From b68806c5f0818249f4e40d839efd5fd9ae06b531 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 24 Dec 2024 11:48:47 +0800 Subject: [PATCH 01/30] Fix: GPR curation for Sphingolipid metabolism --- model/Human-GEM.yml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..6e95fe61 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -116304,7 +116304,7 @@ - MAM02928c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067113 or ENSG00000101577 or ENSG00000132793 or ENSG00000134324 or ENSG00000141934 or ENSG00000162407" + - gene_reaction_rule: "ENSG00000067113 or ENSG00000141934 or ENSG00000162407" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.4" - references: "PMID:12411432;PMID:12815058;PMID:7575445" @@ -116478,7 +116478,7 @@ - MAM03107r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000060642 or ENSG00000069943 or ENSG00000085998 or ENSG00000086062 or ENSG00000102595 or ENSG00000109586 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000119227 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000134910 or ENSG00000136731 or ENSG00000139044 or ENSG00000143315 or ENSG00000147162 or ENSG00000148288 or ENSG00000156966 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000162885 or ENSG00000163527 or ENSG00000167080 or ENSG00000167889 or ENSG00000170340 or ENSG00000172318 or ENSG00000172461 or ENSG00000172728 or ENSG00000175711 or ENSG00000176383 or ENSG00000176597 or ENSG00000177191 or ENSG00000179913 or ENSG00000180549 or ENSG00000182272 or ENSG00000183778 or ENSG00000187676 or ENSG00000196371 or ENSG00000196968 or ENSG00000198488 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" + - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000060642 or ENSG00000086062 or ENSG00000109586 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000119227 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000134910 or ENSG00000139044 or ENSG00000143315 or ENSG00000148288 or ENSG00000156966 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000162885 or ENSG00000163527 or ENSG00000167080 or ENSG00000172318 or ENSG00000176383 or ENSG00000176597 or ENSG00000177191 or ENSG00000179913 or ENSG00000182272 or ENSG00000183778 or ENSG00000187676 or ENSG00000196968 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - references: "PMID:10856719" @@ -116511,7 +116511,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067113 or ENSG00000101577 or ENSG00000105520 or ENSG00000117600 or ENSG00000129951 or ENSG00000132793 or ENSG00000134324 or ENSG00000141934 or ENSG00000147535 or ENSG00000162407 or ENSG00000203805" + - gene_reaction_rule: "ENSG00000067113 or ENSG00000105520 or ENSG00000117600 or ENSG00000129951 or ENSG00000132793 or ENSG00000134324 or ENSG00000141934 or ENSG00000147535 or ENSG00000162407 or ENSG00000203805" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.4" - references: "PMID:8403799" @@ -116546,7 +116546,7 @@ - MAM02930c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067113 or ENSG00000101577 or ENSG00000132793 or ENSG00000134324 or ENSG00000141934 or ENSG00000162407" + - gene_reaction_rule: "ENSG00000067113 or ENSG00000101577 or ENSG00000132793 or ENSG00000141934 or ENSG00000162407" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.4" - references: "PMID:9705349" @@ -116711,7 +116711,6 @@ - MAM03107g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000179913" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - subsystem: @@ -116922,7 +116921,6 @@ - MAM03107g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000179913" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - subsystem: @@ -117644,7 +117642,6 @@ - MAM03107g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000179913" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - subsystem: From 8e40b9b0256f3d6639450c0b95738dc6e97379fa Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Tue, 24 Dec 2024 04:09:18 +0000 Subject: [PATCH 02/30] 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..c049cb07 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 #946** (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 51366ad4d00406daa21691f4d6e3f6a287d5858a Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Sun, 29 Dec 2024 12:20:01 +0800 Subject: [PATCH 03/30] Fix: GPR curation for Glycosphingolipid metabolism --- model/Human-GEM.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..48230f52 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -121215,7 +121215,7 @@ - MAM03091c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000130383 or ENSG00000156413 or ENSG00000171124" + - gene_reaction_rule: "ENSG00000130383 or ENSG00000171124" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.65" - subsystem: @@ -121461,7 +121461,7 @@ - MAM03111c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000170340 or ENSG00000176383 or ENSG00000179913" - rxnFrom: "HMRdatabase" - eccodes: - "2.4.1.149" @@ -122164,7 +122164,7 @@ - MAM03107c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000060642 or ENSG00000069943 or ENSG00000085998 or ENSG00000086062 or ENSG00000102595 or ENSG00000109586 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000119227 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000134910 or ENSG00000136731 or ENSG00000139044 or ENSG00000143315 or ENSG00000147162 or ENSG00000148288 or ENSG00000156966 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000162885 or ENSG00000163527 or ENSG00000167080 or ENSG00000167889 or ENSG00000170340 or ENSG00000172318 or ENSG00000172461 or ENSG00000172728 or ENSG00000175711 or ENSG00000176383 or ENSG00000176597 or ENSG00000177191 or ENSG00000179913 or ENSG00000180549 or ENSG00000182272 or ENSG00000183778 or ENSG00000187676 or ENSG00000196371 or ENSG00000196968 or ENSG00000198488 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" + - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000086062 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000148288 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000167080 or ENSG00000167889 or ENSG00000172318 or ENSG00000183778 or ENSG00000187676 or ENSG00000196968 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - references: "PMID:7930586;PMID:7930586;PMID:7930586" @@ -122181,7 +122181,7 @@ - MAM03107g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000060642 or ENSG00000069943 or ENSG00000085998 or ENSG00000086062 or ENSG00000102595 or ENSG00000109586 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000119227 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000134910 or ENSG00000136731 or ENSG00000139044 or ENSG00000143315 or ENSG00000147162 or ENSG00000148288 or ENSG00000156966 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000162885 or ENSG00000163527 or ENSG00000167080 or ENSG00000167889 or ENSG00000170340 or ENSG00000172318 or ENSG00000172461 or ENSG00000172728 or ENSG00000175711 or ENSG00000176383 or ENSG00000176597 or ENSG00000177191 or ENSG00000179913 or ENSG00000180549 or ENSG00000182272 or ENSG00000183778 or ENSG00000187676 or ENSG00000196371 or ENSG00000196968 or ENSG00000198488 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" + - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000085998 or ENSG00000086062 or ENSG00000109586 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000119227 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000148288 or ENSG00000156966 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000163527 or ENSG00000167080 or ENSG00000172318 or ENSG00000172728 or ENSG00000182272 or ENSG00000183778 or ENSG00000196371 or ENSG00000196968 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - references: "PMID:7930586;PMID:7930586;PMID:7930586" @@ -122199,7 +122199,7 @@ - MAM03107c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000060642 or ENSG00000069943 or ENSG00000085998 or ENSG00000086062 or ENSG00000102595 or ENSG00000109586 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000119227 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000134910 or ENSG00000136731 or ENSG00000139044 or ENSG00000143315 or ENSG00000147162 or ENSG00000148288 or ENSG00000156966 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000162885 or ENSG00000163527 or ENSG00000167080 or ENSG00000167889 or ENSG00000170340 or ENSG00000172318 or ENSG00000172461 or ENSG00000172728 or ENSG00000175711 or ENSG00000176383 or ENSG00000176597 or ENSG00000177191 or ENSG00000179913 or ENSG00000180549 or ENSG00000182272 or ENSG00000183778 or ENSG00000187676 or ENSG00000196371 or ENSG00000196968 or ENSG00000198488 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" + - gene_reaction_rule: "ENSG00000016864 or ENSG00000027847 or ENSG00000086062 or ENSG00000117411 or ENSG00000118017 or ENSG00000118276 or ENSG00000120820 or ENSG00000121578 or ENSG00000124091 or ENSG00000148288 or ENSG00000158470 or ENSG00000158850 or ENSG00000162630 or ENSG00000167080 or ENSG00000172318 or ENSG00000172461 or ENSG00000179913 or ENSG00000182272 or ENSG00000183778 or ENSG00000196371 or ENSG00000196968 or ENSG00000204007 or ENSG00000237172 or ENSG00000251287" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.-" - references: "PMID:11172001;PMID:11172001;PMID:11172001" @@ -122250,7 +122250,7 @@ - MAM03111c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000007541 and ENSG00000100564 and ENSG00000135845 and ENSG00000165195) or ENSG00000138641 or ENSG00000145337 or ENSG00000185808 or ENSG00000255072" + - gene_reaction_rule: "(ENSG00000007541 and ENSG00000100564 and ENSG00000135845 and ENSG00000165195) or ENSG00000145337 or ENSG00000185808 or ENSG00000255072" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.198" - subsystem: @@ -122266,7 +122266,7 @@ - MAM03111r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000007541 and ENSG00000100564 and ENSG00000135845 and ENSG00000165195) or ENSG00000138641 or ENSG00000145337 or ENSG00000185808 or ENSG00000255072" + - gene_reaction_rule: "(ENSG00000007541 and ENSG00000100564 and ENSG00000135845 and ENSG00000165195) or ENSG00000145337 or ENSG00000185808 or ENSG00000255072" - rxnFrom: "HMRdatabase" - eccodes: "2.4.1.198" - subsystem: From 01984c0f10f3cf1a8ef82542625bd2984e6b71e8 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Sun, 29 Dec 2024 04:33:55 +0000 Subject: [PATCH 04/30] 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..92f278ee 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 #950** (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 e2e5e5f59e3c25190f7e31505ce77c393c78a4cd Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 30 Dec 2024 16:14:26 +0800 Subject: [PATCH 05/30] fix: GPR curation for Transport reactions (2) --- model/Human-GEM.yml | 51 ++++++++++----------------------------------- 1 file changed, 11 insertions(+), 40 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..e7e4134c 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -168497,7 +168497,6 @@ - MAM02450e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000059804" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -169238,7 +169237,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117834" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -169546,7 +169544,6 @@ - MAM02578e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000066230 or ENSG00000090020 or ENSG00000115616" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -169748,7 +169745,7 @@ - MAM02938e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000113396 or ENSG00000130304 or ENSG00000143554 or ENSG00000167114" + - gene_reaction_rule: "ENSG00000130304 or ENSG00000143554 or ENSG00000167114" - rxnFrom: "HMRdatabase" - eccodes: "6.2.1.-" - subsystem: @@ -170097,7 +170094,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170113,7 +170110,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170129,7 +170126,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170145,7 +170142,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170161,7 +170158,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170209,7 +170206,7 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170225,7 +170222,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170241,7 +170238,7 @@ - MAM02896e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170257,7 +170254,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000131389 or ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000131389 or ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -172739,7 +172736,7 @@ - MAM01252m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000152779 or ENSG00000165449 or ENSG00000174327" + - gene_reaction_rule: "ENSG00000152779 or ENSG00000174327" - rxnFrom: "HMRdatabase" - references: "PMID:11004451;PMID:911815" - subsystem: @@ -172930,7 +172927,6 @@ - MAM02183m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100075" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173049,7 +173045,6 @@ - MAM02661m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100075" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173554,7 +173549,6 @@ - MAM01637m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173569,7 +173563,6 @@ - MAM01680m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173584,7 +173577,6 @@ - MAM01754m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173614,7 +173606,6 @@ - MAM01680m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173629,7 +173620,6 @@ - MAM01754m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173659,7 +173649,6 @@ - MAM01688m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173674,7 +173663,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173689,7 +173677,6 @@ - MAM01642m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173704,7 +173691,6 @@ - MAM01688m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173719,7 +173705,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -174031,7 +174016,6 @@ - MAM01643m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174073,7 +174057,6 @@ - MAM01754m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174087,7 +174070,6 @@ - MAM01754m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174101,7 +174083,6 @@ - MAM01754m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174143,7 +174124,6 @@ - MAM01747m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174171,7 +174151,6 @@ - MAM01747m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174185,7 +174164,6 @@ - MAM01680m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174213,7 +174191,6 @@ - MAM01643m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174241,7 +174218,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174255,7 +174231,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174269,7 +174244,6 @@ - MAM01643m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174297,7 +174271,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174311,7 +174284,6 @@ - MAM01753m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174325,7 +174297,6 @@ - MAM01753m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" From 7477f6d7332c5a19aaf646a68de29825a2be025b Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 30 Dec 2024 08:35:02 +0000 Subject: [PATCH 06/30] 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..33b081a5 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 #952** (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 e1f77e47471650a1adafc62d1bd633d6eacf1c9b Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 30 Dec 2024 18:05:43 +0800 Subject: [PATCH 07/30] Fix: GPR curation for transport reactions (3) --- model/Human-GEM.yml | 65 +++++++++++---------------------------------- model/genes.tsv | 2 -- 2 files changed, 16 insertions(+), 51 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..89fecc02 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -147989,7 +147989,7 @@ - MAM03134e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000113396 or ENSG00000121769 or ENSG00000130304 or ENSG00000135218 or ENSG00000143554 or ENSG00000145384 or ENSG00000163586 or ENSG00000164434 or ENSG00000164687 or ENSG00000167114 or ENSG00000170231 or ENSG00000170323 or ENSG00000197416 or ENSG00000205186" + - gene_reaction_rule: "ENSG00000121769 or ENSG00000130304 or ENSG00000135218 or ENSG00000143554 or ENSG00000145384 or ENSG00000163586 or ENSG00000164434 or ENSG00000164687 or ENSG00000167114 or ENSG00000170231 or ENSG00000170323 or ENSG00000197416 or ENSG00000205186" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -148152,7 +148152,6 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165029" - rxnFrom: "HMRdatabase" - references: "PMID:16858612" - subsystem: @@ -171079,7 +171078,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000012660 or ENSG00000026652 or ENSG00000100344 or ENSG00000102125 or ENSG00000111684 or ENSG00000123684 or ENSG00000125505 or ENSG00000141446 or ENSG00000143797 or ENSG00000151093 or ENSG00000160216 or ENSG00000169359 or ENSG00000170522 or ENSG00000171320 or ENSG00000176454 or ENSG00000186792 or ENSG00000197977" + - gene_reaction_rule: "ENSG00000151093 or ENSG00000169359 or ENSG00000171320" - rxnFrom: "HMRdatabase" - references: "PMID:14598172;PMID:6361812;PMID:8132483" - subsystem: @@ -174339,7 +174338,6 @@ - MAM01754m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174367,7 +174365,6 @@ - MAM01753m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174381,7 +174378,6 @@ - MAM01753m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174395,7 +174391,6 @@ - MAM01754m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174409,7 +174404,6 @@ - MAM01753m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174423,7 +174417,6 @@ - MAM01645m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174437,7 +174430,6 @@ - MAM01754m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174451,7 +174443,6 @@ - MAM01680m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174479,7 +174470,6 @@ - MAM01645m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174493,7 +174483,6 @@ - MAM01645m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174507,7 +174496,6 @@ - MAM01688m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174535,7 +174523,6 @@ - MAM01754m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174549,7 +174536,6 @@ - MAM01747m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174563,7 +174549,6 @@ - MAM01688m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174577,7 +174562,6 @@ - MAM01688m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174591,7 +174575,6 @@ - MAM01680m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174605,7 +174588,6 @@ - MAM01642m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -175437,7 +175419,7 @@ - MAM02774x: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" + - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000185825" - rxnFrom: "HMRdatabase" - references: "PMID:18619829" - subsystem: @@ -175455,7 +175437,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" + - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000184343 or ENSG00000185825" - rxnFrom: "HMRdatabase" - references: "PMID:18619829" - subsystem: @@ -175473,7 +175455,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" + - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" - rxnFrom: "HMRdatabase" - references: "PMID:18619829" - subsystem: @@ -175491,7 +175473,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" + - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130822 or ENSG00000185825" - rxnFrom: "HMRdatabase" - references: "PMID:18619829" - subsystem: @@ -175509,7 +175491,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" + - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130822 or ENSG00000185825" - rxnFrom: "HMRdatabase" - references: "PMID:18619829" - subsystem: @@ -175811,7 +175793,7 @@ - MAM02819x: 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" - subsystem: @@ -177267,7 +177249,6 @@ - MAM01365l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000123643" - 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: @@ -177305,7 +177286,6 @@ - MAM01628l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000123643" - rxnFrom: "HMRdatabase" - references: "PMID:911815" - subsystem: @@ -177447,7 +177427,7 @@ - MAM03101l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000104044 or ENSG00000123643" + - gene_reaction_rule: "ENSG00000104044" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -179350,7 +179330,7 @@ - MAM03114g: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117620 or ENSG00000130958 or ENSG00000205060" + - gene_reaction_rule: "ENSG00000205060" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -179634,7 +179614,6 @@ - MAM01588g: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000107819" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -180088,7 +180067,7 @@ - MAM01252g: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000152779 or ENSG00000165449 or ENSG00000174327" + - gene_reaction_rule: "ENSG00000174327" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -180185,7 +180164,7 @@ - MAM03114g: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117620 or ENSG00000130958 or ENSG00000205060" + - gene_reaction_rule: "ENSG00000130958" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -188603,7 +188582,6 @@ - MAM02039e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135917" - rxnFrom: "Recon3D" - references: "PMID:14770311;PMID:15623830" - subsystem: @@ -192898,7 +192876,6 @@ - MAM02403m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103569" - rxnFrom: "Recon3D" - eccodes: "2.3.1.21" - references: "PMID:12096044;PMID:16126913;PMID:9733774" @@ -211283,7 +211260,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115902" - rxnFrom: "Recon3D" - references: "PMID:14502423;PMID:11824937" - subsystem: @@ -211960,7 +211936,6 @@ - MAM02319e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149150 or ENSG00000167703" - rxnFrom: "Recon3D" - subsystem: - "Transport reactions" @@ -212902,7 +212877,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000005471 or ENSG00000023839 or ENSG00000103222 or ENSG00000114770 or ENSG00000118777 or ENSG00000121270 or ENSG00000125257" + - gene_reaction_rule: "ENSG00000023839 or ENSG00000103222 or ENSG00000114770 or ENSG00000118777 or ENSG00000125257" - rxnFrom: "Recon3D" - subsystem: - "Transport reactions" @@ -236985,7 +236960,6 @@ - MAM02763e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085563" - rxnFrom: "Recon3D" - references: "PMID:15290871" - subsystem: @@ -237557,7 +237531,6 @@ - MAM02823e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000112759 or ENSG00000174669" - rxnFrom: "Recon3D" - references: "PMID:20956085" - subsystem: @@ -237775,7 +237748,7 @@ - MAM01417e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000015520 or ENSG00000073060 or ENSG00000135218" + - gene_reaction_rule: "ENSG00000073060 or ENSG00000135218" - rxnFrom: "Recon3D" - subsystem: - "Transport reactions" @@ -242644,7 +242617,7 @@ - MAM03512e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000023839 or ENSG00000073734 or ENSG00000108846 or ENSG00000125257" + - gene_reaction_rule: "ENSG00000023839 or ENSG00000108846 or ENSG00000125257" - rxnFrom: "Recon3D" - references: "PMID:25210150;PMID:26579438;PMID:23506869" - subsystem: @@ -242660,7 +242633,7 @@ - MAM03512e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111700 or ENSG00000134538 or ENSG00000163959 or ENSG00000186198" + - gene_reaction_rule: "ENSG00000111700 or ENSG00000134538" - rxnFrom: "Recon3D" - references: "PMID:25210150;PMID:26579438" - subsystem: @@ -262020,9 +261993,6 @@ - !!omap - id: "ENSG00000102100" - name: "SLC35A2" - - !!omap - - id: "ENSG00000102125" - - name: "TAZ" - !!omap - id: "ENSG00000102144" - name: "PGK1" @@ -263220,9 +263190,6 @@ - !!omap - id: "ENSG00000117600" - name: "PLPPR4" - - !!omap - - id: "ENSG00000117620" - - name: "SLC35A3" - !!omap - id: "ENSG00000117643" - name: "MAN1C1" diff --git a/model/genes.tsv b/model/genes.tsv index 67ebb53b..50480c3c 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -515,7 +515,6 @@ "ENSG00000102043" "ENST00000374852;ENST00000478487;ENST00000462447;ENST00000461403" "ENSP00000363985" "Q96EF0" "MTMR8" "55613" "myotubularin related protein 8" "FLJ20126" "Nucleus" "SwissProt" "ENSG00000102078" "ENST00000543953;ENST00000612248;ENST00000495156;ENST00000464342;ENST00000464184;ENST00000424447;ENST00000545805;ENST00000218197;ENST00000467496;ENST00000339231;ENST00000361980;ENST00000478474;ENST00000467346;ENST00000471795;ENST00000465988" "ENSP00000445225;ENSP00000477981;ENSP00000402578;ENSP00000444642;ENSP00000218197;ENSP00000342797;ENSP00000354455" "O95258" "SLC25A14" "9016" "solute carrier family 25 member 14" "BMCP1;UCP5" "Mitochondria" "CellAtlas" "ENSG00000102100" "ENST00000635285;ENST00000247138;ENST00000635460;ENST00000376529;ENST00000635628;ENST00000376521;ENST00000445167;ENST00000413561;ENST00000376515;ENST00000635589;ENST00000616181;ENST00000452555;ENST00000446885;ENST00000635238;ENST00000634665;ENST00000635015;ENST00000376512;ENST00000634461" "ENSP00000489484;ENSP00000247138;ENSP00000489339;ENSP00000365712;ENSP00000489613;ENSP00000365704;ENSP00000402726;ENSP00000393233;ENSP00000365698;ENSP00000489197;ENSP00000478617;ENSP00000416002;ENSP00000415518;ENSP00000489515;ENSP00000489356;ENSP00000489089;ENSP00000365695;ENSP00000489440" "P78381" "SLC35A2" "7355" "solute carrier family 35 member A2" "UGALT;UGAT;UGT;UGT1;UGT2;UGTL" "Golgi apparatus" "SwissProt;CellAtlas" -"ENSG00000102125" "ENST00000613634;ENST00000612460;ENST00000601016;ENST00000613002;ENST00000652682;ENST00000475699;ENST00000615986;ENST00000617701;ENST00000620808;ENST00000615658;ENST00000614595;ENST00000612012;ENST00000652476;ENST00000369776;ENST00000621647;ENST00000652685;ENST00000439735;ENST00000616020;ENST00000476800;ENST00000652358;ENST00000652390;ENST00000483674;ENST00000426231;ENST00000483780;ENST00000476679;ENST00000652354;ENST00000479875;ENST00000470127;ENST00000652644;ENST00000494912;ENST00000498029;ENST00000651139" "ENSP00000481037;ENSP00000469981;ENSP00000478154;ENSP00000498288;ENSP00000419854;ENSP00000480133;ENSP00000481645;ENSP00000479311;ENSP00000482070;ENSP00000358791;ENSP00000398193;ENSP00000483636;ENSP00000498464;ENSP00000498858;ENSP00000406257;ENSP00000498734;ENSP00000498940;ENSP00000498496;ENSP00000498957" "Q16635" "TAZ" "6901" "tafazzin" "BTHS;CMD3A;EFE;EFE2;G4.5;TAZ1;XAP-2" "Cytosol;Inner mitochondria" "SwissProt" "ENSG00000102144" "ENST00000644362;ENST00000477335;ENST00000491291;ENST00000373316;ENST00000474281;ENST00000476531" "ENSP00000496140;ENSP00000362413" "P00558" "PGK1" "5230" "phosphoglycerate kinase 1" "" "Cytosol" "SwissProt" "ENSG00000102172" "ENST00000404933;ENST00000379404;ENST00000478094;ENST00000457085" "ENSP00000385746;ENSP00000368714;ENSP00000407366" "P52788" "SMS" "6611" "spermine synthase" "MRSR;SPMSY;SpS;SRS" "Cytosol;Nucleus" "CellAtlas" "ENSG00000102226" "ENST00000478596;ENST00000377107;ENST00000469080;ENST00000377080;ENST00000377078;ENST00000489111;ENST00000489030;ENST00000480104;ENST00000488848;ENST00000497179;ENST00000467378;ENST00000218348" "ENSP00000366311;ENSP00000366282;ENSP00000366279;ENSP00000218348" "P51784" "USP11" "8237" "ubiquitin specific peptidase 11" "UHX1" "Nucleus;Cytosol" "SwissProt;CellAtlas" @@ -909,7 +908,6 @@ "ENSG00000117592" "ENST00000340385;ENST00000460950;ENST00000470017" "ENSP00000342026" "P30041" "PRDX6" "9588" "peroxiredoxin 6" "1-Cys;aiPLA2;AOP2;KIAA0106;MGC46173;NSGPx;p29;PRX" "Cytosol;Lysosome" "SwissProt;CellAtlas" "ENSG00000117594" "ENST00000615289;ENST00000261465;ENST00000367027;ENST00000367028" "ENSP00000478430;ENSP00000261465;ENSP00000355994;ENSP00000355995" "P28845" "HSD11B1" "3290" "hydroxysteroid 11-beta dehydrogenase 1" "HSD11;HSD11B;SDR26C1" "Endoplasmic reticulum" "SwissProt" "ENSG00000117600" "ENST00000370185;ENST00000457765;ENST00000370184" "ENSP00000359204;ENSP00000394913" "Q7Z2D5" "PLPPR4" "9890" "phospholipid phosphatase related 4" "KIAA0455;LPPR4;PHP1;PRG-1" "Cell membrane" "DeepLoc2" -"ENSG00000117620" "ENST00000638371;ENST00000533028;ENST00000427993;ENST00000639221;ENST00000638336;ENST00000639807;ENST00000640715;ENST00000465289;ENST00000640726;ENST00000639994;ENST00000638988;ENST00000640178;ENST00000640360;ENST00000640732;ENST00000638929;ENST00000640600;ENST00000639088;ENST00000638338;ENST00000638876;ENST00000370155;ENST00000370153;ENST00000532693;ENST00000422078;ENST00000639148" "ENSP00000491146;ENSP00000433849;ENSP00000414947;ENSP00000492169;ENSP00000491145;ENSP00000490964;ENSP00000492801;ENSP00000418527;ENSP00000492128;ENSP00000492135;ENSP00000492681;ENSP00000491771;ENSP00000491598;ENSP00000492771;ENSP00000491789;ENSP00000492308;ENSP00000491533;ENSP00000491185;ENSP00000359174;ENSP00000359172;ENSP00000436938;ENSP00000491383" "Q9Y2D2" "SLC35A3" "23443" "solute carrier family 35 member A3" "" "Golgi apparatus" "SwissProt" "ENSG00000117643" "ENST00000374332;ENST00000611903;ENST00000263979;ENST00000473891;ENST00000374329;ENST00000496532;ENST00000475314;ENST00000487493" "ENSP00000363452;ENSP00000482317;ENSP00000263979;ENSP00000363449" "Q9NR34" "MAN1C1" "57134" "mannosidase alpha class 1C member 1" "HMIC" "Golgi apparatus;Nucleus" "SwissProt;CellAtlas" "ENSG00000117682" "ENST00000434391;ENST00000427245;ENST00000527611;ENST00000374186;ENST00000525682;ENST00000236342;ENST00000526219;ENST00000374185;ENST00000487944;ENST00000360009;ENST00000533087;ENST00000531312;ENST00000525165;ENST00000525326;ENST00000525546;ENST00000528557;ENST00000526278;ENST00000436153;ENST00000529688;ENST00000530781;ENST00000531955;ENST00000525410;ENST00000430232;ENST00000431933;ENST00000416052" "ENSP00000403529;ENSP00000399177;ENSP00000434984;ENSP00000236342;ENSP00000434219;ENSP00000363300;ENSP00000353104;ENSP00000436119;ENSP00000436764;ENSP00000434185;ENSP00000431407;ENSP00000433976;ENSP00000405604;ENSP00000433491;ENSP00000397584;ENSP00000399781;ENSP00000393961" "Q86SQ9" "DHDDS" "79947" "dehydrodolichyl diphosphate synthase subunit" "DS;FLJ13102;hCIT;HDS;RP59" "Endoplasmic reticulum" "SwissProt" "ENSG00000117834" "ENST00000425816;ENST00000533824;ENST00000438567;ENST00000236495;ENST00000493837;ENST00000441260;ENST00000527929;ENST00000525901;ENST00000532322;ENST00000471020" "ENSP00000404982;ENSP00000431900;ENSP00000401730;ENSP00000236495;ENSP00000399991;ENSP00000431196" "Q2M3M2" "SLC5A9" "200010" "solute carrier family 5 member 9" "SGLT4" "Cytosol" "CellAtlas" From 21400800751dbf82bd599c1972fcb7a7f1cd63ef Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 30 Dec 2024 10:49:37 +0000 Subject: [PATCH 08/30] 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..4e381ab0 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 #953** (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 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 09/30] 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 10/30] 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 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 11/30] 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 12/30] 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 1f8445cff964675c0c3d7671639e4db1395f2222 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 30 Dec 2024 21:16:50 +0800 Subject: [PATCH 13/30] fix: GPR curation for transport reactions (6) --- model/Human-GEM.yml | 62 +++++++++++++++++---------------------------- model/genes.tsv | 1 - 2 files changed, 23 insertions(+), 40 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..0818cc8a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -149959,7 +149959,7 @@ - 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: @@ -150129,7 +150129,7 @@ - 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: @@ -150461,7 +150461,6 @@ - MAM02170e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000169710" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.85" - references: "PMID:1550832;PMID:8438778" @@ -151475,7 +151474,7 @@ - MAM01986e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000164363 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000149150 or ENSG00000164363" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151488,7 +151487,7 @@ - MAM01307e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000155465" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151501,7 +151500,7 @@ - MAM01975e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151514,7 +151513,7 @@ - MAM02896e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000149150 or ENSG00000155465" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151527,7 +151526,7 @@ - MAM03089e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151540,7 +151539,7 @@ - MAM02724e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000112394 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151553,7 +151552,7 @@ - MAM01628e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000130876 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151566,7 +151565,7 @@ - MAM02360e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151579,7 +151578,7 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003989 or ENSG00000092068 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "ENSG00000092068 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151592,7 +151591,7 @@ - MAM01369e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151605,7 +151604,7 @@ - MAM03135e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151618,7 +151617,7 @@ - MAM02993e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -155080,7 +155079,7 @@ - MAM02724e: 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: @@ -155284,7 +155283,7 @@ - MAM02896e: -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: @@ -155879,7 +155878,7 @@ - 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: @@ -156015,7 +156014,6 @@ - MAM02724e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157647,7 +157645,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158225,7 +158222,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -161329,7 +161325,7 @@ - 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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161569,7 +161565,7 @@ - MAM02833e: -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: @@ -166585,7 +166581,6 @@ - MAM01517g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000174669" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -170177,7 +170172,7 @@ - MAM02519e: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196517 or ENSG00000268104" + - gene_reaction_rule: "ENSG00000268104" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -173644,7 +173639,6 @@ - MAM01642m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - references: "PMID:14598172" - subsystem: @@ -173734,7 +173728,6 @@ - MAM02914m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000160190" - rxnFrom: "HMRdatabase" - references: "PMID:12811562" - subsystem: @@ -174045,7 +174038,6 @@ - MAM01680m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174283,7 +174275,6 @@ - MAM01756m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -174521,7 +174512,6 @@ - MAM01747m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125454" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -177383,7 +177373,6 @@ - MAM02471l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000123643" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -177498,7 +177487,6 @@ - MAM02993l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000123643" - rxnFrom: "HMRdatabase" - references: "PMID:911815" - subsystem: @@ -179568,7 +179556,7 @@ - MAM02200g: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000065923 or ENSG00000197818" + - gene_reaction_rule: "ENSG00000065923" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -210686,7 +210674,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115902" - rxnFrom: "Recon3D" - references: "PMID:14502423;PMID:11824937" - subsystem: @@ -212934,7 +212921,7 @@ - MAM02946e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000137204 or ENSG00000149452 or ENSG00000168065" + - gene_reaction_rule: "ENSG00000137204 or ENSG00000149452" - rxnFrom: "Recon3D" - subsystem: - "Transport reactions" @@ -215404,7 +215391,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000073734 or ENSG00000108846 or ENSG00000121270" + - gene_reaction_rule: "ENSG00000073734 or ENSG00000108846" - rxnFrom: "Recon3D" - subsystem: - "Transport reactions" @@ -265968,9 +265955,6 @@ - !!omap - id: "ENSG00000160179" - name: "ABCG1" - - !!omap - - id: "ENSG00000160190" - - name: "SLC37A1" - !!omap - id: "ENSG00000160191" - name: "PDE9A" diff --git a/model/genes.tsv b/model/genes.tsv index 67ebb53b..e4359a4b 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -1816,7 +1816,6 @@ "ENSG00000160014" "ENST00000391918;ENST00000597743;ENST00000477244;ENST00000598871;ENST00000291295;ENST00000595072;ENST00000602169;ENST00000594523;ENST00000597868;ENST00000599839;ENST00000596362;ENST00000482455;ENST00000486500" "ENSP00000375785;ENSP00000470308;ENSP00000470502;ENSP00000291295;ENSP00000499372;ENSP00000468877;ENSP00000471225;ENSP00000472141" "P0DP25" "CALM3" "808" "calmodulin 3" "PHKD" "Cytosol" "SwissProt" "ENSG00000160087" "ENST00000450390;ENST00000349431;ENST00000400929;ENST00000464036;ENST00000360466;ENST00000400930;ENST00000467339;ENST00000473215;ENST00000435198;ENST00000509720;ENST00000491779;ENST00000466752;ENST00000503294;ENST00000477894;ENST00000471154;ENST00000422076;ENST00000502382;ENST00000461142;ENST00000488418;ENST00000347370" "ENSP00000407565;ENSP00000305826;ENSP00000383718;ENSP00000423880;ENSP00000353653;ENSP00000383719;ENSP00000427024;ENSP00000393301;ENSP00000425419;ENSP00000422103;ENSP00000425543;ENSP00000423480;ENSP00000401898;ENSP00000424342;ENSP00000427244;ENSP00000344857" "Q8N2K1" "UBE2J2" "118424" "ubiquitin conjugating enzyme E2 J2" "NCUBE2;Ubc6p" "Endoplasmic reticulum" "SwissProt" "ENSG00000160179" "ENST00000398457;ENST00000462050;ENST00000347800;ENST00000450121;ENST00000361802;ENST00000398449;ENST00000343687;ENST00000398437;ENST00000472587;ENST00000467818;ENST00000496783" "ENSP00000381475;ENSP00000291524;ENSP00000414541;ENSP00000354995;ENSP00000381467;ENSP00000339744;ENSP00000381464" "P45844" "ABCG1" "9619" "ATP binding cassette subfamily G member 1" "ABC8" "Endoplasmic reticulum;Golgi apparatus" "SwissProt;CellAtlas" -"ENSG00000160190" "ENST00000454800;ENST00000419522;ENST00000398341;ENST00000484887;ENST00000352133;ENST00000471277;ENST00000398343;ENST00000487951;ENST00000496416" "ENSP00000410129;ENSP00000381383;ENSP00000344648;ENSP00000381385" "P57057" "SLC37A1" "54020" "solute carrier family 37 member 1" "" "Cell membrane;Endoplasmic reticulum" "DeepLoc2" "ENSG00000160191" "ENST00000291539;ENST00000460905;ENST00000472401;ENST00000335512;ENST00000470987;ENST00000490803;ENST00000486902;ENST00000328862;ENST00000335440;ENST00000380328;ENST00000398225;ENST00000398227;ENST00000398229;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000460989;ENST00000462571;ENST00000467403;ENST00000468805;ENST00000495521;ENST00000497805;ENST00000349112;ENST00000398224;ENST00000467162;ENST00000495343;ENST00000489319;ENST00000466472" "ENSP00000291539;ENSP00000335242;ENSP00000328699;ENSP00000335365;ENSP00000369685;ENSP00000381281;ENSP00000381283;ENSP00000381285;ENSP00000381287;ENSP00000381289;ENSP00000381291;ENSP00000344730;ENSP00000381280" "O76083" "PDE9A" "5152" "phosphodiesterase 9A" "" "Endoplasmic reticulum;Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000160194" "ENST00000460259;ENST00000340344;ENST00000354250;ENST00000460740" "ENSP00000342895;ENSP00000346196" "P56181" "NDUFV3" "4731" "NADH:ubiquinone oxidoreductase subunit V3" "CI-10k" "Inner mitochondria" "SwissProt;CellAtlas" "ENSG00000160200" "ENST00000461686;ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000451248;ENST00000462349;ENST00000491776;ENST00000458223;ENST00000430013;ENST00000496485;ENST00000486098;ENST00000441030;ENST00000470912;ENST00000465732;ENST00000488526;ENST00000478709" "ENSP00000381225;ENSP00000381231;ENSP00000352643;ENSP00000344460;ENSP00000402823;ENSP00000408014;ENSP00000405929;ENSP00000388235" "P35520" "CBS" "875" "cystathionine beta-synthase" "HIP4" "Nucleus;Cytosol" "SwissProt;CellAtlas" From bfdf3a0aec9971836813443527f8d45e3c355eac Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 30 Dec 2024 13:39:15 +0000 Subject: [PATCH 14/30] 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..7bce8903 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 #956** (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 6d672e4b841849e5d8e3da743f6ba89ba6e10b3f Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 30 Dec 2024 22:08:09 +0800 Subject: [PATCH 15/30] fix: GPR curation for transport reactions (7) --- model/Human-GEM.yml | 58 +++++++++++++++++++-------------------------- model/genes.tsv | 1 - 2 files changed, 25 insertions(+), 34 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..4da4194a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -151631,7 +151631,7 @@ - MAM02184e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703" + - gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404" - subsystem: @@ -151879,7 +151879,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003989 or ENSG00000072041 or ENSG00000105281 or ENSG00000111371 or ENSG00000115902 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358" + - gene_reaction_rule: "ENSG00000072041 or ENSG00000105281 or ENSG00000111371 or ENSG00000115902 or ENSG00000134294 or ENSG00000139209 or ENSG00000174358" - rxnFrom: "HMRdatabase" - references: "PMID:12845534;PMID:10823827;PMID:11452978;PMID:15632147" - subsystem: @@ -151971,7 +151971,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003989 or ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000168003 or ENSG00000174358" + - gene_reaction_rule: "ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000168003 or ENSG00000174358" - rxnFrom: "HMRdatabase" - references: "PMID:12930836;PMID:17322374" - subsystem: @@ -152029,7 +152029,7 @@ - MAM02724e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003989 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358" + - gene_reaction_rule: "ENSG00000134294 or ENSG00000139209 or ENSG00000174358" - rxnFrom: "HMRdatabase" - subsystem: - "Transport reactions" @@ -152118,7 +152118,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000162383 or ENSG00000174358 or ENSG00000178537" + - gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000162383" - rxnFrom: "HMRdatabase" - references: "PMID:10823827" - subsystem: @@ -152469,7 +152469,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117834 or ENSG00000140675 or ENSG00000148942 or ENSG00000154025 or ENSG00000158865" + - gene_reaction_rule: "ENSG00000117834 or ENSG00000140675 or ENSG00000154025 or ENSG00000158865" - rxnFrom: "HMRdatabase" - references: "PMID:12748858" - subsystem: @@ -153598,7 +153598,7 @@ - MAM03089e: -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: @@ -153613,7 +153613,7 @@ - MAM03135e: -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: @@ -153628,7 +153628,7 @@ - MAM03089e: -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: @@ -153643,7 +153643,7 @@ - MAM03089e: -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: @@ -153658,7 +153658,7 @@ - MAM03089e: -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: @@ -153688,7 +153688,7 @@ - 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: @@ -153703,7 +153703,7 @@ - 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: @@ -153718,7 +153718,7 @@ - MAM02770e: -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: @@ -153733,7 +153733,7 @@ - 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: @@ -153748,7 +153748,7 @@ - MAM03135e: -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: @@ -153763,7 +153763,7 @@ - MAM02993e: -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: @@ -153793,7 +153793,7 @@ - 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: @@ -153883,7 +153883,7 @@ - MAM03101e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257 or ENSG00000188687" + - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154153,7 +154153,6 @@ - MAM02993e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154168,7 +154167,6 @@ - MAM02770e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154655,7 +154653,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154689,7 +154686,6 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -154706,7 +154702,7 @@ - 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: @@ -154774,7 +154770,7 @@ - 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: @@ -154791,7 +154787,7 @@ - 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: @@ -154825,7 +154821,7 @@ - MAM02724e: 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: @@ -154859,7 +154855,7 @@ - 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: @@ -154876,7 +154872,7 @@ - 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: @@ -154927,7 +154923,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000103257" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -265350,9 +265345,6 @@ - !!omap - id: "ENSG00000148834" - name: "GSTO1" - - !!omap - - id: "ENSG00000148942" - - name: "SLC5A12" - !!omap - id: "ENSG00000149016" - name: "TUT1" diff --git a/model/genes.tsv b/model/genes.tsv index 67ebb53b..d381dfb3 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -1611,7 +1611,6 @@ "ENSG00000148795" "ENST00000638971;ENST00000638190;ENST00000369887;ENST00000640633;ENST00000638272;ENST00000639393;ENST00000469683;ENST00000489268" "ENSP00000492313;ENSP00000492539;ENSP00000358903;ENSP00000491508;ENSP00000492651" "P05093" "CYP17A1" "1586" "cytochrome P450 family 17 subfamily A member 1" "CPT7;CYP17;P450C17;S17AH" "Endoplasmic reticulum" "SwissProt" "ENSG00000148832" "ENST00000357296;ENST00000278060;ENST00000356306;ENST00000476834;ENST00000480071;ENST00000483211;ENST00000529585;ENST00000368535;ENST00000528127;ENST00000530555" "ENSP00000349847;ENSP00000278060;ENSP00000348654;ENSP00000432737;ENSP00000435514;ENSP00000434550;ENSP00000432517" "Q6QHF9" "PAOX" "196743" "polyamine oxidase" "PAO" "Peroxisome;Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000148834" "ENST00000470554;ENST00000493946;ENST00000369713;ENST00000445155;ENST00000432659;ENST00000539281;ENST00000369710" "ENSP00000358727;ENSP00000406708;ENSP00000405325;ENSP00000441488;ENSP00000358724" "P78417" "GSTO1" "9446" "glutathione S-transferase omega 1" "GSTTLp28;P28" "Cytosol" "SwissProt" -"ENSG00000148942" "ENST00000396005;ENST00000527405;ENST00000280467;ENST00000533617;ENST00000528822" "ENSP00000379326;ENSP00000436011;ENSP00000280467;ENSP00000435053" "Q1EHB4" "SLC5A12" "159963" "solute carrier family 5 member 12" "MGC52019;SMCT2" "Nucleus" "CellAtlas" "ENSG00000149016" "ENST00000308436;ENST00000476907;ENST00000469480;ENST00000463241;ENST00000278279;ENST00000494385;ENST00000478537" "ENSP00000308000;ENSP00000419607;ENSP00000278279;ENSP00000420739;ENSP00000419792" "Q9H6E5" "TUT1" "64852" "terminal uridylyl transferase 1, U6 snRNA-specific" "FLJ21850;FLJ22267;FLJ22347;PAPD2;RBM21;TENT1;TUTase" "Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000149084" "ENST00000278353;ENST00000527433;ENST00000531185;ENST00000636007;ENST00000395700;ENST00000636722;ENST00000637401;ENST00000638034;ENST00000527213;ENST00000532178;ENST00000533090;ENST00000533802;ENST00000534053;ENST00000525736" "ENSP00000278353;ENSP00000490749;ENSP00000436582;ENSP00000490822;ENSP00000379052;ENSP00000490003;ENSP00000490421;ENSP00000490701" "Q53GQ0" "HSD17B12" "51144" "hydroxysteroid 17-beta dehydrogenase 12" "KAR;SDR12C1" "Endoplasmic reticulum" "SwissProt" "ENSG00000149089" "ENST00000532428;ENST00000395787;ENST00000527830" "ENSP00000474191;ENSP00000379133" "Q96GX9" "APIP" "51074" "APAF1 interacting protein" "APIP2;CGI-29;Mmrp19" "Nucleus;Cytosol" "SwissProt;CellAtlas" From c700a165a61746d39b85a5bb58064ae1048a5647 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 30 Dec 2024 14:26:18 +0000 Subject: [PATCH 16/30] 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..0cfcbceb 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 #957** (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 5948d301676f127cc4b39745e87cc39200b1ca53 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 31 Dec 2024 08:52:11 +0800 Subject: [PATCH 17/30] fix: GPR curation for transport reactions (8) --- model/Human-GEM.yml | 61 +++++++++++++++++---------------------------- 1 file changed, 23 insertions(+), 38 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..33ca679b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -154978,7 +154978,7 @@ - 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: @@ -154995,7 +154995,7 @@ - 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: @@ -155267,7 +155267,7 @@ - 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: @@ -155301,7 +155301,7 @@ - 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: @@ -155335,7 +155335,7 @@ - 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: @@ -155352,7 +155352,7 @@ - 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: @@ -155403,7 +155403,7 @@ - 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: @@ -155420,7 +155420,7 @@ - MAM02896e: -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: @@ -155437,7 +155437,7 @@ - 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: @@ -155454,7 +155454,7 @@ - MAM02993e: 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: @@ -155471,7 +155471,7 @@ - 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: @@ -155522,7 +155522,7 @@ - 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: @@ -155590,7 +155590,7 @@ - MAM02724e: 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: @@ -155641,7 +155641,7 @@ - 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: @@ -155658,7 +155658,7 @@ - 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: @@ -155692,7 +155692,7 @@ - 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: @@ -155726,7 +155726,7 @@ - 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: @@ -155828,7 +155828,7 @@ - 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: @@ -155845,7 +155845,7 @@ - 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: @@ -155862,7 +155862,7 @@ - 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: @@ -155930,7 +155930,7 @@ - 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: @@ -155964,7 +155964,7 @@ - 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: @@ -156066,7 +156066,6 @@ - MAM02896e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156083,7 +156082,6 @@ - MAM02724e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156202,7 +156200,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156219,7 +156216,6 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156270,7 +156266,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156287,7 +156282,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156355,7 +156349,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156406,7 +156399,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156423,7 +156415,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156457,7 +156448,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156474,7 +156464,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156491,7 +156480,6 @@ - MAM03101e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156627,7 +156615,6 @@ - MAM02724e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156644,7 +156631,6 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156712,7 +156698,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156729,7 +156714,7 @@ - MAM02993e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902 or ENSG00000151012" + - gene_reaction_rule: "ENSG00000105281 or ENSG00000115902" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: From 3f06a62ba3320f90187270fe4e1043840434c5ea Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Tue, 31 Dec 2024 01:00:29 +0000 Subject: [PATCH 18/30] 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..2db8e925 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 #958** (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 7b36c5c278d8a2968123d82edc832e23d493dd90 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 31 Dec 2024 09:18:12 +0800 Subject: [PATCH 19/30] fix: GPR curation for transport reactions (9) --- model/Human-GEM.yml | 62 ++++++--------------------------------------- 1 file changed, 8 insertions(+), 54 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..007b9568 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -156797,7 +156797,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156831,7 +156830,6 @@ - MAM02896e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156933,7 +156931,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -156967,7 +156964,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157001,7 +156997,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157052,7 +157047,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157086,7 +157080,6 @@ - MAM02896e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157171,7 +157164,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157188,7 +157180,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157205,7 +157196,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157222,7 +157212,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157256,7 +157245,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157273,7 +157261,6 @@ - MAM02770e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157307,7 +157294,7 @@ - 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: @@ -157324,7 +157311,7 @@ - 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: @@ -157358,7 +157345,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157392,7 +157378,6 @@ - MAM02724e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157426,7 +157411,7 @@ - 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: @@ -157443,7 +157428,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157477,7 +157461,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157511,7 +157494,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157579,7 +157561,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157596,7 +157577,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157613,7 +157593,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157664,7 +157643,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157681,7 +157659,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157715,7 +157692,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157732,7 +157708,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157749,7 +157724,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157766,7 +157740,6 @@ - MAM03135e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157817,7 +157790,7 @@ - MAM02993e: -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: @@ -157919,7 +157892,6 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157936,7 +157908,7 @@ - MAM02993e: -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: @@ -157970,7 +157942,6 @@ - MAM02993e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -157987,7 +157958,7 @@ - MAM02993e: -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: @@ -158004,7 +157975,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158021,7 +157991,6 @@ - MAM02993e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158055,7 +158024,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158072,7 +158040,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158106,7 +158073,6 @@ - MAM02896e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158157,7 +158123,6 @@ - MAM02724e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158174,7 +158139,6 @@ - MAM03101e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158191,7 +158155,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158208,7 +158171,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158242,7 +158204,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158259,7 +158220,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158327,7 +158287,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158378,7 +158337,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158480,7 +158438,6 @@ - MAM02770e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -158514,7 +158471,6 @@ - MAM03135e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -159398,7 +159354,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -159568,7 +159523,6 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064" - rxnFrom: "HMRdatabase" - references: "PMID:14770309;PMID:14770310" - subsystem: @@ -161138,7 +161092,7 @@ - MAM03157e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000104635 or ENSG00000110911 or ENSG00000138821 or ENSG00000139540 or ENSG00000141424 or ENSG00000141873 or ENSG00000143570 or ENSG00000147804 or ENSG00000165794 or ENSG00000196950" + - gene_reaction_rule: "ENSG00000104635 or ENSG00000110911 or ENSG00000138821 or ENSG00000139540 or ENSG00000141424 or ENSG00000141873 or ENSG00000143570 or ENSG00000147804 or ENSG00000165794 or ENSG00000196950" - rxnFrom: "HMRdatabase" - references: "PMID:14530970" - subsystem: @@ -161224,7 +161178,7 @@ - MAM02519e: -3 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103064 or ENSG00000158296" + - gene_reaction_rule: "ENSG00000158296" - rxnFrom: "HMRdatabase" - references: "PMID:12739168;PMID:12915942" - subsystem: From fff9d9a7bcfdf79b5c6d4d3f61e0daf18a719228 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Tue, 31 Dec 2024 01:25:27 +0000 Subject: [PATCH 20/30] 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..9289e6d4 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 #959** (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 cefffae7750565766fd5f4433b19f2a652e9a449 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 31 Dec 2024 09:45:39 +0800 Subject: [PATCH 21/30] fix: GPR curation for transport reactions (10) --- model/Human-GEM.yml | 68 ++++++++++++++++++++++----------------------- 1 file changed, 34 insertions(+), 34 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..03821aba 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -161269,7 +161269,7 @@ - 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: "ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161284,7 +161284,7 @@ - MAM01253e: -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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161299,7 +161299,7 @@ - MAM01833e: -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: "ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161314,7 +161314,7 @@ - MAM02772e: -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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161344,7 +161344,7 @@ - MAM02833e: -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: "ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161359,7 +161359,7 @@ - MAM01253e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161389,7 +161389,7 @@ - MAM01252e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161404,7 +161404,7 @@ - MAM01833e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161419,7 +161419,7 @@ - MAM02772e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161449,7 +161449,7 @@ - MAM01410e: -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 ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161464,7 +161464,7 @@ - MAM02833e: -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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161479,7 +161479,7 @@ - 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: @@ -161494,7 +161494,7 @@ - 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: "ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161509,7 +161509,7 @@ - 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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161524,7 +161524,7 @@ - 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: @@ -161539,7 +161539,7 @@ - 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: @@ -161554,7 +161554,7 @@ - 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: @@ -161584,7 +161584,7 @@ - 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: @@ -161599,7 +161599,7 @@ - MAM01306e: 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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161614,7 +161614,7 @@ - MAM01833e: -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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161629,7 +161629,7 @@ - MAM02772e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161644,7 +161644,7 @@ - MAM01306e: 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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161659,7 +161659,7 @@ - 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: @@ -161674,7 +161674,7 @@ - MAM01410e: -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: "ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161689,7 +161689,7 @@ - MAM02833e: -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: "ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161704,7 +161704,7 @@ - MAM01306e: -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 ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161719,7 +161719,7 @@ - MAM01306e: -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: "ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161734,7 +161734,7 @@ - MAM01833e: -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: "ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161749,7 +161749,7 @@ - MAM02772e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161764,7 +161764,7 @@ - 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: @@ -161779,7 +161779,7 @@ - MAM01410e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161794,7 +161794,7 @@ - MAM02833e: -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: "ENSG00000118596 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161809,7 +161809,7 @@ - MAM01252e: -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: "ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: @@ -161824,7 +161824,7 @@ - MAM02772e: -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: "ENSG00000155380 or ENSG00000168679 or ENSG00000170190" - rxnFrom: "HMRdatabase" - references: "PMID:12739169" - subsystem: From b9390d554587569440f74bbbce60d19626320049 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Tue, 31 Dec 2024 02:07:58 +0000 Subject: [PATCH 22/30] 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..6ab3bd38 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 #960** (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 23/30] 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 24/30] 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 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 25/30] 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 26/30] 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 From 58ada359f4793d908350daba1cb6e77d477a9f53 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:52:02 +0800 Subject: [PATCH 27/30] fix: GPR curation for Arachidonic acid metabolism --- model/Human-GEM.yml | 114 ++++++++++++++++++++++---------------------- 1 file changed, 57 insertions(+), 57 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..2dc65bb6 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -89442,7 +89442,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -89460,7 +89460,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -89478,7 +89478,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -89496,7 +89496,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -91982,7 +91982,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92000,7 +92000,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92018,7 +92018,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92036,7 +92036,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974 or ENSG00000162365 or ENSG00000187048" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974 or ENSG00000162365 or ENSG00000187048" - rxnFrom: "HMRdatabase" - eccodes: - "1.14.14.1" @@ -92056,7 +92056,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92074,7 +92074,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92092,7 +92092,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92110,7 +92110,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92128,7 +92128,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92146,7 +92146,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92164,7 +92164,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92181,7 +92181,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:8651708" @@ -92199,7 +92199,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:8651708" @@ -92235,7 +92235,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92252,7 +92252,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:8651708" @@ -92270,7 +92270,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:8651708" @@ -92306,7 +92306,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92323,7 +92323,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:8651708" @@ -92769,7 +92769,7 @@ - MAM00390c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92783,7 +92783,7 @@ - MAM02040c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92796,7 +92796,7 @@ - MAM00380c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -92810,7 +92810,7 @@ - MAM02040c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -93734,7 +93734,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000242110" + - gene_reaction_rule: "ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227" - rxnFrom: "HMRdatabase" - eccodes: - "1.1.1.35" @@ -94927,7 +94927,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - subsystem: - "Leukotriene metabolism" @@ -94942,7 +94942,7 @@ - MAM02555m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - subsystem: - "Leukotriene metabolism" @@ -94957,7 +94957,7 @@ - MAM02555r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - subsystem: - "Leukotriene metabolism" @@ -94972,7 +94972,7 @@ - MAM02555x: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - subsystem: - "Leukotriene metabolism" @@ -94987,7 +94987,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95004,7 +95004,7 @@ - MAM02555m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95021,7 +95021,7 @@ - MAM02555r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95038,7 +95038,7 @@ - MAM02555x: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95358,7 +95358,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95375,7 +95375,7 @@ - MAM02555m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95392,7 +95392,7 @@ - MAM02555r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -95409,7 +95409,7 @@ - MAM02555x: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9694844" @@ -109909,7 +109909,7 @@ - MAM02630r: -2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - subsystem: - "Steroid metabolism" @@ -109926,7 +109926,7 @@ - MAM02969r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - subsystem: - "Steroid metabolism" @@ -110079,7 +110079,7 @@ - MAM02969r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -111939,7 +111939,7 @@ - MAM02969c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -111955,7 +111955,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -111973,7 +111973,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -111990,7 +111990,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -112006,7 +112006,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -112025,7 +112025,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - subsystem: @@ -112097,7 +112097,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9380738" @@ -112116,7 +112116,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:9380738" @@ -112298,7 +112298,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:12038704;PMID:10337002" @@ -112317,7 +112317,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:12038704;PMID:10337002" @@ -138170,7 +138170,7 @@ - MAM02833c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" - references: "PMID:12091498;PMID:10823918" @@ -202304,7 +202304,7 @@ - MAM02630r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "Recon3D" - eccodes: "1.14.14.1" - references: "PMID:8651708" @@ -203880,7 +203880,7 @@ - MAM03388r: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "Recon3D" - eccodes: "1.14.14.1" - subsystem: @@ -203917,7 +203917,7 @@ - MAM03383r: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "Recon3D" - eccodes: "1.14.14.1" - subsystem: @@ -203999,7 +203999,7 @@ - MAM03385r: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnFrom: "Recon3D" - eccodes: "1.14.14.1" - subsystem: From 7309facf4cb33a055d3772f03d17ed1f925d7e28 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Wed, 8 Jan 2025 12:02:22 +0000 Subject: [PATCH 28/30] 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..ca9ed3b1 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 #962** (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 2e37c56602dc80108dc227af20d3164819565bd1 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Wed, 8 Jan 2025 21:53:57 +0800 Subject: [PATCH 29/30] fix: remove ENSG00000162365 from MAR00934 --- 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 2dc65bb6..f9f2255c 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -92036,7 +92036,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974 or ENSG00000162365 or ENSG00000187048" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974 or ENSG00000187048" - rxnFrom: "HMRdatabase" - eccodes: - "1.14.14.1" From 9f07c5d99524ec3eb794a08fa8181756e2c7c112 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Wed, 8 Jan 2025 20:21:46 +0100 Subject: [PATCH 30/30] 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 ca9ed3b1..e9cd40c6 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 #962** (MACAW) -- **PR #883** (gene essentiality) +- **PR #962** (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