From 44046bf053fa0804c8357f83cc48eb99385346b8 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:26:53 -0500 Subject: [PATCH 01/20] fix: remove MAR05358 for duplicating MAR03452+MAR03453+MAR03454+MAR03455 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 24 ------------------- model/reactions.tsv | 9 ++++--- 3 files changed, 5 insertions(+), 29 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index a1c70245..455497f0 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -282,3 +282,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03322" "" "" "RE3627X" "" "" "HMR_3322" "MNXR124610" "HMR_3322" "RCR14521" "" 0 "" "" "HMR_3322" "MAR03296" "" "" "RE3627M" "" "R-HSA-109343" "HMR_3296" "MNXR124610" "HMR_3296" "RCR12779" "" 0 "" "" "HMR_3296" "MAR04005" "" "" "" "" "" "RE3627C" "" "" "" "" 0 "" "" "RE3627C" +"MAR05358" "" "FAOXC183C163Gm" "" "" "" "FAOXC183C163Gm" "" "" "" "" 0 "" "" "FAOXC183C163Gm" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7e2852a1..d85aaed7 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240657,30 +240657,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05358" - - name: "Fatty Acid Beta Oxidation (C18:3->C16:3), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM01934m: -1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM03274m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778 and ENSG00000084754 and ENSG00000138029" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05359" - name: "Fatty Acid Beta Oxidation (C18:3->C16:3), Mitochondrial" diff --git a/model/reactions.tsv b/model/reactions.tsv index 6197a93d..6b0478e8 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1779,10 +1779,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03448" "" "" "" "" "" "HMR_3448" "" "HMR_3448" "RCR12056" "" 0 "" "" "HMR_3448" "MAR03449" "" "" "RE2986M" "" "" "HMR_3449" "" "HMR_3449" "RCR12057" "" 0 "" "" "HMR_3449" "MAR03450" "" "" "RE2987M" "" "" "HMR_3450" "" "HMR_3450" "RCR12058" "" 0 "" "" "HMR_3450" -"MAR03452" "" "" "RE2997M" "" "" "HMR_3452" "" "HMR_3452" "RCR12060" "" 0 "" "" "HMR_3452" -"MAR03453" "" "" "RE2990M" "" "" "HMR_3453" "" "HMR_3453" "RCR12061" "" 0 "" "" "HMR_3453" -"MAR03454" "" "" "RE2991M" "" "" "HMR_3454" "" "HMR_3454" "RCR12062" "" 0 "" "" "HMR_3454" -"MAR03455" "" "" "RE2989M" "" "" "HMR_3455" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455" +"MAR03452" "" "FAOXC183C163Gm" "RE2997M" "" "" "HMR_3452;FAOXC183C163Gm" "" "HMR_3452" "RCR12060" "" 0 "" "" "HMR_3452;FAOXC183C163Gm;MAR05358" +"MAR03453" "" "FAOXC183C163Gm" "RE2990M" "" "" "HMR_3453;FAOXC183C163Gm" "" "HMR_3453" "RCR12061" "" 0 "" "" "HMR_3453;FAOXC183C163Gm;MAR05358" +"MAR03454" "" "FAOXC183C163Gm" "RE2991M" "" "" "HMR_3454;FAOXC183C163Gm" "" "HMR_3454" "RCR12062" "" 0 "" "" "HMR_3454;FAOXC183C163Gm;MAR05358" +"MAR03455" "" "FAOXC183C163Gm" "RE2989M" "" "" "HMR_3455;FAOXC183C163Gm" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455;FAOXC183C163Gm;MAr05358" "MAR03456" "" "" "RE2994M" "" "" "HMR_3456" "" "HMR_3456" "RCR12064" "" 0 "" "" "HMR_3456" "MAR03457" "" "" "RE2993M" "" "" "HMR_3457" "" "HMR_3457" "RCR12065" "" 0 "" "" "HMR_3457" "MAR03458" "" "" "RE2992M" "" "" "RE2992M" "" "HMR_3458" "RCR12066" "" 0 "" "" "HMR_3458" @@ -9299,7 +9299,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05355" "" "FAOXC181C181OHm" "" "" "" "FAOXC181C181OHm" "" "" "" "" 0 "" "" "FAOXC181C181OHm" "MAR05356" "" "FAOXC182C162m" "" "" "" "FAOXC182C162m" "" "" "" "" 0 "" "" "FAOXC182C162m" "MAR05357" "" "FAOXC182C182OHm" "" "" "" "FAOXC182C182OHm" "" "" "" "" 0 "" "" "FAOXC182C182OHm" -"MAR05358" "" "FAOXC183C163Gm" "" "" "" "FAOXC183C163Gm" "" "" "" "" 0 "" "" "FAOXC183C163Gm" "MAR05359" "" "FAOXC183C163m;HMR_3426" "" "" "" "FAOXC183C163m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC183C163m;HMR_3426;MAR03426" "MAR05360" "" "FAOXC184C163m" "" "" "" "FAOXC184C163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC184C163m;HMR_3422;MAR03422" "MAR05364" "" "FAOXC184C163x" "" "" "" "FAOXC184C163x" "" "" "" "" 0 "" "" "FAOXC184C163x" From 3cc9c2013aaa9aeb0e624c136ffe1b815caf26d9 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:29:29 -0500 Subject: [PATCH 02/20] fix: remove MAR05195 for duplicating MAR03456 --- .../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 455497f0..f74bd38e 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -283,3 +283,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03296" "" "" "RE3627M" "" "R-HSA-109343" "HMR_3296" "MNXR124610" "HMR_3296" "RCR12779" "" 0 "" "" "HMR_3296" "MAR04005" "" "" "" "" "" "RE3627C" "" "" "" "" 0 "" "" "RE3627C" "MAR05358" "" "FAOXC183C163Gm" "" "" "" "FAOXC183C163Gm" "" "" "" "" 0 "" "" "FAOXC183C163Gm" +"MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163C164Gm;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index d85aaed7..7267d7fb 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240113,24 +240113,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05195" - - name: "Fatty Acid Beta Oxidation (C16:3->C16:4), Mitochondrial" - - metabolites: !!omap - - MAM01802m: -1 - - MAM01803m: 1 - - MAM03274m: -1 - - MAM03653m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:17374501" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05196" - name: "Fatty Acid Beta Oxidation (C16:3->C16:4), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index 6b0478e8..46a1ad0d 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1783,7 +1783,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03453" "" "FAOXC183C163Gm" "RE2990M" "" "" "HMR_3453;FAOXC183C163Gm" "" "HMR_3453" "RCR12061" "" 0 "" "" "HMR_3453;FAOXC183C163Gm;MAR05358" "MAR03454" "" "FAOXC183C163Gm" "RE2991M" "" "" "HMR_3454;FAOXC183C163Gm" "" "HMR_3454" "RCR12062" "" 0 "" "" "HMR_3454;FAOXC183C163Gm;MAR05358" "MAR03455" "" "FAOXC183C163Gm" "RE2989M" "" "" "HMR_3455;FAOXC183C163Gm" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455;FAOXC183C163Gm;MAr05358" -"MAR03456" "" "" "RE2994M" "" "" "HMR_3456" "" "HMR_3456" "RCR12064" "" 0 "" "" "HMR_3456" +"MAR03456" "" "FAOXC163C164Gm" "RE2994M" "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422" "" "HMR_3456;HMR_3422" "RCR12064;RCR12667" "" 0 "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422;MAR03422;MAR05195" "MAR03457" "" "" "RE2993M" "" "" "HMR_3457" "" "HMR_3457" "RCR12065" "" 0 "" "" "HMR_3457" "MAR03458" "" "" "RE2992M" "" "" "RE2992M" "" "HMR_3458" "RCR12066" "" 0 "" "" "HMR_3458" "MAR03459" "" "" "RE2985X" "" "" "RE2985X" "" "HMR_3459" "RCR10621" "" 0 "" "" "HMR_3459" @@ -9272,7 +9272,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05192" "" "FAOXC162C162OHm" "" "" "" "FAOXC162C162OHm" "" "" "" "" 0 "" "" "FAOXC162C162OHm" "MAR05193" "" "FAOXC163C142x" "" "" "" "FAOXC163C142x" "" "" "" "" 0 "" "" "FAOXC163C142x" "MAR05194" "" "FAOXC163C143m;HMR_3426" "" "" "" "FAOXC163C143m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC163C143m;HMR_3426;MAR03426" -"MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163C164Gm;HMR_3422;MAR03422" "MAR05196" "" "FAOXC163C164x" "" "" "" "FAOXC163C164x" "" "" "" "" 0 "" "" "FAOXC163C164x" "MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" "MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" From 6f58fd4b20c70a0cbc00c68b4e940bb6ae4c8922 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:31:14 -0500 Subject: [PATCH 03/20] fix: remove MAR05302 for duplicating MAR03457 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 19 ------------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 21 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index f74bd38e..cc65c370 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -284,3 +284,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04005" "" "" "" "" "" "RE3627C" "" "" "" "" 0 "" "" "RE3627C" "MAR05358" "" "FAOXC183C163Gm" "" "" "" "FAOXC183C163Gm" "" "" "" "" 0 "" "" "FAOXC183C163Gm" "MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163C164Gm;HMR_3422;MAR03422" +"MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC164GC163m;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7267d7fb..fe9d58e7 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240284,25 +240284,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05302" - - name: "Fatty Acid Beta Oxidation (C16:4->C16:3), Mitochondrial" - - metabolites: !!omap - - MAM02039m: -1 - - MAM02554m: 1 - - MAM02555m: -1 - - MAM03221m: 1 - - MAM03653m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000104325" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:7818482" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05306" - name: "Isomerization (C16:4), Mitochondrial" diff --git a/model/reactions.tsv b/model/reactions.tsv index 46a1ad0d..26520e24 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1784,7 +1784,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03454" "" "FAOXC183C163Gm" "RE2991M" "" "" "HMR_3454;FAOXC183C163Gm" "" "HMR_3454" "RCR12062" "" 0 "" "" "HMR_3454;FAOXC183C163Gm;MAR05358" "MAR03455" "" "FAOXC183C163Gm" "RE2989M" "" "" "HMR_3455;FAOXC183C163Gm" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455;FAOXC183C163Gm;MAr05358" "MAR03456" "" "FAOXC163C164Gm" "RE2994M" "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422" "" "HMR_3456;HMR_3422" "RCR12064;RCR12667" "" 0 "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422;MAR03422;MAR05195" -"MAR03457" "" "" "RE2993M" "" "" "HMR_3457" "" "HMR_3457" "RCR12065" "" 0 "" "" "HMR_3457" +"MAR03457" "" "FAOXC164GC163m" "RE2993M" "" "" "HMR_3457;FAOXC164GC163m;HMR_3422" "" "HMR_3457;HMR_3422" "RCR12065;RCR12667" "" 0 "" "" "HMR_3457;FAOXC164GC163m;HMR_3422;MAR03422;MAR05302" "MAR03458" "" "" "RE2992M" "" "" "RE2992M" "" "HMR_3458" "RCR12066" "" 0 "" "" "HMR_3458" "MAR03459" "" "" "RE2985X" "" "" "RE2985X" "" "HMR_3459" "RCR10621" "" 0 "" "" "HMR_3459" "MAR03460" "" "" "RE2995X" "" "" "RE2995X" "" "HMR_3460" "RCR12067" "" 0 "" "" "HMR_3460" @@ -9281,7 +9281,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05293" "" "FAOXC164C163x" "" "" "" "FAOXC164C163x" "" "" "" "" 0 "" "" "FAOXC164C163x" "MAR05298" "" "FAOXC164C165m" "" "" "" "FAOXC164C165m" "" "" "" "" 0 "" "" "FAOXC164C165m" "MAR05300" "" "FAOXC164C165x" "" "" "" "FAOXC164C165x" "" "" "" "" 0 "" "" "FAOXC164C165x" -"MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC164GC163m;HMR_3422;MAR03422" "MAR05306" "" "FAOXC164m" "" "" "" "FAOXC164m" "" "" "" "" 0 "" "" "FAOXC164m" "MAR05309" "" "FAOXC164x" "" "" "" "FAOXC164x" "" "" "" "" 0 "" "" "FAOXC164x" "MAR05312" "" "FAOXC165C164m" "" "" "" "FAOXC165C164m" "" "" "" "" 0 "" "" "FAOXC165C164m" From 73fb11d948898dde31d5fc18f742a6c5556abf99 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:33:10 -0500 Subject: [PATCH 04/20] fix: remove MAR05229 for duplicating MAR03458 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 16 ---------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 18 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index cc65c370..b843fb2c 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -285,3 +285,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05358" "" "FAOXC183C163Gm" "" "" "" "FAOXC183C163Gm" "" "" "" "" 0 "" "" "FAOXC183C163Gm" "MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163C164Gm;HMR_3422;MAR03422" "MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC164GC163m;HMR_3422;MAR03422" +"MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index fe9d58e7..903c8ac4 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240153,22 +240153,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05229" - - name: "Isomerization (C16:3), Mitochondrial" - - metabolites: !!omap - - MAM03182m: 1 - - MAM03221m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000167969" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:15351645" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05235" - name: "Isomerization (C16:3), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index 26520e24..03f95fa4 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1785,7 +1785,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03455" "" "FAOXC183C163Gm" "RE2989M" "" "" "HMR_3455;FAOXC183C163Gm" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455;FAOXC183C163Gm;MAr05358" "MAR03456" "" "FAOXC163C164Gm" "RE2994M" "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422" "" "HMR_3456;HMR_3422" "RCR12064;RCR12667" "" 0 "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422;MAR03422;MAR05195" "MAR03457" "" "FAOXC164GC163m" "RE2993M" "" "" "HMR_3457;FAOXC164GC163m;HMR_3422" "" "HMR_3457;HMR_3422" "RCR12065;RCR12667" "" 0 "" "" "HMR_3457;FAOXC164GC163m;HMR_3422;MAR03422;MAR05302" -"MAR03458" "" "" "RE2992M" "" "" "RE2992M" "" "HMR_3458" "RCR12066" "" 0 "" "" "HMR_3458" +"MAR03458" "" "FAOXC163Gm" "RE2992M" "" "" "RE2992M;FAOXC163Gm;HMR_3422" "" "HMR_3458;HMR_3422" "RCR12066;RCR12667" "" 0 "" "" "HMR_3458;FAOXC163Gm;HMR_3422;MAR03422;MAR05229" "MAR03459" "" "" "RE2985X" "" "" "RE2985X" "" "HMR_3459" "RCR10621" "" 0 "" "" "HMR_3459" "MAR03460" "" "" "RE2995X" "" "" "RE2995X" "" "HMR_3460" "RCR12067" "" 0 "" "" "HMR_3460" "MAR03461" "" "" "RE2996X" "" "" "RE2996X" "" "HMR_3461" "RCR12068" "" 0 "" "" "HMR_3461" @@ -9274,7 +9274,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05194" "" "FAOXC163C143m;HMR_3426" "" "" "" "FAOXC163C143m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC163C143m;HMR_3426;MAR03426" "MAR05196" "" "FAOXC163C164x" "" "" "" "FAOXC163C164x" "" "" "" "" 0 "" "" "FAOXC163C164x" "MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" -"MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" "MAR05235" "" "FAOXC163x" "" "" "" "FAOXC163x" "" "" "" "" 0 "" "" "FAOXC163x" "MAR05242" "" "FAOXC164C143m" "" "" "" "FAOXC164C143m" "" "" "" "" 0 "" "" "FAOXC164C143m" "MAR05256" "" "FAOXC164C143x" "" "" "" "FAOXC164C143x" "" "" "" "" 0 "" "" "FAOXC164C143x" From d9a35a64598b73c899a67a98193790949f98611b Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:36:36 -0500 Subject: [PATCH 05/20] fix: remove MAR05208 for duplicating MAR03281+MAR03282+MAR03283 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 22 ------------------- model/reactions.tsv | 7 +++--- 3 files changed, 4 insertions(+), 26 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index b843fb2c..b1f11c99 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -286,3 +286,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163C164Gm;HMR_3422;MAR03422" "MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC164GC163m;HMR_3422;MAR03422" "MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" +"MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 903c8ac4..3acf0109 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240131,28 +240131,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05208" - - name: "Fatty Acid Beta Oxidation (C16:3->C14:2), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM03182m: -1 - - MAM03978m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000084754 and ENSG00000138029" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05235" - name: "Isomerization (C16:3), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index 03f95fa4..0ab72d41 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2764,9 +2764,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03278" "" "" "RE0512M" "" "" "RE0512M" "" "HMR_3278" "RCR12764" "" 0 "" "" "HMR_3278" "MAR03279" "" "" "RE1531M" "" "" "RE1531M" "" "HMR_3279" "RCR12765" "" 0 "" "" "HMR_3279" "MAR03280" "" "" "RE1517M" "" "" "RE1517M" "" "HMR_3280" "RCR12766" "" 0 "" "" "HMR_3280" -"MAR03281" "" "" "RE1522M" "" "" "RE1522M" "" "HMR_3281" "RCR12767" "" 0 "" "" "HMR_3281" -"MAR03282" "" "" "RE1525M" "" "" "RE1525M" "" "HMR_3282" "RCR12768" "" 0 "" "" "HMR_3282" -"MAR03283" "" "" "RE1532M" "" "" "RE1532M" "" "HMR_3283" "RCR12769" "" 0 "" "" "HMR_3283" +"MAR03281" "" "FAOXC163GC142m" "RE1522M" "" "" "RE1522M;FAOXC163GC142m;HMR_3422" "" "HMR_3281;HMR_3422" "RCR12767;RCR12667" "" 0 "" "" "HMR_3281;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" +"MAR03282" "" "FAOXC163GC142m" "RE1525M" "" "" "RE1525M;FAOXC163GC142m;HMR_3422" "" "HMR_3282;HMR_3422" "RCR12768;RCR12667" "" 0 "" "" "HMR_3282;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" +"MAR03283" "" "FAOXC163GC142m" "RE1532M" "" "" "RE1532M;FAOXC163GC142m;HMR_3422" "" "HMR_3283;HMR_3422" "RCR12769;RCR12667" "" 0 "" "" "HMR_3283;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" "MAR03284" "" "" "RE1518M" "" "" "RE1518M" "" "HMR_3284" "RCR12770" "" 0 "" "" "HMR_3284" "MAR03285" "" "" "" "" "" "RE1521M" "" "HMR_3285" "RCR12771" "" 0 "" "" "HMR_3285" "MAR03286" "" "" "" "" "" "RE1526M" "" "HMR_3286" "RCR12772" "" 0 "" "" "HMR_3286" @@ -9273,7 +9273,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05193" "" "FAOXC163C142x" "" "" "" "FAOXC163C142x" "" "" "" "" 0 "" "" "FAOXC163C142x" "MAR05194" "" "FAOXC163C143m;HMR_3426" "" "" "" "FAOXC163C143m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC163C143m;HMR_3426;MAR03426" "MAR05196" "" "FAOXC163C164x" "" "" "" "FAOXC163C164x" "" "" "" "" 0 "" "" "FAOXC163C164x" -"MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" "MAR05235" "" "FAOXC163x" "" "" "" "FAOXC163x" "" "" "" "" 0 "" "" "FAOXC163x" "MAR05242" "" "FAOXC164C143m" "" "" "" "FAOXC164C143m" "" "" "" "" 0 "" "" "FAOXC164C143m" "MAR05256" "" "FAOXC164C143x" "" "" "" "FAOXC164C143x" "" "" "" "" 0 "" "" "FAOXC164C143x" From 5eaebad2ff484cc27ad19459ec3301dc4b5fc5d7 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:40:39 -0500 Subject: [PATCH 06/20] fix: remove MAR05356 for duplicating MAR03275+MAR03277+MAR03278+MAR03279 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 32 +++---------------- model/reactions.tsv | 9 +++--- 3 files changed, 9 insertions(+), 33 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index b1f11c99..892b1aa9 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -287,3 +287,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC164GC163m;HMR_3422;MAR03422" "MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" "MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" +"MAR05356" "" "FAOXC182C162m" "" "" "" "FAOXC182C162m" "" "" "" "" 0 "" "" "FAOXC182C162m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3acf0109..0e78fa2f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -120839,7 +120839,7 @@ - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646" - - rxnNotes: "" + - rxnNotes: "Harpers illustrated Biochemistry (2009) 28th edition page 242, ISBN:9781282335806" - rxnFrom: "HMRdatabase" - eccodes: "1.3.8.7;1.3.8.8;1.3.8.9;1.3.99.-" - references: "PMID:8973539;PMID:10407780;PMID:11356167" @@ -120856,7 +120856,7 @@ - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000084754 and ENSG00000113790 and ENSG00000127884" - - rxnNotes: "" + - rxnNotes: "Harpers illustrated Biochemistry (2009) 28th edition page 242, ISBN:9781282335806" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.17" - references: "PMID:9920399;PMID:10407780;PMID:7923814;PMID:9568246" @@ -120875,7 +120875,7 @@ - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000072506 and ENSG00000084754 and ENSG00000138796" - - rxnNotes: "" + - rxnNotes: "Harpers illustrated Biochemistry (2009) 28th edition page 242, ISBN:9781282335806" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.35;1.1.1.211" - references: "PMID:7846063" @@ -120893,7 +120893,7 @@ - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000084754 and ENSG00000138029 and ENSG00000167315" - - rxnNotes: "" + - rxnNotes: "Harpers illustrated Biochemistry (2009) 28th edition page 242, ISBN:9781282335806" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.16;1.1.1.211" - references: "PMID:10407780;PMID:9920399;PMID:7923814;PMID:9568246" @@ -240539,30 +240539,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05356" - - name: "Fatty Acid Beta Oxidation (C18:2->C16:2), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02391m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM03650m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778 and ENSG00000084754 and ENSG00000138029" - - rxnNotes: "Harpers illustrated Biochemistry (2009) 28th edition page 242, ISBN:9781282335806" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05357" - name: "Fatty Acid Beta Oxidation (C18:2->C18:2Oh), Mitochondrial" diff --git a/model/reactions.tsv b/model/reactions.tsv index 0ab72d41..3d84e774 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2759,10 +2759,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03236" "" "" "" "" "" "HMR_3236" "" "HMR_3236" "RCR12759" "" 0 "" "" "HMR_3236" "MAR03237" "" "" "" "" "" "HMR_3237" "" "HMR_3237" "RCR12760" "" 0 "" "" "HMR_3237" "MAR03239" "R04100" "DCIm" "" "" "" "DCIm" "MNXR97183" "HMR_3239" "RCR12761" "" 0 "RHEA:23719" "RHEA:23716" "HMR_3239" -"MAR03275" "" "" "RE1516M" "" "R-HSA-109339" "RE1516M" "MNXR125224" "HMR_3275" "RCR12762" "" 0 "" "" "HMR_3275" -"MAR03277" "" "" "RE1523M" "" "" "RE1523M" "" "HMR_3277" "RCR12763" "" 0 "" "" "HMR_3277" -"MAR03278" "" "" "RE0512M" "" "" "RE0512M" "" "HMR_3278" "RCR12764" "" 0 "" "" "HMR_3278" -"MAR03279" "" "" "RE1531M" "" "" "RE1531M" "" "HMR_3279" "RCR12765" "" 0 "" "" "HMR_3279" +"MAR03275" "" "FAOXC182C162m" "RE1516M" "" "R-HSA-109339" "RE1516M;FAOXC182C162m" "MNXR125224" "HMR_3275" "RCR12762" "" 0 "" "" "HMR_3275;FAOXC182C162m;MAR05356" +"MAR03277" "" "FAOXC182C162m" "RE1523M" "" "" "RE1523M;FAOXC182C162m" "" "HMR_3277" "RCR12763" "" 0 "" "" "HMR_3277;FAOXC182C162m;MAR05356" +"MAR03278" "" "FAOXC182C162m" "RE0512M" "" "" "RE0512M;FAOXC182C162m" "" "HMR_3278" "RCR12764" "" 0 "" "" "HMR_3278;FAOXC182C162m;MAR05356" +"MAR03279" "" "FAOXC182C162m" "RE1531M" "" "" "RE1531M;FAOXC182C162m" "" "HMR_3279" "RCR12765" "" 0 "" "" "HMR_3279;FAOXC182C162m;MAR05356" "MAR03280" "" "" "RE1517M" "" "" "RE1517M" "" "HMR_3280" "RCR12766" "" 0 "" "" "HMR_3280" "MAR03281" "" "FAOXC163GC142m" "RE1522M" "" "" "RE1522M;FAOXC163GC142m;HMR_3422" "" "HMR_3281;HMR_3422" "RCR12767;RCR12667" "" 0 "" "" "HMR_3281;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" "MAR03282" "" "FAOXC163GC142m" "RE1525M" "" "" "RE1525M;FAOXC163GC142m;HMR_3422" "" "HMR_3282;HMR_3422" "RCR12768;RCR12667" "" 0 "" "" "HMR_3282;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" @@ -9293,7 +9293,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05345" "" "FAOXC181C161m" "" "" "" "FAOXC181C161m" "" "" "" "" 0 "" "" "FAOXC181C161m" "MAR05350" "" "FAOXC181C161x" "" "" "" "FAOXC181C161x" "" "" "" "" 0 "" "" "FAOXC181C161x" "MAR05355" "" "FAOXC181C181OHm" "" "" "" "FAOXC181C181OHm" "" "" "" "" 0 "" "" "FAOXC181C181OHm" -"MAR05356" "" "FAOXC182C162m" "" "" "" "FAOXC182C162m" "" "" "" "" 0 "" "" "FAOXC182C162m" "MAR05357" "" "FAOXC182C182OHm" "" "" "" "FAOXC182C182OHm" "" "" "" "" 0 "" "" "FAOXC182C182OHm" "MAR05359" "" "FAOXC183C163m;HMR_3426" "" "" "" "FAOXC183C163m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC183C163m;HMR_3426;MAR03426" "MAR05360" "" "FAOXC184C163m" "" "" "" "FAOXC184C163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC184C163m;HMR_3422;MAR03422" From 228fa538667d93f6f8a3a2dd206fdd2a4a6e804c Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:45:53 -0500 Subject: [PATCH 07/20] fix: remove MAR05191 for duplicating MAR03280+MAR03281+MAR03282+MAR03283 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 24 ------------------- model/reactions.tsv | 9 ++++--- 3 files changed, 5 insertions(+), 29 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 892b1aa9..f895d3af 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -288,3 +288,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" "MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" "MAR05356" "" "FAOXC182C162m" "" "" "" "FAOXC182C162m" "" "" "" "" 0 "" "" "FAOXC182C162m" +"MAR05191" "" "FAOXC162C142m" "" "" "" "FAOXC162C142m" "" "" "" "" 0 "" "" "FAOXC162C142m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 0e78fa2f..4c41a563 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240024,30 +240024,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05191" - - name: "Fatty Acid Beta Oxidation (C16:2->C14:2), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM03650m: -1 - - MAM03978m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778 and ENSG00000084754 and ENSG00000138029" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05192" - name: "Fatty Acid Beta Oxidation (C16:2->C16:2Oh), Mitochondrial" diff --git a/model/reactions.tsv b/model/reactions.tsv index 3d84e774..c6b5582c 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2763,10 +2763,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03277" "" "FAOXC182C162m" "RE1523M" "" "" "RE1523M;FAOXC182C162m" "" "HMR_3277" "RCR12763" "" 0 "" "" "HMR_3277;FAOXC182C162m;MAR05356" "MAR03278" "" "FAOXC182C162m" "RE0512M" "" "" "RE0512M;FAOXC182C162m" "" "HMR_3278" "RCR12764" "" 0 "" "" "HMR_3278;FAOXC182C162m;MAR05356" "MAR03279" "" "FAOXC182C162m" "RE1531M" "" "" "RE1531M;FAOXC182C162m" "" "HMR_3279" "RCR12765" "" 0 "" "" "HMR_3279;FAOXC182C162m;MAR05356" -"MAR03280" "" "" "RE1517M" "" "" "RE1517M" "" "HMR_3280" "RCR12766" "" 0 "" "" "HMR_3280" -"MAR03281" "" "FAOXC163GC142m" "RE1522M" "" "" "RE1522M;FAOXC163GC142m;HMR_3422" "" "HMR_3281;HMR_3422" "RCR12767;RCR12667" "" 0 "" "" "HMR_3281;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" -"MAR03282" "" "FAOXC163GC142m" "RE1525M" "" "" "RE1525M;FAOXC163GC142m;HMR_3422" "" "HMR_3282;HMR_3422" "RCR12768;RCR12667" "" 0 "" "" "HMR_3282;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" -"MAR03283" "" "FAOXC163GC142m" "RE1532M" "" "" "RE1532M;FAOXC163GC142m;HMR_3422" "" "HMR_3283;HMR_3422" "RCR12769;RCR12667" "" 0 "" "" "HMR_3283;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208" +"MAR03280" "" "FAOXC162C142m" "RE1517M" "" "" "RE1517M;FAOXC162C142m" "" "HMR_3280" "RCR12766" "" 0 "" "" "HMR_3280;FAOXC162C142m;MAR05191" +"MAR03281" "" "FAOXC163GC142m;FAOXC162C142m" "RE1522M" "" "" "RE1522M;FAOXC163GC142m;HMR_3422;FAOXC162C142m" "" "HMR_3281;HMR_3422" "RCR12767;RCR12667" "" 0 "" "" "HMR_3281;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208;FAOXC162C142m;MAR05191" +"MAR03282" "" "FAOXC163GC142m;FAOXC162C142m" "RE1525M" "" "" "RE1525M;FAOXC163GC142m;HMR_3422;FAOXC162C142m" "" "HMR_3282;HMR_3422" "RCR12768;RCR12667" "" 0 "" "" "HMR_3282;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208;FAOXC162C142m;MAR05191" +"MAR03283" "" "FAOXC163GC142m;FAOXC162C142m" "RE1532M" "" "" "RE1532M;FAOXC163GC142m;HMR_3422;FAOXC162C142m" "" "HMR_3283;HMR_3422" "RCR12769;RCR12667" "" 0 "" "" "HMR_3283;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208;FAOXC162C142m;MAR05191" "MAR03284" "" "" "RE1518M" "" "" "RE1518M" "" "HMR_3284" "RCR12770" "" 0 "" "" "HMR_3284" "MAR03285" "" "" "" "" "" "RE1521M" "" "HMR_3285" "RCR12771" "" 0 "" "" "HMR_3285" "MAR03286" "" "" "" "" "" "RE1526M" "" "HMR_3286" "RCR12772" "" 0 "" "" "HMR_3286" @@ -9268,7 +9268,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05188" "" "FAOXC161C141m" "" "" "" "FAOXC161C141m" "" "" "" "" 0 "" "" "FAOXC161C141m" "MAR05189" "" "FAOXC161C141x" "" "" "" "FAOXC161C141x" "" "" "" "" 0 "" "" "FAOXC161C141x" "MAR05190" "" "FAOXC161C161OHm" "" "" "" "FAOXC161C161OHm" "" "" "" "" 0 "" "" "FAOXC161C161OHm" -"MAR05191" "" "FAOXC162C142m" "" "" "" "FAOXC162C142m" "" "" "" "" 0 "" "" "FAOXC162C142m" "MAR05192" "" "FAOXC162C162OHm" "" "" "" "FAOXC162C162OHm" "" "" "" "" 0 "" "" "FAOXC162C162OHm" "MAR05193" "" "FAOXC163C142x" "" "" "" "FAOXC163C142x" "" "" "" "" 0 "" "" "FAOXC163C142x" "MAR05194" "" "FAOXC163C143m;HMR_3426" "" "" "" "FAOXC163C143m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC163C143m;HMR_3426;MAR03426" From 557b5e2ea2ecc4ddfdff80ea5156c5ad86dbba54 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:49:51 -0500 Subject: [PATCH 08/20] fix: remove MAR05123 for duplicating MAR03284+MAR03285+MAR03286+MAR03287 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 24 ------------------- model/reactions.tsv | 9 ++++--- 3 files changed, 5 insertions(+), 29 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index f895d3af..530b32d0 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -289,3 +289,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" "MAR05356" "" "FAOXC182C162m" "" "" "" "FAOXC182C162m" "" "" "" "" 0 "" "" "FAOXC182C162m" "MAR05191" "" "FAOXC162C142m" "" "" "" "FAOXC162C142m" "" "" "" "" 0 "" "" "FAOXC162C142m" +"MAR05123" "" "FAOXC142C122m" "" "" "" "FAOXC142C122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC142C122m;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 4c41a563..cf9d30fa 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -239641,30 +239641,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05123" - - name: "Fatty Acid Beta Oxidation (C14:2->C12:2), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM03203m: 1 - - MAM03978m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778 and ENSG00000084754 and ENSG00000138029" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05175" - name: "Fatty Acid Beta Oxidation (C14:2->C12:2), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index c6b5582c..038bbc36 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2767,10 +2767,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03281" "" "FAOXC163GC142m;FAOXC162C142m" "RE1522M" "" "" "RE1522M;FAOXC163GC142m;HMR_3422;FAOXC162C142m" "" "HMR_3281;HMR_3422" "RCR12767;RCR12667" "" 0 "" "" "HMR_3281;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208;FAOXC162C142m;MAR05191" "MAR03282" "" "FAOXC163GC142m;FAOXC162C142m" "RE1525M" "" "" "RE1525M;FAOXC163GC142m;HMR_3422;FAOXC162C142m" "" "HMR_3282;HMR_3422" "RCR12768;RCR12667" "" 0 "" "" "HMR_3282;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208;FAOXC162C142m;MAR05191" "MAR03283" "" "FAOXC163GC142m;FAOXC162C142m" "RE1532M" "" "" "RE1532M;FAOXC163GC142m;HMR_3422;FAOXC162C142m" "" "HMR_3283;HMR_3422" "RCR12769;RCR12667" "" 0 "" "" "HMR_3283;FAOXC163GC142m;HMR_3422;MAR03422;MAR05208;FAOXC162C142m;MAR05191" -"MAR03284" "" "" "RE1518M" "" "" "RE1518M" "" "HMR_3284" "RCR12770" "" 0 "" "" "HMR_3284" -"MAR03285" "" "" "" "" "" "RE1521M" "" "HMR_3285" "RCR12771" "" 0 "" "" "HMR_3285" -"MAR03286" "" "" "" "" "" "RE1526M" "" "HMR_3286" "RCR12772" "" 0 "" "" "HMR_3286" -"MAR03287" "" "" "" "" "" "RE1533M" "" "HMR_3287" "RCR12773" "" 0 "" "" "HMR_3287" +"MAR03284" "" "FAOXC142C122m" "RE1518M" "" "" "RE1518M;FAOXC142C122m;HMR_3422" "" "HMR_3284;HMR_3422" "RCR12770;RCR12667" "" 0 "" "" "HMR_3284;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" +"MAR03285" "" "FAOXC142C122m" "" "" "" "RE1521M;FAOXC142C122m;HMR_3422" "" "HMR_3285;HMR_3422" "RCR12771;RCR12667" "" 0 "" "" "HMR_3285;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" +"MAR03286" "" "FAOXC142C122m" "" "" "" "RE1526M;FAOXC142C122m;HMR_3422" "" "HMR_3286;HMR_3422" "RCR12772;RCR12667" "" 0 "" "" "HMR_3286;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" +"MAR03287" "" "FAOXC142C122m" "" "" "" "RE1533M;FAOXC142C122m;HMR_3422" "" "HMR_3287;HMR_3422" "RCR12773;RCR12667" "" 0 "" "" "HMR_3287;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" "MAR03288" "R04756" "" "RE1573M" "" "R-HSA-109338" "HMR_3288;RE1573M" "MNXR109096" "HMR_3288" "RCR12774" "" 0 "" "" "HMR_3288" "MAR03290" "" "" "RE1520M" "" "R-HSA-109342" "RE1520M" "MNXR125225" "HMR_3290" "RCR12775" "" 0 "" "" "HMR_3290" "MAR03292" "" "" "RE1527M" "" "" "RE1527M" "" "HMR_3292" "RCR12776" "" 0 "" "" "HMR_3292" @@ -9251,7 +9251,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05111" "" "FAOXC141C121m" "" "" "" "FAOXC141C121m" "" "" "" "" 0 "" "" "FAOXC141C121m" "MAR05119" "" "FAOXC141C121x" "" "" "" "FAOXC141C121x" "" "" "" "" 0 "" "" "FAOXC141C121x" "MAR05120" "" "FAOXC141C141OHm" "" "" "" "FAOXC141C141OHm" "" "" "" "" 0 "" "" "FAOXC141C141OHm" -"MAR05123" "" "FAOXC142C122m" "" "" "" "FAOXC142C122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC142C122m;HMR_3422;MAR03422" "MAR05175" "" "FAOXC142C122x" "" "" "" "FAOXC142C122x" "" "" "" "" 0 "" "" "FAOXC142C122x" "MAR05176" "" "FAOXC142C142OHm" "" "" "" "FAOXC142C142OHm" "" "" "" "" 0 "" "" "FAOXC142C142OHm" "MAR05177" "" "FAOXC143C123m;HMR_3426" "" "" "" "FAOXC143C123m;HMR_3426" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC143C123m;HMR_3426;MAR03426" From b4d2ac4c760845970eaecbf575604e8ed6c73c8a Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:51:30 -0500 Subject: [PATCH 09/20] fix: remove MAR05075 for duplicating MAR03288 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 16 ---------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 18 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 530b32d0..58c578b3 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -290,3 +290,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05356" "" "FAOXC182C162m" "" "" "" "FAOXC182C162m" "" "" "" "" 0 "" "" "FAOXC182C162m" "MAR05191" "" "FAOXC162C142m" "" "" "" "FAOXC162C142m" "" "" "" "" 0 "" "" "FAOXC162C142m" "MAR05123" "" "FAOXC142C122m" "" "" "" "FAOXC142C122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC142C122m;HMR_3422;MAR03422" +"MAR05075" "" "FAOXC122m" "" "" "" "FAOXC122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122m;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index cf9d30fa..1fc62911 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -239275,22 +239275,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05075" - - name: "Isomerization (C12:2), Mitochondrial" - - metabolites: !!omap - - MAM02698m: 1 - - MAM03203m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000167969" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:15351645" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05081" - name: "Isomerization (C12:2), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index 038bbc36..755bcdea 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2771,7 +2771,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03285" "" "FAOXC142C122m" "" "" "" "RE1521M;FAOXC142C122m;HMR_3422" "" "HMR_3285;HMR_3422" "RCR12771;RCR12667" "" 0 "" "" "HMR_3285;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" "MAR03286" "" "FAOXC142C122m" "" "" "" "RE1526M;FAOXC142C122m;HMR_3422" "" "HMR_3286;HMR_3422" "RCR12772;RCR12667" "" 0 "" "" "HMR_3286;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" "MAR03287" "" "FAOXC142C122m" "" "" "" "RE1533M;FAOXC142C122m;HMR_3422" "" "HMR_3287;HMR_3422" "RCR12773;RCR12667" "" 0 "" "" "HMR_3287;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" -"MAR03288" "R04756" "" "RE1573M" "" "R-HSA-109338" "HMR_3288;RE1573M" "MNXR109096" "HMR_3288" "RCR12774" "" 0 "" "" "HMR_3288" +"MAR03288" "R04756" "FAOXC122m" "RE1573M" "" "R-HSA-109338" "HMR_3288;RE1573M;FAOXC122m;HMR_3422" "MNXR109096" "HMR_3288;HMR_3422" "RCR12774;RCR12667" "" 0 "" "" "HMR_3288;FAOXC122m;HMR_3422;MAR03422;MAR05075" "MAR03290" "" "" "RE1520M" "" "R-HSA-109342" "RE1520M" "MNXR125225" "HMR_3290" "RCR12775" "" 0 "" "" "HMR_3290" "MAR03292" "" "" "RE1527M" "" "" "RE1527M" "" "HMR_3292" "RCR12776" "" 0 "" "" "HMR_3292" "MAR03293" "" "" "RE1534M" "" "" "RE1534M" "" "HMR_3293" "RCR12777" "" 0 "" "" "HMR_3293" @@ -9233,7 +9233,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05044" "" "FAOXC121C101m" "" "" "" "FAOXC121C101m" "" "" "" "" 0 "" "" "FAOXC121C101m" "MAR05069" "" "FAOXC121C10x" "" "" "" "FAOXC121C10x" "" "" "" "" 0 "" "" "FAOXC121C10x" "MAR05072" "" "FAOXC122C101m" "" "" "" "FAOXC122C101m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122C101m;HMR_3422;MAR03422" -"MAR05075" "" "FAOXC122m" "" "" "" "FAOXC122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122m;HMR_3422;MAR03422" "MAR05081" "" "FAOXC122x" "" "" "" "FAOXC122x" "" "" "" "" 0 "" "" "FAOXC122x" "MAR05083" "" "FAOXC123C102m;HMR_3426" "" "" "" "FAOXC123C102;HMR_3426m" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC123C102m;HMR_3426;MAR03426" "MAR05086" "" "FAOXC123C102x" "" "" "" "FAOXC123C102x" "" "" "" "" 0 "" "" "FAOXC123C102x" From de7acc85529e90b2186f6dc6294f26898ddf6192 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:55:50 -0500 Subject: [PATCH 10/20] fix: remove MAR05072 for duplicating MAR03290+MAR03292+MAR03293 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 22 ------------------- model/reactions.tsv | 7 +++--- 3 files changed, 4 insertions(+), 26 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 58c578b3..0bc73cc4 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -291,3 +291,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05191" "" "FAOXC162C142m" "" "" "" "FAOXC162C142m" "" "" "" "" 0 "" "" "FAOXC162C142m" "MAR05123" "" "FAOXC142C122m" "" "" "" "FAOXC142C122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC142C122m;HMR_3422;MAR03422" "MAR05075" "" "FAOXC122m" "" "" "" "FAOXC122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122m;HMR_3422;MAR03422" +"MAR05072" "" "FAOXC122C101m" "" "" "" "FAOXC122C101m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122C101m;HMR_3422;MAR03422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 1fc62911..89755ab5 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -239253,28 +239253,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05072" - - name: "Fatty Acid Beta Oxidation (C12:2->C10:1), Mitochondrial" - - metabolites: !!omap - - MAM00980m: 1 - - MAM01261m: 1 - - MAM01597m: -1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM02698m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000127884 and ENSG00000138796 and ENSG00000167315" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05081" - name: "Isomerization (C12:2), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index 755bcdea..55f7b2f4 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2772,9 +2772,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03286" "" "FAOXC142C122m" "" "" "" "RE1526M;FAOXC142C122m;HMR_3422" "" "HMR_3286;HMR_3422" "RCR12772;RCR12667" "" 0 "" "" "HMR_3286;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" "MAR03287" "" "FAOXC142C122m" "" "" "" "RE1533M;FAOXC142C122m;HMR_3422" "" "HMR_3287;HMR_3422" "RCR12773;RCR12667" "" 0 "" "" "HMR_3287;FAOXC142C122m;HMR_3422;MAR03422;MAR05123" "MAR03288" "R04756" "FAOXC122m" "RE1573M" "" "R-HSA-109338" "HMR_3288;RE1573M;FAOXC122m;HMR_3422" "MNXR109096" "HMR_3288;HMR_3422" "RCR12774;RCR12667" "" 0 "" "" "HMR_3288;FAOXC122m;HMR_3422;MAR03422;MAR05075" -"MAR03290" "" "" "RE1520M" "" "R-HSA-109342" "RE1520M" "MNXR125225" "HMR_3290" "RCR12775" "" 0 "" "" "HMR_3290" -"MAR03292" "" "" "RE1527M" "" "" "RE1527M" "" "HMR_3292" "RCR12776" "" 0 "" "" "HMR_3292" -"MAR03293" "" "" "RE1534M" "" "" "RE1534M" "" "HMR_3293" "RCR12777" "" 0 "" "" "HMR_3293" +"MAR03290" "" "FAOXC122C101m" "RE1520M" "" "R-HSA-109342" "RE1520M;FAOXC122C101m;HMR_3422" "MNXR125225" "HMR_3290;HMR_3422" "RCR12775;RCR12667" "" 0 "" "" "HMR_3290;HMR_3422;MAR03422;MAR05072" +"MAR03292" "" "FAOXC122C101m" "RE1527M" "" "" "RE1527M;FAOXC122C101m;HMR_3422" "" "HMR_3292;HMR_3422" "RCR12776;RCR12667" "" 0 "" "" "HMR_3292;HMR_3422;MAR03422;MAR05072" +"MAR03293" "" "FAOXC122C101m" "RE1534M" "" "" "RE1534M;FAOXC122C101m;HMR_3422" "" "HMR_3293;HMR_3422" "RCR12777;RCR12667" "" 0 "" "" "HMR_3293;FAOXC122C101m;HMR_3422;MAR03422;MAR05072" "MAR03294" "" "" "RE1519M" "" "" "FAOXC101C102m;HMR_3422" "" "HMR_3294;HMR_3422" "RCR12778;RCR12667" "" 0 "" "" "HMR_3294;HMR_3422;MAR03422" "MAR03298" "" "" "RE3628M" "" "R-HSA-109998" "RE3628M;FAOXC101m;HMR_3422" "MNXR118942" "HMR_3298;HMR_3422" "RCR12780;RCR12667" "" 0 "RHEA:45753" "RHEA:45752" "HMR_3298;HMR_3422;MAR03422" "MAR01174" "" "" "RE3383M" "" "" "RE3383M" "" "HMR_1174" "RCR12781" "" 0 "" "" "HMR_1174" @@ -9232,7 +9232,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05030" "" "FAOXC11C9m" "" "" "" "FAOXC11C9m" "" "" "" "" 0 "" "" "FAOXC11C9m" "MAR05044" "" "FAOXC121C101m" "" "" "" "FAOXC121C101m" "" "" "" "" 0 "" "" "FAOXC121C101m" "MAR05069" "" "FAOXC121C10x" "" "" "" "FAOXC121C10x" "" "" "" "" 0 "" "" "FAOXC121C10x" -"MAR05072" "" "FAOXC122C101m" "" "" "" "FAOXC122C101m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122C101m;HMR_3422;MAR03422" "MAR05081" "" "FAOXC122x" "" "" "" "FAOXC122x" "" "" "" "" 0 "" "" "FAOXC122x" "MAR05083" "" "FAOXC123C102m;HMR_3426" "" "" "" "FAOXC123C102;HMR_3426m" "" "HMR_3426" "RCR12671" "" 0 "" "" "FAOXC123C102m;HMR_3426;MAR03426" "MAR05086" "" "FAOXC123C102x" "" "" "" "FAOXC123C102x" "" "" "" "" 0 "" "" "FAOXC123C102x" From 15ea8ba72ec6464d1320a6aa5159662a25c7e8bb Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:57:31 -0500 Subject: [PATCH 11/20] fix: replaced MAM03274m with MAM00091m in MAR05360 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 89755ab5..a1ad7fc2 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -240500,6 +240500,7 @@ - id: "MAR05360" - name: "Fatty Acid Beta Oxidation (C18:4->C16:3), Mitochondrial" - metabolites: !!omap + - MAM00091m: 1 - MAM01261m: 1 - MAM01597m: -1 - MAM02039m: 1 @@ -240507,7 +240508,6 @@ - MAM02552m: -1 - MAM02553m: 1 - MAM03194m: -1 - - MAM03274m: 1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000084754 and ENSG00000138029" From 512df3ccf96d81c0215ae4637374c73c1963bc98 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 09:59:33 -0500 Subject: [PATCH 12/20] fix: removed MAM03274m for duplicating MAM00091m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index d935bba1..341a1119 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2263,3 +2263,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02158n" "MAM02158" "" "" "" "" "124985" "" "CE2011" "" "CE2011" "MNXM57006" "" "m02158n" "MAM00678c" "MAM00678" "" "" "" "" "22833562" "" "CE2435" "" "dec24dicoa" "MNXM1601" "" "m00678c" "MAM03035c" "MAM03035" "" "" "" "" "16019966" "" "CE5121" "" "dece3coa" "MNXM90096" "" "m03035c" +"MAM03274m" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index a1ad7fc2..5b287d57 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50633,14 +50633,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03274m" - - name: "4,7,10-Hexadecatrienoyl Coenzyme A" - - compartment: "m" - - formula: "C37H56N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03653m" - name: "2,4,7,10-Hexadecatetraenoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index ffb1efa6..8b36c418 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -162,7 +162,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00089m" "MAM00089" "" "" "" "" "" "" "CE2442" "" "CE2442" "" "m00089m" "m00089m" "MAM00089x" "MAM00089" "" "" "" "" "" "" "CE2442" "" "CE2442" "" "m00089p" "m00089p" "MAM00090x" "MAM00090" "" "" "" "" "53481434" "" "CE5938" "" "CE5938" "MNXM31216" "m00090p" "m00090p" -"MAM00091m" "MAM00091" "" "" "" "" "" "" "CE2440" "" "CE2440" "" "m00091m" "m00091m" +"MAM00091m" "MAM00091" "4hexdtricoa" "" "" "" "" "" "CE2440" "" "CE2440;4hexdtricoa" "" "m00091m" "m00091m;4hexdtricoa_m'MAM03274m" "MAM00091x" "MAM00091" "" "" "" "" "" "" "CE2440" "" "CE2440" "" "m00091p" "m00091p" "MAM00092c" "MAM00092" "dcsptn1crn" "" "" "" "" "" "" "" "dcsptn1crn" "MNXM8558" "m00092c" "m00092c" "MAM00092m" "MAM00092" "dcsptn1crn" "" "" "" "" "" "" "" "dcsptn1crn" "MNXM8558" "m00092m" "m00092m" @@ -6327,7 +6327,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03982m" "MAM03982" "thexddcoa" "" "" "" "" "" "" "" "thexddcoa" "" "" "thexddcoa_m" "MAM03182x" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_p" "MAM03658m" "MAM03658" "hexdtrcoa" "" "" "" "" "" "" "" "hexdtrcoa" "" "" "hexdtrcoa_m" -"MAM03274m" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_m" "MAM03653m" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_m" "MAM03274x" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_p" "MAM03653x" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_p" From 8c404a0c2c20dee95728af3306e9307d01eb99ae Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:01:41 -0500 Subject: [PATCH 13/20] fix: removed MAM03653m for duplicating MAM00072m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 341a1119..4e67e01e 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2264,3 +2264,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00678c" "MAM00678" "" "" "" "" "22833562" "" "CE2435" "" "dec24dicoa" "MNXM1601" "" "m00678c" "MAM03035c" "MAM03035" "" "" "" "" "16019966" "" "CE5121" "" "dece3coa" "MNXM90096" "" "m03035c" "MAM03274m" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_m" +"MAM03653m" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5b287d57..fbdef4e9 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50633,14 +50633,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03653m" - - name: "2,4,7,10-Hexadecatetraenoyl Coenzyme A" - - compartment: "m" - - formula: "C37H54N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03274x" - name: "4,7,10-Hexadecatrienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 8b36c418..36440de1 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -137,7 +137,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00069m" "MAM00069" "" "" "" "" "" "" "" "" "M00069" "" "m00069m" "m00069m" "MAM00070c" "MAM00070" "" "" "" "" "" "" "" "" "M00070" "" "m00070c" "m00070c" "MAM00071m" "MAM00071" "" "" "" "CHEBI:77548" "" "" "" "" "M00071" "MNXM170117" "m00071m" "m00071m" -"MAM00072m" "MAM00072" "" "" "" "" "" "" "CE2441" "" "CE2441" "" "m00072m" "m00072m" +"MAM00072m" "MAM00072" "hexdectecoa" "" "" "" "" "" "CE2441" "" "CE2441;hexdectecoa" "" "m00072m" "m00072m;hexdectecoa_m;MAM03653m" "MAM00072x" "MAM00072" "" "" "" "" "" "" "CE2441" "" "CE2441" "" "m00072p" "m00072p" "MAM00073m" "MAM00073" "" "" "" "" "" "" "CE2437" "" "CE2437" "" "m00073m" "m00073m" "MAM00073x" "MAM00073" "" "" "" "" "" "" "CE2437" "" "CE2437" "" "m00073p" "m00073p" @@ -6327,7 +6327,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03982m" "MAM03982" "thexddcoa" "" "" "" "" "" "" "" "thexddcoa" "" "" "thexddcoa_m" "MAM03182x" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_p" "MAM03658m" "MAM03658" "hexdtrcoa" "" "" "" "" "" "" "" "hexdtrcoa" "" "" "hexdtrcoa_m" -"MAM03653m" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_m" "MAM03274x" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_p" "MAM03653x" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_p" "MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" From b186b224e774a3a3ebe5d751918e7c7a14fce778 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:03:06 -0500 Subject: [PATCH 14/20] fix: removed MAM03221m for duplicating MAM00089m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 4e67e01e..49787597 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2265,3 +2265,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03035c" "MAM03035" "" "" "" "" "16019966" "" "CE5121" "" "dece3coa" "MNXM90096" "" "m03035c" "MAM03274m" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_m" "MAM03653m" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_m" +"MAM03221m" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index fbdef4e9..085155c1 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50657,14 +50657,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03221m" - - name: "3,7,10-Hexadecatrienoyl Coenzyme A" - - compartment: "m" - - formula: "C37H56N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03221x" - name: "3,7,10-Hexadecatrienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 36440de1..0de7df6d 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -159,7 +159,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00087c" "MAM00087" "" "" "" "" "" "" "CE4840" "" "CE4840" "MNXM163965" "m00087c" "m00087c" "MAM00088m" "MAM00088" "dd3coa" "C02944" "" "CHEBI:27989" "16061154" "LMFA07050009" "" "HC01022" "dd3coa" "MNXM14550" "m00088m" "m00088m" "MAM00088x" "MAM00088" "dd3coa" "C02944" "" "CHEBI:27989" "16061154" "LMFA07050009" "" "HC01022" "dd3coa" "MNXM14550" "m00088p" "m00088p" -"MAM00089m" "MAM00089" "" "" "" "" "" "" "CE2442" "" "CE2442" "" "m00089m" "m00089m" +"MAM00089m" "MAM00089" "3hexdtricoa" "" "" "" "" "" "CE2442" "" "CE2442;3hexdtricoa" "" "m00089m" "m00089m;3hexdtricoa_m;MAM03221m" "MAM00089x" "MAM00089" "" "" "" "" "" "" "CE2442" "" "CE2442" "" "m00089p" "m00089p" "MAM00090x" "MAM00090" "" "" "" "" "53481434" "" "CE5938" "" "CE5938" "MNXM31216" "m00090p" "m00090p" "MAM00091m" "MAM00091" "4hexdtricoa" "" "" "" "" "" "CE2440" "" "CE2440;4hexdtricoa" "" "m00091m" "m00091m;4hexdtricoa_m'MAM03274m" @@ -6330,7 +6330,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03274x" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_p" "MAM03653x" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_p" "MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" -"MAM03221m" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_m" "MAM03221x" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_p" "MAM03181m" "MAM03181" "2hexdtetcoa" "" "" "" "" "" "" "" "2hexdtetcoa" "" "" "2hexdtetcoa_m" "MAM03181x" "MAM03181" "2hexdtetcoa" "" "" "" "" "" "" "" "2hexdtetcoa" "" "" "2hexdtetcoa_p" From b16646e250764f1ed4767b973a1dfb8a409f292b Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:05:18 -0500 Subject: [PATCH 15/20] fix: removed MAM03182m for duplicating MAM03009m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 49787597..dfa98910 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2266,3 +2266,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03274m" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_m" "MAM03653m" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_m" "MAM03221m" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_m" +"MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 085155c1..2661fff6 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50649,14 +50649,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03182m" - - name: "2,7,10-Hexadecatrienoyl Coenzyme A" - - compartment: "m" - - formula: "C37H56N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03221x" - name: "3,7,10-Hexadecatrienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 0de7df6d..d4eb5c8d 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -5211,7 +5211,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03006c" "MAM03006" "" "" "" "" "" "" "" "" "M03006" "" "m03006c" "m03006c" "MAM03007c" "MAM03007" "" "" "" "" "" "" "CE4842" "" "CE4842" "MNXM165186" "m03007c" "m03007c" "MAM03008c" "MAM03008" "" "" "" "" "" "" "" "" "M03008" "" "m03008c" "m03008c" -"MAM03009m" "MAM03009" "" "" "" "" "" "" "CE2433" "" "CE2433" "" "m03009m" "m03009m" +"MAM03009m" "MAM03009" "2hexdtricoa" "" "" "" "" "" "CE2433" "" "CE2433;2hexdtricoa" "" "m03009m" "m03009m;2hexdtricoa_m;MAM03182m" "MAM03009x" "MAM03009" "" "" "" "" "" "" "CE2433" "" "CE2433" "" "m03009p" "m03009p" "MAM03010m" "MAM03010" "" "" "" "" "" "" "CE2434" "" "CE2434" "" "m03010m" "m03010m" "MAM03010x" "MAM03010" "" "" "" "" "" "" "CE2434" "" "CE2434" "" "m03010p" "m03010p" @@ -6329,7 +6329,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03658m" "MAM03658" "hexdtrcoa" "" "" "" "" "" "" "" "hexdtrcoa" "" "" "hexdtrcoa_m" "MAM03274x" "MAM03274" "4hexdtricoa" "" "" "" "" "" "" "" "4hexdtricoa" "" "" "4hexdtricoa_p" "MAM03653x" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_p" -"MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" "MAM03221x" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_p" "MAM03181m" "MAM03181" "2hexdtetcoa" "" "" "" "" "" "" "" "2hexdtetcoa" "" "" "2hexdtetcoa_m" "MAM03181x" "MAM03181" "2hexdtetcoa" "" "" "" "" "" "" "" "2hexdtetcoa" "" "" "2hexdtetcoa_p" From adc489bceb063bc4d4fbbeaa9f273961f10148d2 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:07:04 -0500 Subject: [PATCH 16/20] fix: removed MAM03978m for duplicating MAM01576m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index dfa98910..129cc50b 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2267,3 +2267,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03653m" "MAM03653" "hexdectecoa" "" "" "" "" "" "" "" "hexdectecoa" "" "" "hexdectecoa_m" "MAM03221m" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_m" "MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" +"MAM03978m" "MAM03978" "tetdecdicoa" "" "" "" "21252281" "" "" "" "tetdecdicoa" "" "" "tetdecdicoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 2661fff6..8d3cba99 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50545,14 +50545,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03978m" - - name: "5,8-Tetradecadienoyl Coenzyme A" - - compartment: "m" - - formula: "C35H54N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03978x" - name: "5,8-Tetradecadienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index d4eb5c8d..36d1b910 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -2558,7 +2558,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01574x" "MAM01574" "" "" "" "" "" "" "CE1102" "HC11102" "CE1102" "MNXM167439" "m01574p" "m01574p" "MAM01575m" "MAM01575" "" "C05280" "HMDB0003952" "CHEBI:28002" "5280771" "" "" "" "C05280" "MNXM2008" "m01575m" "m01575m" "MAM01575x" "MAM01575" "" "C05280" "HMDB0003952" "CHEBI:28002" "5280771" "" "" "" "C05280" "MNXM2008" "m01575p" "m01575p" -"MAM01576m" "MAM01576" "" "" "" "" "21252281" "" "CE0785" "" "CE0785" "" "m01576m" "m01576m" +"MAM01576m" "MAM01576" "tetdecdicoa" "" "" "" "21252281" "" "CE0785" "" "CE0785;tetdecdicoa" "" "m01576m" "m01576m;tetdecdicoa_m;MAM03978m" "MAM01576x" "MAM01576" "" "" "" "" "21252281" "" "CE0785" "" "CE0785" "" "m01576p" "m01576p" "MAM01577m" "MAM01577" "" "" "" "" "" "" "CE0849" "" "CE0849" "" "m01577m" "m01577m" "MAM01577x" "MAM01577" "" "" "" "" "" "" "CE0849" "" "CE0849" "" "m01577p" "m01577p" @@ -6316,7 +6316,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03211x" "MAM03211" "3dodtricoa" "" "" "" "" "" "" "" "3dodtricoa" "" "" "3dodtricoa_p" "MAM03490x" "MAM03490" "c12dc" "" "" "" "" "" "" "" "c12dc" "" "" "c12dc_p" "MAM03972m" "MAM03972" "tetd7ecoa" "" "" "" "" "" "" "" "tetd7ecoa" "" "" "tetd7ecoa_m" -"MAM03978m" "MAM03978" "tetdecdicoa" "" "" "" "21252281" "" "" "" "tetdecdicoa" "" "" "tetdecdicoa_m" "MAM03978x" "MAM03978" "tetdecdicoa" "" "" "" "21252281" "" "" "" "tetdecdicoa" "" "" "tetdecdicoa_p" "MAM04041m" "MAM04041" "ttetddcoa" "" "" "" "21252281" "" "" "" "ttetddcoa" "" "" "ttetddcoa_m" "MAM03288m" "MAM03288" "5tedtricoa" "" "" "" "" "" "" "" "5tedtricoa" "" "" "5tedtricoa_m" From 84505c84d144b4d74551156e11b3682e18689e36 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:08:30 -0500 Subject: [PATCH 17/20] fix: removed MAM03203m for duplicating MAM01575m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 129cc50b..d41366f2 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2268,3 +2268,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03221m" "MAM03221" "3hexdtricoa" "" "" "" "" "" "" "" "3hexdtricoa" "" "" "3hexdtricoa_m" "MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" "MAM03978m" "MAM03978" "tetdecdicoa" "" "" "" "21252281" "" "" "" "tetdecdicoa" "" "" "tetdecdicoa_m" +"MAM03203m" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8d3cba99..c0878c9e 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50473,14 +50473,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03203m" - - name: "3,6-Dodecadienoyl Coenzyme A" - - compartment: "m" - - formula: "C33H50N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM02698x" - name: "2,6-Dodecadienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 36d1b910..03ce1c17 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -2556,7 +2556,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01573x" "MAM01573" "" "" "" "" "" "" "" "" "M01573" "" "m01573p" "m01573p" "MAM01574m" "MAM01574" "" "" "" "" "" "" "CE1102" "HC11102" "CE1102" "MNXM167439" "m01574m" "m01574m" "MAM01574x" "MAM01574" "" "" "" "" "" "" "CE1102" "HC11102" "CE1102" "MNXM167439" "m01574p" "m01574p" -"MAM01575m" "MAM01575" "" "C05280" "HMDB0003952" "CHEBI:28002" "5280771" "" "" "" "C05280" "MNXM2008" "m01575m" "m01575m" +"MAM01575m" "MAM01575" "3ddecdicoa" "C05280" "HMDB0003952" "CHEBI:28002" "5280771" "" "" "" "C05280;3ddecdicoa" "MNXM2008" "m01575m" "m01575m;3ddecdicoa;MAM03203m" "MAM01575x" "MAM01575" "" "C05280" "HMDB0003952" "CHEBI:28002" "5280771" "" "" "" "C05280" "MNXM2008" "m01575p" "m01575p" "MAM01576m" "MAM01576" "tetdecdicoa" "" "" "" "21252281" "" "CE0785" "" "CE0785;tetdecdicoa" "" "m01576m" "m01576m;tetdecdicoa_m;MAM03978m" "MAM01576x" "MAM01576" "" "" "" "" "21252281" "" "CE0785" "" "CE0785" "" "m01576p" "m01576p" @@ -6307,7 +6307,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM04004x" "MAM04004" "tmuncoa" "" "" "" "" "" "" "" "tmuncoa" "" "" "tmuncoa_p" "MAM03539m" "MAM03539" "dd5ecoa" "" "" "" "" "" "" "" "dd5ecoa" "" "" "dd5ecoa_m" "MAM02698m" "MAM02698" "2ddecdicoa" "" "" "" "53480665" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_m" -"MAM03203m" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_m" "MAM02698x" "MAM02698" "2ddecdicoa" "" "" "" "53480665" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_p" "MAM03203x" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_p" "MAM03172m" "MAM03172" "2dodtricoa" "" "" "" "" "" "" "" "2dodtricoa" "" "" "2dodtricoa_m" From 79a9c664af4c59a85730200703f1e3137932eaec Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:15:24 -0500 Subject: [PATCH 18/20] fix: removed MAM02698m for duplicating MAM03021m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index d41366f2..ee163390 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2269,3 +2269,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03182m" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_m" "MAM03978m" "MAM03978" "tetdecdicoa" "" "" "" "21252281" "" "" "" "tetdecdicoa" "" "" "tetdecdicoa_m" "MAM03203m" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_m" +"MAM02698m" "MAM02698" "2ddecdicoa" "" "" "" "5280770" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c0878c9e..b91c296c 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50465,14 +50465,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM02698m" - - name: "2,6-Dodecadienoyl Coenzyme A" - - compartment: "m" - - formula: "C33H50N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM02698x" - name: "2,6-Dodecadienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 03ce1c17..fab44537 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -5235,7 +5235,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03019x" "MAM03019" "" "" "" "CHEBI:87717" "" "" "" "" "M03019" "" "m03019p" "m03019p" "MAM03020m" "MAM03020" "" "" "" "CHEBI:77549" "" "" "CE2591" "HC12591" "CE2591" "MNXM683714" "m03020m" "m03020m" "MAM03020x" "MAM03020" "" "" "" "CHEBI:77549" "" "" "CE2591" "HC12591" "CE2591" "MNXM683714" "m03020p" "m03020p" -"MAM03021m" "MAM03021" "" "C05279" "HMDB0011123" "CHEBI:28387" "5280770" "" "" "" "C05279" "MNXM2039" "m03021m" "m03021m" +"MAM03021m" "MAM03021" "2ddecdicoa" "C05279" "HMDB0011123" "CHEBI:28387" "5280770" "" "" "" "C05279;2ddecdicoa" "MNXM2039" "m03021m" "m03021m;2ddecdicoa_m;MAM02698m" "MAM03021x" "MAM03021" "" "C05279" "HMDB0011123" "CHEBI:28387" "5280770" "" "" "" "C05279" "MNXM2039" "m03021p" "m03021p" "MAM03022m" "MAM03022" "" "" "" "CHEBI:87701" "" "" "" "" "M03022" "" "m03022m" "m03022m" "MAM03022x" "MAM03022" "" "" "" "CHEBI:87701" "" "" "" "" "M03022" "" "m03022p" "m03022p" @@ -6306,7 +6306,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03922x" "MAM03922" "sbcoa" "" "" "CHEBI:76317" "" "" "" "" "sbcoa" "MNXM163582" "" "sbcoa_p" "MAM04004x" "MAM04004" "tmuncoa" "" "" "" "" "" "" "" "tmuncoa" "" "" "tmuncoa_p" "MAM03539m" "MAM03539" "dd5ecoa" "" "" "" "" "" "" "" "dd5ecoa" "" "" "dd5ecoa_m" -"MAM02698m" "MAM02698" "2ddecdicoa" "" "" "" "53480665" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_m" "MAM02698x" "MAM02698" "2ddecdicoa" "" "" "" "53480665" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_p" "MAM03203x" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_p" "MAM03172m" "MAM03172" "2dodtricoa" "" "" "" "" "" "" "" "2dodtricoa" "" "" "2dodtricoa_m" From db41d5fc2326aeb1640204ae1bb64723352eaf69 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Dec 2023 10:18:18 -0500 Subject: [PATCH 19/20] fix: removed MAM03650m for duplicating MAM01577m --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 3 +-- 3 files changed, 2 insertions(+), 10 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index ee163390..ffd2c7f7 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2270,3 +2270,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03978m" "MAM03978" "tetdecdicoa" "" "" "" "21252281" "" "" "" "tetdecdicoa" "" "" "tetdecdicoa_m" "MAM03203m" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_m" "MAM02698m" "MAM02698" "2ddecdicoa" "" "" "" "5280770" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_m" +"MAM03650m" "MAM03650" "hexddcoa" "" "" "" "" "" "" "" "hexddcoa" "" "" "hexddcoa_m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b91c296c..b8af8654 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -50577,14 +50577,6 @@ - charge: -4 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03650m" - - name: "7,10-Hexadecadienoyl Coenzyme A" - - compartment: "m" - - formula: "C37H58N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03982m" - name: "Trans7,10-Hexadecadienoyl Coenzyme A" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index fab44537..2997003b 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -2560,7 +2560,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01575x" "MAM01575" "" "C05280" "HMDB0003952" "CHEBI:28002" "5280771" "" "" "" "C05280" "MNXM2008" "m01575p" "m01575p" "MAM01576m" "MAM01576" "tetdecdicoa" "" "" "" "21252281" "" "CE0785" "" "CE0785;tetdecdicoa" "" "m01576m" "m01576m;tetdecdicoa_m;MAM03978m" "MAM01576x" "MAM01576" "" "" "" "" "21252281" "" "CE0785" "" "CE0785" "" "m01576p" "m01576p" -"MAM01577m" "MAM01577" "" "" "" "" "" "" "CE0849" "" "CE0849" "" "m01577m" "m01577m" +"MAM01577m" "MAM01577" "hexddcoa" "" "" "" "" "" "CE0849" "" "CE0849;hexddcoa" "" "m01577m" "m01577m;hexddcoa_m;MAM03650m" "MAM01577x" "MAM01577" "" "" "" "" "" "" "CE0849" "" "CE0849" "" "m01577p" "m01577p" "MAM01578c" "MAM01578" "2coum" "C05838" "" "CHEBI:47921" "5280841" "" "" "" "2coum" "MNXM3237" "m01578c" "m01578c" "MAM01579m" "MAM01579" "c2m26dcoa" "C11946" "HMDB0006540" "" "53477855" "" "" "" "c2m26dcoa" "MNXM10980" "m01579m" "m01579m" @@ -6320,7 +6320,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03288x" "MAM03288" "5tedtricoa" "" "" "" "" "" "" "" "5tedtricoa" "" "" "5tedtricoa_p" "MAM03492x" "MAM03492" "c14dccoa" "" "" "" "" "" "" "" "c14dccoa" "" "" "c14dccoa_p" "MAM03216m" "MAM03216" "3hdeccoa" "" "" "" "" "" "" "" "3hdeccoa" "" "" "3hdeccoa_m" -"MAM03650m" "MAM03650" "hexddcoa" "" "" "" "" "" "" "" "hexddcoa" "" "" "hexddcoa_m" "MAM03982m" "MAM03982" "thexddcoa" "" "" "" "" "" "" "" "thexddcoa" "" "" "thexddcoa_m" "MAM03182x" "MAM03182" "2hexdtricoa" "" "" "" "" "" "" "" "2hexdtricoa" "" "" "2hexdtricoa_p" "MAM03658m" "MAM03658" "hexdtrcoa" "" "" "" "" "" "" "" "hexdtrcoa" "" "" "hexdtrcoa_m" From 1fb40a6faa2cfead7f2a905cbfa9c97e8cf038a6 Mon Sep 17 00:00:00 2001 From: feiranl Date: Sun, 31 Dec 2023 17:04:10 +0800 Subject: [PATCH 20/20] fix a small type in rxn ID --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index 55f7b2f4..f81e1c6a 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1782,7 +1782,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03452" "" "FAOXC183C163Gm" "RE2997M" "" "" "HMR_3452;FAOXC183C163Gm" "" "HMR_3452" "RCR12060" "" 0 "" "" "HMR_3452;FAOXC183C163Gm;MAR05358" "MAR03453" "" "FAOXC183C163Gm" "RE2990M" "" "" "HMR_3453;FAOXC183C163Gm" "" "HMR_3453" "RCR12061" "" 0 "" "" "HMR_3453;FAOXC183C163Gm;MAR05358" "MAR03454" "" "FAOXC183C163Gm" "RE2991M" "" "" "HMR_3454;FAOXC183C163Gm" "" "HMR_3454" "RCR12062" "" 0 "" "" "HMR_3454;FAOXC183C163Gm;MAR05358" -"MAR03455" "" "FAOXC183C163Gm" "RE2989M" "" "" "HMR_3455;FAOXC183C163Gm" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455;FAOXC183C163Gm;MAr05358" +"MAR03455" "" "FAOXC183C163Gm" "RE2989M" "" "" "HMR_3455;FAOXC183C163Gm" "" "HMR_3455" "RCR12063" "" 0 "" "" "HMR_3455;FAOXC183C163Gm;MAR05358" "MAR03456" "" "FAOXC163C164Gm" "RE2994M" "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422" "" "HMR_3456;HMR_3422" "RCR12064;RCR12667" "" 0 "" "" "HMR_3456;FAOXC163C164Gm;HMR_3422;MAR03422;MAR05195" "MAR03457" "" "FAOXC164GC163m" "RE2993M" "" "" "HMR_3457;FAOXC164GC163m;HMR_3422" "" "HMR_3457;HMR_3422" "RCR12065;RCR12667" "" 0 "" "" "HMR_3457;FAOXC164GC163m;HMR_3422;MAR03422;MAR05302" "MAR03458" "" "FAOXC163Gm" "RE2992M" "" "" "RE2992M;FAOXC163Gm;HMR_3422" "" "HMR_3458;HMR_3422" "RCR12066;RCR12667" "" 0 "" "" "HMR_3458;FAOXC163Gm;HMR_3422;MAR03422;MAR05229"