Merge pull request #706 from SysBioChalmers/fix/lipoate_transport

Fix Duplicate Lipoic Acid Transport Reactions
SysBioChalmers · Oct 16, 2023 · 04837d1 · 04837d1
2 parents 4d59404 + bc6d7b6
commit 04837d1
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Showing 3 changed files with 4 additions and 50 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -241,3 +241,5 @@ 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"
+"MAR01483"	""	"LIPOti"	""	""	""	"LIPOti"	"MNXR101093"	""	""	""	0	""	""	"LIPOti"
+"MAR06406"	""	"LIPOti"	"RT1089"	""	""	""	"MNXR101093"	"HMR_6406"	"RCR41534"	""	0	""	""	"HMR_6406"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -188389,29 +188389,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR06406"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01285c: 1
-          - MAM01371c: -1
-          - MAM02039c: 1
-          - MAM02040c: -1
-          - MAM02394c: 1
-          - MAM02394e: -1
-          - MAM02519c: 2
-          - MAM02519e: -2
-          - MAM02751c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000138074"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: "PMID:16415531"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR06424"
       - name: ""
@@ -194172,7 +194149,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
-      - references: ""
+      - references: "PMID:9516450;PMID:10329687;PMID:15561972"
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
@@ -224010,29 +223987,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR01483"
-      - name: "Transport of Lipoate  via Sodium Symport"
-      - metabolites: !!omap
-          - MAM01285c: 1
-          - MAM01371c: -1
-          - MAM02039c: 1
-          - MAM02040c: -1
-          - MAM02394c: 1
-          - MAM02394e: -1
-          - MAM02519c: 1
-          - MAM02519e: -1
-          - MAM02751c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000138074"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:10329687;PMID:10334869;PMID:12646417;PMID:15561972;PMID:9516450"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR01485"
       - name: "Transport of L-Lactate via Diffusion, Mitochondrial"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -6253,7 +6253,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06383"	""	"HOMt4"	""	"r2480"	""	""	"MNXR100677"	"HMR_6383"	"RCR41531"	"2.A.18.6.8"	0	""	""	"HMR_6383"
 "MAR06384"	""	"HISt4"	""	"r2481"	""	"HISSNAT5tc"	"MNXR100646"	"HMR_6384"	"RCR41532"	"2.A.18.6.2"	0	""	""	"HMR_6384"
 "MAR06392"	""	""	""	"r2505"	""	"r2505"	"MNXR106316"	"HMR_6392"	"RCR41533"	"3.A.1.208.8"	0	""	""	"HMR_6392"
-"MAR06406"	""	"LIPOti"	"RT1089"	""	""	""	"MNXR101093"	"HMR_6406"	"RCR41534"	""	0	""	""	"HMR_6406"
 "MAR06424"	""	"AVITE2t"	"RT1352"	""	""	"AVITE2t"	"MNXR96147"	"HMR_6424"	"RCR40703"	""	0	""	""	"HMR_6424"
 "MAR06439"	""	""	""	""	""	"HMR_6439"	""	"HMR_6439"	"RCR40704"	""	0	""	""	"HMR_6439"
 "MAR06462"	""	""	""	""	""	"YVITEt"	""	"HMR_6462"	"RCR40705"	""	0	""	""	"HMR_6462"
@@ -6587,7 +6586,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR09605"	""	""	""	""	""	"HMR_9605"	""	"HMR_9605"	"RCR41621"	""	0	""	""	"HMR_9605"
 "MAR09606"	""	""	""	""	""	"GLYSNAT5tc"	""	"HMR_9606"	"RCR41622"	""	0	""	""	"HMR_9606"
 "MAR09607"	""	""	""	""	""	"HMR_9607"	""	"HMR_9607"	"RCR41623"	""	0	""	""	"HMR_9607"
-"MAR09608"	""	""	""	""	""	"HMR_9608"	""	"HMR_9608"	"RCR41624"	""	0	""	""	"HMR_9608"
+"MAR09608"	""	"LIPOti"	"RT1089"	""	""	"HMR_9608;LIPOti"	"MNXR101093"	"HMR_9608;HMR_6406"	"RCR41624;RCR41534"	""	0	"RHEA:73380"	"RHEA:73379"	"HMR_9608;LIPOti;HMR_6406;MAR01483;MAR06406"
 "MAR09609"	""	""	""	""	""	"HMR_9609"	""	"HMR_9609"	"RCR41625"	""	0	""	""	"HMR_9609"
 "MAR09610"	""	""	""	""	""	"HMR_9610"	""	"HMR_9610"	"RCR41626"	""	0	""	""	"HMR_9610"
 "MAR09611"	""	""	""	""	""	"INSTt2r"	""	"HMR_9611"	"RCR40899"	""	0	""	""	"HMR_9611"
@@ -8375,7 +8374,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR01480"	""	"LEUt5m"	""	""	""	"LEUt5m"	"MNXR101057"	""	""	""	0	""	""	"LEUt5m"
 "MAR01481"	""	"LGNCCPT2"	""	""	""	"LGNCCPT2"	"MNXR101063"	""	""	""	0	""	""	"LGNCCPT2"
 "MAR01482"	""	"LGNCCRNt"	""	""	""	"LGNCCRNt"	"MNXR101064"	""	""	""	0	""	""	"LGNCCRNt"
-"MAR01483"	""	"LIPOti"	""	""	""	"LIPOti"	"MNXR101093"	""	""	""	0	""	""	"LIPOti"
 "MAR01485"	""	"L_LACtcm"	""	""	""	"L_LACtcm"	"MNXR100999"	""	""	""	0	""	""	"L_LACtcm"
 "MAR01486"	""	"LNELDCCRNt"	""	""	""	"LNELDCCRNt"	"MNXR101102"	""	""	""	0	""	""	"LNELDCCRNt"
 "MAR01487"	""	"LNLCCRNt"	""	""	""	"LNLCCRNt"	"MNXR101106"	""	""	""	0	""	""	"LNLCCRNt"