fix: remove MAR01009 for being redundant with MAR03885 and MAR03149,5…

…0,51,53,56,57,58,60,63,64,66
SysBioChalmers · Dec 8, 2023 · 08aa570 · 08aa570
1 parent df8c072
commit 08aa570
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Showing 3 changed files with 13 additions and 36 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -266,3 +266,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06283"	""	"FAOXC6C4m"	""	""	""	"FAOXC6C4m"	""	""	""	""	0	""	""	"FAOXC6C4m"
 "MAR06279"	""	"FAOXC61C4m"	""	""	""	"FAOXC61C4m"	""	""	""	""	0	""	""	"FAOXC61C4m"
 "MAR05449"	""	"FAOXC4020m"	""	""	""	"FAOXC4C2m"	"MNXR99368"	""	""	""	0	""	""	"FAOXC4C2m"
+"MAR01009"	""	"FAOXC80"	""	""	""	"FAOXC80"	"MNXR99373"	""	""	""	0	""	""	"FAOXC80"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -222432,29 +222432,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR01009"
-      - name: "Beta Oxidation of Med/Long Chain Fatty Acid"
-      - metabolites: !!omap
-          - MAM01261m: 4
-          - MAM01597m: -3
-          - MAM01802m: -3
-          - MAM01803m: 3
-          - MAM02039m: 3
-          - MAM02040m: -3
-          - MAM02552m: -3
-          - MAM02553m: 3
-          - MAM02644m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "1.3.99.3"
-      - references: "PMID:2565344;PMID:3035565"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR01012"
       - name: "Fatty Acyl Coenzyme A Synthase (N-C10:0CoA)"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -178,7 +178,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00719"	"R08198"	""	""	""	""	"HMR_0719"	"MNXR111769"	"HMR_0719"	"RCR11097"	""	0	""	"RHEA:13449"	"HMR_0719"
 "MAR01434"	"R00238"	"ACACT1r"	"R00238M"	"r0069"	""	"ACACT1r"	"MNXR95194"	"HMR_1434"	"RCR10465"	""	0	"RHEA:21039"	"RHEA:21036"	"HMR_1434"
 "MAR01436"	"R01357"	"AACOAT"	"R01357M"	"r0320"	""	"AACOAT"	"MNXR95136"	"HMR_1436"	"RCR10466"	""	0	"RHEA:16118"	"RHEA:16117"	"HMR_1436"
-"MAR03163"	"R01175"	"ACOAD1fm;FAOXC4020m"	""	""	"R-HSA-77319"	"ACOAD1fm;FAOXC4C2m"	"MNXR95302"	"HMR_3163"	"RCR11098"	""	0	""	"RHEA:24004"	"HMR_3163;FAOXC4C2m;MAR05449"
+"MAR03163"	"R01175"	"ACOAD1fm;FAOXC4020m;FAOXC80"	""	""	"R-HSA-77319"	"ACOAD1fm;FAOXC4C2m;FAOXC80"	"MNXR95302"	"HMR_3163"	"RCR11098"	""	0	""	"RHEA:24004"	"HMR_3163;FAOXC4C2m;MAR05449;FAOXC80;MAR01009"
 "MAR04461"	"R01361"	"BDHm"	"R01361C"	"r0323"	""	"BDHm"	"MNXR96232"	"HMR_4461"	"RCR10467"	""	0	"RHEA:20524"	"RHEA:20521"	"HMR_4461"
 "MAR04604"	"R01978"	""	"R01978C"	"r0463"	""	"r0463"	"MNXR100660;MNXR107257"	"HMR_4604"	"RCR11099"	""	0	""	"RHEA:10188"	"HMR_4604"
 "MAR05351"	"R01000"	""	""	""	""	"2HBO"	"MNXR94796"	"HMR_5351"	"RCR10152"	""	0	""	"RHEA:36371"	"HMR_5351"
@@ -740,9 +740,9 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08026"	""	"LYSMTF2n"	""	""	""	"LYSMTF2n"	"MNXR101260"	"HMR_8026"	"RCR11349"	""	0	""	""	"HMR_8026"
 "MAR08027"	"R04867"	"LYSMTF3n"	""	""	""	"LYSMTF3n"	"MNXR101261"	"HMR_8027"	"RCR11350"	""	0	""	"RHEA:54200"	"HMR_8027"
 "MAR08029"	""	"PLYSPSer"	""	""	""	"PLYSPSer"	"MNXR103039"	"HMR_8029"	"RCR14338"	""	0	""	""	"HMR_8029"
-"MAR03164"	"R03026"	"ECOAH1m;FAOXC4020m"	"R03026M"	"r0588"	""	"ECOAH1m;FAOXC4C2m"	"MNXR97883"	"HMR_3164"	"RCR11351"	""	0	""	"RHEA:26558"	"HMR_3164;FAOXC4C2m;MAR05449"
-"MAR03166"	"R01975"	"HACD1m;FAOXC4020m"	"R01975M"	"r0460"	""	"HACD1m;FAOXC4C2m"	"MNXR100541"	"HMR_3166"	"RCR11352"	""	0	""	"RHEA:30799"	"HMR_3166;FAOXC4C2m;MAR05449"
-"MAR03885"	"R00238"	"ACACT1m;FAOXC4020m"	"R00238M"	"r0070"	""	"ACACT1rm;FAOXC4C2m"	"MNXR95194"	"HMR_3885"	"RCR10247"	""	0	"RHEA:21039"	"RHEA:21036"	"HMR_3885;FAOXC4C2m;MAR05449"
+"MAR03164"	"R03026"	"ECOAH1m;FAOXC4020m;FAOXC80"	"R03026M"	"r0588"	""	"ECOAH1m;FAOXC4C2m;FAOXC80"	"MNXR97883"	"HMR_3164"	"RCR11351"	""	0	""	"RHEA:26558"	"HMR_3164;FAOXC4C2m;MAR05449;FAOXC80;MAR01009"
+"MAR03166"	"R01975"	"HACD1m;FAOXC4020m;FAOXC80"	"R01975M"	"r0460"	""	"HACD1m;FAOXC4C2m;FAOXC80"	"MNXR100541"	"HMR_3166"	"RCR11352"	""	0	""	"RHEA:30799"	"HMR_3166;FAOXC4C2m;MAR05449;FAOXC80;MAR01009"
+"MAR03885"	"R00238"	"ACACT1m;FAOXC4020m;FAOXC80"	"R00238M"	"r0070"	""	"ACACT1rm;FAOXC4C2m;FAOXC80"	"MNXR95194"	"HMR_3885"	"RCR10247"	""	0	"RHEA:21039"	"RHEA:21036"	"HMR_3885;FAOXC4C2m;MAR05449;FAOXC80;MAR01009"
 "MAR04250"	"R04293"	"QUILSYN"	""	"r0675"	""	"QUILSYN"	"MNXR103396"	"HMR_4250"	"RCR11353"	""	1	""	"RHEA:25147"	"HMR_4250"
 "MAR08091"	""	"3HXKYNDCL"	""	""	""	"3HXKYNDCL"	"MNXR94906"	"HMR_8091"	"RCR11354"	""	0	""	""	"HMR_8091"
 "MAR08092"	"R04907"	"3HXKYNOXDA"	""	""	""	"3HXKYNOXDA"	"MNXR94907"	"HMR_8092"	"RCR11355"	""	0	""	""	"HMR_8092"
@@ -2649,14 +2649,14 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03143"	"R04744"	""	"R04744X"	"r0728"	""	"r0728"	"MNXR97889"	"HMR_3143"	"RCR12646"	""	0	""	"RHEA:31191"	"HMR_3143"
 "MAR03144"	"R04743"	""	"R04743X"	"r0726"	""	"r0726"	"MNXR100545"	"HMR_3144"	"RCR12647"	""	0	""	"RHEA:31187"	"HMR_3144"
 "MAR03146"	"R03778"	""	"R03778X"	"r0634"	""	"r0634"	"MNXR95198"	"HMR_3146"	"RCR12648"	""	0	"RHEA:31089"	"RHEA:31087"	"HMR_3146"
-"MAR03149"	"R03777"	"r1448;FAOXC8C6m"	""	""	"R-HSA-77338"	"HMR_3149;r1448i;FAOXC6C8m"	"MNXR95304"	"HMR_3149"	"RCR12649"	""	0	""	"RHEA:30943"	"HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329"
-"MAR03150"	"R04746"	"FAOXC8C6m"	"R04746M"	"r0731"	""	"r0731;FAOXC8C6m"	"MNXR97888"	"HMR_3150"	"RCR12650"	""	0	""	"RHEA:31199"	"HMR_3150;FAOXC6C8m;MAR06329"
-"MAR03151"	"R04745"	"FAOXC8C6m"	"R04745M"	"r0730"	""	"r0730;FAOXC8C6m"	"MNXR100544"	"HMR_3151"	"RCR12651"	""	0	""	"RHEA:31195"	"HMR_3151;FAOXC8C6m;MAR06329"
-"MAR03153"	"R04747"	"FAOXC8C6m"	"R04747M"	"r0732"	""	"r0732;FAOXC8C6m"	"MNXR109092"	"HMR_3153"	"RCR12652"	""	0	"RHEA:31205"	"RHEA:31203"	"HMR_3153;FAOXC8C6m;MAR06329"
-"MAR03156"	"R04751"	"r1450;FAOXC6C4m"	""	""	"R-HSA-77327"	"HMR_3156;r1450;FAOXC6C4m"	"MNXR109093"	"HMR_3156"	"RCR12653"	""	0	""	"RHEA:31207"	"HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283"
-"MAR03157"	"R04749"	"FAOXC6C4m;FAOXC61C4m"	"R04749M"	"r0734"	""	"r0734;FAOXC6C4m;FAOXC61C4m"	"MNXR97886"	"HMR_3157"	"RCR12654"	""	0	""	"RHEA:30547"	"HMR_3157;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279"
-"MAR03158"	"R04748"	"FAOXC6C4m;FAOXC61C4m"	"R04748M"	"r0733"	"R-HSA-77323"	"r0733;FAOXC6C4m;FAOXC61C4m"	"MNXR100543"	"HMR_3158"	"RCR12655"	""	0	""	"RHEA:31143"	"HMR_3158;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279"
-"MAR03160"	"R01177"	"FAOXC6C4m;FAOXC61C4m"	"R01177M"	"r0287"	"R-HSA-77321"	"r0287;FAOXC6C4m;FAOXC61C4m"	"MNXR95196"	"HMR_3160"	"RCR12656"	""	0	""	"RHEA:31111"	"HMR_3160;FAOXC6C4m;MAR03160;FAOXC61C4m;MAR06279"
+"MAR03149"	"R03777"	"r1448;FAOXC8C6m;FAOXC80"	""	""	"R-HSA-77338"	"HMR_3149;r1448i;FAOXC6C8m;FAOXC80"	"MNXR95304"	"HMR_3149"	"RCR12649"	""	0	""	"RHEA:30943"	"HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009"
+"MAR03150"	"R04746"	"FAOXC8C6m;FAOXC80"	"R04746M"	"r0731"	""	"r0731;FAOXC8C6m;FAOXC80"	"MNXR97888"	"HMR_3150"	"RCR12650"	""	0	""	"RHEA:31199"	"HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009"
+"MAR03151"	"R04745"	"FAOXC8C6m;FAOXC80"	"R04745M"	"r0730"	""	"r0730;FAOXC8C6m;FAOXC80"	"MNXR100544"	"HMR_3151"	"RCR12651"	""	0	""	"RHEA:31195"	"HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009"
+"MAR03153"	"R04747"	"FAOXC8C6m;FAOXC80"	"R04747M"	"r0732"	""	"r0732;FAOXC8C6m;FAOXC80"	"MNXR109092"	"HMR_3153"	"RCR12652"	""	0	"RHEA:31205"	"RHEA:31203"	"HMR_3153;FAOXC8C6m;MAR06329;FAOXC80;MAR01009"
+"MAR03156"	"R04751"	"r1450;FAOXC6C4m;FAOXC80"	""	""	"R-HSA-77327"	"HMR_3156;r1450;FAOXC6C4m;FAOXC80"	"MNXR109093"	"HMR_3156"	"RCR12653"	""	0	""	"RHEA:31207"	"HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283;FAOXC80;MAR01009"
+"MAR03157"	"R04749"	"FAOXC6C4m;FAOXC61C4m;FAOXC80"	"R04749M"	"r0734"	""	"r0734;FAOXC6C4m;FAOXC61C4m;FAOXC80"	"MNXR97886"	"HMR_3157"	"RCR12654"	""	0	""	"RHEA:30547"	"HMR_3157;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009"
+"MAR03158"	"R04748"	"FAOXC6C4m;FAOXC61C4m;FAOXC80"	"R04748M"	"r0733"	"R-HSA-77323"	"r0733;FAOXC6C4m;FAOXC61C4m;FAOXC80"	"MNXR100543"	"HMR_3158"	"RCR12655"	""	0	""	"RHEA:31143"	"HMR_3158;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009"
+"MAR03160"	"R01177"	"FAOXC6C4m;FAOXC61C4m;FAOXC80"	"R01177M"	"r0287"	"R-HSA-77321"	"r0287;FAOXC6C4m;FAOXC61C4m;FAOXC80"	"MNXR95196"	"HMR_3160"	"RCR12656"	""	0	""	"RHEA:31111"	"HMR_3160;FAOXC6C4m;MAR03160;FAOXC61C4m;MAR06279;FAOXC80;MAR01009"
 "MAR03398"	""	"HMR_3398"	""	""	""	"HMR_3398"	""	"HMR_3398"	"RCR12657"	""	0	""	""	"HMR_3398"
 "MAR03406"	""	"HMR_3406"	""	""	""	"HMR_3406"	""	"HMR_3406"	"RCR12658"	""	0	""	""	"HMR_3406"
 "MAR03407"	""	""	""	""	""	"HMR_3407"	""	"HMR_3407"	"RCR12659"	""	0	""	""	"HMR_3407"
@@ -8291,7 +8291,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00982"	""	"FAOXC2452256x"	""	""	""	"FAOXC2452256x"	"MNXR99365"	""	""	""	0	""	""	"FAOXC2452256x"
 "MAR01001"	""	"FAOXC246226x"	""	""	""	"FAOXC246226x"	"MNXR99366"	""	""	""	0	""	""	"FAOXC246226x"
 "MAR01005"	""	"FAOXC260240x"	""	""	""	"FAOXC260240x"	"MNXR99367"	""	""	""	0	""	""	"FAOXC260240x"
-"MAR01009"	""	"FAOXC80"	""	""	""	"FAOXC80"	"MNXR99373"	""	""	""	0	""	""	"FAOXC80"
 "MAR01012"	""	"FAS100COA"	""	""	""	"FAS100COA"	"MNXR99385"	""	""	""	0	""	""	"FAS100COA"
 "MAR01019"	""	"FAS120COA"	""	""	""	"FAS120COA"	"MNXR99389"	""	""	""	0	""	""	"FAS120COA"
 "MAR01024"	""	"FAS140COA"	""	""	""	"FAS140COA"	"MNXR99393"	""	""	""	0	""	""	"FAS140COA"