Update tsv, md and png files

_data/WP3925-datanodes.tsv

@@ -1,4 +1,5 @@
 Label	Type	Identifier	Comment	Ensembl	NCBI gene	HGNC	UniProt	Wikidata	ChEBI	InChI	PubChem	ChemSpider	HMDB	KEGG	LipidMaps
+OH-indole acetaldehyde	Metabolite	chebi:50157	""					wikidata:Q27073985	chebi:50157	inchikey:OBFAPCIUSYHFIE-UHFFFAOYSA-N	pubchem.compound:74688	chemspider:67261	hmdb:HMDB0004073	kegg.compound:C05634	
 Ethanol	Metabolite	hmdb:HMDB0000108	""						chebi:16236	inchikey:LFQSCWFLJHTTHZ-UHFFFAOYSA-N	pubchem.compound:702	chemspider:682	hmdb:HMDB0000108	kegg.compound:C00469	
 Methionine	Metabolite	hmdb:HMDB0000696	""						chebi:16643	inchikey:FFEARJCKVFRZRR-BYPYZUCNSA-N	pubchem.compound:6137	chemspider:5907	hmdb:HMDB0000696	kegg.compound:C00073	
 Indoleacetate	Metabolite	hmdb:HMDB0000197	""						chebi:16411	inchikey:SEOVTRFCIGRIMH-UHFFFAOYSA-N	pubchem.compound:802	chemspider:780	hmdb:HMDB0000197	kegg.compound:C00954	
@@ -84,8 +85,8 @@ OH-methylglutaryl-CoA	Metabolite	hmdb:HMDB0001375	""						chebi:15467	inchikey:C
 methacrylyl-CoA	Metabolite	chebi:27754	""					wikidata:Q28487605	chebi:27754	inchikey:NPALUEYCDZWBOV-NDZSKPAWSA-N	pubchem.compound:165390	chemspider:144985	hmdb:HMDB0001011	kegg.compound:C03460	lipidmaps:LMFA07050350
 OH-isobutyrate	Metabolite	chebi:19641	""					wikidata:Q27109235	chebi:19641	inchikey:BWLBGMIXKSTLSX-UHFFFAOYSA-M	pubchem.compound:4277439	chemspider:3484177	hmdb:HMDB0242161		
 Tiglyl-CoA	Metabolite	hmdb:HMDB0002054	""						chebi:15478	inchikey:PMWATMXOQQZNBX-DKBZLLMOSA-N	pubchem.compound:6443760	chemspider:4947725	hmdb:HMDB0002054	kegg.compound:C03345	
-OH-isovaleryl-CoA	Metabolite	hmdb:HMDB0006870	""						chebi:28291	inchikey:PEVZKILCBDEOBT-XBTRWLRFSA-N	pubchem.compound:11953876	chemspider:10128175	hmdb:HMDB0006870	kegg.compound:C05998	
-Methylacetoacetyl-CoA	Metabolite	hmdb:HMDB0001157	""						chebi:15476	inchikey:NHNODHRSCRALBF-XSSXAYJJSA-N			hmdb:HMDB0001157	kegg.compound:C03344	
+OH-isovaleryl-CoA	Metabolite	chebi:28291	""					wikidata:Q27103612	chebi:28291	inchikey:PEVZKILCBDEOBT-XBTRWLRFSA-N;inchikey:PEVZKILCBDEOBT-CITAKDKDSA-N	pubchem.compound:11953876;pubchem.compound:11966188	chemspider:10128175;chemspider:10140181	hmdb:HMDB0006870	kegg.compound:C05998	lipidmaps:LMFA07050222
+Methylacetoacetyl-CoA	Metabolite	chebi:15476	""					wikidata:Q2813820	chebi:15476	inchikey:NHNODHRSCRALBF-NQNBQJKNSA-N;inchikey:NHNODHRSCRALBF-XSSXAYJJSA-N	pubchem.compound:193425	chemspider:17216071	hmdb:HMDB0001157	kegg.compound:C03344	lipidmaps:LMFA07050189
 OH-isobutyryl-CoA	Metabolite	hmdb:HMDB0001052	""						chebi:28259	inchikey:WWEOGFZEFHPUAM-UHFFFAOYSA-N	pubchem.compound:88	chemspider:86	hmdb:HMDB0001052	kegg.compound:C06000	
 Methylcrotonyl-CoA	Metabolite	hmdb:HMDB0001493	""						chebi:15486	inchikey:BXIPALATIYNHJN-ZMHDXICWSA-N	pubchem.compound:9549326	chemspider:7828242	hmdb:HMDB0001493	kegg.compound:C03069	
 Methyl-OH-butyryl-CoA	Metabolite	hmdb:HMDB0001356	""						chebi:15449	inchikey:PEKYNTFSOBAABV-LQUDNSJZSA-N	pubchem.compound:11966220	chemspider:10140213	hmdb:HMDB0001356	kegg.compound:C04405	

_data/WP662-datanodes.tsv

@@ -85,7 +85,7 @@ methacrylyl-CoA	Metabolite	chebi:27754	""					wikidata:Q28487605	chebi:27754	inc
 OH-isobutyrate	Metabolite	chebi:19641	""					wikidata:Q27109235	chebi:19641	inchikey:BWLBGMIXKSTLSX-UHFFFAOYSA-M	pubchem.compound:4277439	chemspider:3484177	hmdb:HMDB0242161		
 Tiglyl-CoA	Metabolite	hmdb:HMDB0002054	""						chebi:15478	inchikey:PMWATMXOQQZNBX-DKBZLLMOSA-N	pubchem.compound:6443760	chemspider:4947725	hmdb:HMDB0002054	kegg.compound:C03345	
 OH-isovaleryl-CoA	Metabolite	hmdb:HMDB0006870	""						chebi:28291	inchikey:PEVZKILCBDEOBT-XBTRWLRFSA-N	pubchem.compound:11953876	chemspider:10128175	hmdb:HMDB0006870	kegg.compound:C05998	
-Methylacetoacetyl-CoA	Metabolite	hmdb:HMDB0001157	""						chebi:15476	inchikey:NHNODHRSCRALBF-XSSXAYJJSA-N			hmdb:HMDB0001157	kegg.compound:C03344	
+Methylacetoacetyl-CoA	Metabolite	chebi:15476	""					wikidata:Q2813820	chebi:15476	inchikey:NHNODHRSCRALBF-NQNBQJKNSA-N;inchikey:NHNODHRSCRALBF-XSSXAYJJSA-N	pubchem.compound:193425	chemspider:17216071	hmdb:HMDB0001157	kegg.compound:C03344	lipidmaps:LMFA07050189
 OH-isobutyryl-CoA	Metabolite	hmdb:HMDB0001052	""						chebi:28259	inchikey:WWEOGFZEFHPUAM-UHFFFAOYSA-N	pubchem.compound:88	chemspider:86	hmdb:HMDB0001052	kegg.compound:C06000	
 Methylcrotonyl-CoA	Metabolite	hmdb:HMDB0001493	""						chebi:15486	inchikey:BXIPALATIYNHJN-ZMHDXICWSA-N	pubchem.compound:9549326	chemspider:7828242	hmdb:HMDB0001493	kegg.compound:C03069	
 Methyl-OH-butyryl-CoA	Metabolite	hmdb:HMDB0001356	""						chebi:15449	inchikey:PEKYNTFSOBAABV-LQUDNSJZSA-N	pubchem.compound:11966220	chemspider:10140213	hmdb:HMDB0001356	kegg.compound:C04405	

_pathways/WP111.md

@@ -1,13 +1,13 @@
 ---
 annotations:
-- id: PW:0000034
-  parent: classic metabolic pathway
-  type: Pathway Ontology
-  value: electron transport chain pathway
 - id: PW:0000002
   parent: classic metabolic pathway
   type: Pathway Ontology
   value: classic metabolic pathway
+- id: PW:0000034
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: electron transport chain pathway
 authors:
 - Kdahlquist
 - MaintBot
@@ -96,15 +96,15 @@ description: 'An electron transport chain(ETC) couples a chemical reaction betwe
   that drives the transfer of H+ ions. Source: Wikipedia ([[wikipedia:Electron_transport_chain]])  Proteins
   on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP111
   CPTAC Assay Portal]'
-last-edited: 2024-06-30
+last-edited: 2024-12-22
 ndex: c1699c36-8b5f-11eb-9e72-0ac135e8bacf
 organisms:
 - Homo sapiens
 redirect_from:
 - /index.php/Pathway:WP111
 - /instance/WP111
-- /instance/WP111_r134131
-revision: r134131
+- /instance/WP111_r136175
+revision: r136175
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP111.html

_pathways/WP3925.md

@@ -1,5 +1,21 @@
 ---
 annotations:
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
 - id: PW:0000011
   parent: classic metabolic pathway
   type: Pathway Ontology
@@ -32,15 +48,15 @@ communities:
 description: A complete overview of the metabolism of all 20 amino acids.  Proteins
   on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3925
   CPTAC Assay Portal]
-last-edited: 2021-05-16
+last-edited: 2024-12-22
 ndex: 6091f57b-8b68-11eb-9e72-0ac135e8bacf
 organisms:
 - Homo sapiens
 redirect_from:
 - /index.php/Pathway:WP3925
 - /instance/WP3925
-- /instance/WP3925_r123124
-revision: r123124
+- /instance/WP3925_r136171
+revision: r136171
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP3925.html
@@ -178,6 +194,7 @@ schema-jsonld:
   - OAT
   - ODC1
   - OGDH
+  - OH-indole acetaldehyde
   - OH-indoleacetate
   - OH-isobutyrate
   - OH-isobutyryl-CoA

_pathways/WP4815.md

@@ -1,13 +1,13 @@
 ---
 annotations:
-- id: PW:0000002
-  parent: classic metabolic pathway
-  type: Pathway Ontology
-  value: classic metabolic pathway
 - id: PW:0001154
   parent: classic metabolic pathway
   type: Pathway Ontology
   value: glycosaminoglycan degradation pathway
+- id: PW:0000002
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: classic metabolic pathway
 authors:
 - Rlee
 - Khanspers
@@ -24,7 +24,7 @@ description: 'Taken from KEGG: Glycosaminoglycan degradation - Homo sapiens (hum
   could not be found, these have been left on the diagram as unannotated GeneProducts.  Linked
   with a dotted arrow to the GeneProduct nodes are diseases caused by mutation in
   the respective gene.'
-last-edited: 2024-12-21
+last-edited: 2024-12-22
 ndex: d37d9242-8b6d-11eb-9e72-0ac135e8bacf
 organisms:
 - Homo sapiens

_pathways/WP5173.md

@@ -1,65 +1,65 @@
 ---
 annotations:
-- id: PW:0000042
+- id: PW:0000005
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: galactose metabolic pathway
-- id: DOID:2747
+  value: carbohydrate metabolic pathway
+- id: DOID:0111458
   parent: genetic disease
   type: Disease Ontology
-  value: glycogen storage disease
-- id: PW:0000002
+  value: galactose epimerase deficiency
+- id: DOID:2754
+  parent: genetic disease
+  type: Disease Ontology
+  value: glycogen storage disease VI
+- id: DOID:2750
+  parent: genetic disease
+  type: Disease Ontology
+  value: glycogen storage disease IV
+- id: DOID:0050579
+  parent: genetic disease
+  type: Disease Ontology
+  value: glycogen storage disease XV
+- id: PW:0000042
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: classic metabolic pathway
+  value: galactose metabolic pathway
 - id: DOID:9870
   parent: genetic disease
   type: Disease Ontology
   value: galactosemia
+- id: DOID:0080570
+  parent: genetic disease
+  type: Disease Ontology
+  value: congenital disorder of glycosylation It
 - id: PW:0000013
   parent: disease pathway
   type: Pathway Ontology
   value: disease pathway
-- id: DOID:0080570
+- id: DOID:2747
   parent: genetic disease
   type: Disease Ontology
-  value: congenital disorder of glycosylation It
+  value: glycogen storage disease
 - id: PW:0002093
   parent: disease pathway
   type: Pathway Ontology
   value: GALE deficiency pathway
-- id: DOID:0111458
-  parent: genetic disease
-  type: Disease Ontology
-  value: galactose epimerase deficiency
-- id: DOID:2750
-  parent: genetic disease
-  type: Disease Ontology
-  value: glycogen storage disease IV
-- id: DOID:0050579
-  parent: genetic disease
-  type: Disease Ontology
-  value: glycogen storage disease XV
-- id: PW:0000306
+- id: PW:0000640
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: altered galactose metabolic pathway
-- id: DOID:2754
-  parent: genetic disease
-  type: Disease Ontology
-  value: glycogen storage disease VI
+  value: glycolysis pathway
 - id: DOID:14695
   parent: genetic disease
   type: Disease Ontology
   value: galactokinase deficiency
-- id: PW:0000005
+- id: PW:0000306
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: carbohydrate metabolic pathway
-- id: PW:0000640
+  value: altered galactose metabolic pathway
+- id: PW:0000002
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: glycolysis pathway
+  value: classic metabolic pathway
 authors:
 - Alexandrabosch
 - EnzoChiaradia
@@ -84,15 +84,15 @@ description: 'Galactose is converted into glucose 1-phosphate (G1P) through a se
   GALT-D) and uridine diphosphate galactose 4-epimerase deficiency (GALE-D). Among
   these, galactosemia is the most common and most severe. This pathway was inspired
   by Chapter 18, figure 18.3 of the book of Blau (4th edition; ISBN: 978-3-642-40337-8). '
-last-edited: 2024-07-22
+last-edited: 2024-12-22
 ndex: null
 organisms:
 - Homo sapiens
 redirect_from:
 - /index.php/Pathway:WP5173
 - /instance/WP5173
-- /instance/WP5173_r134383
-revision: r134383
+- /instance/WP5173_r136172
+revision: r136172
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP5173.html

_pathways/WP5507.md

@@ -1,33 +1,33 @@
 ---
 annotations:
-- id: PW:0000440
-  parent: classic metabolic pathway
-  type: Pathway Ontology
-  value: glycine metabolic pathway
-- id: PW:0000011
+- id: PW:0001086
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: amino acid metabolic pathway
-- id: PW:0000013
+  value: glutamine metabolic pathway
+- id: PW:0000605
   parent: disease pathway
   type: Pathway Ontology
-  value: disease pathway
+  value: cancer pathway
 - id: DOID:1612
   parent: disease of cellular proliferation
   type: Disease Ontology
   value: breast cancer
-- id: PW:0001086
-  parent: classic metabolic pathway
-  type: Pathway Ontology
-  value: glutamine metabolic pathway
 - id: DOID:0060081
   parent: disease of cellular proliferation
   type: Disease Ontology
   value: triple-receptor negative breast cancer
-- id: PW:0000605
+- id: PW:0000013
   parent: disease pathway
   type: Pathway Ontology
-  value: cancer pathway
+  value: disease pathway
+- id: PW:0000440
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: glycine metabolic pathway
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
 - id: PW:0001084
   parent: classic metabolic pathway
   type: Pathway Ontology
@@ -38,20 +38,21 @@ annotations:
   value: amino acid metabolic disorder
 authors:
 - Daanvanbeek
+- Egonw
 citedin: ''
 communities:
 - MetaKids
 description: Reflecting the pathway as shown in Figure 43.2 of Blau et al. "Physician’s
   guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases"
-last-edited: 2024-12-21
+last-edited: 2024-12-22
 ndex: null
 organisms:
 - Homo sapiens
 redirect_from:
 - /index.php/Pathway:WP5507
 - /instance/WP5507
-- /instance/WP5507_r136142
-revision: r136142
+- /instance/WP5507_r136173
+revision: r136173
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP5507.html

_pathways/WP662.md

@@ -1,5 +1,17 @@
 ---
 annotations:
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
+- id: PW:0000011
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: amino acid metabolic pathway
 - id: PW:0000011
   parent: classic metabolic pathway
   type: Pathway Ontology
@@ -20,15 +32,17 @@ citedin:
 - link: 10.1038/s41467-024-52306-5
   title: Podocyte-specific KLF6 primes proximal tubule CaMK1D signaling to attenuate
     diabetic kidney disease (2024)
+communities: []
 description: A complete overview of the metabolism of all 20 amino acids
-last-edited: 2021-05-14
+last-edited: 2024-12-22
+ndex: null
 organisms:
 - Mus musculus
 redirect_from:
 - /index.php/Pathway:WP662
 - /instance/WP662
-- /instance/WP662_r122074
-revision: r122074
+- /instance/WP662_r136168
+revision: r136168
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP662.html