Merge branch 'develop' into fix-LDH

SysBioChalmers · Apr 23, 2023 · 1a44fc6 · 1a44fc6
2 parents 6405dcf + 981b6fc
commit 1a44fc6
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diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2191,3 +2191,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00156c"	"MAM00156"	""	""	""	""	"53481438"	""	"CE2196"	""	"CE2196"	"MNXM31535"	"m00156c"	"m00156c"
 "MAM02045c"	"MAM02045"	""	"C09209"	""	"CHEBI:5623"	"5281404"	""	""	""	"C09209"	"MNXM11747"	"m02045c"	"m02045c"
 "MAM00077x"	"MAM00077"	"CE2416"	""	""	""	""	""	"CE2416"	""	""	"MNXM165274"	"m00077p"	"m00077p"
+"MAM01703m"	"MAM01703"	"dhlpro"	"C02972"	""	"CHEBI:16194"	""	""	""	""	"dhlpro"	"MNXM1663"	"m01703m"	"m01703m"
+"MAM02400m"	"MAM02400"	"lpro"	"C02051"	""	"CHEBI:15804"	""	""	""	""	"lpro"	"MNXM998"	"m02400m"	"m02400m"
+"MAM02879m"	"MAM02879"	"alpro"	"C01242"	""	"CHEBI:16882"	""	""	""	""	"alpro"	"MNXM81221"	"m02879m"	"m02879m"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -72,3 +72,8 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04588"	""	""	""	"r0425"	""	"r0425"	"MNXR105341"	"HMR_4588"	"RCR11669"	""	0	""	""	"HMR_4588"
 "MAR03488"	""	""	"RE3073X"	""	""	""	"MNXR95747"	"HMR_3488"	"RCR12589"	""	0	""	""	"HMR_3488"
 "MAR03489"	""	""	"RE3079X"	""	""	""	""	"HMR_3489"	"RCR12590"	""	0	""	""	"HMR_3489"
+"MAR04456"	"R01324"	"ACONTm"	"R01324C"	"r0316"	""	"ACONTm"	"MNXR95384"	"HMR_4456"	"RCR10351"	""	0	""	"RHEA:10336"	"HMR_4456"
+"MAR08435"	"R03425"	"GCCcm"	""	""	""	"GCCam"	"MNXR100067;MNXR100069"	"HMR_8435"	"RCR10246"	""	0	""	"RHEA:24304"	"HMR_8435"
+"MAR08436"	"R04125"	"GCHOLAt"	""	""	""	"GCCbim"	"MNXR100068;MNXR100070"	"HMR_8436"	"RCR11319"	""	0	""	"RHEA:16945"	"HMR_8436"
+"MAR08437"	"R03815"	"GCHOLAt2"	""	""	""	"GCCcm"	"MNXR100069;MNXR100071"	"HMR_8437"	"RCR11320"	""	0	""	""	"HMR_8437"
+"MAR03923"	"R01221"	"GLYCLm"	"R01221C"	"r0295"	""	"r0295"	"MNXR100330"	"HMR_3923"	"RCR10962"	""	0	""	"RHEA:27758"	"HMR_3923"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -23044,14 +23044,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM01703m"
-      - name: "dihydrolipoylprotein"
-      - compartment: "m"
-      - formula: "H2S2X"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM01704c"
       - name: "dihydroneopterin"
@@ -32860,14 +32852,6 @@
       - charge: 0
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM02400m"
-      - name: "lipoylprotein"
-      - compartment: "m"
-      - formula: "S2X"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02401c"
       - name: "L-isoleucyl-tRNA(ile)"
@@ -39812,14 +39796,6 @@
       - charge: 1
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM02879m"
-      - name: "S-aminomethyldihydrolipoylprotein"
-      - compartment: "m"
-      - formula: "CH6NS2X"
-      - charge: 1
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02880c"
       - name: "sarcosine"
@@ -80422,7 +80398,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.4.19.9"
-      - references: "PMID:12909365;PMID:16859665"
+      - references: "PMID:12909365;PMID:16859665;PMID:17171578"
       - subsystem:
           - "Glycine, serine and threonine metabolism"
       - confidence_score: 0
@@ -80437,7 +80413,7 @@
           - MAM02553m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
+      - gene_reaction_rule: "ENSG00000091140"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.8.1.4;2.1.2.10"
@@ -80493,11 +80469,11 @@
           - MAM02878m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
+      - gene_reaction_rule: "ENSG00000140905 and ENSG00000178445"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.8.1.4;2.1.2.10"
-      - references: ""
+      - references: "PMID:24798336"
       - subsystem:
           - "Glycine, serine and threonine metabolism"
       - confidence_score: 0
@@ -80513,69 +80489,11 @@
           - MAM02980m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.8.1.4;2.1.2.10"
-      - references: ""
-      - subsystem:
-          - "Glycine, serine and threonine metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR08435"
-      - name: "glycine:lipoylprotein oxidoreductase (decarboxylating and acceptor-aminomethylating)"
-      - metabolites: !!omap
-          - MAM01596m: 1
-          - MAM01986m: -1
-          - MAM02039m: -1
-          - MAM02400m: -1
-          - MAM02879m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.4.4.2"
-      - references: ""
-      - subsystem:
-          - "Glycine, serine and threonine metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR08436"
-      - name: "[protein]-S8-aminomethyldihydrolipoyllysine:tetrahydrofolate aminomethyltransferase (ammonia-forming)"
-      - metabolites: !!omap
-          - MAM01045m: 1
-          - MAM01703m: 1
-          - MAM02039m: 1
-          - MAM02578m: 1
-          - MAM02879m: -1
-          - MAM02980m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
+      - gene_reaction_rule: "ENSG00000140905 and ENSG00000145020"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.8.1.4;2.1.2.10"
-      - references: ""
-      - subsystem:
-          - "Glycine, serine and threonine metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR08437"
-      - name: "dihydrolipoylprotein:NAD+ oxidoreductase"
-      - metabolites: !!omap
-          - MAM01703m: 1
-          - MAM02039m: -1
-          - MAM02400m: -1
-          - MAM02552m: 1
-          - MAM02553m: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.8.1.4;2.1.2.10"
-      - references: ""
+      - references: "PMID:24798336"
       - subsystem:
           - "Glycine, serine and threonine metabolism"
       - confidence_score: 0
@@ -94538,23 +94456,7 @@
           - MAM02183c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000122729 or ENSG00000136381"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "4.2.1.3"
-      - references: "PMID:15263083;PMID:16511074"
-      - subsystem:
-          - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR04456"
-      - name: "citrate hydroxymutase"
-      - metabolites: !!omap
-          - MAM01587m: -1
-          - MAM02183m: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729"
+      - gene_reaction_rule: "ENSG00000122729"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.3"
@@ -94571,7 +94473,7 @@
           - MAM02040m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729"
+      - gene_reaction_rule: "ENSG00000100412"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.3"
@@ -94607,7 +94509,7 @@
           - MAM02183m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729"
+      - gene_reaction_rule: "ENSG00000100412"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.3"
@@ -95072,7 +94974,7 @@
           - MAM02630m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111775 and ENSG00000112695 and ENSG00000126267 and ENSG00000127184 and ENSG00000131143 and ENSG00000131174 and ENSG00000135940 and ENSG00000164919 and ENSG00000176340 and ENSG00000178741 and ENSG00000198712 and ENSG00000198804 and ENSG00000198938 and ENSG00000189043"
+      - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.9.3.1"
@@ -153357,28 +153259,6 @@
       - subsystem:
           - "Inositol phosphate metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR03923"
-      - name: "glycine:NAD+ 2-oxidoreductase (tetrahydrofolate-methylene-adding)"
-      - metabolites: !!omap
-          - MAM01045m: 1
-          - MAM01596m: 1
-          - MAM01986m: -1
-          - MAM02039m: 1
-          - MAM02552m: -1
-          - MAM02553m: 1
-          - MAM02578m: 1
-          - MAM02980m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.8.1.4;2.1.2.10"
-      - references: "PMID:7916605"
-      - subsystem:
-          - "Folate metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR03925"
       - name: "5,6,7,8-tetrahydrobiopterin:NAD+ oxidoreductase"
@@ -210078,7 +209958,7 @@
           - MAM01968r: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105220 or ENSG00000137700"
+      - gene_reaction_rule: "ENSG00000281500"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -210574,7 +210454,7 @@
           - MAM02751r: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000137700"
+      - gene_reaction_rule: "ENSG00000281500"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -226875,7 +226755,7 @@
           - MAM02751r: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000137700"
+      - gene_reaction_rule: "ENSG00000281500"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -302937,9 +302817,9 @@
           - MAM02630m: -1
           - MAM02631m: 0.02
       - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111775 and ENSG00000112695 and ENSG00000126267 and ENSG00000127184 and ENSG00000131055 and ENSG00000131143 and ENSG00000131174 and ENSG00000135940 and ENSG00000156885 and ENSG00000160471 and ENSG00000161281 and ENSG00000164919 and ENSG00000170516 and ENSG00000176340 and ENSG00000178741 and ENSG00000187581 and ENSG00000198712 and ENSG00000198804 and ENSG00000198938"
-      - rxnNotes: ""
+      - upper_bound: 0
+      - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043"
+      - rxnNotes: "This is ROS version of Complex IV, and blocked by default"
       - rxnFrom: "Recon3D"
       - eccodes: ""
       - references: ""
@@ -309398,8 +309278,6 @@
       - id: "ENSG00000136267"
     - !!omap
       - id: "ENSG00000136371"
-    - !!omap
-      - id: "ENSG00000136381"
     - !!omap
       - id: "ENSG00000136448"
     - !!omap
@@ -309470,8 +309348,6 @@
       - id: "ENSG00000137563"
     - !!omap
       - id: "ENSG00000137574"
-    - !!omap
-      - id: "ENSG00000137700"
     - !!omap
       - id: "ENSG00000137731"
     - !!omap
@@ -311934,8 +311810,6 @@
       - id: "ENSG00000187555"
     - !!omap
       - id: "ENSG00000187566"
-    - !!omap
-      - id: "ENSG00000187581"
     - !!omap
       - id: "ENSG00000187630"
     - !!omap
@@ -312586,6 +312460,8 @@
       - id: "ENSG00000277893"
     - !!omap
       - id: "ENSG00000278540"
+    - !!omap
+      - id: "ENSG00000281500"
     - !!omap
       - id: "ENSG00000288702"
     - !!omap