Merge pull request #952 from SysBioChalmers/Fix-transport_rxns_2

fix: GPR curation for Transport reactions (2)
SysBioChalmers · Jan 13, 2025 · 1c425c9 · 1c425c9
2 parents 1e02d01 + bc0cf34
commit 1c425c9
Showing 1 changed file with 11 additions and 40 deletions.
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -168369,7 +168369,6 @@
           - MAM02450e: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000059804"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -169110,7 +169109,6 @@
           - MAM02519e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117834"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -169418,7 +169416,6 @@
           - MAM02578e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000066230 or ENSG00000090020 or ENSG00000115616"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -169620,7 +169617,7 @@
           - MAM02938e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000113396 or ENSG00000130304 or ENSG00000143554 or ENSG00000167114"
+      - gene_reaction_rule: "ENSG00000130304 or ENSG00000143554 or ENSG00000167114"
       - rxnFrom: "HMRdatabase"
       - eccodes: "6.2.1.-"
       - subsystem:
@@ -169969,7 +169966,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -169985,7 +169982,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170001,7 +169998,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170017,7 +170014,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170033,7 +170030,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170081,7 +170078,7 @@
           - MAM03135e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170097,7 +170094,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170113,7 +170110,7 @@
           - MAM02896e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -170129,7 +170126,7 @@
           - MAM02519e: -2
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000131389 or ENSG00000196517 or ENSG00000268104"
+      - gene_reaction_rule: "ENSG00000131389 or ENSG00000268104"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -172611,7 +172608,7 @@
           - MAM01252m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000152779 or ENSG00000165449 or ENSG00000174327"
+      - gene_reaction_rule: "ENSG00000152779 or ENSG00000174327"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:11004451;PMID:911815"
       - subsystem:
@@ -172802,7 +172799,6 @@
           - MAM02183m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100075"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -172921,7 +172917,6 @@
           - MAM02661m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100075"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173426,7 +173421,6 @@
           - MAM01637m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173441,7 +173435,6 @@
           - MAM01680m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173456,7 +173449,6 @@
           - MAM01754m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173486,7 +173478,6 @@
           - MAM01680m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173501,7 +173492,6 @@
           - MAM01754m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173530,7 +173520,6 @@
           - MAM01688m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173545,7 +173534,6 @@
           - MAM01756m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173560,7 +173548,6 @@
           - MAM01642m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173575,7 +173562,6 @@
           - MAM01688m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173590,7 +173576,6 @@
           - MAM01756m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:14598172"
       - subsystem:
@@ -173901,7 +173886,6 @@
           - MAM01643m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -173942,7 +173926,6 @@
           - MAM01754m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -173956,7 +173939,6 @@
           - MAM01754m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -173970,7 +173952,6 @@
           - MAM01754m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174012,7 +173993,6 @@
           - MAM01747m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174040,7 +174020,6 @@
           - MAM01747m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174054,7 +174033,6 @@
           - MAM01680m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174082,7 +174060,6 @@
           - MAM01643m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174109,7 +174086,6 @@
           - MAM01756m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174123,7 +174099,6 @@
           - MAM01756m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174137,7 +174112,6 @@
           - MAM01643m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174164,7 +174138,6 @@
           - MAM01756m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174178,7 +174151,6 @@
           - MAM01753m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"
@@ -174192,7 +174164,6 @@
           - MAM01753m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125454"
       - rxnFrom: "HMRdatabase"
       - subsystem:
           - "Transport reactions"