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diff --git a/_data/WP214-bibliography.tsv b/_data/WP214-bibliography.tsv
@@ -1 +1,2 @@
 ID	Database	Citation
+https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PYRUVDEHYD-PWY	URL	
diff --git a/_data/WP214-datanodes.tsv b/_data/WP214-datanodes.tsv
@@ -1,14 +1,15 @@
-Label	Type	Identifier	Comment	Ensembl	NCBI gene	HGNC	UniProt	Wikidata	ChEBI	InChI
-NAD	Metabolite	chebi:13389						wikidata:Q12499775	chebi:13389;chebi:13389	
-S-Acetyldihydrolipoamide	Metabolite	hmdb:HMDB0001526							chebi:16807;chebi:16807	inchikey:ARGXEXVCHMNAQU-UHFFFAOYSA-N
-pyruvate	Metabolite	chebi:15361						wikidata:Q27089397	chebi:15361;chebi:15361	inchikey:LCTONWCANYUPML-UHFFFAOYSA-M
-Coenzyme A	Metabolite	cas:64885-97-8						wikidata:Q412727	chebi:16848;chebi:16848	inchikey:XXFFZHQKSZLLIT-NALJQGANSA-N;inchikey:GEHSZWRGPHDXJO-NALJQGANSA-N
-NADH	Metabolite	cas:53-84-9						wikidata:Q71535049;wikidata:Q12499775	chebi:15846;chebi:44215;chebi:13389;chebi:13389;chebi:44215	inchikey:BAWFJGJZGIEFAR-NNYOXOHSSA-N
-lipoamide	Metabolite	cas:940-69-2						wikidata:Q63611085	chebi:17460;chebi:17460	inchikey:FCCDDURTIIUXBY-UHFFFAOYSA-N
-lipoamide	Metabolite	cas:940-69-2						wikidata:Q63611085	chebi:17460;chebi:17460	inchikey:FCCDDURTIIUXBY-UHFFFAOYSA-N
-acetyl-CoA	Metabolite	cas:72-89-9						wikidata:Q715317	chebi:15351;chebi:15351	inchikey:ZSLZBFCDCINBPY-ZSJPKINUSA-N
-dihydrolipoamide	Metabolite	cas:3884-47-7						wikidata:Q3027880	chebi:17694;chebi:17694	inchikey:VLYUGYAKYZETRF-UHFFFAOYSA-N
-PDA1	GeneProduct	sgd:S000000980		ensembl:YER178W	ncbigene:856925		uniprot:P16387			
-PDB1	GeneProduct	sgd:S000000425		ensembl:YBR221C	ncbigene:852522		uniprot:P32473			
-LPD1	GeneProduct	sgd:S000001876		ensembl:YFL018C	ncbigene:850527		uniprot:P09624			
-LAT1	GeneProduct	sgd:S000005015		ensembl:YNL071W	ncbigene:855653		uniprot:P12695			
+Label	Type	Identifier	Comment	Ensembl	NCBI gene	HGNC	UniProt	Wikidata	ChEBI	InChI	PubChem	ChemSpider	HMDB	KEGG	LipidMaps
+H+	Metabolite	hmdb:HMDB59597	""					wikidata:Q506710	chebi:15378	inchikey:GPRLSGONYQIRFK-UHFFFAOYSA-N	pubchem.compound:1038	chemspider:1010	hmdb:HMDB0059597	kegg.compound:C00080	
+CO2	Metabolite	chebi:16526	""					wikidata:Q1997	chebi:16526	inchikey:CURLTUGMZLYLDI-UHFFFAOYSA-N	pubchem.compound:280	chemspider:274	hmdb:HMDB0001967	kegg.compound:C00011	
+NAD	Metabolite	chebi:13389	""					wikidata:Q12499775	chebi:13389		pubchem.compound:5892	chemspider:5681			
+S-Acetyldihydrolipoamide	Metabolite	hmdb:HMDB0001526	""						chebi:16807	inchikey:ARGXEXVCHMNAQU-UHFFFAOYSA-N	pubchem.compound:1076	chemspider:1046	hmdb:HMDB0001526	kegg.compound:C01136	
+pyruvate	Metabolite	chebi:15361	""					wikidata:Q27089397	chebi:15361	inchikey:LCTONWCANYUPML-UHFFFAOYSA-M	pubchem.compound:107735	chemspider:96901		kegg.compound:C00022	
+Coenzyme A	Metabolite	cas:64885-97-8	""					wikidata:Q412727	chebi:16848	inchikey:XXFFZHQKSZLLIT-NALJQGANSA-N;inchikey:GEHSZWRGPHDXJO-NALJQGANSA-N	pubchem.compound:123996	chemspider:110515		kegg.compound:C00876	
+NADH	Metabolite	cas:53-84-9	""					wikidata:Q71535049;wikidata:Q12499775	chebi:15846;chebi:44215;chebi:13389	inchikey:BAWFJGJZGIEFAR-NNYOXOHSSA-N	pubchem.compound:5892	chemspider:5682;chemspider:5681	hmdb:HMDB0000902	kegg.compound:C00003	
+lipoamide	Metabolite	cas:940-69-2	""					wikidata:Q63611085	chebi:17460	inchikey:FCCDDURTIIUXBY-UHFFFAOYSA-N	pubchem.compound:863	chemspider:840	hmdb:HMDB0000962	kegg.compound:C00248	lipidmaps:LMFA08010006
+acetyl-CoA	Metabolite	cas:72-89-9	""					wikidata:Q715317	chebi:15351	inchikey:ZSLZBFCDCINBPY-ZSJPKINUSA-N	pubchem.compound:444493	chemspider:392413	hmdb:HMDB0001206	kegg.compound:C00024	lipidmaps:LMFA07050281
+dihydrolipoamide	Metabolite	cas:3884-47-7	""					wikidata:Q3027880	chebi:17694	inchikey:VLYUGYAKYZETRF-UHFFFAOYSA-N	pubchem.compound:663	chemspider:21230390;chemspider:643	hmdb:HMDB0000985	kegg.compound:C00579	lipidmaps:LMFA08010019
+PDA1	GeneProduct	sgd:S000000980	""	ensembl:YER178W	ncbigene:856925		uniprot:P16387								
+PDB1	GeneProduct	sgd:S000000425	""	ensembl:YBR221C	ncbigene:852522		uniprot:P32473								
+LPD1	GeneProduct	sgd:S000001876	""	ensembl:YFL018C	ncbigene:850527		uniprot:P09624								
+LAT1	GeneProduct	sgd:S000005015	""	ensembl:YNL071W	ncbigene:855653		uniprot:P12695								
diff --git a/_data/WP416-bibliography.tsv b/_data/WP416-bibliography.tsv
@@ -1 +1,2 @@
 ID	Database	Citation
+https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=PRPP-PWY-1	URL	
diff --git a/_data/WP514-bibliography.tsv b/_data/WP514-bibliography.tsv
@@ -2,3 +2,4 @@ ID	Database	Citation
 8852895	Pubmed	"Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Alifano P, Fani R, Liò P, Lazcano A, Bazzicalupo M, Carlomagno MS, et al. Microbiol Rev. 1996 Mar;60(1):44–69.  <a href=""http://www.ncbi.nlm.nih.gov/pubmed/8852895"" target=""_blank"" class=""external"" rel=""nofollow"">PubMed</a> <a href=""https://europepmc.org/abstract/MED/8852895"" target=""_blank"" class=""external"" rel=""nofollow"">Europe PMC</a> <a href=""https://scholia.toolforge.org/pubmed/8852895"" target=""_blank"" class=""external"" rel=""nofollow"">Scholia</a>"
 9822821	Pubmed	"Role of the myb-like protein bas1p in Saccharomyces cerevisiae: a proteome analysis. Denis V, Boucherie H, Monribot C, Daignan-Fornier B. Mol Microbiol. 1998 Nov;30(3):557–66.  <a href=""http://www.ncbi.nlm.nih.gov/pubmed/9822821"" target=""_blank"" class=""external"" rel=""nofollow"">PubMed</a> <a href=""https://europepmc.org/abstract/MED/9822821"" target=""_blank"" class=""external"" rel=""nofollow"">Europe PMC</a> <a href=""https://scholia.toolforge.org/pubmed/9822821"" target=""_blank"" class=""external"" rel=""nofollow"">Scholia</a>"
 15744050	Pubmed	"Revisiting purine-histidine cross-pathway regulation in Saccharomyces cerevisiae: a central role for a small molecule. Rébora K, Laloo B, Daignan-Fornier B. Genetics. 2005 May;170(1):61–70.  <a href=""http://www.ncbi.nlm.nih.gov/pubmed/15744050"" target=""_blank"" class=""external"" rel=""nofollow"">PubMed</a> <a href=""https://europepmc.org/abstract/MED/15744050"" target=""_blank"" class=""external"" rel=""nofollow"">Europe PMC</a> <a href=""https://scholia.toolforge.org/pubmed/15744050"" target=""_blank"" class=""external"" rel=""nofollow"">Scholia</a>"
+https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=HISTSYN-PWY	URL	
diff --git a/_data/WP541-bibliography.tsv b/_data/WP541-bibliography.tsv
@@ -1 +1,2 @@
 ID	Database	Citation
+https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=NADSYN-PWY	URL	
diff --git a/_data/WP67-bibliography.tsv b/_data/WP67-bibliography.tsv
@@ -1 +1,2 @@
 ID	Database	Citation
+https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=ASPARAGINE-BIOSYNTHESIS-1	URL	
diff --git a/_pathways/WP214.md b/_pathways/WP214.md
@@ -4,6 +4,10 @@ annotations:
   parent: classic metabolic pathway
   type: Pathway Ontology
   value: pyruvate metabolic pathway
+- id: PW:0000002
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: classic metabolic pathway
 authors:
 - J.Heckman
 - MaintBot
@@ -12,17 +16,21 @@ authors:
 - Maxvanson
 - Eweitz
 - AlexanderPico
+- Khanspers
+citedin: ''
+communities: []
 description: Pyruvate dehydrogenase is a multiple enzyme complex that catalyzes the
   production of acetyl-CoA from pyruvate produced by glycolysis. The final step re-oxidizes
   the lipoyl group of dihydrolipoamide to form lipoamide and NADH.
-last-edited: 2023-02-24
+last-edited: 2024-09-06
+ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP214
 - /instance/WP214
-- /instance/WP214_r125509
-revision: r125509
+- /instance/WP214_r135426
+revision: r135426
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP214.html
@@ -34,7 +42,9 @@ schema-jsonld:
     the production of acetyl-CoA from pyruvate produced by glycolysis. The final step
     re-oxidizes the lipoyl group of dihydrolipoamide to form lipoamide and NADH.
   keywords:
+  - CO2
   - Coenzyme A
+  - H+
   - LAT1
   - LPD1
   - NAD

diff --git a/_pathways/WP250.md b/_pathways/WP250.md
@@ -19,25 +19,25 @@ citedin: ''
 communities: []
 description: 'Yeast cells contain 3 pathways for the synthesis of glutamate.  Two
   pathways are mediated by two isoforms of glutamate dehydrogenase, encoded by GDH1
-  and GDH3 (CITS: [2989290])(CITS: [9287019]).  The third pathway is driven by the
-  combined activities of glutamine synthetase and glutamate synthase, encoded by GLN1
-  and GLT1, respectively (CITS: [2570348])(CITS: [8923741]).  Studies of GDH1 and
-  GDH3 regulation indicate that the cell uses these isoforms under different growth
-  conditions (CITS: [11562373]).  Expression of GDH3 is induced by ethanol and repressed
-  by glucose, whereas GDH1 expression is high in either carbon source.  Gdh1p uses
-  alpha-ketoglutarate at a higher rate than Gdh3p.  Thus, under fermentative growth
-  conditions, Gdh1p drives glutamate biosynthesis, whereas in nonfermentable or limiting
-  carbon sources, Gdh3p is the key isoform involved in balancing distribution of alpha-ketoglutarate
-  to glutamate biosynthesis and energy metabolism.  SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html'
-last-edited: 2024-08-16
+  and GDH3.  The third pathway is driven by the combined activities of glutamine synthetase
+  and glutamate synthase, encoded by GLN1 and GLT1, respectively.  Studies of GDH1
+  and GDH3 regulation indicate that the cell uses these isoforms under different growth
+  conditions.  Expression of GDH3 is induced by ethanol and repressed by glucose,
+  whereas GDH1 expression is high in either carbon source.  Gdh1p uses alpha-ketoglutarate
+  at a higher rate than Gdh3p.  Thus, under fermentative growth conditions, Gdh1p
+  drives glutamate biosynthesis, whereas in nonfermentable or limiting carbon sources,
+  Gdh3p is the key isoform involved in balancing distribution of alpha-ketoglutarate
+  to glutamate biosynthesis and energy metabolism.   SOURCE: [https://pathway.yeastgenome.org/
+  YeastPathways].'
+last-edited: 2024-09-06
 ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP250
 - /instance/WP250
-- /instance/WP250_r135303
-revision: r135303
+- /instance/WP250_r135459
+revision: r135459
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP250.html
@@ -47,17 +47,16 @@ schema-jsonld:
     name: WikiPathways
   description: 'Yeast cells contain 3 pathways for the synthesis of glutamate.  Two
     pathways are mediated by two isoforms of glutamate dehydrogenase, encoded by GDH1
-    and GDH3 (CITS: [2989290])(CITS: [9287019]).  The third pathway is driven by the
-    combined activities of glutamine synthetase and glutamate synthase, encoded by
-    GLN1 and GLT1, respectively (CITS: [2570348])(CITS: [8923741]).  Studies of GDH1
-    and GDH3 regulation indicate that the cell uses these isoforms under different
-    growth conditions (CITS: [11562373]).  Expression of GDH3 is induced by ethanol
-    and repressed by glucose, whereas GDH1 expression is high in either carbon source.  Gdh1p
-    uses alpha-ketoglutarate at a higher rate than Gdh3p.  Thus, under fermentative
-    growth conditions, Gdh1p drives glutamate biosynthesis, whereas in nonfermentable
-    or limiting carbon sources, Gdh3p is the key isoform involved in balancing distribution
-    of alpha-ketoglutarate to glutamate biosynthesis and energy metabolism.  SOURCE:
-    SGD pathways, http://pathway.yeastgenome.org/server.html'
+    and GDH3.  The third pathway is driven by the combined activities of glutamine
+    synthetase and glutamate synthase, encoded by GLN1 and GLT1, respectively.  Studies
+    of GDH1 and GDH3 regulation indicate that the cell uses these isoforms under different
+    growth conditions.  Expression of GDH3 is induced by ethanol and repressed by
+    glucose, whereas GDH1 expression is high in either carbon source.  Gdh1p uses
+    alpha-ketoglutarate at a higher rate than Gdh3p.  Thus, under fermentative growth
+    conditions, Gdh1p drives glutamate biosynthesis, whereas in nonfermentable or
+    limiting carbon sources, Gdh3p is the key isoform involved in balancing distribution
+    of alpha-ketoglutarate to glutamate biosynthesis and energy metabolism.   SOURCE:
+    [https://pathway.yeastgenome.org/ YeastPathways].'
   keywords:
   - 2,3-Dihydroxy-3-methylvalerate
   - 2-Aceto-2-hydroxybutyrate

diff --git a/_pathways/WP4010.md b/_pathways/WP4010.md
@@ -1,5 +1,9 @@
 ---
 annotations:
+- id: CL:0000182
+  parent: native cell
+  type: Cell Type Ontology
+  value: hepatocyte
 - id: DOID:9452
   parent: genetic disease
   type: Disease Ontology
@@ -8,10 +12,6 @@ annotations:
   parent: disease pathway
   type: Pathway Ontology
   value: disease pathway
-- id: CL:0000182
-  parent: native cell
-  type: Cell Type Ontology
-  value: hepatocyte
 authors:
 - JJvdHeijden
 - AlexanderPico
@@ -34,7 +34,7 @@ description: 'This liver steatosis AOP starts from the top with different molecu
   into three main categories: alcoholic liver disease (ALD), non-alcoholic  liver
   disease (NAFLD), and toxicant-associated liver disease (TAFLD).[https://pubmed.ncbi.nlm.nih.gov/28210688/
   Review on liver steatosis]'
-last-edited: 2024-09-05
+last-edited: 2024-09-06
 ndex: 1605d5b7-8b69-11eb-9e72-0ac135e8bacf
 organisms:
 - Homo sapiens

diff --git a/_pathways/WP416.md b/_pathways/WP416.md
@@ -1,5 +1,9 @@
 ---
 annotations:
+- id: PW:0000002
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: classic metabolic pathway
 - id: PW:0000012
   parent: classic metabolic pathway
   type: Pathway Ontology
@@ -17,15 +21,15 @@ authors:
 citedin: ''
 communities: []
 description: ''
-last-edited: 2024-08-17
+last-edited: 2024-09-06
 ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP416
 - /instance/WP416
-- /instance/WP416_r135314
-revision: r135314
+- /instance/WP416_r135448
+revision: r135448
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP416.html

diff --git a/_pathways/WP514.md b/_pathways/WP514.md
@@ -19,24 +19,45 @@ authors:
 - Eweitz
 citedin: ''
 communities: []
-description: ''
-last-edited: 2024-08-17
+description: Histidine is synthesized from phosphoribosyl pyrophosphate (PRPP), which
+  is produced in the pentose phosphate pathway. The first step in the pathway is the
+  condensation of PRPP and ATP by ATP-phosphoribosyl transferase (HIS1). HIS4 then
+  hydrolyzes phosphoribosyl-ATP, which produces phosphoribosyl-AMP (PRAMP). Next,
+  HIS4 catalyzes the formation of phosphoribosylformiminoAICAR-phosphate, which is
+  converted to phosphoribulosylformimino-AICAR-P by the HIS6 gene product. HIS7 splits
+  phosphoribulosylformimino-AICAR-P to form d-erythro-imidazole-glycerol-phosphate.
+  HIS3 forms imidazole acetol-phosphate releasing water. HIS5 then makes l-histidinol-phosphate,
+  which is hydrolyzed by HIS2 making histidinol. HIS4 catalyzes the oxidation of l-histidinol
+  to form l-histidinal. In the last step, l-histidinal is converted to l-histidine.  Description
+  adapted from [https://en.wikipedia.org/wiki/Histidine Wikipedia].
+last-edited: 2024-09-06
 ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP514
 - /instance/WP514
-- /instance/WP514_r135310
-revision: r135310
+- /instance/WP514_r135454
+revision: r135454
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP514.html
   '@type': Dataset
   creator:
     '@type': Organization
     name: WikiPathways
-  description: ''
+  description: Histidine is synthesized from phosphoribosyl pyrophosphate (PRPP),
+    which is produced in the pentose phosphate pathway. The first step in the pathway
+    is the condensation of PRPP and ATP by ATP-phosphoribosyl transferase (HIS1).
+    HIS4 then hydrolyzes phosphoribosyl-ATP, which produces phosphoribosyl-AMP (PRAMP).
+    Next, HIS4 catalyzes the formation of phosphoribosylformiminoAICAR-phosphate,
+    which is converted to phosphoribulosylformimino-AICAR-P by the HIS6 gene product.
+    HIS7 splits phosphoribulosylformimino-AICAR-P to form d-erythro-imidazole-glycerol-phosphate.
+    HIS3 forms imidazole acetol-phosphate releasing water. HIS5 then makes l-histidinol-phosphate,
+    which is hydrolyzed by HIS2 making histidinol. HIS4 catalyzes the oxidation of
+    l-histidinol to form l-histidinal. In the last step, l-histidinal is converted
+    to l-histidine.  Description adapted from [https://en.wikipedia.org/wiki/Histidine
+    Wikipedia].
   keywords:
   - 2-oxoglutarate
   - AICAR

diff --git a/_pathways/WP54.md b/_pathways/WP54.md
@@ -13,24 +13,56 @@ authors:
 - Khanspers
 citedin: ''
 communities: []
-description: ''
-last-edited: 2024-09-05
+description: Under conditions where optimal sources of nitrogen are unavailable, S.
+  cerevisiae is able to utilize arginine as its sole nitrogen source. Arginine catabolism
+  occurs in the cytosol with the hydrolysis of arginine to proline, releasing three
+  nitrogen atoms that can be used by the cell. In the absence of oxygen, the proline
+  ring is unable to be further degraded. The utilization of arginine as a nitrogen
+  source is repressed if better nitrogen compounds such as ammonia, asparagine or
+  glutamine are present. This is known as nitrogen catabolite repression (NCR). The
+  CAR1 gene is subject to the effect of this repression which is mediated by the negative
+  regulator Ure2p. In the presence of arginine and the absence of a preferred nitrogen
+  source, NCR is released by the GATA transcriptional activators Gln3p and Gat1p.
+  Unrelated to NCR, the presence of arginine also induces CAR1 and CAR2 expression
+  by the regulators Arg80p, Arg81p and Mcm1p. The CAR genes are also activated by
+  the globally acting transcription factors Rap1p and Abf1p. Conversely, CAR1 and
+  CAR2 expression is repressed by the Ume6p-Sin2p-Rpd3p complex. Additionally, CAR2
+  expression is induced by the two positive regulators Dal81p and Dal82p as well as
+  allophanate, a degradation product of urea.  Description from [https://pathway.yeastgenome.org
+  YeastPathways].
+last-edited: 2024-09-06
 ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP54
 - /instance/WP54
-- /instance/WP54_r135415
-revision: r135415
+- /instance/WP54_r135444
+revision: r135444
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP54.html
   '@type': Dataset
   creator:
     '@type': Organization
     name: WikiPathways
-  description: ''
+  description: Under conditions where optimal sources of nitrogen are unavailable,
+    S. cerevisiae is able to utilize arginine as its sole nitrogen source. Arginine
+    catabolism occurs in the cytosol with the hydrolysis of arginine to proline, releasing
+    three nitrogen atoms that can be used by the cell. In the absence of oxygen, the
+    proline ring is unable to be further degraded. The utilization of arginine as
+    a nitrogen source is repressed if better nitrogen compounds such as ammonia, asparagine
+    or glutamine are present. This is known as nitrogen catabolite repression (NCR).
+    The CAR1 gene is subject to the effect of this repression which is mediated by
+    the negative regulator Ure2p. In the presence of arginine and the absence of a
+    preferred nitrogen source, NCR is released by the GATA transcriptional activators
+    Gln3p and Gat1p. Unrelated to NCR, the presence of arginine also induces CAR1
+    and CAR2 expression by the regulators Arg80p, Arg81p and Mcm1p. The CAR genes
+    are also activated by the globally acting transcription factors Rap1p and Abf1p.
+    Conversely, CAR1 and CAR2 expression is repressed by the Ume6p-Sin2p-Rpd3p complex.
+    Additionally, CAR2 expression is induced by the two positive regulators Dal81p
+    and Dal82p as well as allophanate, a degradation product of urea.  Description
+    from [https://pathway.yeastgenome.org YeastPathways].
   keywords:
   - 2-oxoglutarate
   - CAR1