From 4eebb7242e9a4bbb253042abeb4a824d5b6836d6 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 30 Dec 2024 19:09:43 +0800 Subject: [PATCH 1/4] fix: GPR curation for transport reactions (4) --- model/Human-GEM.yml | 73 +++++++++++++++------------------------------ 1 file changed, 24 insertions(+), 49 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..e80990fd 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -148360,7 +148360,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148447,7 +148446,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148859,7 +148857,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148946,7 +148943,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -149064,7 +149060,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -149122,7 +149117,6 @@ - MAM03153e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -149211,7 +149205,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -149502,7 +149495,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - references: "PMID:16858612" - subsystem: @@ -149942,7 +149934,7 @@ - MAM02617e: -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: @@ -149976,7 +149968,7 @@ - MAM02901e: 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: @@ -150782,7 +150774,7 @@ - MAM02946e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000091138 or ENSG00000112053 or ENSG00000145217 or ENSG00000147606 or ENSG00000155850 or ENSG00000174502 or ENSG00000181045" + - gene_reaction_rule: "ENSG00000112053 or ENSG00000145217 or ENSG00000147606 or ENSG00000155850 or ENSG00000174502 or ENSG00000181045" - rxnFrom: "HMRdatabase" - references: "PMID:12759755" - subsystem: @@ -151069,7 +151061,7 @@ - MAM01962e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117394 or ENSG00000163581 or ENSG00000181856" + - gene_reaction_rule: "ENSG00000117394 or ENSG00000181856" - rxnFrom: "HMRdatabase" - references: "PMID:12750891" - subsystem: @@ -151436,7 +151428,7 @@ - MAM02426e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003989 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349" + - gene_reaction_rule: "ENSG00000003989 or ENSG00000139514 or ENSG00000165349" - rxnFrom: "HMRdatabase" - references: "PMID:17466261;PMID:7718542;PMID:10049700;PMID:10072483;PMID:10391915;PMID:10574970;PMID:11004451;PMID:11311135;PMID:11389679;PMID:11557028;PMID:11564694;PMID:11742812;PMID:11827462;PMID:12117417;PMID:12824232;PMID:14574404;PMID:14770310;PMID:7690540;PMID:9751058;PMID:9759917;PMID:12883891;PMID:16288981;PMID:1904693;PMID:4424190;PMID:6432599;PMID:9868191;PMID:15465786;PMID:16082501" - subsystem: @@ -152103,7 +152095,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000178537" + - gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436" - rxnFrom: "HMRdatabase" - references: "PMID:10823827" - subsystem: @@ -152698,7 +152690,6 @@ - MAM01986e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -153673,7 +153664,7 @@ - MAM03101e: -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: @@ -154587,7 +154578,7 @@ - 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: @@ -154893,7 +154884,7 @@ - MAM02770e: 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: @@ -154910,7 +154901,7 @@ - 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: @@ -155012,7 +155003,7 @@ - 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: @@ -155216,7 +155207,7 @@ - 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: @@ -155539,7 +155530,7 @@ - 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: @@ -155573,7 +155564,7 @@ - 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: @@ -155624,7 +155615,7 @@ - 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: @@ -155811,7 +155802,7 @@ - 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: @@ -155913,7 +155904,7 @@ - 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: @@ -155947,7 +155938,7 @@ - MAM03135e: 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: @@ -156134,7 +156125,6 @@ - MAM02724e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156372,7 +156362,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156542,7 +156531,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902" + - gene_reaction_rule: "ENSG00000115902" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156576,7 +156565,7 @@ - MAM02896e: 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: @@ -156899,7 +156888,6 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157035,7 +157023,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157137,7 +157124,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157375,7 +157361,6 @@ - MAM03089e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157409,7 +157394,6 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157460,7 +157444,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157630,7 +157613,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157868,7 +157850,6 @@ - MAM02993e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158140,7 +158121,6 @@ - MAM03089e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158412,7 +158392,6 @@ - MAM02724e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158463,7 +158442,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158548,7 +158526,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -159653,7 +159630,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -159823,7 +159799,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -161374,7 +161349,7 @@ - MAM02819e: -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" - subsystem: @@ -161989,7 +161964,7 @@ - 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" - subsystem: @@ -169823,7 +169798,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000113396 or ENSG00000130304 or ENSG00000143554 or ENSG00000167114" + - gene_reaction_rule: "ENSG00000113396 or ENSG00000143554 or ENSG00000167114" - rxnFrom: "HMRdatabase" - eccodes: "6.2.1.-" - subsystem: @@ -170193,7 +170168,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" From ce3dc8b4c79e78de53f4a3df558340881c23749c Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 30 Dec 2024 11:31:47 +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..5da8ad0e 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 #954** (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 4bdb0bcdaa61effdbf5f400f4243447ad6ca185a Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Sun, 5 Jan 2025 11:43:24 +0800 Subject: [PATCH 3/4] Fix: remove ENSG00000100156 from MAR06054 --- 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 e80990fd..07475790 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -162054,7 +162054,7 @@ - MAM00648e: -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: "ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: From 0477d10b9b5ac652552d20ead0e5ab483cc94f47 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Sun, 5 Jan 2025 08:26:45 +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 5da8ad0e..5b56b301 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 #954** (MACAW) -- **PR #883** (gene essentiality) +- **PR #954** (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