fix: removed MAR04843, MAR07823, MAR07926, and MAR09019 for being uns…

…upported by evidence
SysBioChalmers · Oct 16, 2023 · a7a9252 · a7a9252
1 parent 8e11d3a
commit a7a9252
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Showing 3 changed files with 4 additions and 70 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -241,3 +241,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR07790"	""	"FADtx"	""	""	""	"FADtx"	"MNXR99217"	"HMR_7790"	"RCR20203"	""	0	""	""	"HMR_7790"
 "MAR08564"	""	"KYNAKGAT"	""	""	""	"KYNAKGAT"	"MNXR100948"	"HMR_8564"	"RCR11356"	""	0	""	""	"HMR_8564"
 "MAR08565"	"R03445"	"KYNATESYN"	""	""	""	"KYNATESYN"	"MNXR100949"	"HMR_8565"	"RCR11357"	""	0	""	"RHEA:42452"	"HMR_8565"
+"MAR04843"	""	""	""	"r0801"	""	"r0801"	"MNXR105390"	"HMR_4843"	"RCR20168"	""	0	""	""	"HMR_4843"
+"MAR09019"	""	""	""	""	""	"HMR_9019"	""	"HMR_9019"	"RCR20242"	""	0	""	""	"HMR_9019"
+"MAR07823"	""	"DNDPt51m"	""	""	""	"DCTPtm"	"MNXR97204"	""	""	""	0	""	""	"DCTPtm"
+"MAR07926"	""	"DGTPtm"	""	""	""	"DGTPtm"	"MNXR97327"	""	""	""	0	""	""	"DGTPtm"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -195112,22 +195112,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR09019"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01424c: -1
-          - MAM01424m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR09020"
       - name: ""
@@ -196237,24 +196221,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04843"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01948c: -1
-          - MAM01948m: 1
-          - MAM02034c: 1
-          - MAM02034m: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: "PMID:11078702"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04850"
       - name: ""
@@ -244901,38 +244867,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR07823"
-      - name: "Transport of dCTP into Mitochondria"
-      - metabolites: !!omap
-          - MAM01645c: -1
-          - MAM01645m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:16816105;PMID:17403938"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR07926"
-      - name: "Transport of dGTP into Mitochondria"
-      - metabolites: !!omap
-          - MAM01688c: -1
-          - MAM01688m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:16816105;PMID:17403938"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR08111"
       - name: "Transport of Dihydroxyacetone Phosphate into Cytosol"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -6644,7 +6644,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08022"	""	"2AMADPTm"	""	""	""	"2AMADPTm"	"MNXR94780"	"HMR_8022"	"RCR20241"	""	0	""	""	"HMR_8022"
 "MAR08070"	""	""	""	""	""	"SLDtm"	""	"HMR_8070"	"RCR20536"	""	0	""	""	"HMR_8070"
 "MAR09015"	""	""	""	""	""	"AMETtd"	""	"HMR_9015"	"RCR20135"	""	0	""	""	"HMR_9015"
-"MAR09019"	""	""	""	""	""	"HMR_9019"	""	"HMR_9019"	"RCR20242"	""	0	""	""	"HMR_9019"
 "MAR09020"	""	""	""	""	""	"FADtm"	""	"HMR_9020"	"RCR20537"	""	0	""	""	"HMR_9020"
 "MAR00157"	""	""	""	""	""	"HMR_0157"	""	"HMR_0157"	"RCR20164"	""	0	""	""	"HMR_0157"
 "MAR00158"	""	""	""	"r1401"	""	"r1401"	"MNXR105470"	"HMR_0158"	"RCR20165"	""	0	""	""	"HMR_0158"
@@ -6712,7 +6711,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04754"	""	"PPPG9tm"	""	"r0976"	""	"PPPG9tm"	"MNXR103127"	"HMR_4754"	"RCR20570"	"3.A.1.210"	0	"RHEA:27649"	"RHEA:27646"	"HMR_4754"
 "MAR04756"	""	"HMR_4756"	""	""	""	"HMR_4756"	""	"HMR_4756"	"RCR20262"	""	0	""	""	"HMR_4756"
 "MAR04760"	""	"PHEMEtm"	""	"r0880"	""	"PHEMEtm"	"MNXR102625"	"HMR_4760"	"RCR20571"	"3.A.1.210"	0	""	""	"HMR_4760"
-"MAR04843"	""	""	""	"r0801"	""	"r0801"	"MNXR105390"	"HMR_4843"	"RCR20168"	""	0	""	""	"HMR_4843"
 "MAR04850"	""	""	""	"r0818"	""	"r0818"	"MNXR97813"	"HMR_4850"	"RCR20572"	""	0	""	""	"HMR_4850"
 "MAR04851"	""	""	""	"r0819"	""	"r0819"	"MNXR105393"	"HMR_4851"	"RCR20573"	"2.A.29.2.2"	0	""	""	"HMR_4851"
 "MAR04852"	""	"AKGMALtm"	""	"r0820"	""	"AKGMALtm"	"MNXR95659"	"HMR_4852"	"RCR20169"	"2.A.29.2.2"	0	""	""	"HMR_4852"
@@ -9516,8 +9514,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR07817"	""	"CYSAMOe"	""	""	""	"CYSAMOe"	"MNXR96988"	""	""	""	0	"RHEA:14410"	"RHEA:14409"	"CYSAMOe"
 "MAR07819"	""	"Coqe"	""	""	""	"Coqe"	"MNXR97066"	""	""	""	0	""	""	"Coqe"
 "MAR07821"	""	"DATPtm_cho"	""	""	""	"DATPtm"	"MNXR97176"	""	""	""	0	""	""	"DATPtm"
-"MAR07823"	""	"DNDPt51m"	""	""	""	"DCTPtm"	"MNXR97204"	""	""	""	0	""	""	"DCTPtm"
-"MAR07926"	""	"DGTPtm"	""	""	""	"DGTPtm"	"MNXR97327"	""	""	""	0	""	""	"DGTPtm"
 "MAR08111"	""	"DHAPtm"	""	""	""	"DHAPtc"	"MNXR97366"	""	""	""	0	""	""	"DHAPtc"
 "MAR08204"	""	"DPCOAPPe"	""	""	""	"DPCOAPPe"	"MNXR97763"	""	""	""	0	""	""	"DPCOAPPe"
 "MAR08218"	""	"DSREDUCr"	""	""	""	"DSREDUCr"	""	""	""	""	0	""	""	"DSREDUCr"