigene:523798		uniprot:Q2KIW1			
+thio esters	Metabolite	chebi:51277	""					wikidata:Q422794	chebi:51277;chebi:51277	
+Phosphoric acid esters	Metabolite	chebi:37734	""					wikidata:Q411097	chebi:37734;chebi:37734	
+thio esters	Metabolite	chebi:51277	""					wikidata:Q422794	chebi:51277;chebi:51277	
+carboxylic acid esters	Metabolite	chebi:33308	""					wikidata:Q355518	chebi:33308;chebi:33308	
+amides	Metabolite	chebi:32988	""					wikidata:Q188777	chebi:32988;chebi:32988	
+carboxylic acid esters	Metabolite	chebi:33308	""					wikidata:Q355518	chebi:33308;chebi:33308	
+Phosphoric acid esters	Metabolite	chebi:37734	""					wikidata:Q411097	chebi:37734;chebi:37734	
+amides	Metabolite	chebi:32988	""					wikidata:Q188777	chebi:32988;chebi:32988	
+CES5A	GeneProduct	ensembl:ENSBTAG00000011164	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000159398"	ensembl:ENSBTAG00000011164	ncbigene:513992		uniprot:E1BN79			
+ESD	GeneProduct	ensembl:ENSBTAG00000003415	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000139684"	ensembl:ENSBTAG00000003415	ncbigene:535653		uniprot:A0A3Q1MAU7;uniprot:Q08E20			
+LIPA	GeneProduct	ensembl:ENSBTAG00000003636	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000107798"	ensembl:ENSBTAG00000003636	ncbigene:100125267		uniprot:A0A3Q1M1X5;uniprot:A6H713			
+PON3	GeneProduct	ensembl:ENSBTAG00000034645	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000105852"	ensembl:ENSBTAG00000034645	ncbigene:510953		uniprot:Q1JQD3			
+CES2	GeneProduct	ensembl:ENSBTAG00000005093	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000172831"	ensembl:ENSBTAG00000005093	ncbigene:505928		uniprot:F1MU22			
+PON2	GeneProduct	ensembl:ENSBTAG00000008361	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000105854"	ensembl:ENSBTAG00000008361	ncbigene:281417		uniprot:Q58DS7;uniprot:A0A3Q1M1W2			
+CES1	GeneProduct	ensembl:ENSBTAG00000011021	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000198848"	ensembl:ENSBTAG00000011021	ncbigene:512098		uniprot:A0A3S5ZPA1;uniprot:A0A3Q1LYA7;uniprot:A0A3Q1MQJ1			
+PON1	GeneProduct	ensembl:ENSBTAG00000015654	"Homology Mapping from Homo sapiens to Bos taurus: Original ID = En:ENSG00000005421"	ensembl:ENSBTAG00000015654	ncbigene:523798		uniprot:Q2KIW1			

pathways/WP1021/WP1021.gpml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Phase I biotransformations, non P450" Data-Source="WikiPathways" Version="WP1021_r125260" Author="[MaintBot, Khanspers, Mkutmon, Larsgw]" Last-Modified="20230131120927" Organism="Bos taurus">
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Phase I biotransformations, non-P450" Data-Source="WikiPathways" Version="WP1021_r128191" Author="[MaintBot, Khanspers, Mkutmon, Larsgw, Eweitz]" Last-Modified="20240129003440" Organism="Bos taurus">
   <Comment Source="WikiPathways-description">This pathway lists several phase 1 biotransformations and their related enzymes.</Comment>
   <Comment Source="HomologyMapper">This pathway was inferred from Homo sapiens pathway [http://wikipathways.org/instance/WP136_r95126 WP136(r95126)] with a 100.0% conversion rate.</Comment>
   <BiopaxRef>b69</BiopaxRef>
@@ -131,11 +131,6 @@
   <Group GroupId="efe95" GraphId="d55f1" />
   <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">cytochrome P450-independent phase I biotransformation 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:0000376</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="b69">
       <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">978-0-07-138914-3</bp:ID>
       <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ISBN</bp:DB>
@@ -145,6 +140,11 @@
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Klaassen, C.D.</bp:AUTHORS>
       <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Watkins III, J.B.</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">cytochrome P450-independent phase I biotransformation 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:0000376</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>
 

pathways/WP1021/WP1021.json

@@ -26,10 +26,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:51277",
         "Metabolite",
+        "CompactIdentifier:chebi:51277",
+        "thio esters",
+        "Wikidata:Q422794",
         "ChEBI:51277",
-        "P683:51277",
-        "P683:CHEBI:51277",
-        "Wikidata:Q422794"
+        "ChEBI:51277"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -66,10 +67,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:37734",
         "Metabolite",
+        "CompactIdentifier:chebi:37734",
+        "Phosphoric acid esters",
+        "Wikidata:Q411097",
         "ChEBI:37734",
-        "P683:37734",
-        "P683:CHEBI:37734",
-        "Wikidata:Q411097"
+        "ChEBI:37734"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -175,9 +177,11 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000011164",
         "GeneProduct",
-        "P594:ENSBTAG00000011164",
+        "CompactIdentifier:ensembl:ENSBTAG00000011164",
+        "CES5A",
+        "Ensembl:ENSBTAG00000011164",
         "Entrez Gene:513992",
-        "P351:513992"
+        "UniProt:E1BN79"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -338,10 +342,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:51277",
         "Metabolite",
+        "CompactIdentifier:chebi:51277",
+        "thio esters",
+        "Wikidata:Q422794",
         "ChEBI:51277",
-        "P683:51277",
-        "P683:CHEBI:51277",
-        "Wikidata:Q422794"
+        "ChEBI:51277"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -385,9 +390,12 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000003415",
         "GeneProduct",
-        "P594:ENSBTAG00000003415",
+        "CompactIdentifier:ensembl:ENSBTAG00000003415",
+        "ESD",
+        "Ensembl:ENSBTAG00000003415",
         "Entrez Gene:535653",
-        "P351:535653"
+        "UniProt:A0A3Q1MAU7",
+        "UniProt:Q08E20"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -431,9 +439,12 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000003636",
         "GeneProduct",
-        "P594:ENSBTAG00000003636",
+        "CompactIdentifier:ensembl:ENSBTAG00000003636",
+        "LIPA",
+        "Ensembl:ENSBTAG00000003636",
         "Entrez Gene:100125267",
-        "P351:100125267"
+        "UniProt:A0A3Q1M1X5",
+        "UniProt:A6H713"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -471,10 +482,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:33308",
         "Metabolite",
+        "CompactIdentifier:chebi:33308",
+        "carboxylic acid esters",
+        "Wikidata:Q355518",
         "ChEBI:33308",
-        "P683:33308",
-        "P683:CHEBI:33308",
-        "Wikidata:Q355518"
+        "ChEBI:33308"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -518,9 +530,11 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000034645",
         "GeneProduct",
-        "P594:ENSBTAG00000034645",
+        "CompactIdentifier:ensembl:ENSBTAG00000034645",
+        "PON3",
+        "Ensembl:ENSBTAG00000034645",
         "Entrez Gene:510953",
-        "P351:510953"
+        "UniProt:Q1JQD3"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -558,10 +572,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:32988",
         "Metabolite",
+        "CompactIdentifier:chebi:32988",
+        "amides",
+        "Wikidata:Q188777",
         "ChEBI:32988",
-        "P683:32988",
-        "P683:CHEBI:32988",
-        "Wikidata:Q188777"
+        "ChEBI:32988"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -599,10 +614,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:33308",
         "Metabolite",
+        "CompactIdentifier:chebi:33308",
+        "carboxylic acid esters",
+        "Wikidata:Q355518",
         "ChEBI:33308",
-        "P683:33308",
-        "P683:CHEBI:33308",
-        "Wikidata:Q355518"
+        "ChEBI:33308"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -938,10 +954,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:37734",
         "Metabolite",
+        "CompactIdentifier:chebi:37734",
+        "Phosphoric acid esters",
+        "Wikidata:Q411097",
         "ChEBI:37734",
-        "P683:37734",
-        "P683:CHEBI:37734",
-        "Wikidata:Q411097"
+        "ChEBI:37734"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -985,9 +1002,11 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000005093",
         "GeneProduct",
-        "P594:ENSBTAG00000005093",
+        "CompactIdentifier:ensembl:ENSBTAG00000005093",
+        "CES2",
+        "Ensembl:ENSBTAG00000005093",
         "Entrez Gene:505928",
-        "P351:505928"
+        "UniProt:F1MU22"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -1031,9 +1050,12 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000008361",
         "GeneProduct",
-        "P594:ENSBTAG00000008361",
+        "CompactIdentifier:ensembl:ENSBTAG00000008361",
+        "PON2",
+        "Ensembl:ENSBTAG00000008361",
         "Entrez Gene:281417",
-        "P351:281417"
+        "UniProt:Q58DS7",
+        "UniProt:A0A3Q1M1W2"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -1135,10 +1157,11 @@
         "SingleFreeNode",
         "ChEBI:CHEBI:32988",
         "Metabolite",
+        "CompactIdentifier:chebi:32988",
+        "amides",
+        "Wikidata:Q188777",
         "ChEBI:32988",
-        "P683:32988",
-        "P683:CHEBI:32988",
-        "Wikidata:Q188777"
+        "ChEBI:32988"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -1214,9 +1237,13 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000011021",
         "GeneProduct",
-        "P594:ENSBTAG00000011021",
+        "CompactIdentifier:ensembl:ENSBTAG00000011021",
+        "CES1",
+        "Ensembl:ENSBTAG00000011021",
         "Entrez Gene:512098",
-        "P351:512098"
+        "UniProt:A0A3S5ZPA1",
+        "UniProt:A0A3Q1LYA7",
+        "UniProt:A0A3Q1MQJ1"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -1324,9 +1351,11 @@
         "SingleFreeNode",
         "Ensembl:ENSBTAG00000015654",
         "GeneProduct",
-        "P594:ENSBTAG00000015654",
+        "CompactIdentifier:ensembl:ENSBTAG00000015654",
+        "PON1",
+        "Ensembl:ENSBTAG00000015654",
         "Entrez Gene:523798",
-        "P351:523798"
+        "UniProt:Q2KIW1"
       ],
       "verticalAlign": "middle",
       "whiteSpace": "pre",
@@ -1373,7 +1402,7 @@
         "@base": "WP1021/"
       }
     ],
-    "author": "[MaintBot, Khanspers, Mkutmon, Larsgw]",
+    "author": "[MaintBot, Khanspers, Mkutmon, Larsgw, Eweitz]",
     "comments": [
       {
         "content": "This pathway lists several phase 1 biotransformations and their related enzymes.",
@@ -1397,8 +1426,8 @@
       "aa661",
       "ab569"
     ],
-    "dataSourceVersion": "WP1021_r125260",
-    "displayName": "Phase I biotransformations, non P450",
+    "dataSourceVersion": "WP1021_r128191",
+    "displayName": "Phase I biotransformations, non-P450",
     "drawAs": "rect",
     "fill": "white",
     "fontSize": 12,
@@ -1407,16 +1436,16 @@
     "height": 408,
     "id": "WP1021",
     "kaavioType": "Group",
-    "lastModified": "20230131120927",
-    "name": "Phase I biotransformations, non P450",
+    "lastModified": "20240129003440",
+    "name": "Phase I biotransformations, non-P450",
     "organism": "Bos taurus",
     "padding": 5,
     "pathwayVersion": "WP1021",
-    "standardName": "Phase I biotransformations, non P450",
+    "standardName": "Phase I biotransformations, non-P450",
     "stroke": "black",
     "strokeWidth": 0,
     "textAlign": "left",
-    "textContent": "Name: Phase I biotransformations, non P450\nLast Modified: 20230131120927\nOrganism: Bos taurus",
+    "textContent": "Name: Phase I biotransformations, non-P450\nLast Modified: 20240129003440\nOrganism: Bos taurus",
     "type": [
       "Pathway",
       "http://identifiers.org/pw/PW:0000376"