diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 69cfefad..39779b48 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -300,3 +300,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745" "MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747" "MAR07799" "" "ATPasel" "" "" "" "" "MNXR96136" "HMR_7799" "RCR20334" "" 0 "" "" "HMR_7799" +"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180" +"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m" diff --git a/data/testResults/README.md b/data/testResults/README.md index 5b0034ab..5a49a7d3 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #675** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #820** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index aa73eeed..112e0ccf 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -8250,9 +8250,7 @@ MAR00759,4 MAM01597x + 4 MAM01802x + 4 MAM02040x + 4 MAM02552x + MAM02678x --> 4 MAR00764,MAM00051m + 4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00772,4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m + MAM02677m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00774,7 MAM01597m + 7 MAM01802m + 7 MAM02040m + MAM02101m + 7 MAM02552m --> 7 MAM01261m + 7 MAM01803m + 7 MAM02039m + 7 MAM02553m + MAM02774m,ok,ok,ok,ok,N/A -MAR00776,MAM01597m + MAM01802m + MAM02040m + MAM02552m + MAM02941m --> MAM01261m + MAM01803m + MAM02039m + MAM02553m + MAM02678m,ok,ok,ok,ok,N/A MAR00777,MAM01597x + MAM01802x + MAM02040x + MAM02552x + MAM02941x --> MAM01261x + MAM01803x + MAM02039x + MAM02553x + MAM02678x,ok,ok,ok,ok,N/A -MAR00778,MAM00057m + 5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00780,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM03791m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00784,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM02647m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00785,5 MAM01597m + 3 MAM01802m + 5 MAM02040m + MAM02391m + 5 MAM02552m --> 5 MAM01261m + 3 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e9484f6b..e6e2ecff 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -118350,7 +118350,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.3.8.7;1.3.8.8;1.3.8.9;1.3.99.-" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118367,7 +118367,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.17" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118386,7 +118386,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.35;1.1.1.211" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118404,7 +118404,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.16;1.1.1.211" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -221482,30 +221482,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR00776" - - name: "Beta Oxidation of Long Chain Fatty Acid" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM02678m: 1 - - MAM02941m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "1.3.99.3" - - references: "PMID:2565344;PMID:3035565" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR00777" - name: "Beta Oxidation of Long Chain Fatty Acid" @@ -221530,30 +221506,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR00778" - - name: "Beta Oxidation Fatty Acid" - - metabolites: !!omap - - MAM00057m: -1 - - MAM01261m: 5 - - MAM01597m: -5 - - MAM01802m: -4 - - MAM01803m: 4 - - MAM02039m: 5 - - MAM02040m: -5 - - MAM02552m: -5 - - MAM02553m: 5 - - MAM02644m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "4.2.1.74" - - references: "" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR00780" - name: "Beta Oxidation Fatty Acid" diff --git a/model/reactions.tsv b/model/reactions.tsv index 1a9770d5..4fa8c7c9 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2624,26 +2624,26 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03112" "" "" "" "" "" "HMR_3112" "" "HMR_3112" "RCR12626" "" 0 "" "" "HMR_3112" "MAR03113" "" "" "" "" "" "HMR_3113" "" "HMR_3113" "RCR12627" "" 0 "" "" "HMR_3113" "MAR03114" "" "" "" "" "" "HMR_3114" "" "HMR_3114" "RCR12628" "" 0 "" "" "HMR_3114" -"MAR03115" "" "" "" "" "" "HMR_3115" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115" -"MAR03116" "R07760" "" "" "" "" "HMR_3116" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116" -"MAR03117" "" "" "" "" "" "HMR_3117" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117" -"MAR03118" "" "" "" "" "" "HMR_3118" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118" -"MAR03121" "R01279" "r0310" "" "" "R-HSA-77299" "HMR_3121;r0310" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035" -"MAR03122" "R04738" "" "R04738X" "r0716" "" "r0716" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122" -"MAR03123" "R04737" "" "R04737X" "r0714" "" "r0714" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123" -"MAR03125" "R03991" "" "R03991X" "r0653" "" "r0653" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125" -"MAR03128" "R03990" "r1449" "" "" "R-HSA-77274" "HMR_3128;r1449" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370" -"MAR03129" "R04740" "" "R04740X" "r0720" "" "r0720" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129" -"MAR03130" "R04739" "" "R04739X" "r0718" "" "r0718" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130" -"MAR03132" "R03858" "" "R03858X" "r0639" "" "r0639" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132" -"MAR03135" "R03857" "r1447" "" "" "R-HSA-77263" "HMR_3135;r1447" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367" -"MAR03136" "R04170" "r1446" "R04170X" "r0660" "" "r0660;r1446" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366" -"MAR03137" "R04741" "" "R04741X" "r0722" "" "r0722" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137" -"MAR03139" "R04742" "" "R04742X" "r0724" "" "r0724" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139" -"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024" -"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" -"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" -"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" +"MAR03115" "" "FAOXC180" "" "" "" "HMR_3115;FAOXC180" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115;FAOXC180;MAR00776" +"MAR03116" "R07760" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3116;FAOXC180;FAOXC1811601m" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03117" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3117;FAOXC180;FAOXC1811601m" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03118" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3118;FAOXC180;FAOXC1811601m" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03121" "R01279" "r0310;FAOXC1811601m" "" "" "R-HSA-77299" "HMR_3121;r0310;FAOXC1811601m" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035;FAOXC1811601m;MAR00778" +"MAR03122" "R04738" "FAOXC1811601m" "R04738X" "r0716" "" "r0716;FAOXC1811601m" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122;FAOXC1811601m;MAR00778" +"MAR03123" "R04737" "FAOXC1811601m" "R04737X" "r0714" "" "r0714;FAOXC1811601m" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123;FAOXC1811601m;MAR00778" +"MAR03125" "R03991" "FAOXC1811601m" "R03991X" "r0653" "" "r0653;FAOXC1811601m" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125;FAOXC1811601m;MAR00778" +"MAR03128" "R03990" "r1449;FAOXC1811601m" "" "" "R-HSA-77274" "HMR_3128;r1449;FAOXC1811601m" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370;FAOXC1811601m;MAR00778" +"MAR03129" "R04740" "FAOXC1811601m" "R04740X" "r0720" "" "r0720;FAOXC1811601m" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129;FAOXC1811601m;MAR00778" +"MAR03130" "R04739" "FAOXC1811601m" "R04739X" "r0718" "" "r0718;FAOXC1811601m" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130;FAOXC1811601m;MAR00778" +"MAR03132" "R03858" "FAOXC1811601m" "R03858X" "r0639" "" "r0639;FAOXC1811601m" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132;FAOXC1811601m;MAR00778" +"MAR03135" "R03857" "r1447;FAOXC1811601m" "" "" "R-HSA-77263" "HMR_3135;r1447;FAOXC1811601m" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367;FAOXC1811601m;MAR00778" +"MAR03136" "R04170" "r1446;FAOXC1811601m" "R04170X" "r0660" "" "r0660;r1446;FAOXC1811601m" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366;FAOXC1811601m;MAR00778" +"MAR03137" "R04741" "FAOXC1811601m" "R04741X" "r0722" "" "r0722;FAOXC1811601m" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137;FAOXC1811601m;MAR00778" +"MAR03139" "R04742" "FAOXC1811601m" "R04742X" "r0724" "" "r0724;FAOXC1811601m" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139;FAOXC1811601m;MAR00778" +"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m;FAOXC1811601m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m;FAOXC1811601m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" "MAR03149" "R03777" "r1448;FAOXC8C6m;FAOXC80" "" "" "R-HSA-77338" "HMR_3149;r1448;FAOXC6C8m;FAOXC80;HMR_3422" "MNXR95304" "HMR_3149;HMR_3422" "RCR12649;RCR12667" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03150" "R04746" "FAOXC8C6m;FAOXC80" "R04746M" "r0731" "" "r0731;FAOXC8C6m;FAOXC80;HMR_3422" "MNXR97888" "HMR_3150;HMR_3422" "RCR12650;RCR12667" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03151" "R04745" "FAOXC8C6m;FAOXC80" "R04745M" "r0730" "" "r0730;FAOXC8C6m;FAOXC80;HMR_3422" "MNXR100544" "HMR_3151;HMR_3422" "RCR12651;RCR12667" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" @@ -8249,9 +8249,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00764" "" "FAOXC161802m" "" "" "" "FAOXC161802m" "MNXR99301" "" "" "" 0 "" "" "FAOXC161802m" "MAR00772" "" "FAOXC16180m" "" "" "" "FAOXC16180m" "MNXR99302" "" "" "" 0 "" "" "FAOXC16180m" "MAR00774" "" "FAOXC170m" "" "" "" "FAOXC170m" "MNXR99312" "" "" "" 0 "" "" "FAOXC170m" -"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180" "MAR00777" "" "FAOXC180x" "" "" "" "FAOXC180x" "MNXR99314" "" "" "" 0 "" "" "FAOXC180x" -"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m" "MAR00780" "" "FAOXC1811602m" "" "" "" "FAOXC1811602m" "MNXR99316" "" "" "" 0 "" "" "FAOXC1811602m" "MAR00784" "" "FAOXC1811603m" "" "" "" "FAOXC1811603m" "MNXR99317" "" "" "" 0 "" "" "FAOXC1811603m" "MAR00785" "" "FAOXC182806m" "" "" "" "FAOXC182806m" "MNXR99321" "" "" "" 0 "" "" "FAOXC182806m"