Merge pull request #937 from SysBioChalmers/Fix-Sulfur_metabolism

Fix: GPR curation for Sulfur metabolism
SysBioChalmers · Dec 16, 2024 · 0e0d55a · 0e0d55a
2 parents 5e88b8a + 05cd3f4
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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 #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.

diff --git 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.-"