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Fix gpr curation for histidine metabolism, propanoate metabolism and …
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…nucleotide metabolism (#884)

* Fix-GPR curation for Histidine metabolism/Propanoate metabolism/Nucleotide metabolism

* Fix-remove unused genes

* chore: add macaw test result

---------

Co-authored-by: JHL-452b <JHL-452b@users.noreply.github.com>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
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@JHL-452b @edkerk
3 people authored Dec 17, 2024
1 parent ba8a4f3 commit dcfcf71
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Showing 2 changed files with 28 additions and 40 deletions.
65 changes: 28 additions & 37 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -70769,7 +70769,7 @@
- MAM02553m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000116133"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.59"
Expand Down Expand Up @@ -70847,7 +70847,7 @@
- MAM03168m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857"
- gene_reaction_rule: "ENSG00000100867 or ENSG00000109854 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.-"
Expand Down Expand Up @@ -74688,7 +74688,7 @@
- MAM02759m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125877"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.6.1.19"
Expand Down Expand Up @@ -74724,7 +74724,7 @@
- MAM01755c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000168393"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.4.9"
Expand Down Expand Up @@ -75044,7 +75044,7 @@
- MAM02039c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000196839"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.76;2.7.1.76"
Expand All @@ -75062,7 +75062,7 @@
- MAM01755m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000168393"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.4.4;2.7.4.9"
Expand Down Expand Up @@ -75293,7 +75293,7 @@
- MAM02751l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309"
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.5"
Expand All @@ -75311,7 +75311,7 @@
- MAM03123l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309"
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.5"
Expand Down Expand Up @@ -75347,7 +75347,7 @@
- MAM02751l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309"
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.5"
Expand All @@ -75365,7 +75365,7 @@
- MAM02996l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309"
- gene_reaction_rule: "ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000185013 or ENSG00000205309"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.-"
Expand All @@ -75383,7 +75383,7 @@
- MAM02751l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309"
- gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.5"
Expand Down Expand Up @@ -75795,7 +75795,7 @@
- MAM03130m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
- gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.4.6"
Expand Down Expand Up @@ -75921,7 +75921,7 @@
- MAM01645m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
- gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.4.6"
Expand Down Expand Up @@ -76011,7 +76011,7 @@
- MAM02193m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
- gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.4.6"
Expand All @@ -76029,7 +76029,7 @@
- MAM02040n: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268"
- gene_reaction_rule: "ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.4.35"
Expand All @@ -76047,7 +76047,7 @@
- MAM02040g: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268"
- gene_reaction_rule: "ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000172572 or ENSG00000185527 or ENSG00000186642"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.4.17"
Expand All @@ -76065,7 +76065,7 @@
- MAM02040g: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268"
- gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.4.17"
Expand All @@ -76084,7 +76084,7 @@
- MAM02040c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000165609 or ENSG00000170222 or ENSG00000170502"
- gene_reaction_rule: "ENSG00000165609 or ENSG00000170222"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.6.1.13"
Expand All @@ -76103,7 +76103,7 @@
- MAM02454c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000165609 or ENSG00000170222 or ENSG00000170502"
- gene_reaction_rule: "ENSG00000165609 or ENSG00000170222"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.6.1.13"
Expand Down Expand Up @@ -76194,7 +76194,7 @@
- MAM01688c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000162368"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.4.14"
Expand Down Expand Up @@ -76623,7 +76623,7 @@
- MAM02751e: 2
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000054179 or ENSG00000138185 or ENSG00000168032 or ENSG00000171302 or ENSG00000187097 or ENSG00000188833 or ENSG00000197217 or ENSG00000197586"
- gene_reaction_rule: "ENSG00000054179 or ENSG00000138185 or ENSG00000168032 or ENSG00000187097 or ENSG00000188833 or ENSG00000197217 or ENSG00000197586"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.6.1.5;3.6.1.6;3.6.1.42"
Expand Down Expand Up @@ -80558,7 +80558,7 @@
- MAM02039c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000102030 or ENSG00000122390 or ENSG00000139977 or ENSG00000156269 or ENSG00000164134 or ENSG00000173418"
- gene_reaction_rule: "ENSG00000102030 or ENSG00000122390 or ENSG00000164134"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.88"
Expand All @@ -80576,7 +80576,7 @@
- MAM02125c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000132437 or ENSG00000140287"
- gene_reaction_rule: "ENSG00000140287"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "4.1.1.22;4.1.1.28"
Expand Down Expand Up @@ -80727,7 +80727,7 @@
- MAM02867c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000078124 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531"
- gene_reaction_rule: "ENSG00000077463 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000187531"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.5.1.-"
Expand All @@ -80744,7 +80744,7 @@
- MAM03124c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665"
- gene_reaction_rule: "ENSG00000054267 or ENSG00000120942"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.5.1.-"
Expand All @@ -80763,7 +80763,7 @@
- MAM02867c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000012660 or ENSG00000066322 or ENSG00000118402 or ENSG00000119915 or ENSG00000164181 or ENSG00000170522 or ENSG00000197977"
- gene_reaction_rule: "ENSG00000066322 or ENSG00000119915 or ENSG00000164181 or ENSG00000197977"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.199"
Expand All @@ -80781,7 +80781,7 @@
- MAM02867c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000078124 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531"
- gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.5.1.-"
Expand All @@ -80799,7 +80799,7 @@
- MAM02867c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000078124 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531"
- gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000156795 or ENSG00000157045 or ENSG00000187531"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.5.1.-"
Expand Down Expand Up @@ -308873,9 +308873,6 @@
- !!omap
- id: "ENSG00000139914"
- name: "FITM1"
- !!omap
- id: "ENSG00000139977"
- name: "NAA30"
- !!omap
- id: "ENSG00000139988"
- name: "RDH12"
Expand Down Expand Up @@ -309869,9 +309866,6 @@
- !!omap
- id: "ENSG00000156256"
- name: "USP16"
- !!omap
- id: "ENSG00000156269"
- name: "NAA11"
- !!omap
- id: "ENSG00000156411"
- name: "ATP5MJ"
Expand Down Expand Up @@ -312020,9 +312014,6 @@
- !!omap
- id: "ENSG00000183654"
- name: "MARCHF11"
- !!omap
- id: "ENSG00000183665"
- name: "TRMT12"
- !!omap
- id: "ENSG00000183696"
- name: "UPP1"
Expand Down
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