Update frontmatter .md files

pathways/WP178/WP178.md

@@ -1,5 +1,9 @@
 ---
 annotations:
+- id: PW:0000002
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: classic metabolic pathway
 - id: PW:0001269
   parent: classic metabolic pathway
   type: Pathway Ontology
@@ -10,36 +14,38 @@ authors:
 - Ddigles
 - Egonw
 - Eweitz
+- Khanspers
+citedin: ''
+communities: []
 description: 'While Saccharomyces cerevisiae can use most amino acids as their sole
   nitrogen source, they can only use a few amino acids as a carbon source to support
-  growth (CITS:[Large86][Cooper82]).  This is in contrast to most eukaryotes and some
-  fungi, which can metabolize amino acids completely, utilizing them as sole sources
-  of carbon and nitrogen (CITS:[Stryer88][Large 86]). S. cerevisiae degrade the branched-chain
-  amino acids (iso-leucine, leucine, and valine) and the aromatic amino acids (tryptophan,
-  phenylalanine, and tyrosine) via the Ehrlich pathway (CITS:[Sentheshanmuganathan60][10989420]).  This
-  pathway is comprised of the following steps:  1) deamination of the amino acid to
-  the corresponding alpha-keto acid; 2) decarboxylation of the resulting alpha-keto
-  acid to the respective aldehyde; and, 3) reduction of the aldehyde to form the corresponding
-  long chain or complex alcohol, known as a fusel alcohol or fusel oil (CITS:[10989420][Large
-  86]).  Fusel alcohols are important flavor and aroma compounds in yeast-fermented
-  food products and beverages (as reported in (CITS:[9546164])  Each of the three
-  steps in branched-chain amino acid degradation can be catalyzed by more than one
-  isozyme; which enzyme is used appears to depend on the amino acid, the carbon source
-  and the stage of growth of the culture (CITS:[12499363]). The initial transamination
-  step in iso-leucine degradation can be catalyzed by either of the branched-chain
-  amino acid transaminases BAT1 (mitochondrial) or BAT2 (cytosolic) (CITS:[10989445][8798704][8702755]).
+  growth.  This is in contrast to most eukaryotes and some fungi, which can metabolize
+  amino acids completely, utilizing them as sole sources of carbon and nitrogen. S.
+  cerevisiae degrade the branched-chain amino acids (iso-leucine, leucine, and valine)
+  and the aromatic amino acids (tryptophan, phenylalanine, and tyrosine) via the Ehrlich
+  pathway.  This pathway is comprised of the following steps:  1) deamination of the
+  amino acid to the corresponding alpha-keto acid; 2) decarboxylation of the resulting
+  alpha-keto acid to the respective aldehyde; and, 3) reduction of the aldehyde to
+  form the corresponding long chain or complex alcohol, known as a fusel alcohol or
+  fusel oil.  Fusel alcohols are important flavor and aroma compounds in yeast-fermented
+  food products and beverages  Each of the three steps in branched-chain amino acid
+  degradation can be catalyzed by more than one isozyme; which enzyme is used appears
+  to depend on the amino acid, the carbon source and the stage of growth of the culture.
+  The initial transamination step in iso-leucine degradation can be catalyzed by either
+  of the branched-chain amino acid transaminases BAT1 (mitochondrial) or BAT2 (cytosolic).
   The subsequent decarboxylation step can be catalyzed by any one of the five decarboxylases
-  (Pdc1p, Pdc5p, Pdc6p, Thi3p, and Aro10p) (CITS:[9546164][10753893]) and the final
-  step can be catalyzed by any one of six alcohol dehydrogenases (Adh1p, Adh2p, Adh3p,
-  Adh4p, Adh5p, and Sfa1p) (CITS:[12499363]).  SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html'
-last-edited: 2021-05-20
+  (Pdc1p, Pdc5p, Pdc6p, Thi3p, and Aro10p) and the final step can be catalyzed by
+  any one of six alcohol dehydrogenases (Adh1p, Adh2p, Adh3p, Adh4p, Adh5p, and Sfa1p).  SOURCE:
+  SGD pathways, http://pathway.yeastgenome.org/server.html'
+last-edited: 2024-09-21
+ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP178
 - /instance/WP178
-- /instance/WP178_r117305
-revision: r117305
+- /instance/WP178_r135519
+revision: r135519
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP178.html
@@ -49,35 +55,44 @@ schema-jsonld:
     name: WikiPathways
   description: 'While Saccharomyces cerevisiae can use most amino acids as their sole
     nitrogen source, they can only use a few amino acids as a carbon source to support
-    growth (CITS:[Large86][Cooper82]).  This is in contrast to most eukaryotes and
-    some fungi, which can metabolize amino acids completely, utilizing them as sole
-    sources of carbon and nitrogen (CITS:[Stryer88][Large 86]). S. cerevisiae degrade
-    the branched-chain amino acids (iso-leucine, leucine, and valine) and the aromatic
-    amino acids (tryptophan, phenylalanine, and tyrosine) via the Ehrlich pathway
-    (CITS:[Sentheshanmuganathan60][10989420]).  This pathway is comprised of the following
-    steps:  1) deamination of the amino acid to the corresponding alpha-keto acid;
-    2) decarboxylation of the resulting alpha-keto acid to the respective aldehyde;
-    and, 3) reduction of the aldehyde to form the corresponding long chain or complex
-    alcohol, known as a fusel alcohol or fusel oil (CITS:[10989420][Large 86]).  Fusel
-    alcohols are important flavor and aroma compounds in yeast-fermented food products
-    and beverages (as reported in (CITS:[9546164])  Each of the three steps in branched-chain
-    amino acid degradation can be catalyzed by more than one isozyme; which enzyme
-    is used appears to depend on the amino acid, the carbon source and the stage of
-    growth of the culture (CITS:[12499363]). The initial transamination step in iso-leucine
+    growth.  This is in contrast to most eukaryotes and some fungi, which can metabolize
+    amino acids completely, utilizing them as sole sources of carbon and nitrogen.
+    S. cerevisiae degrade the branched-chain amino acids (iso-leucine, leucine, and
+    valine) and the aromatic amino acids (tryptophan, phenylalanine, and tyrosine)
+    via the Ehrlich pathway.  This pathway is comprised of the following steps:  1)
+    deamination of the amino acid to the corresponding alpha-keto acid; 2) decarboxylation
+    of the resulting alpha-keto acid to the respective aldehyde; and, 3) reduction
+    of the aldehyde to form the corresponding long chain or complex alcohol, known
+    as a fusel alcohol or fusel oil.  Fusel alcohols are important flavor and aroma
+    compounds in yeast-fermented food products and beverages  Each of the three steps
+    in branched-chain amino acid degradation can be catalyzed by more than one isozyme;
+    which enzyme is used appears to depend on the amino acid, the carbon source and
+    the stage of growth of the culture. The initial transamination step in iso-leucine
     degradation can be catalyzed by either of the branched-chain amino acid transaminases
-    BAT1 (mitochondrial) or BAT2 (cytosolic) (CITS:[10989445][8798704][8702755]).
-    The subsequent decarboxylation step can be catalyzed by any one of the five decarboxylases
-    (Pdc1p, Pdc5p, Pdc6p, Thi3p, and Aro10p) (CITS:[9546164][10753893]) and the final
-    step can be catalyzed by any one of six alcohol dehydrogenases (Adh1p, Adh2p,
-    Adh3p, Adh4p, Adh5p, and Sfa1p) (CITS:[12499363]).  SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html'
+    BAT1 (mitochondrial) or BAT2 (cytosolic). The subsequent decarboxylation step
+    can be catalyzed by any one of the five decarboxylases (Pdc1p, Pdc5p, Pdc6p, Thi3p,
+    and Aro10p) and the final step can be catalyzed by any one of six alcohol dehydrogenases
+    (Adh1p, Adh2p, Adh3p, Adh4p, Adh5p, and Sfa1p).  SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html'
   keywords:
+  - (S)-3-methyl-2-oxopentanoate
+  - 2-methylbutanal
+  - 2-methylbutanol
+  - 2-oxoglutarate
+  - ADH4
+  - ADH5
   - ARO10
   - BAT1
   - BAT2
+  - CO2
+  - H+
   - L-glutamate
+  - L-isoleucine
+  - NAD+
+  - NADH
   - PDC1
   - PDC5
   - PDC6
+  - SFA1
   - THI3
   license: CC0
   name: Isoleucine degradation

pathways/WP23/WP23.md

@@ -97,15 +97,15 @@ description: 'The functional B-cell receptor is a multi-protein complex consisti
   A. (2010). NetPath: A public resource of curated signal transduction pathways. <i>Genome
   Biology</i>. 11:R3.  Proteins on this pathway have targeted assays available via
   the [https://assays.cancer.gov/available_assays?wp_id=WP23 CPTAC Assay Portal]'
-last-edited: 2024-09-20
+last-edited: 2024-09-21
 ndex: 6ec414d7-8b5f-11eb-9e72-0ac135e8bacf
 organisms:
 - Homo sapiens
 redirect_from:
 - /index.php/Pathway:WP23
 - /instance/WP23
-- /instance/WP23_r135492
-revision: r135492
+- /instance/WP23_r135495
+revision: r135495
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP23.html

pathways/WP266/WP266.md

@@ -1,5 +1,9 @@
 ---
 annotations:
+- id: PW:0000002
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: classic metabolic pathway
 - id: PW:0000736
   parent: classic metabolic pathway
   type: Pathway Ontology
@@ -10,64 +14,59 @@ authors:
 - Ddigles
 - Egonw
 - Eweitz
-description: 'Sphingolipids are essential components of the plasma membrane in all
-  eukaryotic cells.  S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide
-  (IPC), mannose-inositol-phosphoceramide (MIPC), and mannose-(inositol phosphate)2-ceramide
-  (M(IP)2C)(CITS: [12069845]).  In the yeast plasma membrane sphingolipids concentrate
-  with ergosterol to form lipid rafts, specialized membrane microdomains implicated
-  in a variety of cellular processes, including sorting of membrane proteins and lipids,
-  as well as organizing and regulating signaling cascades (CITS: [12452424]).  Intermediates
-  in sphingolipid biosynthesis have been shown to play important roles as signaling
-  molecules and growth regulators.  Sphingolipid long chain bases (LCBs), dihydrosphingosine
-  (DHS) and phytosphingosine (PHS), have been implicated as secondary messengers in
-  signaling pathways that regulate heat stress response (CITS: [9405471])(CITS: [11967828]).  Other
-  intermediates, phytoceramide and long-chain base phosphates (LCBPs), have been shown
-  to be components of the tightly-controlled ceramide/LCBP rheostat, which regulates
-  cell growth (CITS: [12684378]).  Since phosphoinositol-containing sphingolipids
-  are unique to fungi, the sphingolipid biosynthesis pathway is considered a target
-  for antifungal drugs (CITS: [9092515])(CITS: [15578972]).  SOURCE: SGD pathways,
-  http://pathway.yeastgenome.org/server.html'
-last-edited: 2023-01-18
+- Khanspers
+citedin: ''
+communities: []
+description: 'Triacylglycerol (TAG) is the major lipid reserve in plants and animals.
+  The assembly of TAG occurs in the endoplasmic reticulum (ER). Four consecutive reactions
+  are catalyzed by ER membrane bound enzymes. The two intermediates, phosphatidate
+  and 1,2-diacylglycerol, are also substrates for the synthesis of membrane lipids
+  glycosylglycerides and phosphoglycerides. Thus, the last step in the pathway, catalyzed
+  by diacylglycerol acyltransferase, is the only dedicated step in triacylglycerol
+  synthesis.  Source: https://pathway.yeastgenome.org/.'
+last-edited: 2024-09-21
+ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP266
 - /instance/WP266
-- /instance/WP266_r124926
-revision: r124926
+- /instance/WP266_r135515
+revision: r135515
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP266.html
   '@type': Dataset
   creator:
     '@type': Organization
     name: WikiPathways
-  description: 'Sphingolipids are essential components of the plasma membrane in all
-    eukaryotic cells.  S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide
-    (IPC), mannose-inositol-phosphoceramide (MIPC), and mannose-(inositol phosphate)2-ceramide
-    (M(IP)2C)(CITS: [12069845]).  In the yeast plasma membrane sphingolipids concentrate
-    with ergosterol to form lipid rafts, specialized membrane microdomains implicated
-    in a variety of cellular processes, including sorting of membrane proteins and
-    lipids, as well as organizing and regulating signaling cascades (CITS: [12452424]).  Intermediates
-    in sphingolipid biosynthesis have been shown to play important roles as signaling
-    molecules and growth regulators.  Sphingolipid long chain bases (LCBs), dihydrosphingosine
-    (DHS) and phytosphingosine (PHS), have been implicated as secondary messengers
-    in signaling pathways that regulate heat stress response (CITS: [9405471])(CITS:
-    [11967828]).  Other intermediates, phytoceramide and long-chain base phosphates
-    (LCBPs), have been shown to be components of the tightly-controlled ceramide/LCBP
-    rheostat, which regulates cell growth (CITS: [12684378]).  Since phosphoinositol-containing
-    sphingolipids are unique to fungi, the sphingolipid biosynthesis pathway is considered
-    a target for antifungal drugs (CITS: [9092515])(CITS: [15578972]).  SOURCE: SGD
-    pathways, http://pathway.yeastgenome.org/server.html'
+  description: 'Triacylglycerol (TAG) is the major lipid reserve in plants and animals.
+    The assembly of TAG occurs in the endoplasmic reticulum (ER). Four consecutive
+    reactions are catalyzed by ER membrane bound enzymes. The two intermediates, phosphatidate
+    and 1,2-diacylglycerol, are also substrates for the synthesis of membrane lipids
+    glycosylglycerides and phosphoglycerides. Thus, the last step in the pathway,
+    catalyzed by diacylglycerol acyltransferase, is the only dedicated step in triacylglycerol
+    synthesis.  Source: https://pathway.yeastgenome.org/.'
   keywords:
-  - CDP-choline
-  - CPT1
-  - Coenzyme A
+  - 1,2-diacyl-sn-glycerol
+  - 1,2-diacyl-sn-glycerol 3-phosphate
+  - 1-acyl-sn-glycero-3-phosphocholine
+  - 1-acyl-sn-glycerol 3-phosphate
+  - Acyl-CoA
+  - COENZYME A
   - DGA1
-  - ISC1
+  - DPP1
+  - GPT2
+  - H2O
+  - LPP1
+  - LRO1
+  - PAH1
+  - Phosphate
+  - SCT1
   - SLC1
-  - acyl-CoA
-  - phosphate
+  - phosphatidylcholine
+  - sn-glycerol 3-phosphate
+  - triacyl-sn-glycerol
   license: CC0
   name: Triglyceride biosynthesis
 seo: CreativeWork

pathways/WP432/WP432.md

@@ -12,26 +12,40 @@ authors:
 - Khanspers
 citedin: ''
 communities: []
-description: 'ter Schure, E.G. et al suggest that in yeast, degradation of nitrogen
-  sources yields either ammonia or glutamate.  SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html'
-last-edited: 2024-09-20
+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'
+last-edited: 2024-09-21
 ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP432
 - /instance/WP432
-- /instance/WP432_r135491
-revision: r135491
+- /instance/WP432_r135498
+revision: r135498
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP432.html
   '@type': Dataset
   creator:
     '@type': Organization
     name: WikiPathways
-  description: 'ter Schure, E.G. et al suggest that in yeast, degradation of nitrogen
-    sources yields either ammonia or glutamate.  SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html'
+  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'
   keywords:
   - 2-oxoglutarate
   - AAT1

pathways/WP503/WP503.md

@@ -1,9 +1,13 @@
 ---
 annotations:
-- id: PW:0001382
+- id: PW:0000002
   parent: classic metabolic pathway
   type: Pathway Ontology
-  value: glutamate degradation pathway III
+  value: classic metabolic pathway
+- id: PW:0001389
+  parent: classic metabolic pathway
+  type: Pathway Ontology
+  value: glutamate degradation pathway IX
 authors:
 - J.Heckman
 - MaintBot
@@ -14,24 +18,34 @@ authors:
 - Eweitz
 citedin: ''
 communities: []
-description: Based on BioCyc.
-last-edited: 2024-07-22
+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/.
+last-edited: 2024-09-21
 ndex: null
 organisms:
 - Saccharomyces cerevisiae
 redirect_from:
 - /index.php/Pathway:WP503
 - /instance/WP503
-- /instance/WP503_r134374
-revision: r134374
+- /instance/WP503_r135505
+revision: r135505
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP503.html
   '@type': Dataset
   creator:
     '@type': Organization
     name: WikiPathways
-  description: Based on BioCyc.
+  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/.
   keywords:
   - 2-Oxoglutarate
   - Ammonia
@@ -42,8 +56,8 @@ schema-jsonld:
   - NAD
   - NADH
   license: CC0
-  name: Glutamate degradation III
+  name: Glutamate degradation IX
 seo: CreativeWork
-title: Glutamate degradation III
+title: Glutamate degradation IX
 wpid: WP503
 ---