fix: GPR curation for transport reactions (7)

SysBioChalmers · Dec 30, 2024 · 6d672e4 · 6d672e4
1 parent 008b443
commit 6d672e4
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Showing 2 changed files with 25 additions and 34 deletions.
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -151631,7 +151631,7 @@
           - MAM02184e: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
+      - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
       - subsystem:
@@ -151879,7 +151879,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000003989 or ENSG00000072041 or ENSG00000105281 or ENSG00000111371 or ENSG00000115902 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358"
+      - gene_reaction_rule: "ENSG00000072041 or ENSG00000105281 or ENSG00000111371 or ENSG00000115902 or ENSG00000134294 or ENSG00000139209 or ENSG00000174358"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:12845534;PMID:10823827;PMID:11452978;PMID:15632147"
       - subsystem:
@@ -151971,7 +151971,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000003989 or ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000168003 or ENSG00000174358"
+      - gene_reaction_rule: "ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000168003 or ENSG00000174358"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:12930836;PMID:17322374"
       - subsystem:
@@ -152029,7 +152029,7 @@
           - MAM02724e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000003989 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358"
+      - gene_reaction_rule: "ENSG00000134294 or ENSG00000139209 or ENSG00000174358"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -152118,7 +152118,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000162383 or ENSG00000174358 or ENSG00000178537"
+      - gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000162383"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:10823827"
       - subsystem:
@@ -152469,7 +152469,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117834 or ENSG00000140675 or ENSG00000148942 or ENSG00000154025 or ENSG00000158865"
+      - gene_reaction_rule: "ENSG00000117834 or ENSG00000140675 or ENSG00000154025 or ENSG00000158865"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:12748858"
       - subsystem:
@@ -153598,7 +153598,7 @@
           - MAM03089e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153613,7 +153613,7 @@
           - MAM03135e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153628,7 +153628,7 @@
           - MAM03089e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153643,7 +153643,7 @@
           - MAM03089e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153658,7 +153658,7 @@
           - MAM03089e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153688,7 +153688,7 @@
           - MAM02724e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153703,7 +153703,7 @@
           - MAM02724e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153718,7 +153718,7 @@
           - MAM02770e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153733,7 +153733,7 @@
           - MAM02724e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153748,7 +153748,7 @@
           - MAM03135e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153763,7 +153763,7 @@
           - MAM02993e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153793,7 +153793,7 @@
           - MAM02724e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -153883,7 +153883,7 @@
           - MAM03101e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257 or ENSG00000188687"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154153,7 +154153,6 @@
           - MAM02993e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154168,7 +154167,6 @@
           - MAM02770e: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154655,7 +154653,6 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154689,7 +154686,6 @@
           - MAM02993e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154706,7 +154702,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154774,7 +154770,7 @@
           - MAM02896e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902"
+      - gene_reaction_rule: "ENSG00000105281 or ENSG00000115902"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154791,7 +154787,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154825,7 +154821,7 @@
           - MAM02724e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154859,7 +154855,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902"
+      - gene_reaction_rule: "ENSG00000105281 or ENSG00000115902"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154876,7 +154872,7 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
+      - gene_reaction_rule: "ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -154927,7 +154923,6 @@
           - MAM03135e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14770309;PMID:14770310"
       - subsystem:
@@ -265350,9 +265345,6 @@
     - !!omap
       - id: "ENSG00000148834"
       - name: "GSTO1"
-    - !!omap
-      - id: "ENSG00000148942"
-      - name: "SLC5A12"
     - !!omap
       - id: "ENSG00000149016"
       - name: "TUT1"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -1611,7 +1611,6 @@
 "ENSG00000148795"	"ENST00000638971;ENST00000638190;ENST00000369887;ENST00000640633;ENST00000638272;ENST00000639393;ENST00000469683;ENST00000489268"	"ENSP00000492313;ENSP00000492539;ENSP00000358903;ENSP00000491508;ENSP00000492651"	"P05093"	"CYP17A1"	"1586"	"cytochrome P450 family 17 subfamily A member 1"	"CPT7;CYP17;P450C17;S17AH"	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000148832"	"ENST00000357296;ENST00000278060;ENST00000356306;ENST00000476834;ENST00000480071;ENST00000483211;ENST00000529585;ENST00000368535;ENST00000528127;ENST00000530555"	"ENSP00000349847;ENSP00000278060;ENSP00000348654;ENSP00000432737;ENSP00000435514;ENSP00000434550;ENSP00000432517"	"Q6QHF9"	"PAOX"	"196743"	"polyamine oxidase"	"PAO"	"Peroxisome;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000148834"	"ENST00000470554;ENST00000493946;ENST00000369713;ENST00000445155;ENST00000432659;ENST00000539281;ENST00000369710"	"ENSP00000358727;ENSP00000406708;ENSP00000405325;ENSP00000441488;ENSP00000358724"	"P78417"	"GSTO1"	"9446"	"glutathione S-transferase omega 1"	"GSTTLp28;P28"	"Cytosol"	"SwissProt"
-"ENSG00000148942"	"ENST00000396005;ENST00000527405;ENST00000280467;ENST00000533617;ENST00000528822"	"ENSP00000379326;ENSP00000436011;ENSP00000280467;ENSP00000435053"	"Q1EHB4"	"SLC5A12"	"159963"	"solute carrier family 5 member 12"	"MGC52019;SMCT2"	"Nucleus"	"CellAtlas"
 "ENSG00000149016"	"ENST00000308436;ENST00000476907;ENST00000469480;ENST00000463241;ENST00000278279;ENST00000494385;ENST00000478537"	"ENSP00000308000;ENSP00000419607;ENSP00000278279;ENSP00000420739;ENSP00000419792"	"Q9H6E5"	"TUT1"	"64852"	"terminal uridylyl transferase 1, U6 snRNA-specific"	"FLJ21850;FLJ22267;FLJ22347;PAPD2;RBM21;TENT1;TUTase"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000149084"	"ENST00000278353;ENST00000527433;ENST00000531185;ENST00000636007;ENST00000395700;ENST00000636722;ENST00000637401;ENST00000638034;ENST00000527213;ENST00000532178;ENST00000533090;ENST00000533802;ENST00000534053;ENST00000525736"	"ENSP00000278353;ENSP00000490749;ENSP00000436582;ENSP00000490822;ENSP00000379052;ENSP00000490003;ENSP00000490421;ENSP00000490701"	"Q53GQ0"	"HSD17B12"	"51144"	"hydroxysteroid 17-beta dehydrogenase 12"	"KAR;SDR12C1"	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000149089"	"ENST00000532428;ENST00000395787;ENST00000527830"	"ENSP00000474191;ENSP00000379133"	"Q96GX9"	"APIP"	"51074"	"APAF1 interacting protein"	"APIP2;CGI-29;Mmrp19"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"