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fix: GPR curation for Transport reactions (2) #952

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merged 3 commits into from
Jan 13, 2025
Merged

fix: GPR curation for Transport reactions (2) #952

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e2e5e5f
fix: GPR curation for Transport reactions (2)
JHL-452b Dec 30, 2024
7477f6d
chore: add macaw test result
JHL-452b Dec 30, 2024
bc0cf34
Merge branch 'develop' into Fix-transport_rxns_2
feiranl Jan 13, 2025
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51 changes: 11 additions & 40 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -168369,7 +168369,6 @@
- MAM02450e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000059804"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -169110,7 +169109,6 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117834"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -172802,7 +172799,6 @@
- MAM02183m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100075"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand Down Expand Up @@ -172921,7 +172917,6 @@
- MAM02661m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100075"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand Down Expand Up @@ -173426,7 +173421,6 @@
- MAM01637m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173441,7 +173435,6 @@
- MAM01680m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173456,7 +173449,6 @@
- MAM01754m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand Down Expand Up @@ -173486,7 +173478,6 @@
- MAM01680m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173501,7 +173492,6 @@
- MAM01754m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand Down Expand Up @@ -173530,7 +173520,6 @@
- MAM01688m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173545,7 +173534,6 @@
- MAM01756m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173560,7 +173548,6 @@
- MAM01642m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173575,7 +173562,6 @@
- MAM01688m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand All @@ -173590,7 +173576,6 @@
- MAM01756m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand Down Expand Up @@ -173901,7 +173886,6 @@
- MAM01643m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -173942,7 +173926,6 @@
- MAM01754m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -173956,7 +173939,6 @@
- MAM01754m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -173970,7 +173952,6 @@
- MAM01754m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -174012,7 +173993,6 @@
- MAM01747m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -174040,7 +174020,6 @@
- MAM01747m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174054,7 +174033,6 @@
- MAM01680m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -174082,7 +174060,6 @@
- MAM01643m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174109,7 +174086,6 @@
- MAM01756m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174123,7 +174099,6 @@
- MAM01756m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174137,7 +174112,6 @@
- MAM01643m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174164,7 +174138,6 @@
- MAM01756m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174178,7 +174151,6 @@
- MAM01753m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174192,7 +174164,6 @@
- MAM01753m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down
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