From 9ac4f79cc32c0f8c5df4afbe926428e44432a1f2 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Wed, 6 Nov 2024 19:21:25 +0800
Subject: [PATCH 01/16] fix-GPR_curation_for_Xenobiotics_metabolism

---
 model/Human-GEM.yml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index e9484f6b..7a41c271 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -159340,7 +159340,7 @@
           - MAM02630c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.14.1"
@@ -159382,7 +159382,7 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.14.1"
@@ -159695,7 +159695,7 @@
           - MAM03043c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
+      - gene_reaction_rule: "ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.1"
@@ -159971,7 +159971,7 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.14.1"
@@ -160084,7 +160084,7 @@
           - MAM02555c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000104808 or ENSG00000117594 or ENSG00000151632 or ENSG00000159228 or ENSG00000159231 or ENSG00000187134 or ENSG00000196139 or ENSG00000198610"
+      - gene_reaction_rule: "ENSG00000104808 or ENSG00000151632 or ENSG00000159228 or ENSG00000159231 or ENSG00000187134 or ENSG00000196139 or ENSG00000198610"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.146;1.1.1.184;1.3.1.20"
@@ -160786,7 +160786,7 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.14.1"
@@ -161269,7 +161269,7 @@
           - MAM02156c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
+      - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000167419"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.11.1.7"
@@ -161288,7 +161288,7 @@
           - MAM02591c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
+      - gene_reaction_rule: "ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.11.1.7"
@@ -161306,7 +161306,7 @@
           - MAM02754e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000014257 or ENSG00000102575 or ENSG00000134575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162551 or ENSG00000162836 or ENSG00000163283 or ENSG00000163286 or ENSG00000163295 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000134575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162551 or ENSG00000162836 or ENSG00000163283 or ENSG00000163286 or ENSG00000163295"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.1;3.1.3.2;3.1.3.41"
@@ -235503,7 +235503,7 @@
           - MAM03381r: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.14.14.1"
@@ -235704,7 +235704,7 @@
           - MAM03386r: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.14.14.1"
@@ -235797,7 +235797,7 @@
           - MAM03388r: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
+      - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.14.14.1"

From d2b35bf49ff9c9de75ee95b6b323865c0d0d2c1c Mon Sep 17 00:00:00 2001
From: JHL-452b <JHL-452b@users.noreply.github.com>
Date: Wed, 6 Nov 2024 11:46:10 +0000
Subject: [PATCH 02/16] chore: add macaw test result

---
 data/testResults/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index 160c9df5..adfaae5b 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #882** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

From d17703cdcda1d2d70d8a0c77b89a0a8cd62ca4f6 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Fri, 6 Dec 2024 12:31:59 +0800
Subject: [PATCH 03/16] Fix: GPR curation for Starch and sucrose metabolism

---
 model/Human-GEM.yml | 23 ++++++++++-------------
 model/genes.tsv     |  1 -
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 7a41c271..6ad11be3 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -68303,7 +68303,7 @@
           - MAM02450e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000092529 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335"
+      - gene_reaction_rule: "ENSG00000171298 or ENSG00000214013 or ENSG00000257335"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.20"
@@ -68340,7 +68340,7 @@
           - MAM03039e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000118094 or ENSG00000142102"
+      - gene_reaction_rule: "ENSG00000118094"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.28"
@@ -68500,7 +68500,7 @@
           - MAM02448c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68572,7 +68572,7 @@
           - MAM02447c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68608,7 +68608,7 @@
           - MAM02449c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68644,7 +68644,7 @@
           - MAM02451c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68680,7 +68680,7 @@
           - MAM02452c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68770,7 +68770,7 @@
           - MAM02452c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68787,7 +68787,7 @@
           - MAM02450c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -218065,7 +218065,7 @@
           - MAM03622e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000021488 and ENSG00000138079) or ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "3.2.1.1"
@@ -305846,9 +305846,6 @@
     - !!omap
       - id: "ENSG00000092295"
       - name: "TGM1"
-    - !!omap
-      - id: "ENSG00000092529"
-      - name: "CAPN3"
     - !!omap
       - id: "ENSG00000092621"
       - name: "PHGDH"
diff --git a/model/genes.tsv b/model/genes.tsv
index 763bde13..375d8282 100644
--- a/model/genes.tsv
+++ b/model/genes.tsv
@@ -389,7 +389,6 @@ ENSG00000092068	"ENST00000339733;ENST00000316902;ENST00000397310;ENST00000422941
 ENSG00000092098	"ENST00000560875;ENST00000559308;ENST00000558634;ENST00000557878;ENST00000559533;ENST00000557991;ENST00000559438;ENST00000560071;ENST00000559275;ENST00000324103;ENST00000559882;ENST00000559260;ENST00000560342;ENST00000558907;ENST00000560787;ENST00000559583;ENST00000491351;ENST00000559071;ENST00000560754;ENST00000558452;ENST00000559449;ENST00000483895;ENST00000559719;ENST00000559491;ENST00000560631"	"ENSP00000454032;ENSP00000453471;ENSP00000454048;ENSP00000453423;ENSP00000453948;ENSP00000453574;ENSP00000315112;ENSP00000453645;ENSP00000453601;ENSP00000452972;ENSP00000499015;ENSP00000453595;ENSP00000454140;ENSP00000453672;ENSP00000452820"	Q96EP0	RNF31	55072	ring finger protein 31	"FLJ10111;FLJ23501;HOIP;Paul;ZIBRA"	Cytosol	"SwissProt;CellAtlas"
 ENSG00000092148	"ENST00000554882;ENST00000399332;ENST00000555843;ENST00000611816;ENST00000553700;ENST00000556281;ENST00000557695;ENST00000555311;ENST00000553957;ENST00000557321;ENST00000554027;ENST00000555915;ENST00000556004;ENST00000557369;ENST00000554850;ENST00000556224;ENST00000554471;ENST00000553616;ENST00000556474"	"ENSP00000451260;ENSP00000382269;ENSP00000484981;ENSP00000450697;ENSP00000451860;ENSP00000450920;ENSP00000452233;ENSP00000452015;ENSP00000479695"	Q9ULT8	HECTD1	25831	HECT domain E3 ubiquitin protein ligase 1	KIAA1131	Nucleus	CellAtlas
 ENSG00000092295	"ENST00000206765;ENST00000544573;ENST00000559669;ENST00000559136;ENST00000558074;ENST00000560443;ENST00000560478;ENST00000560226;ENST00000561067"	"ENSP00000206765;ENSP00000439446;ENSP00000453701;ENSP00000453337;ENSP00000453840;ENSP00000452822;ENSP00000453234;ENSP00000454070;ENSP00000452690"	P22735	TGM1	7051	transglutaminase 1	"ICR2;LI;LI1;TGASE;TGK"	Cytosol	DeepLoc2
-ENSG00000092529	"ENST00000349748;ENST00000397163;ENST00000357568;ENST00000638141;ENST00000673705;ENST00000673658;ENST00000673813;ENST00000397200;ENST00000569827;ENST00000673646;ENST00000567071;ENST00000673854;ENST00000674093;ENST00000569136;ENST00000673936;ENST00000673890;ENST00000674149;ENST00000673771;ENST00000337571;ENST00000673743;ENST00000673939;ENST00000674146;ENST00000674119;ENST00000674064;ENST00000673692;ENST00000565173;ENST00000674052;ENST00000561817;ENST00000674018;ENST00000397204;ENST00000673886;ENST00000674139;ENST00000673851;ENST00000673839;ENST00000673978;ENST00000673987;ENST00000673928;ENST00000674041;ENST00000565559;ENST00000673750;ENST00000674011;ENST00000674135;ENST00000674012;ENST00000565274;ENST00000674140;ENST00000564503;ENST00000673774;ENST00000673950;ENST00000466222;ENST00000673687;ENST00000674027;ENST00000674130;ENST00000562199;ENST00000673893;ENST00000673684;ENST00000568153;ENST00000567817;ENST00000356316;ENST00000318023"	"ENSP00000183936;ENSP00000380349;ENSP00000350181;ENSP00000501021;ENSP00000380384;ENSP00000454379;ENSP00000501007;ENSP00000456607;ENSP00000501303;ENSP00000455254;ENSP00000501189;ENSP00000501293;ENSP00000501112;ENSP00000501023;ENSP00000336840;ENSP00000500989;ENSP00000501129;ENSP00000501175;ENSP00000501217;ENSP00000501138;ENSP00000501057;ENSP00000456575;ENSP00000501271;ENSP00000380387;ENSP00000501155;ENSP00000501054;ENSP00000501142;ENSP00000501188;ENSP00000500976;ENSP00000501231;ENSP00000501099;ENSP00000500956;ENSP00000457878;ENSP00000501173;ENSP00000501171;ENSP00000501178;ENSP00000457759;ENSP00000457898;ENSP00000501034;ENSP00000500987;ENSP00000454937;ENSP00000456514;ENSP00000348667;ENSP00000326281"	P20807	CAPN3	825	calpain 3	"CANP3;LGMD2;LGMD2A;nCL-1;p94"	"Cytosol;Nucleus"	SwissProt
 ENSG00000092621	"ENST00000641597;ENST00000493622;ENST00000641720;ENST00000642041;ENST00000641947;ENST00000641213;ENST00000641074;ENST00000496756;ENST00000641115;ENST00000642021;ENST00000641491;ENST00000369409;ENST00000641023;ENST00000641513;ENST00000641573;ENST00000641587;ENST00000641570;ENST00000641891;ENST00000641375;ENST00000462324;ENST00000641371;ENST00000641272;ENST00000641247;ENST00000641756;ENST00000641711;ENST00000641927;ENST00000641314;ENST00000369407;ENST00000641811;ENST00000641847;ENST00000641455;ENST00000469443;ENST00000641939;ENST00000482968"	"ENSP00000493382;ENSP00000493433;ENSP00000492948;ENSP00000493415;ENSP00000492994;ENSP00000493079;ENSP00000493446;ENSP00000493264;ENSP00000493187;ENSP00000358417;ENSP00000493175;ENSP00000493398;ENSP00000493453;ENSP00000493213;ENSP00000493288;ENSP00000493089;ENSP00000493305;ENSP00000493432;ENSP00000492955;ENSP00000493147;ENSP00000493296"	O43175	PHGDH	26227	phosphoglycerate dehydrogenase	"PDG;PGDH;SERA"	"Cytosol;Nucleus"	CellAtlas
 ENSG00000092964	"ENST00000521913;ENST00000493789;ENST00000311151;ENST00000523027;ENST00000523690;ENST00000523093;ENST00000521983;ENST00000474808"	"ENSP00000427985;ENSP00000427954;ENSP00000309539;ENSP00000431117"	Q16555	DPYSL2	1808	dihydropyrimidinase like 2	"CRMP2;DHPRP2;DRP-2;DRP2"	Cytosol	"SwissProt;CellAtlas"
 ENSG00000093000	"ENST00000347635;ENST00000407019;ENST00000424634;ENST00000417702;ENST00000497960;ENST00000461437;ENST00000434760;ENST00000430547;ENST00000484186;ENST00000445721;ENST00000493456;ENST00000396096;ENST00000461194;ENST00000432340;ENST00000419387;ENST00000422489;ENST00000486184;ENST00000491860;ENST00000469163"	"ENSP00000345895;ENSP00000385555;ENSP00000415062;ENSP00000394450;ENSP00000388426;ENSP00000397960;ENSP00000398297;ENSP00000379403;ENSP00000400465;ENSP00000391987;ENSP00000416264"	Q9UKX7	NUP50	10762	nucleoporin 50	NPAP60L	Nucleus	"SwissProt;CellAtlas"

From 548d5fa5208b57fc58a435558a808a1bddc2b0d7 Mon Sep 17 00:00:00 2001
From: JHL-452b <JHL-452b@users.noreply.github.com>
Date: Fri, 6 Dec 2024 04:58:02 +0000
Subject: [PATCH 04/16] chore: add macaw test result

---
 data/testResults/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index adfaae5b..39140d5d 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

From 8a855e87d7fb17e5a7b760da3038430f9550c5ce Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Sat, 7 Dec 2024 11:03:57 +0800
Subject: [PATCH 05/16] Fix: GPR curation for subsystems related with amino
 acid

---
 model/Human-GEM.yml | 21 +++++++++------------
 model/genes.tsv     |  1 -
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 7a41c271..278e3b90 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -77405,7 +77405,7 @@
           - MAM02943m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000134333"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.16"
@@ -80744,7 +80744,7 @@
           - MAM03124c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006695 or ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665"
+      - gene_reaction_rule: "ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.5.1.-"
@@ -85711,7 +85711,7 @@
           - MAM02555c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000181652 or ENSG00000184470 or ENSG00000197763 or ENSG00000198431"
+      - gene_reaction_rule: "ENSG00000184470 or ENSG00000197763 or ENSG00000198431"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.8.1.9"
@@ -86410,7 +86410,7 @@
           - MAM02041e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116157 or ENSG00000117450 or ENSG00000117592 or ENSG00000126432 or ENSG00000164294 or ENSG00000165672 or ENSG00000167468 or ENSG00000167815 or ENSG00000176153 or ENSG00000198704 or ENSG00000211445 or ENSG00000224586 or ENSG00000233276"
+      - gene_reaction_rule: "ENSG00000116157 or ENSG00000117450 or ENSG00000117592 or ENSG00000126432 or ENSG00000164294 or ENSG00000167468 or ENSG00000167815 or ENSG00000176153 or ENSG00000198704 or ENSG00000211445 or ENSG00000224586 or ENSG00000233276"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.11.1.9;1.11.1.15"
@@ -86668,7 +86668,7 @@
           - MAM02039c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000128683 or ENSG00000136750"
+      - gene_reaction_rule: "ENSG00000136750"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.1.1.11;4.1.1.15"
@@ -86882,7 +86882,7 @@
           - MAM02885c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000138801 or ENSG00000198682"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.7.4"
@@ -88067,7 +88067,7 @@
           - 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"
@@ -93247,7 +93247,7 @@
           - MAM03135c: 28
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000165996 or ENSG00000206527"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.134"
@@ -218356,7 +218356,7 @@
           - MAM02553m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423"
+      - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.5.1.12"
@@ -311948,9 +311948,6 @@
     - !!omap
       - id: "ENSG00000181555"
       - name: "SETD2"
-    - !!omap
-      - id: "ENSG00000181652"
-      - name: "ATG9B"
     - !!omap
       - id: "ENSG00000181788"
       - name: "SIAH2"
diff --git a/model/genes.tsv b/model/genes.tsv
index 763bde13..1178753a 100644
--- a/model/genes.tsv
+++ b/model/genes.tsv
@@ -2407,7 +2407,6 @@ ENSG00000181192	"ENST00000263035;ENST00000437298;ENST00000465617;ENST00000415935
 ENSG00000181222	"ENST00000674977;ENST00000617998;ENST00000572844;ENST00000576952;ENST00000575547;ENST00000576114;ENST00000576718;ENST00000574158;ENST00000573603;ENST00000576553"	ENSP00000502190	A0A6Q8PGB0	POLR2A	5430	RNA polymerase II subunit A	"POLR2;POLRA;RPB1"	"Cytosol;Nucleus"	CellAtlas
 ENSG00000181523	"ENST00000575484;ENST00000571156;ENST00000572257;ENST00000326317;ENST00000575282;ENST00000573150;ENST00000576856;ENST00000570923;ENST00000576941;ENST00000574505;ENST00000572208;ENST00000571051;ENST00000576707;ENST00000570427;ENST00000571675;ENST00000575188;ENST00000571075"	"ENSP00000461827;ENSP00000314606;ENSP00000459280;ENSP00000460720;ENSP00000458200;ENSP00000461160;ENSP00000459708;ENSP00000461128;ENSP00000459765"	P51688	SGSH	6448	N-sulfoglucosamine sulfohydrolase	"HSS;MPS3A;SFMD"	Lysosome	SwissProt
 ENSG00000181555	"ENST00000431180;ENST00000330022;ENST00000409792;ENST00000445387;ENST00000479832;ENST00000492397;ENST00000638947;ENST00000484689;ENST00000412450"	"ENSP00000388349;ENSP00000332415;ENSP00000386759;ENSP00000411901;ENSP00000491413;ENSP00000416401"	Q9BYW2	SETD2	29072	SET domain containing 2, histone lysine methyltransferase	"FLJ23184;HIF-1;HYPB;KIAA1732;KMT3A"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
-ENSG00000181652	"ENST00000498521;ENST00000605952;ENST00000639579;ENST00000617967;ENST00000404733;ENST00000476282;ENST00000471797;ENST00000611177;ENST00000469530;ENST00000473409;ENST00000473134;ENST00000466157"	"ENSP00000475737;ENSP00000491504;ENSP00000479879"	Q674R7	ATG9B	285973	autophagy related 9B	"APG9L2;FLJ14885;NOS3AS;SONE"	Cytosol	SwissProt
 ENSG00000181788	"ENST00000312960;ENST00000482706;ENST00000472885"	"ENSP00000322457;ENSP00000417619"	O43255	SIAH2	6478	siah E3 ubiquitin protein ligase 2		"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000181789	"ENST00000314797;ENST00000513965;ENST00000515725;ENST00000504350;ENST00000509208;ENST00000504547;ENST00000513410;ENST00000509889;ENST00000514478;ENST00000512034"	"ENSP00000325002;ENSP00000426457;ENSP00000422478;ENSP00000420916"	Q9Y678	COPG1	22820	COPI coat complex subunit gamma 1	COPG	"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000181804	"ENST00000316549;ENST00000483124;ENST00000474727;ENST00000474151;ENST00000498717"	"ENSP00000320246;ENSP00000419090;ENSP00000418627"	Q8IVB4	SLC9A9	285195	solute carrier family 9 member A9	"FLJ35613;NHE9"	"Cell membrane;Lysosome"	DeepLoc2

From bc79aec5d1921ad51098a12fc2a0b80d02d7e86c Mon Sep 17 00:00:00 2001
From: JHL-452b <JHL-452b@users.noreply.github.com>
Date: Sat, 7 Dec 2024 03:19:20 +0000
Subject: [PATCH 06/16] chore: add macaw test result

---
 data/testResults/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index adfaae5b..c83a2491 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

From de496404b4c87f2bb75d14fe84839e9e8f1ab287 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Sat, 7 Dec 2024 14:26:57 +0800
Subject: [PATCH 07/16] Fix: GPR curation for Sulfur metabolism

---
 model/Human-GEM.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 7a41c271..89c2a606 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -93535,7 +93535,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000104331 or ENSG00000162813"
+      - gene_reaction_rule: "ENSG00000162813"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.7"
@@ -93611,7 +93611,7 @@
           - MAM02877c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000006534 or ENSG00000132746 or ENSG00000184254"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.5"
@@ -140094,7 +140094,7 @@
           - MAM02946l: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000106304 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614"
+      - gene_reaction_rule: "ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.35;3.2.1.52"
@@ -140337,7 +140337,7 @@
           - MAM02946l: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
+      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
@@ -140412,7 +140412,7 @@
           - MAM02946l: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
+      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
@@ -140508,7 +140508,7 @@
           - MAM02946l: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
+      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
@@ -140602,7 +140602,7 @@
           - MAM02946l: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
+      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
@@ -140735,7 +140735,7 @@
           - MAM02946l: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
+      - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
@@ -142090,7 +142090,7 @@
           - MAM02682g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196"
+      - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.8.2.-"

From 05cd3f4821d60ee58d778f07610a79e988a00e81 Mon Sep 17 00:00:00 2001
From: JHL-452b <JHL-452b@users.noreply.github.com>
Date: Sat, 7 Dec 2024 06:58:30 +0000
Subject: [PATCH 08/16] chore: add macaw test result

---
 data/testResults/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index adfaae5b..1e25d652 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #937** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

From f9d560dbf290e630a6801958f4d1b7f47d0184bb Mon Sep 17 00:00:00 2001
From: feiranl <feiranl@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:44:51 +0000
Subject: [PATCH 09/16] chore: add macaw test result

---
 data/testResults/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index 1e25d652..c83a2491 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #937** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

From 30975e88bf12e4a8ff8d7dd5dfff151b76307aa5 Mon Sep 17 00:00:00 2001
From: feiranl <feiranl@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:53:46 +0000
Subject: [PATCH 10/16] chore: add macaw test result

---
 data/testResults/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index c83a2491..39140d5d 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

From ccc8b29ba9b9ce9a09cb15ed09b04c996fc4c851 Mon Sep 17 00:00:00 2001
From: Devlin-Moyer <33460176+Devlin-Moyer@users.noreply.github.com>
Date: Mon, 16 Dec 2024 19:16:15 -0500
Subject: [PATCH 11/16] Fix Duplicate Stearoyl-CoA Beta-Oxidation Reactions
 (#820)

* fix: removed MAR00776 and MAR00778 from YAML file

* feat: added appropriate refs for MAR03115-8 since refs from MAR00776 weren't appropriate

* chore: merged annotations for MAR00776 with those for MAR03115-8 in reactions.tsv and moved MAR00776 to deprecatedReactions.tsv

* chore: merged annotations for MAR00778 with those for MAR03116-MAR03146 in reactions.tsv and moved MAR00778 to deprecatedReactions.tsv

* fix: indentation error in YAML file

* fix: removed incorrect MetaNetX IDs for MAR03117 and MAR03118

* chore: add macaw test result

* chore: add macaw test result

---------

Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
Co-authored-by: Devlin-Moyer <Devlin-Moyer@users.noreply.github.com>
Co-authored-by: edkerk <edkerk@users.noreply.github.com>
---
 .../deprecatedReactions.tsv                   |  2 +
 data/testResults/README.md                    |  2 +-
 data/testResults/macaw_results.csv            |  2 -
 model/Human-GEM.yml                           | 56 ++-----------------
 model/reactions.tsv                           | 42 +++++++-------
 5 files changed, 27 insertions(+), 77 deletions(-)

diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
index 69cfefad..39779b48 100644
--- a/data/deprecatedIdentifiers/deprecatedReactions.tsv
+++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -300,3 +300,5 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08745"	""	"THMMPtm"	""	""	""	""	"MNXR104822"	"HMR_8745"	"RCR20669"	""	0	""	""	"HMR_8745"
 "MAR08747"	""	"THMPPtm"	""	""	""	""	"MNXR104824"	"HMR_8747"	"RCR20670"	""	0	""	""	"HMR_8747"
 "MAR07799"	""	"ATPasel"	""	""	""	""	"MNXR96136"	"HMR_7799"	"RCR20334"	""	0	""	""	"HMR_7799"
+"MAR00776"	""	"FAOXC180"	""	""	""	"FAOXC180"	"MNXR99313"	""	""	""	0	""	""	"FAOXC180"
+"MAR00778"	""	"FAOXC1811601m"	""	""	""	"FAOXC1811601m"	"MNXR99315"	""	""	""	0	""	""	"FAOXC1811601m"
diff --git a/data/testResults/README.md b/data/testResults/README.md
index 39140d5d..5a49a7d3 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #820** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.
diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv
index aa73eeed..112e0ccf 100644
--- a/data/testResults/macaw_results.csv
+++ b/data/testResults/macaw_results.csv
@@ -8250,9 +8250,7 @@ MAR00759,4 MAM01597x + 4 MAM01802x + 4 MAM02040x + 4 MAM02552x + MAM02678x --> 4
 MAR00764,MAM00051m + 4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A
 MAR00772,4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m + MAM02677m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A
 MAR00774,7 MAM01597m + 7 MAM01802m + 7 MAM02040m + MAM02101m + 7 MAM02552m --> 7 MAM01261m + 7 MAM01803m + 7 MAM02039m + 7 MAM02553m + MAM02774m,ok,ok,ok,ok,N/A
-MAR00776,MAM01597m + MAM01802m + MAM02040m + MAM02552m + MAM02941m --> MAM01261m + MAM01803m + MAM02039m + MAM02553m + MAM02678m,ok,ok,ok,ok,N/A
 MAR00777,MAM01597x + MAM01802x + MAM02040x + MAM02552x + MAM02941x --> MAM01261x + MAM01803x + MAM02039x + MAM02553x + MAM02678x,ok,ok,ok,ok,N/A
-MAR00778,MAM00057m + 5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A
 MAR00780,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM03791m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A
 MAR00784,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM02647m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A
 MAR00785,5 MAM01597m + 3 MAM01802m + 5 MAM02040m + MAM02391m + 5 MAM02552m --> 5 MAM01261m + 3 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 5f1cbb0c..568b3f1d 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -118350,7 +118350,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.3.8.7;1.3.8.8;1.3.8.9;1.3.99.-"
-      - references: ""
+      - references: "PMID:20490924"
       - subsystem:
           - "Beta oxidation of even-chain fatty acids (mitochondrial)"
       - confidence_score: 0
@@ -118367,7 +118367,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.17"
-      - references: ""
+      - references: "PMID:20490924"
       - subsystem:
           - "Beta oxidation of even-chain fatty acids (mitochondrial)"
       - confidence_score: 0
@@ -118386,7 +118386,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.35;1.1.1.211"
-      - references: ""
+      - references: "PMID:20490924"
       - subsystem:
           - "Beta oxidation of even-chain fatty acids (mitochondrial)"
       - confidence_score: 0
@@ -118404,7 +118404,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.16;1.1.1.211"
-      - references: ""
+      - references: "PMID:20490924"
       - subsystem:
           - "Beta oxidation of even-chain fatty acids (mitochondrial)"
       - confidence_score: 0
@@ -221482,30 +221482,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR00776"
-      - name: "Beta Oxidation of Long Chain Fatty Acid"
-      - metabolites: !!omap
-          - MAM01261m: 1
-          - MAM01597m: -1
-          - MAM01802m: -1
-          - MAM01803m: 1
-          - MAM02039m: 1
-          - MAM02040m: -1
-          - MAM02552m: -1
-          - MAM02553m: 1
-          - MAM02678m: 1
-          - MAM02941m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "1.3.99.3"
-      - references: "PMID:2565344;PMID:3035565"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR00777"
       - name: "Beta Oxidation of Long Chain Fatty Acid"
@@ -221530,30 +221506,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR00778"
-      - name: "Beta Oxidation Fatty Acid"
-      - metabolites: !!omap
-          - MAM00057m: -1
-          - MAM01261m: 5
-          - MAM01597m: -5
-          - MAM01802m: -4
-          - MAM01803m: 4
-          - MAM02039m: 5
-          - MAM02040m: -5
-          - MAM02552m: -5
-          - MAM02553m: 5
-          - MAM02644m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "4.2.1.74"
-      - references: ""
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR00780"
       - name: "Beta Oxidation Fatty Acid"
diff --git a/model/reactions.tsv b/model/reactions.tsv
index 1a9770d5..4fa8c7c9 100644
--- a/model/reactions.tsv
+++ b/model/reactions.tsv
@@ -2624,26 +2624,26 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03112"	""	""	""	""	""	"HMR_3112"	""	"HMR_3112"	"RCR12626"	""	0	""	""	"HMR_3112"
 "MAR03113"	""	""	""	""	""	"HMR_3113"	""	"HMR_3113"	"RCR12627"	""	0	""	""	"HMR_3113"
 "MAR03114"	""	""	""	""	""	"HMR_3114"	""	"HMR_3114"	"RCR12628"	""	0	""	""	"HMR_3114"
-"MAR03115"	""	""	""	""	""	"HMR_3115"	""	"HMR_3115"	"RCR12629"	""	0	""	""	"HMR_3115"
-"MAR03116"	"R07760"	""	""	""	""	"HMR_3116"	""	"HMR_3116"	"RCR12630"	""	0	"RHEA:35349"	"RHEA:35347"	"HMR_3116"
-"MAR03117"	""	""	""	""	""	"HMR_3117"	""	"HMR_3117"	"RCR12631"	""	0	"RHEA:35276"	"RHEA:35275"	"HMR_3117"
-"MAR03118"	""	""	""	""	""	"HMR_3118"	""	"HMR_3118"	"RCR12632"	""	0	""	""	"HMR_3118"
-"MAR03121"	"R01279"	"r0310"	""	""	"R-HSA-77299"	"HMR_3121;r0310"	"MNXR125070"	"HMR_3121"	"RCR12633"	""	0	""	"RHEA:30747"	"HMR_3121;r0310;MAR02035"
-"MAR03122"	"R04738"	""	"R04738X"	"r0716"	""	"r0716"	"MNXR105372;MNXR97892"	"HMR_3122"	"RCR12634"	""	0	""	"RHEA:31163"	"HMR_3122"
-"MAR03123"	"R04737"	""	"R04737X"	"r0714"	""	"r0714"	"MNXR100548;MNXR105371"	"HMR_3123"	"RCR12635"	""	0	""	"RHEA:31159"	"HMR_3123"
-"MAR03125"	"R03991"	""	"R03991X"	"r0653"	""	"r0653"	"MNXR95203"	"HMR_3125"	"RCR12636"	""	0	""	"RHEA:18161"	"HMR_3125"
-"MAR03128"	"R03990"	"r1449"	""	""	"R-HSA-77274"	"HMR_3128;r1449"	"MNXR95300"	"HMR_3128"	"RCR12637"	""	0	""	"RHEA:28358"	"HMR_3128;r1449;MAR02370"
-"MAR03129"	"R04740"	""	"R04740X"	"r0720"	""	"r0720"	"MNXR105373;MNXR97891"	"HMR_3129"	"RCR12638"	""	0	""	"RHEA:31171"	"HMR_3129"
-"MAR03130"	"R04739"	""	"R04739X"	"r0718"	""	"r0718"	"MNXR100547"	"HMR_3130"	"RCR12639"	""	0	""	"RHEA:31167"	"HMR_3130"
-"MAR03132"	"R03858"	""	"R03858X"	"r0639"	""	"r0639"	"MNXR95201"	"HMR_3132"	"RCR12640"	""	0	""	"RHEA:31091"	"HMR_3132"
-"MAR03135"	"R03857"	"r1447"	""	""	"R-HSA-77263"	"HMR_3135;r1447"	"MNXR95299"	"HMR_3135"	"RCR12641"	""	0	""	"RHEA:31039"	"HMR_3135;r1447;MAR02367"
-"MAR03136"	"R04170"	"r1446"	"R04170X"	"r0660"	""	"r0660;r1446"	"MNXR97890"	"HMR_3136"	"RCR12642"	""	0	""	"RHEA:31075"	"HMR_3136;r1446;MAR02366"
-"MAR03137"	"R04741"	""	"R04741X"	"r0722"	""	"r0722"	"MNXR100546"	"HMR_3137"	"RCR12643"	""	0	""	"RHEA:31179"	"HMR_3137"
-"MAR03139"	"R04742"	""	"R04742X"	"r0724"	""	"r0724"	"MNXR95199;MNXR95200"	"HMR_3139"	"RCR12644"	""	0	"RHEA:31185"	"RHEA:31183"	"HMR_3139"
-"MAR03142"	"R04754"	"r1451;FAOXC10C10OHm;FAOXC10080m"	""	""	"R-HSA-77345"	"HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m"	"MNXR109095"	"HMR_3142"	"RCR12645"	""	0	""	"RHEA:28354"	"HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024"
-"MAR03143"	"R04744"	"FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m"	"R04744X"	"r0728"	""	"r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m"	"MNXR97889"	"HMR_3143;HMR_3422"	"RCR12646;RCR12667"	""	0	""	"RHEA:31191"	"HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024"
-"MAR03144"	"R04743"	"FAOXC101C8m;FAOXC10080m"	"R04743X"	"r0726"	""	"r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m"	"MNXR100545"	"HMR_3144;HMR_3422"	"RCR12647;RCR12667"	""	0	""	"RHEA:31187"	"HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024"
-"MAR03146"	"R03778"	"FAOXC101C8m;FAOXC10080m"	"R03778X"	"r0634"	""	"r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m"	"MNXR95198"	"HMR_3146;HMR_3422"	"RCR12648;RCR12667"	""	0	"RHEA:31089"	"RHEA:31087"	"HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024"
+"MAR03115"	""	"FAOXC180"	""	""	""	"HMR_3115;FAOXC180"	""	"HMR_3115"	"RCR12629"	""	0	""	""	"HMR_3115;FAOXC180;MAR00776"
+"MAR03116"	"R07760"	"FAOXC180;FAOXC1811601m"	""	""	""	"HMR_3116;FAOXC180;FAOXC1811601m"	""	"HMR_3116"	"RCR12630"	""	0	"RHEA:35349"	"RHEA:35347"	"HMR_3116;FAOXC180;MAR00776;FAOXC1811601m;MAR00778"
+"MAR03117"	""	"FAOXC180;FAOXC1811601m"	""	""	""	"HMR_3117;FAOXC180;FAOXC1811601m"	""	"HMR_3117"	"RCR12631"	""	0	"RHEA:35276"	"RHEA:35275"	"HMR_3117;FAOXC180;MAR00776;FAOXC1811601m;MAR00778"
+"MAR03118"	""	"FAOXC180;FAOXC1811601m"	""	""	""	"HMR_3118;FAOXC180;FAOXC1811601m"	""	"HMR_3118"	"RCR12632"	""	0	""	""	"HMR_3118;FAOXC180;MAR00776;FAOXC1811601m;MAR00778"
+"MAR03121"	"R01279"	"r0310;FAOXC1811601m"	""	""	"R-HSA-77299"	"HMR_3121;r0310;FAOXC1811601m"	"MNXR125070"	"HMR_3121"	"RCR12633"	""	0	""	"RHEA:30747"	"HMR_3121;r0310;MAR02035;FAOXC1811601m;MAR00778"
+"MAR03122"	"R04738"	"FAOXC1811601m"	"R04738X"	"r0716"	""	"r0716;FAOXC1811601m"	"MNXR105372;MNXR97892"	"HMR_3122"	"RCR12634"	""	0	""	"RHEA:31163"	"HMR_3122;FAOXC1811601m;MAR00778"
+"MAR03123"	"R04737"	"FAOXC1811601m"	"R04737X"	"r0714"	""	"r0714;FAOXC1811601m"	"MNXR100548;MNXR105371"	"HMR_3123"	"RCR12635"	""	0	""	"RHEA:31159"	"HMR_3123;FAOXC1811601m;MAR00778"
+"MAR03125"	"R03991"	"FAOXC1811601m"	"R03991X"	"r0653"	""	"r0653;FAOXC1811601m"	"MNXR95203"	"HMR_3125"	"RCR12636"	""	0	""	"RHEA:18161"	"HMR_3125;FAOXC1811601m;MAR00778"
+"MAR03128"	"R03990"	"r1449;FAOXC1811601m"	""	""	"R-HSA-77274"	"HMR_3128;r1449;FAOXC1811601m"	"MNXR95300"	"HMR_3128"	"RCR12637"	""	0	""	"RHEA:28358"	"HMR_3128;r1449;MAR02370;FAOXC1811601m;MAR00778"
+"MAR03129"	"R04740"	"FAOXC1811601m"	"R04740X"	"r0720"	""	"r0720;FAOXC1811601m"	"MNXR105373;MNXR97891"	"HMR_3129"	"RCR12638"	""	0	""	"RHEA:31171"	"HMR_3129;FAOXC1811601m;MAR00778"
+"MAR03130"	"R04739"	"FAOXC1811601m"	"R04739X"	"r0718"	""	"r0718;FAOXC1811601m"	"MNXR100547"	"HMR_3130"	"RCR12639"	""	0	""	"RHEA:31167"	"HMR_3130;FAOXC1811601m;MAR00778"
+"MAR03132"	"R03858"	"FAOXC1811601m"	"R03858X"	"r0639"	""	"r0639;FAOXC1811601m"	"MNXR95201"	"HMR_3132"	"RCR12640"	""	0	""	"RHEA:31091"	"HMR_3132;FAOXC1811601m;MAR00778"
+"MAR03135"	"R03857"	"r1447;FAOXC1811601m"	""	""	"R-HSA-77263"	"HMR_3135;r1447;FAOXC1811601m"	"MNXR95299"	"HMR_3135"	"RCR12641"	""	0	""	"RHEA:31039"	"HMR_3135;r1447;MAR02367;FAOXC1811601m;MAR00778"
+"MAR03136"	"R04170"	"r1446;FAOXC1811601m"	"R04170X"	"r0660"	""	"r0660;r1446;FAOXC1811601m"	"MNXR97890"	"HMR_3136"	"RCR12642"	""	0	""	"RHEA:31075"	"HMR_3136;r1446;MAR02366;FAOXC1811601m;MAR00778"
+"MAR03137"	"R04741"	"FAOXC1811601m"	"R04741X"	"r0722"	""	"r0722;FAOXC1811601m"	"MNXR100546"	"HMR_3137"	"RCR12643"	""	0	""	"RHEA:31179"	"HMR_3137;FAOXC1811601m;MAR00778"
+"MAR03139"	"R04742"	"FAOXC1811601m"	"R04742X"	"r0724"	""	"r0724;FAOXC1811601m"	"MNXR95199;MNXR95200"	"HMR_3139"	"RCR12644"	""	0	"RHEA:31185"	"RHEA:31183"	"HMR_3139;FAOXC1811601m;MAR00778"
+"MAR03142"	"R04754"	"r1451;FAOXC10C10OHm;FAOXC10080m;FAOXC1811601m"	""	""	"R-HSA-77345"	"HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m;FAOXC1811601m"	"MNXR109095"	"HMR_3142"	"RCR12645"	""	0	""	"RHEA:28354"	"HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
+"MAR03143"	"R04744"	"FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m;FAOXC1811601m"	"R04744X"	"r0728"	""	"r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m"	"MNXR97889"	"HMR_3143;HMR_3422"	"RCR12646;RCR12667"	""	0	""	"RHEA:31191"	"HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
+"MAR03144"	"R04743"	"FAOXC101C8m;FAOXC10080m;FAOXC1811601m"	"R04743X"	"r0726"	""	"r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m"	"MNXR100545"	"HMR_3144;HMR_3422"	"RCR12647;RCR12667"	""	0	""	"RHEA:31187"	"HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
+"MAR03146"	"R03778"	"FAOXC101C8m;FAOXC10080m;FAOXC1811601m"	"R03778X"	"r0634"	""	"r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m"	"MNXR95198"	"HMR_3146;HMR_3422"	"RCR12648;RCR12667"	""	0	"RHEA:31089"	"RHEA:31087"	"HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
 "MAR03149"	"R03777"	"r1448;FAOXC8C6m;FAOXC80"	""	""	"R-HSA-77338"	"HMR_3149;r1448;FAOXC6C8m;FAOXC80;HMR_3422"	"MNXR95304"	"HMR_3149;HMR_3422"	"RCR12649;RCR12667"	""	0	""	"RHEA:30943"	"HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422"
 "MAR03150"	"R04746"	"FAOXC8C6m;FAOXC80"	"R04746M"	"r0731"	""	"r0731;FAOXC8C6m;FAOXC80;HMR_3422"	"MNXR97888"	"HMR_3150;HMR_3422"	"RCR12650;RCR12667"	""	0	""	"RHEA:31199"	"HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422"
 "MAR03151"	"R04745"	"FAOXC8C6m;FAOXC80"	"R04745M"	"r0730"	""	"r0730;FAOXC8C6m;FAOXC80;HMR_3422"	"MNXR100544"	"HMR_3151;HMR_3422"	"RCR12651;RCR12667"	""	0	""	"RHEA:31195"	"HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422"
@@ -8249,9 +8249,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00764"	""	"FAOXC161802m"	""	""	""	"FAOXC161802m"	"MNXR99301"	""	""	""	0	""	""	"FAOXC161802m"
 "MAR00772"	""	"FAOXC16180m"	""	""	""	"FAOXC16180m"	"MNXR99302"	""	""	""	0	""	""	"FAOXC16180m"
 "MAR00774"	""	"FAOXC170m"	""	""	""	"FAOXC170m"	"MNXR99312"	""	""	""	0	""	""	"FAOXC170m"
-"MAR00776"	""	"FAOXC180"	""	""	""	"FAOXC180"	"MNXR99313"	""	""	""	0	""	""	"FAOXC180"
 "MAR00777"	""	"FAOXC180x"	""	""	""	"FAOXC180x"	"MNXR99314"	""	""	""	0	""	""	"FAOXC180x"
-"MAR00778"	""	"FAOXC1811601m"	""	""	""	"FAOXC1811601m"	"MNXR99315"	""	""	""	0	""	""	"FAOXC1811601m"
 "MAR00780"	""	"FAOXC1811602m"	""	""	""	"FAOXC1811602m"	"MNXR99316"	""	""	""	0	""	""	"FAOXC1811602m"
 "MAR00784"	""	"FAOXC1811603m"	""	""	""	"FAOXC1811603m"	"MNXR99317"	""	""	""	0	""	""	"FAOXC1811603m"
 "MAR00785"	""	"FAOXC182806m"	""	""	""	"FAOXC182806m"	"MNXR99321"	""	""	""	0	""	""	"FAOXC182806m"

From ba8a4f3c02e929dda9bd2daa964cc3433318cd65 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Tue, 17 Dec 2024 08:39:41 +0800
Subject: [PATCH 12/16] Fix-GPR curation for fatty_acid_oxidation and
 Glycerolipid_metabolism (#928)

* fix: GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism

* chore: add macaw test result

---------

Co-authored-by: JHL-452b <JHL-452b@users.noreply.github.com>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
---
 data/testResults/README.md |  2 +-
 model/Human-GEM.yml        | 24 ++++++++++++------------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index 5a49a7d3..78746c32 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #820** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #928** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 568b3f1d..ca0b3fe0 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -131779,7 +131779,7 @@
           - MAM02555c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
+      - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72"
@@ -131818,7 +131818,7 @@
           - MAM02555m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
+      - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72"
@@ -134237,7 +134237,7 @@
           - MAM02877c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000135929"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.1.1.103"
@@ -134255,7 +134255,7 @@
           - MAM02877c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000135929"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.1.1.103"
@@ -223471,7 +223471,7 @@
           - MAM03727c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+      - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "2.3.1.21"
@@ -231805,7 +231805,7 @@
           - MAM03333m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000161533 or ENSG00000196177"
+      - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.99.3"
@@ -232279,7 +232279,7 @@
           - MAM02766x: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000068366 or ENSG00000103740 or ENSG00000119673 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000177465 or ENSG00000197142"
+      - gene_reaction_rule: "ENSG00000140284"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "6.2.1.3"
@@ -237338,7 +237338,7 @@
           - MAM03488c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+      - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -237917,7 +237917,7 @@
           - MAM03496c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+      - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -241061,7 +241061,7 @@
           - MAM03243c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+      - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
       - rxnNotes: "http://www.perkinelmergenetics.com/3Hydroxy3MethylglutarylCoALyaseDeficiency.html"
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -241163,7 +241163,7 @@
           - MAM03409x: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000060971 and ENSG00000113790 and ENSG00000133835 and ENSG00000161533"
+      - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835) and (ENSG00000060971 or ENSG00000116171)"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -272528,7 +272528,7 @@
           - MAM03922x: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000113790 and ENSG00000161533) or (ENSG00000104823 and ENSG00000161533)"
+      - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835)"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.3.6;4.2.1.17"

From dcfcf71f8a21cf60a1e78366954c48330d449c43 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Tue, 17 Dec 2024 08:43:50 +0800
Subject: [PATCH 13/16] Fix gpr curation for histidine metabolism, propanoate
 metabolism and 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>
---
 model/Human-GEM.yml | 65 +++++++++++++++++++--------------------------
 model/genes.tsv     |  3 ---
 2 files changed, 28 insertions(+), 40 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index ca0b3fe0..00b60dbc 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -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"
@@ -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.-"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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.-"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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"
@@ -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.-"
@@ -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.-"
@@ -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"
@@ -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.-"
@@ -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.-"
@@ -308873,9 +308873,6 @@
     - !!omap
       - id: "ENSG00000139914"
       - name: "FITM1"
-    - !!omap
-      - id: "ENSG00000139977"
-      - name: "NAA30"
     - !!omap
       - id: "ENSG00000139988"
       - name: "RDH12"
@@ -309869,9 +309866,6 @@
     - !!omap
       - id: "ENSG00000156256"
       - name: "USP16"
-    - !!omap
-      - id: "ENSG00000156269"
-      - name: "NAA11"
     - !!omap
       - id: "ENSG00000156411"
       - name: "ATP5MJ"
@@ -312020,9 +312014,6 @@
     - !!omap
       - id: "ENSG00000183654"
       - name: "MARCHF11"
-    - !!omap
-      - id: "ENSG00000183665"
-      - name: "TRMT12"
     - !!omap
       - id: "ENSG00000183696"
       - name: "UPP1"
diff --git a/model/genes.tsv b/model/genes.tsv
index 73213a76..5ec73e81 100644
--- a/model/genes.tsv
+++ b/model/genes.tsv
@@ -1408,7 +1408,6 @@ ENSG00000139631	"ENST00000267085;ENST00000475890;ENST00000379850;ENST00000379846
 ENSG00000139684	"ENST00000378720;ENST00000378697;ENST00000412582;ENST00000471867;ENST00000495654"	"ENSP00000367992;ENSP00000367969;ENSP00000391350;ENSP00000476193"	P10768	ESD	2098	esterase D		"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000139718	"ENST00000604567;ENST00000542440;ENST00000619791;ENST00000267197"	"ENSP00000474253;ENSP00000442924;ENSP00000481531;ENSP00000267197"	Q9UPS6	SETD1B	23067	SET domain containing 1B, histone lysine methyltransferase	"KIAA1076;KMT2G;Set1B"	Nucleus	"SwissProt;CellAtlas"
 ENSG00000139914	"ENST00000267426;ENST00000559294"	"ENSP00000267426;ENSP00000453741"	A5D6W6	FITM1	161247	fat storage inducing transmembrane protein 1	FIT1	Endoplasmic reticulum	DeepLoc2
-ENSG00000139977	"ENST00000555166;ENST00000556492;ENST00000554703;ENST00000298406"	"ENSP00000450939;ENSP00000452521;ENSP00000451255;ENSP00000298406"	Q147X3	NAA30	122830	N-alpha-acetyltransferase 30, NatC catalytic subunit	"C14orf35;FLJ35355;MAK3;Mak3p;NAT12"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000139988	"ENST00000551171;ENST00000547463;ENST00000267502;ENST00000552873"	"ENSP00000449079;ENSP00000267502"	Q96NR8	RDH12	145226	retinol dehydrogenase 12	"FLJ30273;LCA13;RP53;SDR7C2"	Endoplasmic reticulum	SwissProt
 ENSG00000140057	"ENST00000267584;ENST00000555570;ENST00000556643;ENST00000554313;ENST00000554706"	"ENSP00000267584;ENSP00000451068;ENSP00000450453"	Q96M32	AK7	122481	adenylate kinase 7	"CFAP75;FAP75;FLJ32864"	Cytosol	SwissProt
 ENSG00000140090	"ENST00000393265;ENST00000532405;ENST00000676001;ENST00000531433;ENST00000554461;ENST00000525557;ENST00000554925;ENST00000556739;ENST00000526482"	"ENSP00000376948;ENSP00000431840;ENSP00000502715;ENSP00000433302;ENSP00000452099;ENSP00000432464"	Q8NFF2	SLC24A4	123041	solute carrier family 24 member 4	NCKX4	Cytosol	SwissProt
@@ -1738,7 +1737,6 @@ ENSG00000156136	"ENST00000509617;ENST00000286648;ENST00000503359;ENST00000504730
 ENSG00000156219	"ENST00000513353;ENST00000510669;ENST00000341029;ENST00000513122;ENST00000504914;ENST00000355810;ENST00000349321;ENST00000513494;ENST00000510423;ENST00000395688;ENST00000504112;ENST00000506667;ENST00000506313;ENST00000511188;ENST00000510863"	"ENSP00000421345;ENSP00000343843;ENSP00000422287;ENSP00000421431;ENSP00000348064;ENSP00000304313;ENSP00000425327;ENSP00000422249"	Q13508	ART3	419	ADP-ribosyltransferase 3 (inactive)	ARTC3	Cell membrane	DeepLoc2
 ENSG00000156222	"ENST00000338602;ENST00000538177;ENST00000394573;ENST00000286749"	"ENSP00000341629;ENSP00000443752;ENSP00000378074;ENSP00000286749"	O00337	SLC28A1	9154	solute carrier family 28 member 1	CNT1	"Cytosol;Nucleus"	CellAtlas
 ENSG00000156256	"ENST00000399975;ENST00000399976;ENST00000334352;ENST00000474835;ENST00000399973;ENST00000485067"	"ENSP00000382857;ENSP00000382858;ENSP00000334808;ENSP00000382855"	Q9Y5T5	USP16	10600	ubiquitin specific peptidase 16	Ubp-M	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
-ENSG00000156269	"ENST00000511542;ENST00000513733;ENST00000286794"	"ENSP00000422022;ENSP00000286794"	Q9BSU3	NAA11	84779	N-alpha-acetyltransferase 11, NatA catalytic subunit	"ARD1B;ARD2;hARD2"	"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000156411	"ENST00000286953;ENST00000554880;ENST00000555030;ENST00000414262;ENST00000553430;ENST00000554287;ENST00000557040;ENST00000553449;ENST00000554089;ENST00000554713;ENST00000557260;ENST00000554528"	"ENSP00000286953;ENSP00000452133;ENSP00000452186;ENSP00000401770;ENSP00000452462;ENSP00000450894;ENSP00000451500"	P56378	ATP5MJ	9556	ATP synthase membrane subunit j	"6.8PL;ATP5MPL;C14orf2;MLQ;MP68"	"Mitochondria;Nucleus"	CellAtlas
 ENSG00000156413	"ENST00000318336;ENST00000524754;ENST00000527106;ENST00000286955;ENST00000592563;ENST00000531085;ENST00000531199;ENST00000532464;ENST00000528505;ENST00000526499;ENST00000591079"	"ENSP00000313398;ENSP00000431708;ENSP00000432954;ENSP00000286955;ENSP00000466016;ENSP00000432161;ENSP00000436413;ENSP00000431880;ENSP00000433811"	P51993	FUT6	2528	fucosyltransferase 6	"FCT3A;FLJ40754;FT1A;FucT-VI"	Golgi apparatus	"SwissProt;CellAtlas"
 ENSG00000156463	"ENST00000359120;ENST00000506591;ENST00000511217;ENST00000509286;ENST00000503848;ENST00000511705;ENST00000504522"	"ENSP00000352028;ENSP00000424497"	Q8TEC5	SH3RF2	153769	SH3 domain containing ring finger 2	"FLJ23654;Hepp1;POSHER;PPP1R39;RNF158"	Nucleus	"SwissProt;CellAtlas"
@@ -2447,7 +2445,6 @@ ENSG00000183479	"ENST00000370231;ENST00000393862;ENST00000330912;ENST00000334497
 ENSG00000183549	"ENST00000575584;ENST00000331849;ENST00000575070;ENST00000570305;ENST00000574748;ENST00000573920;ENST00000577024"	"ENSP00000460112;ENSP00000327916;ENSP00000478073;ENSP00000461752"	Q6NUN0	ACSM5	54988	acyl-CoA synthetase medium chain family member 5	FLJ20581	Mitochondria	SwissProt
 ENSG00000183648	"ENST00000553514;ENST00000605997;ENST00000329559;ENST00000553666;ENST00000555441;ENST00000617122;ENST00000556555"	"ENSP00000451090;ENSP00000475170;ENSP00000330787;ENSP00000450776;ENSP00000483888"	O75438	NDUFB1	4707	NADH:ubiquinone oxidoreductase subunit B1	"CI-MNLL;MNLL"	"Nucleus;Inner mitochondria"	"SwissProt;CellAtlas"
 ENSG00000183654	"ENST00000332432;ENST00000507111;ENST00000505509"	"ENSP00000333181;ENSP00000424425"	A6NNE9	MARCHF11	441061	membrane associated ring-CH-type finger 11	"MARCH-XI;MARCH11;RNF226"	"Cell membrane;Endoplasmic reticulum;Lysosome;Golgi apparatus"	DeepLoc2
-ENSG00000183665	"ENST00000328599;ENST00000521443;ENST00000522518"	"ENSP00000329858;ENSP00000429771"	Q53H54	TRMT12	55039	tRNA methyltransferase 12 homolog	"FLJ20772;Trm12;TYW2"	"Mitochondria;Nucleus"	CellAtlas
 ENSG00000183696	"ENST00000416681;ENST00000331803;ENST00000432131;ENST00000457596;ENST00000421046;ENST00000395564;ENST00000436673;ENST00000395560;ENST00000444999;ENST00000482015;ENST00000417464;ENST00000495446"	"ENSP00000405209;ENSP00000330032;ENSP00000387607;ENSP00000408899;ENSP00000414963;ENSP00000378931;ENSP00000390118;ENSP00000378927;ENSP00000396820;ENSP00000413611"	Q16831	UPP1	7378	uridine phosphorylase 1	"UDRPASE;UP;UPASE;UPP"	Nucleus	CellAtlas
 ENSG00000183747	"ENST00000574251;ENST00000570698;ENST00000573854;ENST00000576361;ENST00000417235;ENST00000575558;ENST00000219054;ENST00000575690;ENST00000571204;ENST00000574692;ENST00000571894;ENST00000396104;ENST00000572921;ENST00000572843;ENST00000576101;ENST00000576119"	"ENSP00000460153;ENSP00000459451;ENSP00000460948;ENSP00000392169;ENSP00000219054;ENSP00000460349;ENSP00000460884;ENSP00000460031;ENSP00000379411"	Q08AH3	ACSM2A	123876	acyl-CoA synthetase medium chain family member 2A	"A-923A4.1;ACSM2;MGC150530"	Mitochondria	SwissProt
 ENSG00000183760	"ENST00000601575;ENST00000331256;ENST00000594229;ENST00000601531"	"ENSP00000469048;ENSP00000327557;ENSP00000470989;ENSP00000470089"	Q6ZNF0	ACP7	390928	acid phosphatase 7, tartrate resistant (putative)	"FLJ16165;PAPL;PAPL1"	"Extracellular;Lysosome"	DeepLoc2

From 8186362a4e2b1e2a7c9e7bbca58d7d57d31d9af2 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Tue, 17 Dec 2024 08:45:19 +0800
Subject: [PATCH 14/16] fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism
 (#885)

* fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism

* chore: add macaw test result

---------

Co-authored-by: JHL-452b <JHL-452b@users.noreply.github.com>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
---
 model/Human-GEM.yml | 25 +++++++++++--------------
 model/genes.tsv     |  1 -
 2 files changed, 11 insertions(+), 15 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 00b60dbc..53204379 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -79545,7 +79545,7 @@
           - MAM02181m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689 or ENSG00000166840"
+      - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.13"
@@ -79619,7 +79619,7 @@
           - MAM02039m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689 or ENSG00000166840"
+      - gene_reaction_rule: "ENSG00000149124"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.13"
@@ -79675,7 +79675,7 @@
           - MAM02530m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000161653"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.1"
@@ -79730,7 +79730,7 @@
           - MAM02896c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111237 or ENSG00000146733"
+      - gene_reaction_rule: "ENSG00000146733"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.3"
@@ -79827,7 +79827,7 @@
           - MAM02553c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000137106"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.79;1.1.1.81"
@@ -79900,7 +79900,7 @@
           - MAM02944m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000023330 or ENSG00000158578 or ENSG00000178773"
+      - gene_reaction_rule: "ENSG00000023330 or ENSG00000178773"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.37"
@@ -80385,7 +80385,7 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882"
+      - gene_reaction_rule: "ENSG00000101323"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.3.15"
@@ -82228,7 +82228,7 @@
           - MAM02553m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000072506 or ENSG00000106049 or ENSG00000138796"
+      - gene_reaction_rule: "ENSG00000072506 or ENSG00000106049"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.31;1.1.1.35"
@@ -82468,7 +82468,7 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000179148 or ENSG00000179477 or ENSG00000188676"
+      - gene_reaction_rule: "ENSG00000179148 or ENSG00000179477"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.13.11.-"
@@ -82487,7 +82487,7 @@
           - MAM02553c: -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 ENSG00000145439 or ENSG00000159692 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000204228 or ENSG00000227471"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.-"
@@ -271474,7 +271474,7 @@
           - MAM03176c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166800 or ENSG00000166816 or ENSG00000171989"
+      - gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166816 or ENSG00000171989"
       - rxnNotes: "https://www.springer.com/gp/book/9789400957800"
       - rxnFrom: "Recon3D"
       - eccodes: "1.1.1.27"
@@ -306836,9 +306836,6 @@
     - !!omap
       - id: "ENSG00000111224"
       - name: "PARP11"
-    - !!omap
-      - id: "ENSG00000111237"
-      - name: "VPS29"
     - !!omap
       - id: "ENSG00000111261"
       - name: "MANSC1"
diff --git a/model/genes.tsv b/model/genes.tsv
index 5ec73e81..c7c3f9e9 100644
--- a/model/genes.tsv
+++ b/model/genes.tsv
@@ -734,7 +734,6 @@ ENSG00000111077	"ENST00000379902;ENST00000314276;ENST00000549498;ENST00000551302
 ENSG00000111144	"ENST00000228740;ENST00000537111;ENST00000552789;ENST00000553041;ENST00000413268;ENST00000548852;ENST00000547393;ENST00000548375;ENST00000547982;ENST00000552091"	"ENSP00000228740;ENSP00000449958;ENSP00000395051;ENSP00000449340"	P09960	LTA4H	4048	leukotriene A4 hydrolase		"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000111181	"ENST00000359674;ENST00000545058;ENST00000424061;ENST00000536824;ENST00000542825;ENST00000535498;ENST00000544782;ENST00000538272;ENST00000540094;ENST00000538580;ENST00000536116;ENST00000537793;ENST00000535347;ENST00000537826;ENST00000538424;ENST00000397296;ENST00000684302"	"ENSP00000352702;ENSP00000399136;ENSP00000444268;ENSP00000439351;ENSP00000446082;ENSP00000380464;ENSP00000508194"	P48065	SLC6A12	6539	solute carrier family 6 member 12	BGT-1	Cell membrane	DeepLoc2
 ENSG00000111224	"ENST00000416739;ENST00000427057;ENST00000458162;ENST00000228820;ENST00000476985;ENST00000453942;ENST00000450737;ENST00000447133"	"ENSP00000392392;ENSP00000397058;ENSP00000399665;ENSP00000228820;ENSP00000395062;ENSP00000387481;ENSP00000405385"	Q9NR21	PARP11	57097	poly(ADP-ribose) polymerase family member 11	"ARTD11;C12orf6"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
-ENSG00000111237	"ENST00000549578;ENST00000360579;ENST00000621131;ENST00000552130;ENST00000447578;ENST00000546588;ENST00000548539;ENST00000549970;ENST00000548259;ENST00000553128;ENST00000551655;ENST00000550267"	"ENSP00000447058;ENSP00000353786;ENSP00000480853;ENSP00000449954;ENSP00000400048;ENSP00000449044;ENSP00000447634"	Q9UBQ0	VPS29	51699	VPS29 retromer complex component	"DC15;DC7;PEP11"	Cytosol	"SwissProt;CellAtlas"
 ENSG00000111261	"ENST00000535902;ENST00000396349;ENST00000545735;ENST00000543314"	"ENSP00000438205;ENSP00000379638;ENSP00000445303;ENSP00000437624"	Q9H8J5	MANSC1	54682	MANSC domain containing 1	"FLJ10298;LOH12CR3"	Golgi apparatus	CellAtlas
 ENSG00000111275	"ENST00000416293;ENST00000261733;ENST00000548536;ENST00000549106;ENST00000551450"	"ENSP00000403349;ENSP00000261733;ENSP00000448179;ENSP00000474669"	P05091	ALDH2	217	aldehyde dehydrogenase 2 family member		Mitochondria	SwissProt
 ENSG00000111339	"ENST00000228936;ENST00000430129;ENST00000544616;ENST00000420600"	"ENSP00000228936;ENSP00000412735;ENSP00000442877;ENSP00000405689"	Q93070	ART4	420	ADP-ribosyltransferase 4 (inactive) (Dombrock blood group)	"ARTC4;CD297;DO;DOK1"	Cytosol	CellAtlas

From 82fa36116b52ba43538ab8d43933298652774264 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Tue, 17 Dec 2024 08:46:16 +0800
Subject: [PATCH 15/16] Fix-GPR curation for Galactose, Fructose and mannose
 metabolism (#886)

* fix-GPR curation for Galactose, Fructose and mannose metabolism

* chore: add macaw test result

---------

Co-authored-by: JHL-452b <JHL-452b@users.noreply.github.com>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
---
 model/Human-GEM.yml | 30 ++++++++++++------------------
 model/genes.tsv     |  2 --
 2 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 53204379..63873688 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -68983,7 +68983,7 @@
           - MAM02945e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000090402 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335"
+      - gene_reaction_rule: "ENSG00000090402 or ENSG00000214013 or ENSG00000257335"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.10;3.2.1.20;3.2.1.48"
@@ -69038,7 +69038,7 @@
           - MAM02040e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000102393 or ENSG00000170266 or ENSG00000241343"
+      - gene_reaction_rule: "ENSG00000102393 or ENSG00000170266"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.22;3.2.1.23"
@@ -69117,7 +69117,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.3"
-      - references: "PMID:33715524"
+      - references: "PMID:33715524;PMID:246961;PMID:19158351"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
@@ -69167,7 +69167,7 @@
           - MAM02555c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074"
+      - gene_reaction_rule: "ENSG00000085662"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.21"
@@ -69281,7 +69281,7 @@
           - MAM02555c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074"
+      - gene_reaction_rule: "ENSG00000085662"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.21"
@@ -69300,7 +69300,7 @@
           - MAM02917c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
+      - gene_reaction_rule: "ENSG00000116199"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.-"
@@ -69319,7 +69319,7 @@
           - MAM02039c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
+      - gene_reaction_rule: "ENSG00000167363 or ENSG00000172456"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.-"
@@ -69357,7 +69357,7 @@
           - MAM02454c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
+      - gene_reaction_rule: "ENSG00000116199"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.-"
@@ -69406,7 +69406,7 @@
           - MAM02455c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100413 or ENSG00000100417 or ENSG00000140650"
+      - gene_reaction_rule: "ENSG00000100417 or ENSG00000140650"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "5.4.2.8"
@@ -69425,7 +69425,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000164068 or ENSG00000173540"
+      - gene_reaction_rule: "ENSG00000173540"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.7.22;2.7.7.13"
@@ -69499,7 +69499,7 @@
           - MAM02759c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116783 or ENSG00000254685"
+      - gene_reaction_rule: "ENSG00000254685"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.7.30"
@@ -223305,7 +223305,7 @@
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "2.7.1.3"
-      - references: "PMID:33715524"
+      - references: "PMID:33715524;PMID:2469615;PMID:19158351"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
@@ -307292,9 +307292,6 @@
     - !!omap
       - id: "ENSG00000116771"
       - name: "AGMAT"
-    - !!omap
-      - id: "ENSG00000116783"
-      - name: "TNNI3K"
     - !!omap
       - id: "ENSG00000116791"
       - name: "CRYZ"
@@ -313025,9 +313022,6 @@
     - !!omap
       - id: "ENSG00000241119"
       - name: "UGT1A9"
-    - !!omap
-      - id: "ENSG00000241343"
-      - name: "RPL36A"
     - !!omap
       - id: "ENSG00000241360"
       - name: "PDXP"
diff --git a/model/genes.tsv b/model/genes.tsv
index c7c3f9e9..2580393e 100644
--- a/model/genes.tsv
+++ b/model/genes.tsv
@@ -884,7 +884,6 @@ ENSG00000116745	ENST00000262340	ENSP00000262340	Q16518	RPE65	6121	retinoid isome
 ENSG00000116748	"ENST00000637080;ENST00000520113;ENST00000369538;ENST00000639274;ENST00000639077;ENST00000638214;ENST00000485564"	"ENSP00000489753;ENSP00000430075;ENSP00000358551"	P23109	AMPD1	270	adenosine monophosphate deaminase 1	"MAD;MADA"	"Cytosol;Nucleus"	DeepLoc2
 ENSG00000116761	"ENST00000411986;ENST00000370938;ENST00000464926;ENST00000346806;ENST00000482383"	"ENSP00000413407;ENSP00000359976;ENSP00000311554"	P32929	CTH	1491	cystathionine gamma-lyase		Cytosol	SwissProt
 ENSG00000116771	ENST00000375826	ENSP00000364986	Q9BSE5	AGMAT	79814	agmatinase	FLJ23384	Mitochondria	DeepLoc2
-ENSG00000116783	"ENST00000326637;ENST00000530184;ENST00000497284;ENST00000526236;ENST00000534020;ENST00000525480;ENST00000370889;ENST00000465473"	"ENSP00000322251;ENSP00000431465;ENSP00000434975;ENSP00000433550"	Q59H18	TNNI3K	51086	TNNI3 interacting kinase	CARK	"Cytosol;Nucleus"	SwissProt
 ENSG00000116791	"ENST00000370872;ENST00000340866;ENST00000492102;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120"	"ENSP00000359909;ENSP00000339399;ENSP00000399805;ENSP00000359908;ENSP00000359907;ENSP00000404289"	Q08257	CRYZ	1429	crystallin zeta		Cytosol	"SwissProt;CellAtlas"
 ENSG00000116882	"ENST00000457318;ENST00000361035;ENST00000325945;ENST00000482991;ENST00000622548"	"ENSP00000393955;ENSP00000354314;ENSP00000316339;ENSP00000483507"	Q9NYQ3	HAO2	51179	hydroxyacid oxidase 2	"GIG16;HAOX2"	"Peroxisome;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000116906	"ENST00000436239;ENST00000366647;ENST00000416000;ENST00000644483;ENST00000492459;ENST00000469332"	"ENSP00000402811;ENSP00000355607;ENSP00000411640;ENSP00000496537"	O15228	GNPAT	8443	glyceronephosphate O-acyltransferase	"DAP-AT;DAPAT;DHAPAT"	Peroxisome	SwissProt
@@ -2778,7 +2777,6 @@ ENSG00000240857	"ENST00000381249;ENST00000468071"	ENSP00000370648	Q9HBH5	RDH14	5
 ENSG00000240891	"ENST00000636933;ENST00000393934;ENST00000477665;ENST00000468174;ENST00000474484"	"ENSP00000490816;ENSP00000377511;ENSP00000420686"	Q0VAA5	PLCXD2	257068	phosphatidylinositol specific phospholipase C X domain containing 2	FLJ31579	Nucleus	CellAtlas
 ENSG00000240972	"ENST00000215754;ENST00000465752;ENST00000498385"	ENSP00000215754	P14174	MIF	4282	macrophage migration inhibitory factor	"GIF;GLIF"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000241119	ENST00000354728	ENSP00000346768	O60656	UGT1A9	54600	UDP glucuronosyltransferase family 1 member A9	"HLUGP4;LUGP4;UGT1AI"	Endoplasmic reticulum	SwissProt
-ENSG00000241343	"ENST00000427805;ENST00000614077;ENST00000392994;ENST00000491851;ENST00000465340;ENST00000553110;ENST00000372849;ENST00000465744;ENST00000471855;ENST00000489407"	"ENSP00000404375;ENSP00000483017;ENSP00000397659;ENSP00000446503;ENSP00000361940;ENSP00000473451"	P83881	RPL36A	6173	ribosomal protein L36a	"L36A;RPL44"	"Endoplasmic reticulum;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000241360	"ENST00000215904;ENST00000403251"	"ENSP00000215904;ENSP00000385336"	Q96GD0	PDXP	57026	pyridoxal phosphatase	"CIN;dJ37E16.5;FLJ32703"	Cytosol	SwissProt
 ENSG00000241404	"ENST00000333845;ENST00000395512;ENST00000432129;ENST00000466239;ENST00000482938;ENST00000489721"	"ENSP00000333380;ENSP00000378888;ENSP00000401694"	Q99944	EGFL8	80864	EGF like domain multiple 8	"C6orf8;NG3"	Nucleus	CellAtlas
 ENSG00000241468	"ENST00000466753;ENST00000414062;ENST00000449683;ENST00000491560;ENST00000359832;ENST00000292475;ENST00000488775;ENST00000394186;ENST00000481899;ENST00000523680;ENST00000485011;ENST00000524321"	"ENSP00000412149;ENSP00000407540;ENSP00000352890;ENSP00000292475;ENSP00000418197;ENSP00000377740;ENSP00000430398"	P56134	ATP5MF	9551	ATP synthase membrane subunit f	"ATP5J2;ATP5JL"	"Nucleus;Inner mitochondria"	"SwissProt;CellAtlas"

From c0f3a66393c0aad09345e7540b490e5e8c185bc2 Mon Sep 17 00:00:00 2001
From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com>
Date: Tue, 17 Dec 2024 08:47:44 +0800
Subject: [PATCH 16/16] Fix-GPR curation for Purine metabolism (#898)

* fix-GPR_curation_for_Purine_metabolism

* chore: add macaw test result

---------

Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
Co-authored-by: edkerk <edkerk@users.noreply.github.com>
---
 model/Human-GEM.yml | 46 ++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 63873688..4e54774f 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -71448,7 +71448,7 @@
           - MAM02751c: 1
       - 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 ENSG00000171302 or ENSG00000187097 or ENSG00000188833 or ENSG00000197586"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.6.1.5;3.6.1.6"
@@ -71465,7 +71465,7 @@
           - MAM02759c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000070019 or ENSG00000078295 or ENSG00000101890 or ENSG00000121281 or ENSG00000129467 or ENSG00000132518 or ENSG00000138031 or ENSG00000143199 or ENSG00000152402 or ENSG00000155897 or ENSG00000159899 or ENSG00000162104 or ENSG00000164742 or ENSG00000169418 or ENSG00000173175 or ENSG00000174233"
+      - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000078295 or ENSG00000121281 or ENSG00000129467 or ENSG00000138031 or ENSG00000143199 or ENSG00000155897 or ENSG00000159899 or ENSG00000162104 or ENSG00000164742 or ENSG00000173175 or ENSG00000174233"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.6.1.1;4.6.1.2"
@@ -71517,7 +71517,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -71535,7 +71535,7 @@
           - MAM02751e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -71553,7 +71553,7 @@
           - MAM02751m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -71590,7 +71590,7 @@
           - MAM02040c: -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 ENSG00000095464 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"
@@ -71625,7 +71625,7 @@
           - MAM02759c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000070019 or ENSG00000078295 or ENSG00000101890 or ENSG00000121281 or ENSG00000129467 or ENSG00000132518 or ENSG00000138031 or ENSG00000143199 or ENSG00000152402 or ENSG00000155897 or ENSG00000159899 or ENSG00000162104 or ENSG00000164742 or ENSG00000169418 or ENSG00000173175 or ENSG00000174233"
+      - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000070019 or ENSG00000078295 or ENSG00000101890 or ENSG00000121281 or ENSG00000132518 or ENSG00000138031 or ENSG00000143199 or ENSG00000152402 or ENSG00000155897 or ENSG00000159899 or ENSG00000169418"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.6.1.1;4.6.1.2"
@@ -71724,7 +71724,7 @@
           - MAM02040c: -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 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 ENSG00000185527 or ENSG00000186642"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.4.17;3.1.4.35"
@@ -71834,7 +71834,7 @@
           - MAM02759c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125877"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.6.1.19;3.6.1.8"
@@ -71927,7 +71927,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -72002,7 +72002,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -72020,7 +72020,7 @@
           - MAM02751e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -72096,7 +72096,7 @@
           - MAM01639c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000004455 or ENSG00000072778 or ENSG00000085231 or ENSG00000087008 or ENSG00000106992 or ENSG00000117054 or ENSG00000140057 or ENSG00000147853 or ENSG00000151498 or ENSG00000154027 or ENSG00000155085 or ENSG00000162433 or ENSG00000165695 or ENSG00000177646"
+      - gene_reaction_rule: "ENSG00000004455 or ENSG00000085231 or ENSG00000106992 or ENSG00000140057 or ENSG00000147853 or ENSG00000154027 or ENSG00000155085 or ENSG00000162433 or ENSG00000165695 or ENSG00000177646"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.4.11;2.7.4.3"
@@ -72265,7 +72265,7 @@
           - MAM02193c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156510 or ENSG00000156515 or ENSG00000159399 or ENSG00000160883"
+      - gene_reaction_rule: "ENSG00000156515 or ENSG00000159399"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.1"
@@ -72284,7 +72284,7 @@
           - MAM02039c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156510 or ENSG00000156515 or ENSG00000159399 or ENSG00000160883"
+      - gene_reaction_rule: "ENSG00000156510 or ENSG00000156515 or ENSG00000159399"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.1"
@@ -72415,7 +72415,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -72603,7 +72603,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -72789,7 +72789,7 @@
           - MAM03150c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -72927,7 +72927,7 @@
           - MAM02872c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000100354 or ENSG00000239900"
+      - gene_reaction_rule: "ENSG00000239900"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.3.2.2"
@@ -73038,7 +73038,7 @@
           - MAM03121e: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
+      - gene_reaction_rule: "ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.11.1.7"
@@ -73257,7 +73257,7 @@
           - MAM01642c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
+      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.4.6"
@@ -73275,7 +73275,7 @@
           - MAM02193c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
+      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.4.6"
@@ -217612,7 +217612,7 @@
           - MAM03200l: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000134575 or ENSG00000162836"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000134575"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "3.1.3.2"