Merge pull request #913 from SysBioChalmers/fix-Xenobiotics_metabolism

fix-GPR curation for Xenobiotics metabolism
SysBioChalmers · Dec 4, 2024 · 5e88b8a · 5e88b8a
2 parents 45b9f45 + d2b35bf
commit 5e88b8a
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diff --git 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.

diff --git 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"