From a7a92529b423527f599d0ff3ab846ffd76dd2647 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 16 Oct 2023 19:56:23 -0400 Subject: [PATCH] fix: removed MAR04843, MAR07823, MAR07926, and MAR09019 for being unsupported by evidence --- .../deprecatedReactions.tsv | 4 ++ model/Human-GEM.yml | 66 ------------------- model/reactions.tsv | 4 -- 3 files changed, 4 insertions(+), 70 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index f4b34adf..d8cca81c 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -241,3 +241,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" "MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564" "MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565" +"MAR04843" "" "" "" "r0801" "" "r0801" "MNXR105390" "HMR_4843" "RCR20168" "" 0 "" "" "HMR_4843" +"MAR09019" "" "" "" "" "" "HMR_9019" "" "HMR_9019" "RCR20242" "" 0 "" "" "HMR_9019" +"MAR07823" "" "DNDPt51m" "" "" "" "DCTPtm" "MNXR97204" "" "" "" 0 "" "" "DCTPtm" +"MAR07926" "" "DGTPtm" "" "" "" "DGTPtm" "MNXR97327" "" "" "" 0 "" "" "DGTPtm" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index dd78dd03..2a401df0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -195112,22 +195112,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR09019" - - name: "" - - metabolites: !!omap - - MAM01424c: -1 - - MAM01424m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR09020" - name: "" @@ -196237,24 +196221,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR04843" - - name: "" - - metabolites: !!omap - - MAM01948c: -1 - - MAM01948m: 1 - - MAM02034c: 1 - - MAM02034m: -1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000108602 or ENSG00000132746 or ENSG00000184254" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "PMID:11078702" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR04850" - name: "" @@ -244901,38 +244867,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR07823" - - name: "Transport of dCTP into Mitochondria" - - metabolites: !!omap - - MAM01645c: -1 - - MAM01645m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:16816105;PMID:17403938" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - - !!omap - - id: "MAR07926" - - name: "Transport of dGTP into Mitochondria" - - metabolites: !!omap - - MAM01688c: -1 - - MAM01688m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:16816105;PMID:17403938" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR08111" - name: "Transport of Dihydroxyacetone Phosphate into Cytosol" diff --git a/model/reactions.tsv b/model/reactions.tsv index a2576ab0..3037a589 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6644,7 +6644,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08022" "" "2AMADPTm" "" "" "" "2AMADPTm" "MNXR94780" "HMR_8022" "RCR20241" "" 0 "" "" "HMR_8022" "MAR08070" "" "" "" "" "" "SLDtm" "" "HMR_8070" "RCR20536" "" 0 "" "" "HMR_8070" "MAR09015" "" "" "" "" "" "AMETtd" "" "HMR_9015" "RCR20135" "" 0 "" "" "HMR_9015" -"MAR09019" "" "" "" "" "" "HMR_9019" "" "HMR_9019" "RCR20242" "" 0 "" "" "HMR_9019" "MAR09020" "" "" "" "" "" "FADtm" "" "HMR_9020" "RCR20537" "" 0 "" "" "HMR_9020" "MAR00157" "" "" "" "" "" "HMR_0157" "" "HMR_0157" "RCR20164" "" 0 "" "" "HMR_0157" "MAR00158" "" "" "" "r1401" "" "r1401" "MNXR105470" "HMR_0158" "RCR20165" "" 0 "" "" "HMR_0158" @@ -6712,7 +6711,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04754" "" "PPPG9tm" "" "r0976" "" "PPPG9tm" "MNXR103127" "HMR_4754" "RCR20570" "3.A.1.210" 0 "RHEA:27649" "RHEA:27646" "HMR_4754" "MAR04756" "" "HMR_4756" "" "" "" "HMR_4756" "" "HMR_4756" "RCR20262" "" 0 "" "" "HMR_4756" "MAR04760" "" "PHEMEtm" "" "r0880" "" "PHEMEtm" "MNXR102625" "HMR_4760" "RCR20571" "3.A.1.210" 0 "" "" "HMR_4760" -"MAR04843" "" "" "" "r0801" "" "r0801" "MNXR105390" "HMR_4843" "RCR20168" "" 0 "" "" "HMR_4843" "MAR04850" "" "" "" "r0818" "" "r0818" "MNXR97813" "HMR_4850" "RCR20572" "" 0 "" "" "HMR_4850" "MAR04851" "" "" "" "r0819" "" "r0819" "MNXR105393" "HMR_4851" "RCR20573" "2.A.29.2.2" 0 "" "" "HMR_4851" "MAR04852" "" "AKGMALtm" "" "r0820" "" "AKGMALtm" "MNXR95659" "HMR_4852" "RCR20169" "2.A.29.2.2" 0 "" "" "HMR_4852" @@ -9516,8 +9514,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07817" "" "CYSAMOe" "" "" "" "CYSAMOe" "MNXR96988" "" "" "" 0 "RHEA:14410" "RHEA:14409" "CYSAMOe" "MAR07819" "" "Coqe" "" "" "" "Coqe" "MNXR97066" "" "" "" 0 "" "" "Coqe" "MAR07821" "" "DATPtm_cho" "" "" "" "DATPtm" "MNXR97176" "" "" "" 0 "" "" "DATPtm" -"MAR07823" "" "DNDPt51m" "" "" "" "DCTPtm" "MNXR97204" "" "" "" 0 "" "" "DCTPtm" -"MAR07926" "" "DGTPtm" "" "" "" "DGTPtm" "MNXR97327" "" "" "" 0 "" "" "DGTPtm" "MAR08111" "" "DHAPtm" "" "" "" "DHAPtc" "MNXR97366" "" "" "" 0 "" "" "DHAPtc" "MAR08204" "" "DPCOAPPe" "" "" "" "DPCOAPPe" "MNXR97763" "" "" "" 0 "" "" "DPCOAPPe" "MAR08218" "" "DSREDUCr" "" "" "" "DSREDUCr" "" "" "" "" 0 "" "" "DSREDUCr"