diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 66f1b180..f20b06bb 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2272,3 +2272,4 @@ MAM00208c MAM00208 C16832 M00208 MNXM21289 m00208c m00208c MAM00209c MAM00209 C16237 M00209 MNXM96070 m00209c m00209c MAM00210c MAM00210 C16236 M00210 MNXM4090 m00210c m00210c MAM01622x MAM01622 b2coa C00877 CHEBI:15473 5280381 HC00572 b2coa MNXM214 m01622p m01622p +MAM02768c MAM02768 pcollglys C16740 HC00904 pcollglys MNXM149166 m02768c m02768c diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index b48534b3..931bc2f7 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -401,3 +401,4 @@ MAR07851 DNDPt62m DNDPt62m MNXR97327 HMR_7851 RCR20193 0 HMR_7851 MAR07852 DNDPt63m DNDPt63m MNXR97676 HMR_7852 RCR20146 0 HMR_7852 MAR07853 DNDPt6m DNDPt6m MNXR97677 HMR_7853 RCR20194 0 HMR_7853 MAR07854 DNDPt7m DNDPt7m MNXR97175 HMR_7854 RCR20122 0 HMR_7854 +MAR09553 PCLYSOX PCLYSOX MNXR102412 HMR_9553 RCR14815 0 HMR_9553 diff --git a/data/testResults/README.md b/data/testResults/README.md index 1b3495b5..cacce41a 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 #1035** (QC) +- **PR #1043** (QC) - **PR #973** (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/macaw_results.csv b/data/testResults/macaw_results.csv index 5b8d58da..6bd0eb06 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -727,9 +727,9 @@ MAR06979,MAM01306c + MAM02517c + MAM02630c --> MAM00789c + MAM01596c + MAM02943c MAR06980,MAM00789c + MAM02039c --> MAM01034c + MAM01986c,ok,ok,ok,ok,N/A MAR06981,MAM01034c + MAM02040c + MAM02552c --> MAM01922c + 2 MAM02039c + MAM02553c,ok,ok,ok,ok,N/A MAR06982,MAM01306c + MAM01922c + MAM02630c --> MAM01596c + MAM02348c + MAM02943c,ok,ok,ok,ok,N/A -MAR06983,MAM00204c + MAM01306c + MAM02630c --> MAM01596c + MAM02767c + MAM02943c,MAM02767c,ok,ok,ok,N/A -MAR06984,MAM02767c + MAM03107c --> MAM01036c + MAM02039c + MAM03106c,MAM01036c;MAM02767c,ok,ok,ok,N/A -MAR06985,MAM01036c + MAM03108c --> MAM00232c + MAM02039c + MAM03106c,MAM00232c;MAM01036c,ok,ok,ok,N/A +MAR06983,MAM00204c + MAM01306c + MAM02630c --> MAM01596c + MAM02767c + MAM02943c,ok,ok,ok,ok,N/A +MAR06984,MAM02767c + MAM03107c --> MAM01036c + MAM02039c + MAM03106c,ok,ok,ok,ok,N/A +MAR06985,MAM01036c + MAM03108c --> MAM00232c + MAM02039c + MAM03106c,ok,ok,ok,ok,N/A MAR08017,MAM01802x + MAM02040x + MAM02426x --> MAM01157x + MAM01803x + MAM02039x + MAM02578x,ok,ok,ok,ok,N/A MAR08018,MAM01157x --> MAM01663x + MAM02040x,ok,ok,ok,ok,N/A MAR08019,MAM01663x + MAM02039x + MAM02553x --> MAM02413x + MAM02552x,ok,ok,ok,ok,N/A @@ -4989,7 +4989,6 @@ MAR09549,MAM02039c + MAM02700c + MAM02871c <=> MAM02699c + MAM02877c,MAM02699c;M MAR09550,2 MAM00188c + MAM02555c + 2 MAM02877c <=> 2 MAM00189c + MAM02039c + MAM02554c + 2 MAM02871c,MAM00188c;MAM00189c,ok,ok,ok,N/A MAR09551,MAM01838c + MAM02040c --> MAM01833c + MAM02039c + MAM02472c,MAM01838c;MAM02472c,ok,ok,ok,N/A MAR09552,MAM01710c + MAM02040c --> MAM02039c + MAM02493c + MAM02751c,MAM01710c;MAM02493c,ok,ok,ok,N/A -MAR09553,MAM01306c + MAM02630c + MAM02768c --> MAM01596c + MAM02767c + MAM02943c,MAM02767c;MAM02768c,ok,ok,ok,N/A MAR09801,MAM02034c + MAM02381c <=> MAM01948c + MAM03167c,only when going backwards,ok,ok,ok,N/A MAR09807,MAM02040c + MAM03167c --> MAM00631c + MAM02039c + MAM02578c + MAM02751c,ok,ok,ok,ok,N/A MAR09554,MAM00683c + 2 MAM02040c --> MAM00774c + 2 MAM02039c + 2 MAM10005c,MAM00683c;MAM00774c,ok,ok,ok,N/A @@ -12876,3 +12875,5 @@ MAR20188,MAM01098m <=> MAM01098c,MAM01098c;MAM01098m,ok,ok,ok,N/A MAR20189,MAM01329c + 2 MAM01824m + 5 MAM02039m --> MAM01328c + 2 MAM01826m + 4 MAM02039i,MAM01328c;MAM01329c,ok,ok,ok,N/A MAR20190,MAM01329c + MAM02039c + MAM02553c --> MAM01328c + MAM02552c,MAM01328c;MAM01329c,ok,ok,ok,N/A MAR20191,MAM01371m + MAM01974m + MAM02578m --> MAM01285m + MAM01975m + MAM02751m,ok,ok,ok,ok,N/A +MAR20192,MAM00232c --> MAM00232e,ok,ok,ok,ok,N/A +MAR20193,MAM00232e <=> ,ok,ok,ok,ok,N/A diff --git a/data/testResults/qc_summary.md b/data/testResults/qc_summary.md index 83524e3e..dc2b4988 100644 --- a/data/testResults/qc_summary.md +++ b/data/testResults/qc_summary.md @@ -2,8 +2,8 @@ ``` Starting dead-end test... - - Found 1384 dead-end metabolites. - - Found 1141 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends. + - Found 1380 dead-end metabolites. + - Found 1137 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends. - Found 1369 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends. Starting duplicate test... - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided. diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 681c03b0..deab1a7d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -3064,6 +3064,13 @@ - formula: "C19H34N3O13R2" - charge: 1 - metFrom: "HMRdatabase" + - !!omap + - id: "MAM00232e" + - name: "1,2-D-glucosyl-5-D-(galactosyloxy)-L-lysine-procollagen" + - compartment: "e" + - formula: "C19H34N3O13R2" + - charge: 1 + - metFrom: "HMRdatabase" - !!omap - id: "MAM00233c" - name: "1,2-diacylglycerol-bile-PC pool" @@ -33612,13 +33619,6 @@ - formula: "C7H14N3O3R2" - charge: 1 - metFrom: "HMRdatabase" - - !!omap - - id: "MAM02768c" - - name: "procollagen-L-lysine" - - compartment: "c" - - formula: "C7H14N3O2R2" - - charge: 1 - - metFrom: "HMRdatabase" - !!omap - id: "MAM02769c" - name: "progesterone" @@ -140067,22 +140067,6 @@ - eccodes: "3.6.1.52" - subsystem: "Isolated" - confidence_score: 0 - - !!omap - - id: "MAR09553" - - metabolites: !!omap - - MAM01306c: -1 - - MAM01596c: 1 - - MAM02630c: -1 - - MAM02767c: 1 - - MAM02768c: -1 - - MAM02943c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000083444 or ENSG00000106397 or ENSG00000152952" - - rxnFrom: "HMRdatabase" - - eccodes: "1.14.11.4" - - subsystem: "Isolated" - - confidence_score: 0 - !!omap - id: "MAR09801" - name: "GTP:5-hydroxy-L-lysine O-phosphotransferase" @@ -245971,6 +245955,25 @@ - references: "PMID:11080211;PMID:1356223;PMID:14583610;PMID:16213501;PMID:7595668;PMID:8838581;PMID:9053810" - subsystem: "Alanine, aspartate and glutamate metabolism" - confidence_score: 0 + - !!omap + - id: "MAR20192" + - name: "Transport of 1,2-D-glucosyl-5-D-(galactosyloxy)-L-lysine-procollagen (Cytosol to Extracellular)" + - metabolites: !!omap + - MAM00232c: -1 + - MAM00232e: 1 + - lower_bound: 0 + - upper_bound: 1000 + - subsystem: "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20193" + - name: "Exchange of 1,2-D-glucosyl-5-D-(galactosyloxy)-L-lysine-procollagen" + - metabolites: !!omap + - MAM00232e: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - subsystem: "Exchange/demand reactions" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 928d9f09..16abc3fb 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -430,6 +430,7 @@ MAM00229c MAM00229 C19591 M00229 MNXM9522 m00229c m00229c MAM00230c MAM00230 107838 CE2152 CE2152 MNXM32042 m00230c m00230c MAM00231c MAM00231 CE5629 CE5629 MNXM32113 m00231c m00231c MAM00232c MAM00232 C04759 M00232 MNXM91041 m00232c m00232c +MAM00232e MAM00232 C04759 MNXM91041 MAM00233c MAM00233 C00641 CHEBI:17815 LMGL02010000 HC02085 HC02085 MNXM59 m00233c m00233c MAM00234e MAM00234 C00641 CHEBI:17815 LMGL02010000 M00234 MNXM59 m00234s m00234s MAM00235c MAM00235 C00641 CHEBI:17815 LMGL02010000 HC02056 HC02056 MNXM59 m00235c m00235c @@ -4756,7 +4757,6 @@ MAM02764c MAM02764 C03428 CHEBI:15442 HC01118 HC01118 MNXM591 m02764c m0276 MAM02765c MAM02765 pd3 C07711 HMDB0006500 11199982 pd3 MNXM7697 m02765c m02765c MAM02766x MAM02766 prist HMDB0000795 CHEBI:51340 123929 LMPR0104010022 CE0932 prist MNXM3342 m02766p m02766p MAM02767c MAM02767 C01211 CHEBI:51807 M02767 MNXM5281 m02767c m02767c -MAM02768c MAM02768 pcollglys C16740 HC00904 pcollglys MNXM149166 m02768c m02768c MAM02769c MAM02769 prgstrn C00410 HMDB0001830 CHEBI:17026 5994 LMST02030135 prgstrn MNXM162773;MNXM307 m02769c m02769c MAM02769r MAM02769 prgstrn C00410 HMDB0001830 CHEBI:17026 5994 LMST02030135 prgstrn MNXM162773;MNXM307 m02769r m02769r MAM02769e MAM02769 prgstrn C00410 HMDB0001830 CHEBI:17026 5994 LMST02030135 prgstrn MNXM162773;MNXM307 m02769s m02769s diff --git a/model/reactions.tsv b/model/reactions.tsv index e5b1099e..3c54f87a 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -4988,7 +4988,6 @@ MAR09549 R04481 HMR_9549 MNXR108915 HMR_9549 RCR14813 0 RHEA:36419 HMR_954 MAR09550 R05182 HMR_9550 MNXR109379 HMR_9550 RCR14814 0 RHEA:23908 HMR_9550 MAR09551 R05635 HMR_9551 MNXR109727 HMR_9551 RCR14150 0 RHEA:24420 HMR_9551 MAR09552 R05777 HMR_9552 MNXR109829 HMR_9552 RCR14151 0 HMR_9552 -MAR09553 PCLYSOX PCLYSOX MNXR102412 HMR_9553 RCR14815 0 HMR_9553 MAR09801 R03378 HMR_9801 MNXR100675 HMR_9801 RCR14816 0 RHEA:19049 HMR_9801 MAR09807 R10270 HMR_9807 MNXR95619 HMR_9807 RCR14152 0 RHEA:34091 HMR_9807 MAR09554 R05792 HMR_9554 MNXR109840 HMR_9554 RCR14817 0 HMR_9554 @@ -12876,3 +12875,5 @@ MAR20188 0 MAR20189 0 MAR20190 0 MAR20191 R00253 GLNS R00253C r0077 GLNS MNXR100024 HMR_3890 RCR10506 0 RHEA:16169 HMR_3890 +MAR20192 0 +MAR20193 0