From 08aa570a3ebf13cf2422bf27cd8d8b9c2aa4d54f Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 09:37:49 -0500 Subject: [PATCH] fix: remove MAR01009 for being redundant with MAR03885 and MAR03149,50,51,53,56,57,58,60,63,64,66 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 23 ----------------- model/reactions.tsv | 25 +++++++++---------- 3 files changed, 13 insertions(+), 36 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index f7610e91..7a07508c 100644 --- 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 index df1c6b03..3ffcbca4 100644 --- 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 index 48e866d4..b4084e75 100644 --- 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"