chore: merge in latest develop branch

SysBioChalmers · Dec 14, 2023 · 1c2060b · 1c2060b
2 parents 08aa570 + f2561c1
commit 1c2060b
Show file tree

Hide file tree

Showing 3 changed files with 41 additions and 104 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -267,3 +267,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06279"	""	"FAOXC61C4m"	""	""	""	"FAOXC61C4m"	""	""	""	""	0	""	""	"FAOXC61C4m"
 "MAR05449"	""	"FAOXC4020m"	""	""	""	"FAOXC4C2m"	"MNXR99368"	""	""	""	0	""	""	"FAOXC4C2m"
 "MAR01009"	""	"FAOXC80"	""	""	""	"FAOXC80"	"MNXR99373"	""	""	""	0	""	""	"FAOXC80"
+"MAR03422"	""	""	""	""	""	"HMR_3422"	""	"HMR_3422"	"RCR12667"	""	0	""	""	"HMR_3422"
+"MAR03748"	"R01210"	"OIVD2m"	"R03171M"	"r0600"	""	"OIVD2m"	"MNXR102173;MNXR107999"	"HMR_3748"	"RCR14420"	""	0	""	"RHEA:13997"	"HMR_3748"
+"MAR03780"	"R03171"	"OIVD3m"	"R03171M"	"r0602"	""	"OIVD3m"	"MNXR102174;MNXR107999"	"HMR_3780"	"RCR10345"	""	0	""	"RHEA:30907"	"HMR_3780"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -87297,26 +87297,6 @@
       - subsystem:
           - "Metabolism of other amino acids"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR03748"
-      - name: "3-methyl-2-oxobutanoate:NAD+ oxidoreductase (CoA-mehtylpropanoylating)"
-      - metabolites: !!omap
-          - MAM00824m: -1
-          - MAM01596m: 1
-          - MAM01597m: -1
-          - MAM02180m: 1
-          - MAM02552m: -1
-          - MAM02553m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.2.1.25"
-      - references: ""
-      - subsystem:
-          - "Valine, leucine, and isoleucine metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR03753"
       - name: "(S)-3-Hydroxyisobutyryl-CoA hydro-lyase"
@@ -87430,26 +87410,6 @@
       - subsystem:
           - "Valine, leucine, and isoleucine metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR03780"
-      - name: "(S)-3-methyl-2-oxopentanoate:NAD+ 2-oxidoreductase (CoA-methylbutanoylating)"
-      - metabolites: !!omap
-          - MAM00663m: 1
-          - MAM00669m: -1
-          - MAM01596m: 1
-          - MAM01597m: -1
-          - MAM02552m: -1
-          - MAM02553m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.2.1.25"
-      - references: ""
-      - subsystem:
-          - "Valine, leucine, and isoleucine metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR03785"
       - name: "(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA hydro-liase"
@@ -119154,29 +119114,6 @@
       - subsystem:
           - "Beta oxidation of even-chain fatty acids (mitochondrial)"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR03422"
-      - name: ""
-      - metabolites: !!omap
-          - MAM00093m: -1
-          - MAM01261m: 11
-          - MAM01597m: -10
-          - MAM01802m: -5
-          - MAM01803m: 5
-          - MAM02039m: 10
-          - MAM02040m: -10
-          - MAM02552m: -10
-          - MAM02553m: 10
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000060971 or ENSG00000072506 or ENSG00000072778 or ENSG00000084754 or ENSG00000115361 or ENSG00000117054 or ENSG00000127884 or ENSG00000138029 or ENSG00000138796 or ENSG00000167315 or ENSG00000177646"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "4.2.1.17;1.1.1.35;1.1.1.211;1.3.8.7;1.3.8.8;1.3.8.9;2.3.1.16"
-      - references: ""
-      - subsystem:
-          - "Beta oxidation of even-chain fatty acids (mitochondrial)"
-      - confidence_score: 0
     - !!omap
       - id: "MAR03423"
       - name: ""
@@ -232035,7 +231972,7 @@
           - MAM03334m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000072506 or ENSG00000084754 or ENSG00000113790 or ENSG00000133835 or ENSG00000138029 or ENSG00000138796"
+      - gene_reaction_rule: "ENSG00000084754 or ENSG00000072506"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.1.1.35"
@@ -232510,7 +232447,7 @@
           - MAM03351m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000072506 or ENSG00000113790 or ENSG00000133835 or ENSG00000138796"
+      - gene_reaction_rule: "ENSG00000084754 or ENSG00000072506"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.1.1.35"