From 94d6b14afd2768c87fdea2637b1477ea4366ee33 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Sat, 14 Oct 2023 18:56:25 -0400 Subject: [PATCH 1/4] fix: removed MAR01483 and MAR06406 for being duplicates of MAR09608 and merged annotations accordingly --- .../deprecatedReactions.tsv | 4 +- model/Human-GEM.yml | 46 ------------------- model/reactions.tsv | 4 +- 3 files changed, 4 insertions(+), 50 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 5524225a..cd80a21a 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -238,4 +238,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771" "MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" "MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" -"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" \ No newline at end of file +"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" +"MAR01483" "" "LIPOti" "" "" "" "LIPOti" "MNXR101093" "" "" "" 0 "" "" "LIPOti" +"MAR06406" "" "LIPOti" "RT1089" "" "" "" "MNXR101093" "HMR_6406" "RCR41534" "" 0 "" "" "HMR_6406" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c6a46e87..eb55ae1a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -188432,29 +188432,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR06406" - - name: "" - - metabolites: !!omap - - MAM01285c: 1 - - MAM01371c: -1 - - MAM02039c: 1 - - MAM02040c: -1 - - MAM02394c: 1 - - MAM02394e: -1 - - MAM02519c: 2 - - MAM02519e: -2 - - MAM02751c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000138074" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "PMID:16415531" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR06424" - name: "" @@ -224053,29 +224030,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR01483" - - name: "Transport of Lipoate via Sodium Symport" - - metabolites: !!omap - - MAM01285c: 1 - - MAM01371c: -1 - - MAM02039c: 1 - - MAM02040c: -1 - - MAM02394c: 1 - - MAM02394e: -1 - - MAM02519c: 1 - - MAM02519e: -1 - - MAM02751c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000138074" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:10329687;PMID:10334869;PMID:12646417;PMID:15561972;PMID:9516450" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR01485" - name: "Transport of L-Lactate via Diffusion, Mitochondrial" diff --git a/model/reactions.tsv b/model/reactions.tsv index 34c5374f..a89647a1 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6255,7 +6255,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06383" "" "HOMt4" "" "r2480" "" "" "MNXR100677" "HMR_6383" "RCR41531" "2.A.18.6.8" 0 "" "" "HMR_6383" "MAR06384" "" "HISt4" "" "r2481" "" "HISSNAT5tc" "MNXR100646" "HMR_6384" "RCR41532" "2.A.18.6.2" 0 "" "" "HMR_6384" "MAR06392" "" "" "" "r2505" "" "r2505" "MNXR106316" "HMR_6392" "RCR41533" "3.A.1.208.8" 0 "" "" "HMR_6392" -"MAR06406" "" "LIPOti" "RT1089" "" "" "" "MNXR101093" "HMR_6406" "RCR41534" "" 0 "" "" "HMR_6406" "MAR06424" "" "AVITE2t" "RT1352" "" "" "AVITE2t" "MNXR96147" "HMR_6424" "RCR40703" "" 0 "" "" "HMR_6424" "MAR06439" "" "" "" "" "" "HMR_6439" "" "HMR_6439" "RCR40704" "" 0 "" "" "HMR_6439" "MAR06462" "" "" "" "" "" "YVITEt" "" "HMR_6462" "RCR40705" "" 0 "" "" "HMR_6462" @@ -6589,7 +6588,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09605" "" "" "" "" "" "HMR_9605" "" "HMR_9605" "RCR41621" "" 0 "" "" "HMR_9605" "MAR09606" "" "" "" "" "" "GLYSNAT5tc" "" "HMR_9606" "RCR41622" "" 0 "" "" "HMR_9606" "MAR09607" "" "" "" "" "" "HMR_9607" "" "HMR_9607" "RCR41623" "" 0 "" "" "HMR_9607" -"MAR09608" "" "" "" "" "" "HMR_9608" "" "HMR_9608" "RCR41624" "" 0 "" "" "HMR_9608" +"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "" "" "HMR_9608;LIPOti;HMR_6406" "MAR09609" "" "" "" "" "" "HMR_9609" "" "HMR_9609" "RCR41625" "" 0 "" "" "HMR_9609" "MAR09610" "" "" "" "" "" "HMR_9610" "" "HMR_9610" "RCR41626" "" 0 "" "" "HMR_9610" "MAR09611" "" "" "" "" "" "INSTt2r" "" "HMR_9611" "RCR40899" "" 0 "" "" "HMR_9611" @@ -8377,7 +8376,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR01480" "" "LEUt5m" "" "" "" "LEUt5m" "MNXR101057" "" "" "" 0 "" "" "LEUt5m" "MAR01481" "" "LGNCCPT2" "" "" "" "LGNCCPT2" "MNXR101063" "" "" "" 0 "" "" "LGNCCPT2" "MAR01482" "" "LGNCCRNt" "" "" "" "LGNCCRNt" "MNXR101064" "" "" "" 0 "" "" "LGNCCRNt" -"MAR01483" "" "LIPOti" "" "" "" "LIPOti" "MNXR101093" "" "" "" 0 "" "" "LIPOti" "MAR01485" "" "L_LACtcm" "" "" "" "L_LACtcm" "MNXR100999" "" "" "" 0 "" "" "L_LACtcm" "MAR01486" "" "LNELDCCRNt" "" "" "" "LNELDCCRNt" "MNXR101102" "" "" "" 0 "" "" "LNELDCCRNt" "MAR01487" "" "LNLCCRNt" "" "" "" "LNLCCRNt" "MNXR101106" "" "" "" 0 "" "" "LNLCCRNt" From 6e1c87a8ff5ee46516aa8a56806f49af1ea0d9ac Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Sat, 14 Oct 2023 18:59:48 -0400 Subject: [PATCH 2/4] feat: updated references and added RHEA IDs for MAR09608 --- model/Human-GEM.yml | 2 +- model/reactions.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index eb55ae1a..0ba3fc88 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -194192,7 +194192,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID:9516450;PMID:10329687;PMID:15561972" - subsystem: - "Transport reactions" - confidence_score: 0 diff --git a/model/reactions.tsv b/model/reactions.tsv index a89647a1..d8e41d92 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6588,7 +6588,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09605" "" "" "" "" "" "HMR_9605" "" "HMR_9605" "RCR41621" "" 0 "" "" "HMR_9605" "MAR09606" "" "" "" "" "" "GLYSNAT5tc" "" "HMR_9606" "RCR41622" "" 0 "" "" "HMR_9606" "MAR09607" "" "" "" "" "" "HMR_9607" "" "HMR_9607" "RCR41623" "" 0 "" "" "HMR_9607" -"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "" "" "HMR_9608;LIPOti;HMR_6406" +"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "RHEA:73379" "RHEA:73380" "HMR_9608;LIPOti;HMR_6406" "MAR09609" "" "" "" "" "" "HMR_9609" "" "HMR_9609" "RCR41625" "" 0 "" "" "HMR_9609" "MAR09610" "" "" "" "" "" "HMR_9610" "" "HMR_9610" "RCR41626" "" 0 "" "" "HMR_9610" "MAR09611" "" "" "" "" "" "INSTt2r" "" "HMR_9611" "RCR40899" "" 0 "" "" "HMR_9611" From d33211d697586079b08bcdc113cb3ad8f8449bc0 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Sat, 14 Oct 2023 19:21:46 -0400 Subject: [PATCH 3/4] fix: accidentally swapped master and direction-specific RHEA IDs in annotations for MAR09608 --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index d8e41d92..793c98b1 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6588,7 +6588,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09605" "" "" "" "" "" "HMR_9605" "" "HMR_9605" "RCR41621" "" 0 "" "" "HMR_9605" "MAR09606" "" "" "" "" "" "GLYSNAT5tc" "" "HMR_9606" "RCR41622" "" 0 "" "" "HMR_9606" "MAR09607" "" "" "" "" "" "HMR_9607" "" "HMR_9607" "RCR41623" "" 0 "" "" "HMR_9607" -"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "RHEA:73379" "RHEA:73380" "HMR_9608;LIPOti;HMR_6406" +"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "RHEA:73380" "RHEA:73379" "HMR_9608;LIPOti;HMR_6406" "MAR09609" "" "" "" "" "" "HMR_9609" "" "HMR_9609" "RCR41625" "" 0 "" "" "HMR_9609" "MAR09610" "" "" "" "" "" "HMR_9610" "" "HMR_9610" "RCR41626" "" 0 "" "" "HMR_9610" "MAR09611" "" "" "" "" "" "INSTt2r" "" "HMR_9611" "RCR40899" "" 0 "" "" "HMR_9611" From bc6d7b6d93dcb3ab4db0755babd9dccbf75068ba Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 16 Oct 2023 09:45:48 -0400 Subject: [PATCH 4/4] fix: added removed reactions to rxnRetired column for MAR09608 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 0cab64f8..926f2dcf 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6586,7 +6586,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09605" "" "" "" "" "" "HMR_9605" "" "HMR_9605" "RCR41621" "" 0 "" "" "HMR_9605" "MAR09606" "" "" "" "" "" "GLYSNAT5tc" "" "HMR_9606" "RCR41622" "" 0 "" "" "HMR_9606" "MAR09607" "" "" "" "" "" "HMR_9607" "" "HMR_9607" "RCR41623" "" 0 "" "" "HMR_9607" -"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "RHEA:73380" "RHEA:73379" "HMR_9608;LIPOti;HMR_6406" +"MAR09608" "" "LIPOti" "RT1089" "" "" "HMR_9608;LIPOti" "MNXR101093" "HMR_9608;HMR_6406" "RCR41624;RCR41534" "" 0 "RHEA:73380" "RHEA:73379" "HMR_9608;LIPOti;HMR_6406;MAR01483;MAR06406" "MAR09609" "" "" "" "" "" "HMR_9609" "" "HMR_9609" "RCR41625" "" 0 "" "" "HMR_9609" "MAR09610" "" "" "" "" "" "HMR_9610" "" "HMR_9610" "RCR41626" "" 0 "" "" "HMR_9610" "MAR09611" "" "" "" "" "" "INSTt2r" "" "HMR_9611" "RCR40899" "" 0 "" "" "HMR_9611"