From ce1c33c5d2357b4814d8998ea1c0861e1677e6a8 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 28 Jul 2023 09:57:29 -0400 Subject: [PATCH 1/6] fix: remove MAR06400 for being a less accurate duplicate of MAR06403 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 25 ------------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 27 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index a23bb63c..970bc613 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -200,3 +200,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00096" "" "BUP2" "" "" "" "BUP2" "MNXR96346" "" "" "" 0 "" "" "BUP2" "MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193" "MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034" +"MAR06400" "R07768" "" "R07768C" "" "" "HMR_6400" "MNXR111356" "HMR_6400" "RCR11944" "" 0 "" "" "HMR_6400" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 94385efb..4bbeb1bf 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -101009,31 +101009,6 @@ - subsystem: - "Lipoic acid metabolism" - confidence_score: 0 - - !!omap - - id: "MAR06400" - - name: "" - - metabolites: !!omap - - MAM01098c: 2 - - MAM02039c: -5 - - MAM02040c: 6 - - MAM02397c: 1 - - MAM02471c: 2 - - MAM02554c: 7 - - MAM02555c: -7 - - MAM02643c: -1 - - MAM02681c: 2 - - MAM02682c: -2 - - MAM02877c: -2 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000121897 or ENSG00000175536" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "2.8.1.8;2.3.1.181" - - references: "" - - subsystem: - - "Lipoic acid metabolism" - - confidence_score: 0 - !!omap - id: "MAR06401" - name: "lipoyl-[acp]:protein N6-lipoyltransferase" diff --git a/model/reactions.tsv b/model/reactions.tsv index 99a89d3d..0da37484 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1671,10 +1671,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06397" "" "" "RE2882C" "" "" "HMR_6397" "" "HMR_6397" "RCR10619" "" 0 "" "" "HMR_6397" "MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398" "MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399" -"MAR06400" "R07768" "" "R07768C" "" "" "HMR_6400" "MNXR111356" "HMR_6400" "RCR11944" "" 0 "" "" "HMR_6400" "MAR06401" "R07769" "" "R07769C" "" "" "HMR_6401" "MNXR111357" "HMR_6401" "RCR11945" "" 0 "" "" "HMR_6401" "MAR06402" "R07766" "" "R07766C" "" "" "HMR_6402" "MNXR111354" "HMR_6402" "RCR11946" "" 0 "" "RHEA:17665" "HMR_6402" -"MAR06403" "R07767" "" "R07767C" "" "" "HMR_6403" "MNXR111355" "HMR_6403" "RCR11947" "" 0 "" "RHEA:16585" "HMR_6403" +"MAR06403" "R07767;R07768" "" "R07767C;R07768C" "" "" "HMR_6403;HMR_6400" "MNXR111355" "HMR_6403;HMR_6400" "RCR11947;RCR11948" "" 0 "" "RHEA:16585" "HMR_6403;HMR_6400;MAR06400" "MAR06404" "R08550" "" "R08550C" "" "" "HMR_6404" "MNXR112089" "HMR_6404" "RCR14491" "" 0 "" "" "HMR_6404" "MAR02472" "" "HMR_2472" "RE3109C" "" "" "HMR_2472" "" "HMR_2472" "RCR11948" "" 0 "" "" "HMR_2472" "MAR02475" "" "RE3110C" "RE3110C" "" "" "RE3110C" "MNXR103792" "HMR_2475" "RCR11949" "" 0 "" "" "HMR_2475" From 83aab8065c8925d46229bd5b2533b85e0fe59ded Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 28 Jul 2023 10:01:55 -0400 Subject: [PATCH 2/6] fix: remove MAR06401 for being a duplicate of MAR06402 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 18 ------------------ model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 20 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 970bc613..ebc76196 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -201,3 +201,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193" "MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034" "MAR06400" "R07768" "" "R07768C" "" "" "HMR_6400" "MNXR111356" "HMR_6400" "RCR11944" "" 0 "" "" "HMR_6400" +"MAR06401" "R07769" "" "R07769C" "" "" "HMR_6401" "MNXR111357" "HMR_6401" "RCR11945" "" 0 "" "" "HMR_6401" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 4bbeb1bf..6784e174 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -101009,24 +101009,6 @@ - subsystem: - "Lipoic acid metabolism" - confidence_score: 0 - - !!omap - - id: "MAR06401" - - name: "lipoyl-[acp]:protein N6-lipoyltransferase" - - metabolites: !!omap - - MAM00184c: 1 - - MAM00209c: 1 - - MAM01350c: -1 - - MAM02397c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000175536" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "2.3.1.181" - - references: "" - - subsystem: - - "Lipoic acid metabolism" - - confidence_score: 0 - !!omap - id: "MAR06402" - name: "octanoyl-[acp]:protein N6-octanoyltransferase" diff --git a/model/reactions.tsv b/model/reactions.tsv index 0da37484..ee787009 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1671,8 +1671,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06397" "" "" "RE2882C" "" "" "HMR_6397" "" "HMR_6397" "RCR10619" "" 0 "" "" "HMR_6397" "MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398" "MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399" -"MAR06401" "R07769" "" "R07769C" "" "" "HMR_6401" "MNXR111357" "HMR_6401" "RCR11945" "" 0 "" "" "HMR_6401" -"MAR06402" "R07766" "" "R07766C" "" "" "HMR_6402" "MNXR111354" "HMR_6402" "RCR11946" "" 0 "" "RHEA:17665" "HMR_6402" +"MAR06402" "R07766;R07769" "" "R07766C;R07769C" "" "" "HMR_6402;HMR_6401" "MNXR111354" "HMR_6402;HMR_6401" "RCR11946;RCR11945" "" 0 "" "RHEA:17665" "HMR_6402;HMR_6401;MAR06401" "MAR06403" "R07767;R07768" "" "R07767C;R07768C" "" "" "HMR_6403;HMR_6400" "MNXR111355" "HMR_6403;HMR_6400" "RCR11947;RCR11948" "" 0 "" "RHEA:16585" "HMR_6403;HMR_6400;MAR06400" "MAR06404" "R08550" "" "R08550C" "" "" "HMR_6404" "MNXR112089" "HMR_6404" "RCR14491" "" 0 "" "" "HMR_6404" "MAR02472" "" "HMR_2472" "RE3109C" "" "" "HMR_2472" "" "HMR_2472" "RCR11948" "" 0 "" "" "HMR_2472" From a9e732a0cd1dea02ec3f29d44abdcde3bcd94c36 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 28 Jul 2023 10:06:30 -0400 Subject: [PATCH 3/6] fix: remove MAM02397c --- model/Human-GEM.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6784e174..2168b4c5 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -32769,14 +32769,6 @@ - charge: -1 - inchis: "" - metFrom: "HMRdatabase" - - !!omap - - id: "MAM02397c" - - name: "lipoyl-[ACP]" - - compartment: "c" - - formula: "C19H33N2O8PRS3" - - charge: -1 - - inchis: "" - - metFrom: "HMRdatabase" - !!omap - id: "MAM02398c" - name: "lipoyl-AMP" From a171e1765f082a22a4931b81c81b5df29e750833 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 28 Jul 2023 10:07:08 -0400 Subject: [PATCH 4/6] fix: update metabolite annotation files --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/metabolites.tsv | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index cd098958..db6b5abb 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2229,3 +2229,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03368x" "MAM03368" "" "C05467" "HMDB0006891" "CHEBI:27379" "440690" "" "CE5169" "" "CE5169" "" "" "CE5169_p" "MAM00902c" "MAM00902" "" "" "" "" "" "" "CE4820" "" "CE4820" "MNXM164259" "m00902c" "m00902c" "MAM00759c" "MAM00759" "" "C13712" "" "" "" "LMST02030130" "" "" "M00759" "MNXM3494" "m00759c" "m00759c" +"MAM02397c" "MAM02397" "" "C16239" "" "" "" "" "" "" "M02397" "MNXM19093" "m02397c" "m02397c" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index ad06d2fc..0c1df8c0 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -4094,7 +4094,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02396n" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396n" "m02396n" "MAM02396x" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396p" "m02396p" "MAM02396r" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396r" "m02396r" -"MAM02397c" "MAM02397" "" "C16239" "" "" "" "" "" "" "M02397" "MNXM19093" "m02397c" "m02397c" "MAM02398c" "MAM02398" "" "C16238" "" "" "23724672" "" "CE5656" "" "CE5656" "MNXM2392" "m02398c" "m02398c" "MAM02399c" "MAM02399" "" "" "" "" "53481572" "" "CE2102" "" "CE2102" "MNXM60228" "m02399c" "m02399c" "MAM02401c" "MAM02401" "" "C03127" "" "CHEBI:29160" "" "" "" "" "M02401" "MNXM89832" "m02401c" "m02401c" From 4dcfc780f35bdd954591103014d6bab214c4b594 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Sat, 14 Oct 2023 19:24:50 -0400 Subject: [PATCH 5/6] feat: added direction-specific RHEA IDs for MAR06402 and MAR06403 --- model/reactions.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index 0ac385b6..8a88ee0c 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1668,8 +1668,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06397" "" "" "RE2882C" "" "" "HMR_6397" "" "HMR_6397" "RCR10619" "" 0 "" "" "HMR_6397" "MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398" "MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399" -"MAR06402" "R07766;R07769" "" "R07766C;R07769C" "" "" "HMR_6402;HMR_6401" "MNXR111354" "HMR_6402;HMR_6401" "RCR11946;RCR11945" "" 0 "" "RHEA:17665" "HMR_6402;HMR_6401;MAR06401" -"MAR06403" "R07767;R07768" "" "R07767C;R07768C" "" "" "HMR_6403;HMR_6400" "MNXR111355" "HMR_6403;HMR_6400" "RCR11947;RCR11948" "" 0 "" "RHEA:16585" "HMR_6403;HMR_6400;MAR06400" +"MAR06402" "R07766;R07769" "" "R07766C;R07769C" "" "" "HMR_6402;HMR_6401" "MNXR111354" "HMR_6402;HMR_6401" "RCR11946;RCR11945" "" 0 "RHEA:17666" "RHEA:17665" "HMR_6402;HMR_6401;MAR06401" +"MAR06403" "R07767;R07768" "" "R07767C;R07768C" "" "" "HMR_6403;HMR_6400" "MNXR111355" "HMR_6403;HMR_6400" "RCR11947;RCR11948" "" 0 "RHEA:16586" "RHEA:16585" "HMR_6403;HMR_6400;MAR06400" "MAR06404" "R08550" "" "R08550C" "" "" "HMR_6404" "MNXR112089" "HMR_6404" "RCR14491" "" 0 "" "" "HMR_6404" "MAR02472" "" "HMR_2472" "RE3109C" "" "" "HMR_2472" "" "HMR_2472" "RCR11948" "" 0 "" "" "HMR_2472" "MAR02475" "" "RE3110C" "RE3110C" "" "" "RE3110C" "MNXR103792" "HMR_2475" "RCR11949" "" 0 "" "" "HMR_2475" From 01a5d1e2d28bb4ebe790c0e4b324bf7c368cb9b1 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Mon, 16 Oct 2023 17:03:15 +0200 Subject: [PATCH 6/6] doc: update Rhea ids for MAR01706 - update Rhea ids as mentioned in #670 --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index f558d1ed..3f161dcc 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -4061,7 +4061,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR01702" "" "" "" "r1012" "" "" "MNXR105423" "HMR_1702" "RCR20518" "" 0 "" "" "HMR_1702" "MAR01703" "R08739" "" "" "" "R-HSA-193452" "HMR_1703" "MNXR124748" "HMR_1703" "RCR13627" "" 0 "" "" "HMR_1703" "MAR01704" "" "" "" "" "R-HSA-193369" "HMR_1704" "MNXR124227" "HMR_1704" "RCR13628" "" 0 "" "" "HMR_1704" -"MAR01706" "R04809" "" "" "" "R-HSA-193535" "HMR_1706" "MNXR123029" "HMR_1706" "RCR13629" "" 0 "" "" "HMR_1706" +"MAR01706" "R04809" "" "" "" "R-HSA-193535" "HMR_1706" "MNXR123029" "HMR_1706" "RCR13629" "" 0 "RHEA:47409" "RHEA:47408" "HMR_1706" "MAR01708" "R04810" "" "" "r1021" "R-HSA-193508" "HMR_1708" "MNXR124228" "HMR_1708" "RCR13630" "" 0 "" "" "HMR_1708" "MAR01710" "R04811" "" "" "" "R-HSA-193533" "HMR_1710" "MNXR109135" "HMR_1710" "RCR13631" "" 0 "" "" "HMR_1710" "MAR01716" "R03974" "" "RE1835X" "" "" "RE1835X" "MNXR103559" "HMR_1716" "RCR14626" "" 0 "" "RHEA:31511" "HMR_1716"