Fix: GPR curation for miscellaneous isolated drug metabolism (#931)

* Fix: GPR curation for Miscellaneous_Isolated_Drug_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b <[email protected]> Co-authored-by: Eduard Kerkhoven <[email protected]>
SysBioChalmers · Dec 17, 2024 · 18782b4 · 18782b4
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commit 18782b4
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diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -161378,7 +161378,7 @@
           - MAM02553c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
+      - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.244"
@@ -161486,7 +161486,7 @@
           - MAM02470l: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000005381 or ENSG00000115705 or ENSG00000117592 or ENSG00000121053 or ENSG00000167419"
+      - gene_reaction_rule: "ENSG00000005381 or ENSG00000117592 or ENSG00000121053 or ENSG00000167419"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.11.1.7;1.11.1.8;1.11.2.2"
@@ -161523,7 +161523,7 @@
           - MAM02040c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000090402 or ENSG00000114982 or ENSG00000168137 or ENSG00000243056 or ENSG00000257335"
+      - gene_reaction_rule: "ENSG00000090402 or ENSG00000114982 or ENSG00000257335"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.3;3.2.1.10"
@@ -161559,7 +161559,7 @@
           - MAM02039c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
+      - gene_reaction_rule: "ENSG00000167363"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.-"
@@ -161578,7 +161578,7 @@
           - MAM02039c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
+      - gene_reaction_rule: "ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.-"
@@ -161908,7 +161908,7 @@
           - MAM02527c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111261 or ENSG00000133048 or ENSG00000133063 or ENSG00000134216"
+      - gene_reaction_rule: "ENSG00000111261 or ENSG00000133063 or ENSG00000134216"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.14"
@@ -162075,7 +162075,7 @@
           - MAM02128c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000005339 and ENSG00000124151) or ENSG00000083168 or ENSG00000084676 or ENSG00000100393 or ENSG00000103510 or ENSG00000108773 or ENSG00000114166 or ENSG00000125484 or ENSG00000128708 or ENSG00000129873 or ENSG00000134014 or ENSG00000134852 or ENSG00000136504 or ENSG00000156650 or ENSG00000172288 or ENSG00000172352 or ENSG00000172977 or ENSG00000182415 or ENSG00000198408"
+      - gene_reaction_rule: "(ENSG00000005339 and ENSG00000124151) or ENSG00000083168 or ENSG00000084676 or ENSG00000100393 or ENSG00000103510 or ENSG00000108773 or ENSG00000114166 or ENSG00000125484 or ENSG00000128708 or ENSG00000129873 or ENSG00000134014 or ENSG00000134852 or ENSG00000136504 or ENSG00000156650 or ENSG00000172288 or ENSG00000172352 or ENSG00000172977 or ENSG00000182415"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.48"
@@ -162149,7 +162149,7 @@
           - MAM02918c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000131238 or ENSG00000221988 or ENSG00000241404"
+      - gene_reaction_rule: "ENSG00000131238 or ENSG00000241404"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.2.22"
@@ -162410,7 +162410,7 @@
           - MAM02577c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000153904 or ENSG00000213722"
+      - gene_reaction_rule: "ENSG00000153904"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.5.3.18"
@@ -226820,7 +226820,7 @@
           - MAM02555m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.2.1.5"
@@ -226860,7 +226860,7 @@
           - MAM02555m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.2.1.5"
@@ -226900,7 +226900,7 @@
           - MAM03136m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.2.1.5"
@@ -242378,7 +242378,7 @@
           - MAM03164c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000133313 or ENSG00000150656"
+      - gene_reaction_rule: "ENSG00000133313"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -288366,7 +288366,7 @@
           - MAM03418e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000197506"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -288580,7 +288580,7 @@
           - MAM03418e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000137860 or ENSG00000156222 or ENSG00000197506"
+      - gene_reaction_rule: "ENSG00000137860"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -310952,9 +310952,6 @@
     - !!omap
       - id: "ENSG00000168092"
       - name: "PAFAH1B2"
-    - !!omap
-      - id: "ENSG00000168137"
-      - name: "SETD5"
     - !!omap
       - id: "ENSG00000168159"
       - name: "RNF187"
@@ -312593,9 +312590,6 @@
     - !!omap
       - id: "ENSG00000198380"
       - name: "GFPT1"
-    - !!omap
-      - id: "ENSG00000198408"
-      - name: "OGA"
     - !!omap
       - id: "ENSG00000198431"
       - name: "TXNRD1"
@@ -312848,9 +312842,6 @@
     - !!omap
       - id: "ENSG00000213689"
       - name: "TREX1"
-    - !!omap
-      - id: "ENSG00000213722"
-      - name: "DDAH2"
     - !!omap
       - id: "ENSG00000213759"
       - name: "UGT2B11"
@@ -313058,9 +313049,6 @@
     - !!omap
       - id: "ENSG00000242612"
       - name: "DECR2"
-    - !!omap
-      - id: "ENSG00000243056"
-      - name: "EIF4EBP3"
     - !!omap
       - id: "ENSG00000243477"
       - name: "NAA80"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -2095,7 +2095,6 @@ ENSG00000168003	"ENST00000680729;ENST00000680002;ENST00000377890;ENST00000681467
 ENSG00000168032	"ENST00000301825;ENST00000647765;ENST00000439533;ENST00000456402;ENST00000445129"	"ENSP00000301825;ENSP00000497683;ENSP00000406555;ENSP00000401565;ENSP00000404671"	O75355	ENTPD3	956	ectonucleoside triphosphate diphosphohydrolase 3	"CD39L3;HB6;NTPDase-3"	Cell membrane	DeepLoc2
 ENSG00000168065	"ENST00000377585;ENST00000301891;ENST00000377581;ENST00000490834;ENST00000478051;ENST00000460745;ENST00000428570;ENST00000416590"	"ENSP00000366809;ENSP00000301891;ENSP00000366804;ENSP00000394043;ENSP00000413508"	Q9NSA0	SLC22A11	55867	solute carrier family 22 member 11	OAT4	Cell membrane	DeepLoc2
 ENSG00000168092	"ENST00000419197;ENST00000527958;ENST00000304808;ENST00000529887;ENST00000526888;ENST00000530272;ENST00000533206;ENST00000533677"	"ENSP00000388742;ENSP00000435289;ENSP00000304006;ENSP00000434951;ENSP00000431365"	P68402	PAFAH1B2	5049	platelet activating factor acetylhydrolase 1b catalytic subunit 2		"Nucleus;Cytosol"	"SwissProt;CellAtlas"
-ENSG00000168137	"ENST00000431285;ENST00000402198;ENST00000683012;ENST00000463180;ENST00000478475;ENST00000415650;ENST00000682536;ENST00000663774;ENST00000683262;ENST00000684606;ENST00000665872;ENST00000666307;ENST00000443339;ENST00000406341;ENST00000670063;ENST00000468208;ENST00000684055;ENST00000407969;ENST00000490791;ENST00000493918;ENST00000399686;ENST00000497213;ENST00000413704;ENST00000466242;ENST00000464410;ENST00000682236;ENST00000488236;ENST00000421188;ENST00000478961;ENST00000476740;ENST00000486465;ENST00000492939;ENST00000459941;ENST00000479538;ENST00000466826"	"ENSP00000397076;ENSP00000385852;ENSP00000506933;ENSP00000395959;ENSP00000507956;ENSP00000499452;ENSP00000507464;ENSP00000506817;ENSP00000499600;ENSP00000499402;ENSP00000393221;ENSP00000383939;ENSP00000499725;ENSP00000499609;ENSP00000507953;ENSP00000384114;ENSP00000507055;ENSP00000382593;ENSP00000401554;ENSP00000507801;ENSP00000399993;ENSP00000506929;ENSP00000507322"	Q9C0A6	SETD5	55209	SET domain containing 5	FLJ10707	Nucleus	"SwissProt;CellAtlas"
 ENSG00000168159	"ENST00000305943;ENST00000482739"	ENSP00000306396	Q5TA31	RNF187	149603	ring finger protein 187	"RACO-1;RACO1"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000168237	"ENST00000461183;ENST00000305690;ENST00000473032;ENST00000486393;ENST00000436784;ENST00000471180;ENST00000473583;ENST00000477382;ENST00000489173"	"ENSP00000417264;ENSP00000301965;ENSP00000418951;ENSP00000419868;ENSP00000389175;ENSP00000417526;ENSP00000419008"	Q8IVS8	GLYCTK	132158	glycerate kinase	"HBEBP2;HBEBP4"	"Golgi apparatus;Mitochondria;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000168282	ENST00000305386	ENSP00000307423	Q10469	MGAT2	4247	alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase	GNT-II	Golgi apparatus	"SwissProt;CellAtlas"
@@ -2634,7 +2633,6 @@ ENSG00000198276	"ENST00000354216;ENST00000369908;ENST00000632800;ENST00000430743
 ENSG00000198363	"ENST00000379454;ENST00000541428;ENST00000521909;ENST00000524173;ENST00000521499;ENST00000522349;ENST00000523897;ENST00000523927;ENST00000522919;ENST00000356457;ENST00000519234;ENST00000518068;ENST00000517903;ENST00000517847;ENST00000518441;ENST00000522835;ENST00000519678;ENST00000519264;ENST00000518306;ENST00000520198;ENST00000517856;ENST00000517928;ENST00000389204;ENST00000522603;ENST00000379449;ENST00000517661;ENST00000522325;ENST00000522036;ENST00000522343;ENST00000445642"	"ENSP00000368767;ENSP00000437864;ENSP00000479945;ENSP00000429718;ENSP00000478706;ENSP00000430516;ENSP00000348841;ENSP00000427823;ENSP00000429286;ENSP00000430245;ENSP00000429954;ENSP00000429160;ENSP00000483443;ENSP00000479830;ENSP00000427877;ENSP00000429743;ENSP00000373856;ENSP00000436188;ENSP00000368762;ENSP00000428060;ENSP00000394013"	Q12797	ASPH	444	aspartate beta-hydroxylase	"BAH;CASQ2BP1;HAAH;JCTN"	Endoplasmic reticulum	"SwissProt;CellAtlas"
 ENSG00000198373	"ENST00000359154;ENST00000561780;ENST00000569620;ENST00000568845;ENST00000563659;ENST00000569658;ENST00000569174;ENST00000544162;ENST00000567986;ENST00000563618;ENST00000570104;ENST00000569297;ENST00000567579;ENST00000566463;ENST00000568684;ENST00000568185;ENST00000568818;ENST00000567161;ENST00000567303;ENST00000356003"	"ENSP00000352069;ENSP00000456451;ENSP00000456582;ENSP00000455347;ENSP00000455311;ENSP00000456216;ENSP00000348283"	O00308	WWP2	11060	WW domain containing E3 ubiquitin protein ligase 2	AIP2	Nucleus	SwissProt
 ENSG00000198380	"ENST00000357308;ENST00000361060;ENST00000674507;ENST00000674438;ENST00000494201"	"ENSP00000349860;ENSP00000354347;ENSP00000501332;ENSP00000501469;ENSP00000501359"	Q06210	GFPT1	2673	glutamine--fructose-6-phosphate transaminase 1	"GFA;GFAT;GFAT1;GFPT"	Nucleus	CellAtlas
-ENSG00000198408	"ENST00000439817;ENST00000361464;ENST00000462994;ENST00000482611;ENST00000357797;ENST00000494347;ENST00000479811;ENST00000461645;ENST00000492204;ENST00000370094;ENST00000429860"	"ENSP00000409973;ENSP00000354850;ENSP00000350445;ENSP00000359112;ENSP00000414235"	O60502	OGA	10724	O-GlcNAcase	"MEA5;MGEA5;NCOAT"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000198431	"ENST00000429002;ENST00000525566;ENST00000534282;ENST00000526006;ENST00000526266;ENST00000503506;ENST00000354940;ENST00000388854;ENST00000397736;ENST00000526691;ENST00000531691;ENST00000526390;ENST00000531689;ENST00000529546;ENST00000529751;ENST00000526207;ENST00000528079;ENST00000526580;ENST00000529784;ENST00000524698;ENST00000527688;ENST00000527335;ENST00000526950;ENST00000525265"	"ENSP00000412045;ENSP00000434516;ENSP00000431294;ENSP00000421934;ENSP00000347020;ENSP00000373506;ENSP00000380844;ENSP00000435929;ENSP00000431925;ENSP00000435123;ENSP00000433507;ENSP00000434919;ENSP00000432273;ENSP00000433732;ENSP00000433887;ENSP00000436229;ENSP00000433425;ENSP00000433935;ENSP00000433599;ENSP00000432812"	Q16881	TXNRD1	7296	thioredoxin reductase 1	"GRIM-12;Trxr1;TXNR"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000198488	"ENST00000528622;ENST00000622824"	"ENSP00000435628;ENSP00000484640"	Q6ZMB0	B3GNT6	192134	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6	B3Gn-T6	Golgi apparatus	SwissProt
 ENSG00000198569	"ENST00000673865;ENST00000538474;ENST00000673835;ENST00000673953;ENST00000361134"	"ENSP00000501101;ENSP00000442397;ENSP00000501114;ENSP00000501108;ENSP00000355353"	Q8N130	SLC34A3	142680	solute carrier family 34 member 3	"FLJ38680;NPTIIc"	"Cell membrane;Lysosome"	DeepLoc2
@@ -2719,7 +2717,6 @@ ENSG00000213614	"ENST00000268097;ENST00000683243;ENST00000684263;ENST00000683853
 ENSG00000213619	"ENST00000533507;ENST00000529276;ENST00000528192;ENST00000530295;ENST00000534208;ENST00000534716;ENST00000263774;ENST00000533105;ENST00000524568;ENST00000677462;ENST00000678975;ENST00000531351;ENST00000525378;ENST00000525212;ENST00000527178"	"ENSP00000433753;ENSP00000432099;ENSP00000431588;ENSP00000433405;ENSP00000263774"	O75489	NDUFS3	4722	NADH:ubiquinone oxidoreductase core subunit S3	CI-30	"Nucleus;Inner mitochondria"	"SwissProt;CellAtlas"
 ENSG00000213648	"ENST00000360423;ENST00000569544;ENST00000565290;ENST00000563944;ENST00000562941"	"ENSP00000353600;ENSP00000455063;ENSP00000456834;ENSP00000457597"	P0DMN0	SULT1A4	445329	sulfotransferase family 1A member 4		Cytosol	SwissProt
 ENSG00000213689	"ENST00000433541;ENST00000444177;ENST00000625293;ENST00000492235;ENST00000635452;ENST00000456089"	"ENSP00000412404;ENSP00000415972;ENSP00000486676;ENSP00000494511;ENSP00000492023;ENSP00000411331"	Q9NSU2	TREX1	11277	three prime repair exonuclease 1	"AGS1;DRN3"	"Endoplasmic reticulum;Nucleus;Cytosol"	"SwissProt;CellAtlas"
-ENSG00000213722	"ENST00000437288;ENST00000436437;ENST00000469963;ENST00000416410;ENST00000480913;ENST00000483792;ENST00000375787;ENST00000375792;ENST00000375789;ENST00000488119"	"ENSP00000413164;ENSP00000395759;ENSP00000397466;ENSP00000364943;ENSP00000364949;ENSP00000364945"	O95865	DDAH2	23564	dimethylarginine dimethylaminohydrolase 2	G6A	"Mitochondria;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000213759	"ENST00000446444;ENST00000513315"	ENSP00000387683	O75310	UGT2B11	10720	UDP glucuronosyltransferase family 2 member B11		Endoplasmic reticulum	SwissProt
 ENSG00000213760	"ENST00000376151;ENST00000303892;ENST00000483251;ENST00000415099;ENST00000483170;ENST00000481998"	"ENSP00000365321;ENSP00000302194;ENSP00000419698;ENSP00000390148"	O95670	ATP6V1G2	534	ATPase H+ transporting V1 subunit G2	"ATP6G;ATP6G2;Em:AC004181.3;NG38;Vma10"	Cytosol	SwissProt
 ENSG00000213920	"ENST00000530222;ENST00000396833;ENST00000288087;ENST00000532557;ENST00000531553;ENST00000525696;ENST00000533536;ENST00000532742;ENST00000528849;ENST00000466422"	"ENSP00000380045;ENSP00000288087"	Q86V88	MDP1	145553	magnesium dependent phosphatase 1	"FN6Pase;MGC5987"	Nucleus	CellAtlas
@@ -2789,7 +2786,6 @@ ENSG00000242110	"ENST00000335606;ENST00000382072;ENST00000506639;ENST00000514195
 ENSG00000242366	ENST00000373450	ENSP00000362549	Q9HAW9	UGT1A8	54576	UDP glucuronosyltransferase family 1 member A8	UGT1H	Endoplasmic reticulum	SwissProt
 ENSG00000242515	"ENST00000344644;ENST00000373445"	"ENSP00000343838;ENSP00000362544"	Q9HAW8	UGT1A10	54575	UDP glucuronosyltransferase family 1 member A10	UGT1J	Endoplasmic reticulum	SwissProt
 ENSG00000242612	"ENST00000627716;ENST00000424398;ENST00000633923;ENST00000631605;ENST00000219481;ENST00000439661;ENST00000437024;ENST00000633348;ENST00000445291;ENST00000633025;ENST00000461802;ENST00000632744;ENST00000461947;ENST00000465166;ENST00000429116;ENST00000461749;ENST00000469922"	"ENSP00000486613;ENSP00000400374;ENSP00000487776;ENSP00000488859;ENSP00000219481;ENSP00000399697;ENSP00000402180;ENSP00000488501;ENSP00000395913;ENSP00000488142;ENSP00000393382"	Q9NUI1	DECR2	26063	2,4-dienoyl-CoA reductase 2	"PDCR;SDR17C1"	Peroxisome	"SwissProt;CellAtlas"
-ENSG00000243056	ENST00000310331	ENSP00000308472	O60516	EIF4EBP3	8637	eukaryotic translation initiation factor 4E binding protein 3	4E-BP3	"Cytosol;Nucleus"	DeepLoc2
 ENSG00000243477	"ENST00000443094;ENST00000354862;ENST00000417393;ENST00000443842;ENST00000450489;ENST00000442620;ENST00000452674"	"ENSP00000410610;ENSP00000346927;ENSP00000391893;ENSP00000400559;ENSP00000388316;ENSP00000391158;ENSP00000413623"	Q93015	NAA80	24142	N-alpha-acetyltransferase 80, NatH catalytic subunit	"FUS2;NAT6"	Cytosol	SwissProt
 ENSG00000243480	"ENST00000423678;ENST00000414303;ENST00000497748;ENST00000682202"	"ENSP00000390832;ENSP00000397582"	P04746	AMY2A	279	amylase alpha 2A	AMY2	Extracellular	DeepLoc2
 ENSG00000243678	"ENST00000514264;ENST00000513177;ENST00000512737;ENST00000503064;ENST00000393183;ENST00000485076;ENST00000393190;ENST00000570801;ENST00000573262"	"ENSP00000426976;ENSP00000425581;ENSP00000421064;ENSP00000426901;ENSP00000376880;ENSP00000376886"	P22392	NME2	4831	NME/NM23 nucleoside diphosphate kinase 2	"NDPKB;NM23-H2"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"