fix-GPR_curation_for_Serotonin and melatonin biosynthesis and Keratan… (

#907) * fix-GPR_curation_for_Serotonin and melatonin biosynthesis and Keratan sulfate biosynthesis * chore: add macaw test result --------- Co-authored-by: JHL-452b <[email protected]> Co-authored-by: Eduard Kerkhoven <[email protected]>
SysBioChalmers · Dec 17, 2024 · 7ebff3f · 7ebff3f
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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 #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.
+The test results shown here were obtained by the GitHub Actions run in **PR #907** (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
@@ -141463,7 +141463,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141501,7 +141501,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141520,7 +141520,7 @@
           - 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.-"
@@ -141558,7 +141558,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141577,7 +141577,7 @@
           - 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.-"
@@ -141615,7 +141615,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141634,7 +141634,7 @@
           - 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.-"
@@ -141672,7 +141672,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141691,7 +141691,7 @@
           - 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.-"
@@ -141729,7 +141729,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141748,7 +141748,7 @@
           - 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.-"
@@ -141786,7 +141786,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141805,7 +141805,7 @@
           - 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.-"
@@ -141843,7 +141843,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141862,7 +141862,7 @@
           - 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.-"
@@ -141900,7 +141900,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141919,7 +141919,7 @@
           - 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.-"
@@ -141957,7 +141957,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -141976,7 +141976,7 @@
           - 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.-"
@@ -142014,7 +142014,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142033,7 +142033,7 @@
           - 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.-"
@@ -142071,7 +142071,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142185,7 +142185,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142223,7 +142223,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142242,7 +142242,7 @@
           - 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.-"
@@ -142280,7 +142280,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142394,7 +142394,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142432,7 +142432,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142451,7 +142451,7 @@
           - 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.-"
@@ -142489,7 +142489,7 @@
           - MAM03111g: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
+      - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -142508,7 +142508,7 @@
           - 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.-"
@@ -156497,7 +156497,7 @@
           - MAM02949c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000070614 or ENSG00000111962 or ENSG00000115526 or ENSG00000124302 or ENSG00000130540 or ENSG00000135702 or ENSG00000136720 or ENSG00000138653 or ENSG00000140835 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000154252 or ENSG00000164100 or ENSG00000166507 or ENSG00000171004 or ENSG00000173597 or ENSG00000175040 or ENSG00000175229 or ENSG00000183196 or ENSG00000185352 or ENSG00000197093 or ENSG00000198075 or ENSG00000198203 or ENSG00000261052"
+      - gene_reaction_rule: "ENSG00000070614 or ENSG00000115526 or ENSG00000130540 or ENSG00000135702 or ENSG00000138653 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000173597 or ENSG00000197093 or ENSG00000198203 or ENSG00000261052"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.8.2.-"