From aee9aa37a7339ae41cb6fd7a3a43277f12394f21 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 30 Dec 2024 19:51:45 +0800 Subject: [PATCH 1/4] Fix: GPR curation for transport reactions (5) --- model/Human-GEM.yml | 68 +++++++++++---------------------------------- 1 file changed, 16 insertions(+), 52 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..38713e85 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -148269,7 +148269,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148330,7 +148329,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - references: "PMID:16858612" - subsystem: @@ -148389,7 +148387,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148597,7 +148594,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - references: "PMID:16858612" - subsystem: @@ -148656,7 +148652,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148714,7 +148709,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -149152,7 +149146,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - references: "PMID:16858612" - subsystem: @@ -150010,7 +150003,7 @@ - MAM02900e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnFrom: "HMRdatabase" - references: "PMID:14579113" - subsystem: @@ -150044,7 +150037,7 @@ - MAM02046e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnFrom: "HMRdatabase" - references: "PMID:14579113" - subsystem: @@ -150738,7 +150731,7 @@ - MAM02039e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" + - gene_reaction_rule: "ENSG00000100156 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12107270;PMID:12739169;PMID:12829793;PMID:17173541;PMID:17245649;PMID:18305372;PMID:18375207;PMID:8476015;PMID:8557697;PMID:9651205;PMID:9786900" - subsystem: @@ -152683,7 +152676,6 @@ - MAM02770e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -153778,7 +153770,7 @@ - MAM02724e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257 or ENSG00000165029" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154303,7 +154295,6 @@ - MAM02993e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154502,7 +154493,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154808,7 +154799,7 @@ - MAM03089e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154842,7 +154833,7 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154961,7 +154952,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -155165,7 +155156,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000105281" + - gene_reaction_rule: "ENSG00000105281" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -155386,7 +155377,7 @@ - MAM02896e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -155607,7 +155598,7 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -155709,7 +155700,7 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -155981,7 +155972,7 @@ - MAM03089e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156168,7 +156159,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156236,7 +156226,6 @@ - MAM02724e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156338,7 +156327,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156695,7 +156683,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902" + - gene_reaction_rule: "ENSG00000105281 or ENSG00000115902" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156746,7 +156734,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156984,7 +156971,6 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157103,7 +157089,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157120,7 +157105,6 @@ - MAM03089e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157154,7 +157138,6 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157239,7 +157222,6 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157528,7 +157510,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157885,7 +157866,6 @@ - MAM03089e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158089,7 +158069,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158123,7 +158102,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158276,7 +158254,6 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158293,7 +158270,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158361,7 +158337,6 @@ - MAM02896e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158531,7 +158506,6 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158633,7 +158607,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -159058,7 +159031,6 @@ - MAM03089e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -161254,7 +161226,7 @@ - MAM02403e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" + - gene_reaction_rule: "ENSG00000100156 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169;PMID:18305372;PMID:11101640;PMID:23935841;PMID:31719150" - subsystem: @@ -173351,7 +173323,7 @@ - MAM02658m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000102743 or ENSG00000120329" + - gene_reaction_rule: "ENSG00000120329" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -174227,7 +174199,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174353,7 +174324,6 @@ - MAM01753m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174465,7 +174435,6 @@ - MAM01645m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -179376,7 +179345,6 @@ - MAM03114g: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000205060" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -231785,7 +231753,6 @@ - MAM02039e: -2 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100170" - rxnFrom: "Recon3D" - eccodes: "2.4.1.92" - references: "PMID:11024018;PMID:11034615;PMID:12748858;PMID:2490366;PMID:8063771" @@ -232375,7 +232342,6 @@ - MAM02519e: 3 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165970" - rxnFrom: "Recon3D" - references: "PMID:20649585;PMID:12719981" - subsystem: @@ -235364,7 +235330,6 @@ - MAM02147e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000173638" - rxnFrom: "Recon3D" - references: "PMID:17687501" - subsystem: @@ -237185,7 +237150,6 @@ - MAM01681e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000142583" - rxnFrom: "Recon3D" - references: "PMID:23084044" - subsystem: From 3d1a0445b0ae2e26c0d6b026ca4a999357b71bf6 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 30 Dec 2024 12:11:47 +0000 Subject: [PATCH 2/4] 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 24c52291..7151ab9e 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: -- **PR #830** (MACAW) +- **PR #955** (MACAW) - **PR #883** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. From 7f3c86f8d59a7eca447e235f0b2a13a00d258cff Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Wed, 8 Jan 2025 14:32:24 +0800 Subject: [PATCH 3/4] fix: curated the GPR of MAR05606 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 38713e85..4e0823b8 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -154799,7 +154799,7 @@ - MAM03089e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: From 2abf6618fddf5ea65a74c407e548a7ddc81ed21f Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Wed, 8 Jan 2025 11:15:51 +0100 Subject: [PATCH 4/4] chore: add gene essentiality test result --- data/testResults/README.md | 2 +- data/testResults/gene-essential.csv | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 7151ab9e..8070791f 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -5,7 +5,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: - **PR #955** (MACAW) -- **PR #883** (gene essentiality) +- **PR #955** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 90a498c1..c918efe0 100644 --- a/data/testResults/gene-essential.csv +++ b/data/testResults/gene-essential.csv @@ -1,7 +1,7 @@ cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC -DLD1,37,2165,62,277,0.8666,0.1178,0.9722,0.1792,0.1531 -GBM,34,2147,65,294,0.8587,0.1037,0.9706,0.1593,0.1287 -HCT116,46,2189,57,305,0.8606,0.1311,0.9746,0.2026,0.1851 -HELA,31,2246,72,249,0.8764,0.1107,0.9689,0.1619,0.1266 -RPE1,15,2186,84,255,0.8665,0.05556,0.963,0.0813,0.02954 -all,7,2386,96,109,0.9211,0.06034,0.9613,0.06393,0.02293 +DLD1,50,2147,85,272,0.8602,0.1553,0.9619,0.2188,0.1739 +GBM,57,2138,78,280,0.8598,0.1691,0.9648,0.2415,0.2026 +HCT116,71,2179,70,289,0.8624,0.1972,0.9689,0.2834,0.2534 +HELA,35,2219,106,251,0.8633,0.1224,0.9544,0.1639,0.1061 +RPE1,21,2163,114,255,0.8555,0.07609,0.9499,0.1022,0.0361 +all,8,2357,133,113,0.9058,0.06612,0.9466,0.06107,0.01181