Merge pull request #714 from SysBioChalmers/fix/LIPT1

Fix Representation of LIPT1
SysBioChalmers · Oct 29, 2023 · 48eda9c · 48eda9c
2 parents 84198f7 + 7e3fd18
commit 48eda9c
Show file tree

Hide file tree

Showing 5 changed files with 27 additions and 86 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2252,3 +2252,5 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM20020r"	"MAM20020"	"C00061"	""	""	"CHEBI:58210"	""	""	""	""	""	"MNXM1105928"	""	""
 "MAM20022i"	"MAM20022"	"C01847"	""	""	"CHEBI:57618"	""	""	""	""	""	"MNXM1107623"	""	""
 "MAM20023i"	"MAM20023"	"C00061"	""	""	"CHEBI:58210"	""	""	""	""	""	"MNXM1105928"	""	""
+"MAM02398c"	"MAM02398"	""	"C16238"	""	""	"23724672"	""	"CE5656"	""	"CE5656"	"MNXM2392"	"m02398c"	"m02398c"
+"MAM01701c"	"MAM01701"	"dhlam"	"C00579"	"HMDB0000985"	"CHEBI:17694"	"663"	""	""	"HC00437"	"dhlam"	"MNXM1277"	"m01701c"	"m01701c"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -253,3 +253,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00482"	"R00848;R00849"	"G3PD2m"	"R00848C"	"r0205"	""	"HMR_0482;r0205"	"MNXR99875;MNXR106713"	"HMR_0482;HMR_0483"	"RCR14578;RCR21050"	""	0	""	"RHEA:31283;RHEA:18977"	"HMR_0482;HMR_0483;MAR00483"
 "MAR20012"	"R02123"	"HMR_6647;RADH;R_HMR_6647;R_RADH"	""	""	""	""	"MNXR146215"	""	""	""	0	"RHEA:42080"	""	""
 "MAR20089"	"R02701"	""	""	""	""	""	"MNXR151808"	""	""	""	0	"RHEA:18533"	""	""
+"MAR06398"	"R07770"	""	"R07770C"	""	""	"RE1944C"	"MNXR101081"	"HMR_6398"	"RCR14489"	""	0	""	"RHEA:12913"	"HMR_6398"
+"MAR06399"	"R07771"	""	"R07771C"	""	""	"HMR_6399"	"MNXR111358"	"HMR_6399"	"RCR14490"	""	0	""	"RHEA:20473"	"HMR_6399"
+"MAR06408"	""	""	"RT0295"	""	""	"HMR_6408"	""	"HMR_6408"	"RCR21069"	""	0	""	""	"HMR_6408"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -22849,14 +22849,6 @@
       - charge: -2
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM01701c"
-      - name: "dihydrolipoamide"
-      - compartment: "c"
-      - formula: "C8H17NOS2"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM01701m"
       - name: "dihydrolipoamide"
@@ -32657,14 +32649,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM02398c"
-      - name: "lipoyl-AMP"
-      - compartment: "c"
-      - formula: "C18H25N5O8PS2"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02399c"
       - name: "lipoyllysine"
@@ -80471,7 +80455,7 @@
           - MAM01596m: 1
           - MAM01986m: -1
           - MAM02039m: -1
-          - MAM02393m: -1
+          - MAM00209c: -1
           - MAM02878m: 1
       - lower_bound: 0
       - upper_bound: 1000
@@ -80488,7 +80472,7 @@
       - name: ""
       - metabolites: !!omap
           - MAM01045m: 1
-          - MAM01701m: 1
+          - MAM00208c: 1
           - MAM02039m: 1
           - MAM02578m: 1
           - MAM02878m: -1
@@ -100667,44 +100651,6 @@
       - subsystem:
           - "Lipoic acid metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR06398"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01371c: -1
-          - MAM02039c: -1
-          - MAM02394c: -1
-          - MAM02398c: 1
-          - MAM02759c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000144182"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.7.7.63"
-      - references: "PMID:10103005"
-      - subsystem:
-          - "Lipoic acid metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR06399"
-      - name: ""
-      - metabolites: !!omap
-          - MAM00209c: 1
-          - MAM01334c: 1
-          - MAM01350c: -1
-          - MAM02039c: 1
-          - MAM02398c: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000144182"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.7.7.63"
-      - references: ""
-      - subsystem:
-          - "Lipoic acid metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR06402"
       - name: "octanoyl-[acp]:protein N6-octanoyltransferase"
@@ -105524,7 +105470,7 @@
           - MAM02538c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000144182 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
+      - gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.-"
@@ -105543,7 +105489,7 @@
           - MAM02538n: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000144182 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
+      - gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.-"
@@ -198496,24 +198442,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR06408"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01701c: -1
-          - MAM01701m: 1
-          - MAM02039i: -1
-          - MAM02039m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR06431"
       - name: ""
@@ -270321,8 +270249,6 @@
       - id: "MAR11346"
       - name: "Lipoamide Transport"
       - metabolites: !!omap
-          - MAM02039c: 1
-          - MAM02039e: -1
           - MAM02393c: 1
           - MAM02393e: -1
       - lower_bound: -1000
@@ -270558,11 +270484,9 @@
       - id: "MAR11361"
       - name: "Transport of Lipoamide, Mitochondrial"
       - metabolites: !!omap
-          - MAM02039i: -1
-          - MAM02039m: 1
           - MAM02393c: -1
           - MAM02393m: 1
-      - lower_bound: 0
+      - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""
       - rxnNotes: ""
@@ -305321,6 +305245,22 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
+    - !!omap
+      - id: "MAR20168"
+      - name: "MAR20168"
+      - metabolites: !!omap
+          - MAM00209c: -1
+          - MAM02393m: 1
+      - lower_bound: 0
+      - upper_bound: 1000
+      - gene_reaction_rule: "ENSG00000144182"
+      - rxnNotes: ""
+      - rxnFrom: ""
+      - eccodes: ""
+      - references: "PMID:29987032"
+      - subsystem:
+          - "Miscellaneous"
+      - confidence_score: 0
 - genes:
     - !!omap
       - id: "ENSG00000000419"

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -2854,7 +2854,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01700l"	"MAM01700"	"dhf"	"C00415"	""	"CHEBI:15633"	"98792"	""	""	"HC00340"	"dhf"	"MNXM281"	"m01700l"	"m01700l"
 "MAM01700m"	"MAM01700"	"dhf"	"C00415"	""	"CHEBI:15633"	"98792"	""	""	"HC00340"	"dhf"	"MNXM281"	"m01700m"	"m01700m"
 "MAM01700e"	"MAM01700"	"dhf"	"C00415"	""	"CHEBI:15633"	"98792"	""	""	"HC00340"	"dhf"	"MNXM281"	"m01700s"	"m01700s"
-"MAM01701c"	"MAM01701"	"dhlam"	"C00579"	"HMDB0000985"	"CHEBI:17694"	"663"	""	""	"HC00437"	"dhlam"	"MNXM1277"	"m01701c"	"m01701c"
 "MAM01701m"	"MAM01701"	"dhlam"	"C00579"	"HMDB0000985"	"CHEBI:17694"	"663"	""	""	"HC00437"	"dhlam"	"MNXM1277"	"m01701m"	"m01701m"
 "MAM01702c"	"MAM01702"	""	"C02147"	"HMDB0012210"	"CHEBI:18047"	"421"	"LMFA01130003"	""	""	"C02147"	"MNXM3585"	"m01702c"	"m01702c"
 "MAM01704c"	"MAM01704"	""	"C04874"	""	"CHEBI:17001"	"65074"	""	""	"HC01361"	"HC01361"	"MNXM993"	"m01704c"	"m01704c"
@@ -4080,7 +4079,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02396n"	"MAM02396"	""	"C06315"	"HMDB0005082"	"CHEBI:6499"	"5280915"	"LMFA03040002"	""	""	"C06315"	"MNXM12130"	"m02396n"	"m02396n"
 "MAM02396x"	"MAM02396"	""	"C06315"	"HMDB0005082"	"CHEBI:6499"	"5280915"	"LMFA03040002"	""	""	"C06315"	"MNXM12130"	"m02396p"	"m02396p"
 "MAM02396r"	"MAM02396"	""	"C06315"	"HMDB0005082"	"CHEBI:6499"	"5280915"	"LMFA03040002"	""	""	"C06315"	"MNXM12130"	"m02396r"	"m02396r"
-"MAM02398c"	"MAM02398"	""	"C16238"	""	""	"23724672"	""	"CE5656"	""	"CE5656"	"MNXM2392"	"m02398c"	"m02398c"
 "MAM02399c"	"MAM02399"	""	""	""	""	"53481572"	""	"CE2102"	""	"CE2102"	"MNXM60228"	"m02399c"	"m02399c"
 "MAM02401c"	"MAM02401"	""	"C03127"	""	"CHEBI:29160"	""	""	""	""	"M02401"	"MNXM89832"	"m02401c"	"m02401c"
 "MAM02402c"	"MAM02402"	""	"C03990"	"HMDB0000761"	"CHEBI:16325"	"11740284"	"LMST04010003"	""	"HC02191"	"HC02191"	"MNXM886"	"m02402c"	"m02402c"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -1664,8 +1664,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR02469"	""	""	"RE3264C"	""	""	"RE3264C"	""	"HMR_2469"	"RCR11942"	""	0	""	""	"HMR_2469"
 "MAR02470"	""	""	"RE3264R"	""	""	"RE3264R"	"MNXR103858"	"HMR_2470"	"RCR11943"	""	0	""	""	"HMR_2470"
 "MAR06397"	""	""	"RE2882C"	""	""	"HMR_6397"	""	"HMR_6397"	"RCR10619"	""	0	""	""	"HMR_6397"
-"MAR06398"	"R07770"	""	"R07770C"	""	""	"RE1944C"	"MNXR101081"	"HMR_6398"	"RCR14489"	""	0	""	"RHEA:12913"	"HMR_6398"
-"MAR06399"	"R07771"	""	"R07771C"	""	""	"HMR_6399"	"MNXR111358"	"HMR_6399"	"RCR14490"	""	0	""	"RHEA:20473"	"HMR_6399"
 "MAR06402"	"R07766;R07769"	""	"R07766C;R07769C"	""	""	"HMR_6402;HMR_6401"	"MNXR111354"	"HMR_6402;HMR_6401"	"RCR11946;RCR11945"	""	0	"RHEA:17666"	"RHEA:17665"	"HMR_6402;HMR_6401;MAR06401"
 "MAR06403"	"R07767;R07768"	""	"R07767C;R07768C"	""	""	"HMR_6403;HMR_6400"	"MNXR111355"	"HMR_6403;HMR_6400"	"RCR11947;RCR11948"	""	0	"RHEA:16586"	"RHEA:16585"	"HMR_6403;HMR_6400;MAR06400"
 "MAR06404"	"R08550"	""	"R08550C"	""	""	"HMR_6404"	"MNXR112089"	"HMR_6404"	"RCR14491"	""	0	""	""	"HMR_6404"
@@ -6839,7 +6837,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06343"	""	"DNDPt42m"	""	"r2432"	""	"DNDPt42m"	"MNXR97655"	"HMR_6343"	"RCR20276"	"2.A.29.16.1"	0	""	""	"HMR_6343"
 "MAR06389"	""	"r2472"	""	"r2472"	""	"r2472"	"MNXR100321"	"HMR_6389"	"RCR20616"	"2.A.1.4.7"	0	""	""	"HMR_6389"
 "MAR06391"	""	""	""	"r2520"	""	"r2520"	"MNXR106328"	"HMR_6391"	"RCR20063"	""	0	""	""	"HMR_6391"
-"MAR06408"	""	""	"RT0295"	""	""	"HMR_6408"	""	"HMR_6408"	"RCR21069"	""	0	""	""	"HMR_6408"
 "MAR06431"	""	""	""	""	""	"HMR_6431"	""	"HMR_6431"	"RCR20617"	""	0	""	""	"HMR_6431"
 "MAR06438"	""	""	""	""	""	"HMR_6438"	""	"HMR_6438"	"RCR20618"	""	0	""	""	"HMR_6438"
 "MAR06446"	""	""	""	""	""	"HMR_6446"	""	"HMR_6446"	"RCR20619"	""	0	""	""	"HMR_6446"
@@ -12997,3 +12994,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20164"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR20165"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR20166"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
+"MAR20168"	""	""	""	""	""	""	""	""	""	""	0	""	""	""