fix: update GPRs for Cytochrome C Oxidoreductase and remove MAR04456 that is duplicated to MAR04458+MAR04589

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -72,3 +72,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04588"	""	""	""	"r0425"	""	"r0425"	"MNXR105341"	"HMR_4588"	"RCR11669"	""	0	""	""	"HMR_4588"
 "MAR03488"	""	""	"RE3073X"	""	""	""	"MNXR95747"	"HMR_3488"	"RCR12589"	""	0	""	""	"HMR_3488"
 "MAR03489"	""	""	"RE3079X"	""	""	""	""	"HMR_3489"	"RCR12590"	""	0	""	""	"HMR_3489"
+"MAR04456"	"R01324"	"ACONTm"	"R01324C"	"r0316"	""	"ACONTm"	"MNXR95384"	"HMR_4456"	"RCR10351"	""	0	""	"RHEA:10336"	"HMR_4456"

model/Human-GEM.yml

@@ -94538,23 +94538,7 @@
           - MAM02183c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000122729 or ENSG00000136381"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "4.2.1.3"
-      - references: "PMID:15263083;PMID:16511074"
-      - subsystem:
-          - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR04456"
-      - name: "citrate hydroxymutase"
-      - metabolites: !!omap
-          - MAM01587m: -1
-          - MAM02183m: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729"
+      - gene_reaction_rule: "ENSG00000122729"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.3"
@@ -94571,7 +94555,7 @@
           - MAM02040m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729"
+      - gene_reaction_rule: "ENSG00000100412"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.3"
@@ -94607,7 +94591,7 @@
           - MAM02183m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729"
+      - gene_reaction_rule: "ENSG00000100412"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.3"
@@ -95072,7 +95056,7 @@
           - MAM02630m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111775 and ENSG00000112695 and ENSG00000126267 and ENSG00000127184 and ENSG00000131143 and ENSG00000131174 and ENSG00000135940 and ENSG00000164919 and ENSG00000176340 and ENSG00000178741 and ENSG00000198712 and ENSG00000198804 and ENSG00000198938 and ENSG00000189043"
+      - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.9.3.1"
@@ -302937,9 +302921,9 @@
           - MAM02630m: -1
           - MAM02631m: 0.02
       - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111775 and ENSG00000112695 and ENSG00000126267 and ENSG00000127184 and ENSG00000131055 and ENSG00000131143 and ENSG00000131174 and ENSG00000135940 and ENSG00000156885 and ENSG00000160471 and ENSG00000161281 and ENSG00000164919 and ENSG00000170516 and ENSG00000176340 and ENSG00000178741 and ENSG00000187581 and ENSG00000198712 and ENSG00000198804 and ENSG00000198938"
-      - rxnNotes: ""
+      - upper_bound: 0
+      - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043"
+      - rxnNotes: "This is ROS version of Complex IV, and blocked by default"
       - rxnFrom: "Recon3D"
       - eccodes: ""
       - references: ""
@@ -309398,8 +309382,6 @@
       - id: "ENSG00000136267"
     - !!omap
       - id: "ENSG00000136371"
-    - !!omap
-      - id: "ENSG00000136381"
     - !!omap
       - id: "ENSG00000136448"
     - !!omap
@@ -311934,8 +311916,6 @@
       - id: "ENSG00000187555"
     - !!omap
       - id: "ENSG00000187566"
-    - !!omap
-      - id: "ENSG00000187581"
     - !!omap
       - id: "ENSG00000187630"
     - !!omap

model/genes.tsv

@@ -1302,7 +1302,6 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000136250"	"ENST00000617537;ENST00000621510;ENST00000617267;ENST00000614254;ENST00000491444;ENST00000487014;ENST00000495942;ENST00000480201;ENST00000543742;ENST00000435386;ENST00000414637;ENST00000612871"	"ENSP00000483783;ENSP00000479664;ENSP00000416051;ENSP00000416472;ENSP00000484305"	"P28039"	"AOAH"	"313"	"acyloxyacyl hydrolase"	""	"Cytosol"	"SwissProt"
 "ENSG00000136267"	"ENST00000403951;ENST00000402815;ENST00000407950;ENST00000493142;ENST00000406247;ENST00000403963;ENST00000471732;ENST00000477401;ENST00000464065;ENST00000467449;ENST00000437998;ENST00000463981;ENST00000399322"	"ENSP00000385780;ENSP00000384909;ENSP00000385031;ENSP00000386066;ENSP00000405569;ENSP00000382260"	"Q9Y6T7"	"DGKB"	"1607"	"diacylglycerol kinase beta"	"DAGK2;DGK;DGK-BETA;KIAA0718"	"Cytosol"	"SwissProt"
 "ENSG00000136371"	"ENST00000560261;ENST00000258874;ENST00000559722;ENST00000560919"	"ENSP00000454318;ENSP00000258874;ENSP00000489076;ENSP00000454626"	"P49914"	"MTHFS"	"10588"	"methenyltetrahydrofolate synthetase"	"HsT19268"	"Cytosol"	"SwissProt;CellAtlas"
-"ENSG00000136381"	"ENST00000560840;ENST00000559215;ENST00000258886;ENST00000558525;ENST00000560440;ENST00000558570;ENST00000560454;ENST00000559427;ENST00000559676;ENST00000559091"	"ENSP00000453172;ENSP00000453532;ENSP00000258886;ENSP00000453058;ENSP00000452938;ENSP00000454063;ENSP00000453863"	"P48200"	"IREB2"	"3658"	"iron responsive element binding protein 2"	"IRP2"	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136448"	"ENST00000678938;ENST00000592782;ENST00000676828;ENST00000590310;ENST00000677949;ENST00000591931;ENST00000678606;ENST00000587014;ENST00000587670;ENST00000258960;ENST00000678576;ENST00000543908;ENST00000676753;ENST00000678332;ENST00000590114;ENST00000585561;ENST00000592654;ENST00000588455;ENST00000587120"	"ENSP00000503621;ENSP00000468424;ENSP00000504192;ENSP00000503657;ENSP00000504048;ENSP00000504365;ENSP00000258960;ENSP00000503635;ENSP00000439263;ENSP00000503505;ENSP00000504484;ENSP00000504284;ENSP00000466777;ENSP00000466827"	"P30419"	"NMT1"	"4836"	"N-myristoyltransferase 1"	"NMT"	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136504"	"ENST00000675278;ENST00000454930;ENST00000259021;ENST00000509773;ENST00000510819;ENST00000424009;ENST00000509124;ENST00000506533;ENST00000435742;ENST00000513171;ENST00000514540;ENST00000513980;ENST00000512616;ENST00000508594;ENST00000509794;ENST00000510426;ENST00000513075;ENST00000503101;ENST00000503635"	"ENSP00000502732;ENSP00000413415;ENSP00000259021;ENSP00000424577;ENSP00000423385;ENSP00000398961;ENSP00000421368;ENSP00000409477"	"O95251"	"KAT7"	"11143"	"lysine acetyltransferase 7"	"HBO1;HBOA;MYST2;ZC2HC7"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136521"	"ENST00000488002;ENST00000611971;ENST00000493866;ENST00000259037;ENST00000472629;ENST00000468210;ENST00000359944;ENST00000477177;ENST00000482604;ENST00000480374;ENST00000496904;ENST00000473500;ENST00000491054;ENST00000471112;ENST00000476587;ENST00000493716"	"ENSP00000481703;ENSP00000419656;ENSP00000259037;ENSP00000419248;ENSP00000420538;ENSP00000353026;ENSP00000418354;ENSP00000419099;ENSP00000419501"	"O43674"	"NDUFB5"	"4711"	"NADH:ubiquinone oxidoreductase subunit B5"	"CI-SGDH;MGC12314;SGDH"	"Nucleus;Inner mitochondria"	"SwissProt;CellAtlas"
@@ -2570,7 +2569,6 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000187531"	"ENST00000574992;ENST00000572976;ENST00000571832;ENST00000328666;ENST00000536038;ENST00000574153;ENST00000576156;ENST00000571233;ENST00000572902;ENST00000572350;ENST00000577065;ENST00000574495;ENST00000573367;ENST00000571915;ENST00000575360;ENST00000575244;ENST00000570367;ENST00000572671;ENST00000571213;ENST00000573576;ENST00000574915"	"ENSP00000329466;ENSP00000461044;ENSP00000459524"	"Q9NRC8"	"SIRT7"	"51547"	"sirtuin 7"	""	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000187555"	"ENST00000344836;ENST00000673704;ENST00000563961;ENST00000381886;ENST00000565455;ENST00000563085;ENST00000567113;ENST00000565883;ENST00000562615;ENST00000563043;ENST00000562051;ENST00000567692;ENST00000569448;ENST00000566131;ENST00000570256;ENST00000567329;ENST00000542333;ENST00000566004;ENST00000569230;ENST00000566273;ENST00000564117;ENST00000566224"	"ENSP00000343535;ENSP00000501290;ENSP00000454362;ENSP00000371310;ENSP00000456258;ENSP00000454795;ENSP00000459594;ENSP00000458027;ENSP00000439272;ENSP00000456150;ENSP00000457237;ENSP00000455719;ENSP00000457815"	"Q93009"	"USP7"	"7874"	"ubiquitin specific peptidase 7"	"HAUSP"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000187566"	"ENST00000340650"	"ENSP00000345464"	"Q6VVB1"	"NHLRC1"	"378884"	"NHL repeat containing E3 ubiquitin protein ligase 1"	"bA204B7.2;EPM2B"	"Endoplasmic reticulum;Nucleus"	"SwissProt"
-"ENSG00000187581"	"ENST00000342144"	"ENSP00000340568"	"Q7Z4L0"	"COX8C"	"341947"	"cytochrome c oxidase subunit 8C"	"COX8-3"	"Mitochondria"	"DeepLoc2"
 "ENSG00000187630"	"ENST00000534993;ENST00000543805;ENST00000621761;ENST00000397071;ENST00000559411;ENST00000558753;ENST00000537912;ENST00000335125;ENST00000559387;ENST00000557812;ENST00000560276"	"ENSP00000441095;ENSP00000441433;ENSP00000481066;ENSP00000380261;ENSP00000453889;ENSP00000453845;ENSP00000439942;ENSP00000334801;ENSP00000453173;ENSP00000452875"	"Q6PKH6"	"DHRS4L2"	"317749"	"dehydrogenase/reductase 4 like 2"	"SDR25C3"	"Nucleus"	"CellAtlas"
 "ENSG00000187676"	"ENST00000343307;ENST00000461652"	"ENSP00000343002"	"Q6Y288"	"B3GLCT"	"145173"	"beta 3-glucosyltransferase"	"B3GALTL;B3Glc-T;B3GTL"	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000187714"	"ENST00000374115"	"ENSP00000363229"	"Q16572"	"SLC18A3"	"6572"	"solute carrier family 18 member A3"	"VACHT"	"Cell membrane;Lysosome"	"DeepLoc2"

model/reactions.tsv

@@ -1347,7 +1347,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04408"	"R01082"	"FUM"	"R01082C"	"r0258"	""	"FUM"	"MNXR99705"	"HMR_4408"	"RCR10105"	""	0	""	"RHEA:12460"	"HMR_4408"
 "MAR04410"	"R01082"	"FUMm"	"R01082C"	"r0259"	""	"FUMm"	"MNXR99705"	"HMR_4410"	"RCR11665"	""	0	""	"RHEA:12460"	"HMR_4410"
 "MAR04454"	"R01324"	"ACONT"	"R01324C"	"r0315"	""	"ACONT"	"MNXR95384"	"HMR_4454"	"RCR10028"	""	0	""	"RHEA:10336"	"HMR_4454"
-"MAR04456"	"R01324"	"ACONTm"	"R01324C"	"r0316"	""	"ACONTm"	"MNXR95384"	"HMR_4456"	"RCR10351"	""	0	""	"RHEA:10336"	"HMR_4456"
 "MAR04458"	"R01325"	""	"R01325C"	"r0317"	""	"r0317"	"MNXR105321;MNXR95386"	"HMR_4458"	"RCR10106"	""	0	"RHEA:10231"	"RHEA:10228"	"HMR_4458"
 "MAR04465"	"R01392"	"HPYRRy"	"R01392C"	"r0327"	""	"HPYRRy"	"MNXR100336"	"HMR_4465"	"RCR11666"	""	0	""	"RHEA:18657"	"HMR_4465"
 "MAR04589"	"R01900"	""	"R01900C"	"r0426"	""	"r0426"	"MNXR105342;MNXR95387"	"HMR_4589"	"RCR10352"	""	0	""	"RHEA:22144"	"HMR_4589"