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 <[email protected]> Co-authored-by: Eduard Kerkhoven <[email protected]>
SysBioChalmers · Dec 17, 2024 · ba8a4f3 · ba8a4f3
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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 #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
@@ -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"