From bf88f4e5b086962cc63f9fb6585f1b253b5cbcc2 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 8 Nov 2023 16:51:38 -0500 Subject: [PATCH 1/7] fix: removed MAR04940 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 18 ------------------ model/reactions.tsv | 1 - 3 files changed, 1 insertion(+), 19 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 3fed26a3..7eed79f3 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -259,3 +259,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3" "MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" "MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc" +"MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8eebb91e..555e41f1 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -196414,24 +196414,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR04940" - - name: "" - - metabolites: !!omap - - MAM02026c: -1 - - MAM02026m: 1 - - MAM02751c: 1 - - MAM02751m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000183048" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "PMID:15845418;PMID:16600197;PMID:9639574" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR04944" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 7a7e75d4..7829b155 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6725,7 +6725,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04914" "" "COAtim" "" "r0863" "" "COAtm" "MNXR96815" "HMR_4914" "RCR20001" "" 0 "" "" "HMR_4914" "MAR04922" "" "CO2tm" "" "r0868" "" "CO2tm" "MNXR96810" "HMR_4922" "RCR20011" "" 0 "" "" "HMR_4922" "MAR04926" "" "PYRt2m" "" "r0872" "" "PYRt2m" "MNXR103385" "HMR_4926" "RCR20136" "" 0 "" "" "HMR_4926" -"MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" "MAR04944" "" "FORtm" "" "r0888" "" "FORt2m" "MNXR99620" "HMR_4944" "RCR20583" "" 0 "RHEA:29682" "RHEA:29679" "HMR_4944" "MAR04951" "" "UREAtm" "" "r0897" "" "UREAtm" "MNXR105156" "HMR_4951" "RCR20266" "" 0 "RHEA:32802" "RHEA:32799" "HMR_4951" "MAR04953" "" "BALAtmr" "" "r0900" "" "BALAtmr" "MNXR95682" "HMR_4953" "RCR20584" "" 0 "" "" "HMR_4953" From 5dbfb45284244cff33ec832d1278754712eaa55d Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 8 Nov 2023 16:52:47 -0500 Subject: [PATCH 2/7] fix: removed MAR06391 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 18 ------------------ model/reactions.tsv | 1 - 3 files changed, 1 insertion(+), 19 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 7eed79f3..7312d142 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -260,3 +260,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" "MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc" "MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" +"MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 555e41f1..330accae 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -198398,24 +198398,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR06391" - - name: "" - - metabolites: !!omap - - MAM01306c: -1 - - MAM01306m: 1 - - MAM02026c: 1 - - MAM02026m: -1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000108528" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "PMID:15845418" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR06431" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 7829b155..899eed9f 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6835,7 +6835,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06342" "" "DNDPt58m" "" "r2431" "" "DNDPt58m" "MNXR97671" "HMR_6342" "RCR20140" "2.A.29.16.1" 0 "" "" "HMR_6342" "MAR06343" "" "DNDPt42m" "" "r2432" "" "DNDPt42m" "MNXR97655" "HMR_6343" "RCR20276" "2.A.29.16.1" 0 "" "" "HMR_6343" "MAR06389" "" "r2472" "" "r2472" "" "r2472" "MNXR100321" "HMR_6389" "RCR20616" "2.A.1.4.7" 0 "" "" "HMR_6389" -"MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" "MAR06431" "" "" "" "" "" "HMR_6431" "" "HMR_6431" "RCR20617" "" 0 "" "" "HMR_6431" "MAR06438" "" "" "" "" "" "HMR_6438" "" "HMR_6438" "RCR20618" "" 0 "" "" "HMR_6438" "MAR06446" "" "" "" "" "" "HMR_6446" "" "HMR_6446" "RCR20619" "" 0 "" "" "HMR_6446" From 698976cdd8854bcc27a2ac29c70c3032072f679a Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 8 Nov 2023 16:55:12 -0500 Subject: [PATCH 3/7] fix: made MAR08771 ATP-independent & added references --- model/Human-GEM.yml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 330accae..3b148207 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -86676,20 +86676,15 @@ - id: "MAR08771" - name: "" - metabolites: !!omap - - MAM01285c: 1 - - MAM01371c: -1 - MAM02026c: -1 - MAM02026m: 1 - - MAM02039c: 1 - - MAM02040c: -1 - - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" + - gene_reaction_rule: "ENSG00000013306 or ENSG00000075303" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID:25637873;PMID:34707288;PMID:35513392" - subsystem: - "Transport reactions" - confidence_score: 0 From 71e7b2d6ab81804ba069e3ec8c1e9dc7636dfb38 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 8 Nov 2023 17:00:44 -0500 Subject: [PATCH 4/7] fix: updated RHEA ID for MAR08771 and merged annotations from MAR04940 & MAR06391 in reactions.tsv --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index 899eed9f..9d97ba68 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1015,7 +1015,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04708" "R02743" "" "R02743C" "r0568" "" "r0568" "MNXR105350" "HMR_4708" "RCR14413" "" 0 "" "" "HMR_4708" "MAR08769" "" "GTMLTe" "" "" "" "GTMLTe" "MNXR100452" "HMR_8769" "RCR40314" "" 0 "" "" "HMR_8769" "MAR08770" "" "GGLUCT" "" "" "" "GGLUCT" "MNXR100126" "HMR_8770" "RCR40168" "" 0 "" "" "HMR_8770" -"MAR08771" "" "GTHRDt" "" "" "" "GTHRDt" "MNXR100447" "HMR_8771" "RCR20224" "" 0 "RHEA:29792" "RHEA:29791" "HMR_8771" +"MAR08771" "" "GTHRDt" "" "r0885;r2520" "" "GTHRDt;r0885;r2520" "MNXR100447;MNXR105402;MNXR106328" "HMR_8771;HMR_4940;HMR_6391" "RCR20224;RCR20265;RCR20063" "2.A.29.2.7" 0 "" "RHEA:74819" "HMR_8771;MAR04940;HMR_4940;MAR06391;HMR_6391" "MAR04078" "R09076" "" "" "" "" "HMR_4078" "" "HMR_4078" "RCR10551" "" 0 "" "RHEA:25804" "HMR_4078" "MAR04079" "" "" "" "" "" "HMR_4079" "" "HMR_4079" "RCR11506" "" 0 "" "" "HMR_4079" "MAR04174" "R00489" "ASP1DC" "R00489C" "r0128" "" "ASP1DC" "MNXR96077" "HMR_4174" "RCR10095" "" 0 "" "RHEA:19497" "HMR_4174" From 5cfb14b2a09354f1dbe3d9026b7621fb06fd9035 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 8 Nov 2023 17:16:58 -0500 Subject: [PATCH 5/7] fix: added new gene entries for SLC25A39 and SLC25A40 to model/Human-GEM.yml and model/genes.tsv --- model/Human-GEM.yml | 6 ++++++ model/genes.tsv | 2 ++ 2 files changed, 8 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3b148207..b7d61583 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -305464,6 +305464,9 @@ - !!omap - id: "ENSG00000013288" - name: "MAN2B2" + - !!omap + - id: "ENSG00000013306" + - name: "SLC25A39" - !!omap - id: "ENSG00000013375" - name: "PGM3" @@ -306058,6 +306061,9 @@ - !!omap - id: "ENSG00000075239" - name: "ACAT1" + - !!omap + - id: "ENSG00000075303" + - name: "SLC25A40" - !!omap - id: "ENSG00000075415" - name: "SLC25A3" diff --git a/model/genes.tsv b/model/genes.tsv index ecde1bbc..0ea7072e 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2888,3 +2888,5 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000114120" "ENST00000324194;ENST00000446041;ENST00000507429;ENST00000453248;ENST00000513887;ENST00000648615;ENST00000502594;ENST00000512023;ENST00000512506;ENST00000631654" "ENSP00000320688;ENSP00000401938;ENSP00000421470;ENSP00000391521;ENSP00000422265;ENSP00000497436;ENSP00000423319;ENSP00000424505;ENSP00000423711;ENSP00000487839" "Q96CQ1" "SLC25A36" "55186" "solute carrier family 25 member 36" "" "" "" "ENSG00000159445" "ENST00000368814.8;ENST00000489410.1;ENST00000471464.5;ENST00000477437.1;ENST00000483207.5" "ENSP00000357804.3;ENSP00000433304.1;ENSP00000431288.1" "Q5T1C6" "THEM4" "117145" "thioesterase superfamily member 4" "CTMP" "Cytosol;Inner mitochondria" "SwissProt" "ENSG00000196407" "ENST00000368817.10;ENST00000453881.2" "ENSP00000357807.4;ENSP00000406809.2" "Q8N1Q8" "THEM5" "284486" "thioesterase superfamily member 5" "ACOT15" "Inner mitochondria" "SwissProt" +"ENSG00000013306" "ENST00000377095;ENST00000225308;ENST00000590194;ENST00000537904;ENST00000586016;ENST00000588049;ENST00000592857;ENST00000588767;ENST00000585523;ENST00000586633;ENST00000585636;ENST00000593166;ENST00000591006;ENST00000588315;ENST00000585695;ENST00000592372;ENST00000591151" "ENSP00000366299;ENSP00000225308;ENSP00000467681;ENSP00000444540;ENSP00000466676;ENSP00000465182;ENSP00000467956;ENSP00000466615;ENSP00000466144;ENSP00000465594;ENSP00000465554" "Q9BZJ4" "SLC25A39" "51629" "solute carrier family 25 member 39" "" "" "" +"ENSG00000075303" "ENST00000341119" "" "Q8TBP6" "SLC25A40" "55972" "solute carrier family 25 member 40" "MCFP" "" "" From 083c97baed9e8fad9d023f8124ea51fd7ac35fb1 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 8 Nov 2023 17:24:03 -0500 Subject: [PATCH 6/7] feat: added Ensembl transcript and protein IDs for SLC25A40 --- model/genes.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/genes.tsv b/model/genes.tsv index 0ea7072e..0d9de8df 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2889,4 +2889,4 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000159445" "ENST00000368814.8;ENST00000489410.1;ENST00000471464.5;ENST00000477437.1;ENST00000483207.5" "ENSP00000357804.3;ENSP00000433304.1;ENSP00000431288.1" "Q5T1C6" "THEM4" "117145" "thioesterase superfamily member 4" "CTMP" "Cytosol;Inner mitochondria" "SwissProt" "ENSG00000196407" "ENST00000368817.10;ENST00000453881.2" "ENSP00000357807.4;ENSP00000406809.2" "Q8N1Q8" "THEM5" "284486" "thioesterase superfamily member 5" "ACOT15" "Inner mitochondria" "SwissProt" "ENSG00000013306" "ENST00000377095;ENST00000225308;ENST00000590194;ENST00000537904;ENST00000586016;ENST00000588049;ENST00000592857;ENST00000588767;ENST00000585523;ENST00000586633;ENST00000585636;ENST00000593166;ENST00000591006;ENST00000588315;ENST00000585695;ENST00000592372;ENST00000591151" "ENSP00000366299;ENSP00000225308;ENSP00000467681;ENSP00000444540;ENSP00000466676;ENSP00000465182;ENSP00000467956;ENSP00000466615;ENSP00000466144;ENSP00000465594;ENSP00000465554" "Q9BZJ4" "SLC25A39" "51629" "solute carrier family 25 member 39" "" "" "" -"ENSG00000075303" "ENST00000341119" "" "Q8TBP6" "SLC25A40" "55972" "solute carrier family 25 member 40" "MCFP" "" "" +"ENSG00000075303" "ENST00000341119;ENST00000429674;ENST00000444363;ENST00000446236;ENST00000470328;ENST00000483810;ENST00000491499;ENST00000496348" "ENSP00000344831;ENSP00000401473;ENSP00000405566;ENSP00000407780" "Q8TBP6" "SLC25A40" "55972" "solute carrier family 25 member 40" "MCFP" "" "" From 39005dc4faf1e1bf021621575c97d216f8f0e023 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Thu, 9 Nov 2023 22:09:22 +0100 Subject: [PATCH 7/7] doc: update Rhea id to MAR08771 --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index 9d97ba68..f6f302a3 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1015,7 +1015,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04708" "R02743" "" "R02743C" "r0568" "" "r0568" "MNXR105350" "HMR_4708" "RCR14413" "" 0 "" "" "HMR_4708" "MAR08769" "" "GTMLTe" "" "" "" "GTMLTe" "MNXR100452" "HMR_8769" "RCR40314" "" 0 "" "" "HMR_8769" "MAR08770" "" "GGLUCT" "" "" "" "GGLUCT" "MNXR100126" "HMR_8770" "RCR40168" "" 0 "" "" "HMR_8770" -"MAR08771" "" "GTHRDt" "" "r0885;r2520" "" "GTHRDt;r0885;r2520" "MNXR100447;MNXR105402;MNXR106328" "HMR_8771;HMR_4940;HMR_6391" "RCR20224;RCR20265;RCR20063" "2.A.29.2.7" 0 "" "RHEA:74819" "HMR_8771;MAR04940;HMR_4940;MAR06391;HMR_6391" +"MAR08771" "" "GTHRDt" "" "r0885;r2520" "" "GTHRDt;r0885;r2520" "MNXR100447;MNXR105402;MNXR106328" "HMR_8771;HMR_4940;HMR_6391" "RCR20224;RCR20265;RCR20063" "2.A.29.2.7" 0 "RHEA:74821" "RHEA:74819" "HMR_8771;MAR04940;HMR_4940;MAR06391;HMR_6391" "MAR04078" "R09076" "" "" "" "" "HMR_4078" "" "HMR_4078" "RCR10551" "" 0 "" "RHEA:25804" "HMR_4078" "MAR04079" "" "" "" "" "" "HMR_4079" "" "HMR_4079" "RCR11506" "" 0 "" "" "HMR_4079" "MAR04174" "R00489" "ASP1DC" "R00489C" "r0128" "" "ASP1DC" "MNXR96077" "HMR_4174" "RCR10095" "" 0 "" "RHEA:19497" "HMR_4174"