diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 66f1b180..2b4ab6b5 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2272,3 +2272,6 @@ 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 + +MAM00348c MAM00348 13_cis_oretn 13_cis_oretn MNXM146866 m00348c m00348c +MAM00348n MAM00348 13_cis_oretn 13_cis_oretn MNXM146866 m00348n \ No newline at end of file diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index b48534b3..d2705614 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -401,3 +401,6 @@ 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 + +MAR08704 RAI4 RAI4 MNXR103425 HMR_8704 RCR13922 0 HMR_8704 +MAR01564 ORETNtn2 ORETNtn2 MNXR102215 0 ORETNtn2 \ No newline at end of file diff --git a/data/testResults/README.md b/data/testResults/README.md index 1b3495b5..3aeeaab4 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 #1044** (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..62f9248d 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -4627,9 +4627,8 @@ MAR08698,2 MAM02039c + MAM02555c + MAM02833c <=> MAM02040c + MAM02554c + MAM0283 MAR08699,MAM00349c + MAM02040c + MAM02554c <=> MAM00350c + 2 MAM02039c + MAM02555c,ok,ok,ok,ok,N/A MAR08700,MAM02039c + MAM02555c + MAM02630c + MAM02833c --> MAM01006c + MAM02040c + MAM02554c,ok,ok,ok,ok,N/A MAR08702,MAM01230c <=> MAM02832c,ok,ok,ok,ok,N/A -MAR08703,MAM02630c + 2 MAM02833c --> 2 MAM01026c,MAM01026c,ok,ok,ok,N/A -MAR08704,MAM00348c <=> MAM01026c,MAM00348c;MAM01026c,ok,ok,ok,N/A -MAR08706,2 MAM00350c + MAM02630c --> 2 MAM00348c,MAM00348c,ok,ok,ok,N/A +MAR08703,MAM02630c + 2 MAM02833c --> 2 MAM00993c,ok,ok,ok,ok,N/A +MAR08706,2 MAM00350c + MAM02630c --> 2 MAM01026c,MAM01026c,ok,ok,ok,N/A MAR08709,MAM00290c + MAM02039c + MAM02555c <=> MAM00291c + MAM02554c,ok,ok,ok,ok,N/A MAR08710,MAM00349c + MAM02039c + MAM02553c <=> MAM00351c + MAM02552c,only when going forwards,ok,ok,ok,N/A MAR08711,MAM00291c <=> MAM02834c,ok,ok,ok,ok,N/A @@ -8290,7 +8289,6 @@ MAR01560,MAM02040e + MAM03622e --> MAM01965e + MAM03623e,ok,ok,ok,ok,N/A MAR01561,MAM02644c <=> MAM02644x,ok,ok,ok,ok,N/A MAR01562,MAM02647c <=> MAM02647x,ok,ok,ok,ok,N/A MAR01563,MAM01026c <=> MAM01026n,MAM01026c;MAM01026n,ok,ok,ok,N/A -MAR01564,MAM00348c <=> MAM00348n,MAM00348c;MAM00348n,ok,ok,ok,N/A MAR01566,MAM02661x --> MAM02661c,ok,ok,ok,ok,N/A MAR01567,MAM01093m + MAM02039m + MAM02555m + MAM02630m --> MAM00756m + 2 MAM02040m + MAM02554m,ok,ok,ok,ok,N/A MAR01569,MAM00610r + MAM02039r + MAM02555r + MAM02630r --> MAM01446r + MAM02040r + MAM02554r,ok,ok,ok,ok,N/A diff --git a/data/testResults/qc_summary.md b/data/testResults/qc_summary.md index 83524e3e..8b160799 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 1382 dead-end metabolites. + - Found 1138 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..87a1edfb 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -4535,13 +4535,6 @@ - formula: "C28H39O4" - charge: -1 - metFrom: "HMRdatabase" - - !!omap - - id: "MAM00348c" - - name: "13-cis-oxo-retinoate" - - compartment: "c" - - formula: "C20H27O3" - - charge: -1 - - metFrom: "HMRdatabase" - !!omap - id: "MAM00349c" - name: "13-cis-retinal" @@ -11333,14 +11326,14 @@ - metFrom: "HMRdatabase" - !!omap - id: "MAM01026c" - - name: "4-oxo-13-cis-retinoate" + - name: "4-hydroxy-13-cis-retinoate" - compartment: "c" - formula: "C20H27O3" - charge: -1 - metFrom: "HMRdatabase" - !!omap - id: "MAM01026r" - - name: "4-oxo-13-cis-retinoate" + - name: "4-hydroxy-13-cis-retinoate" - compartment: "r" - formula: "C20H27O3" - charge: -1 @@ -39428,13 +39421,6 @@ - charge: 0 - inchis: "InChI=1S/C27H42O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h7,9-10,19,21,23-25,28H,6,8,11-17H2,1-5H3/t19-,21+,23-,24+,25+,26+,27-/m1/s1" - metFrom: "Recon3D" - - !!omap - - id: "MAM00348n" - - name: "13-cis-oxo-retinoate" - - compartment: "n" - - formula: "C20H27O3" - - charge: -1 - - metFrom: "Recon3D" - !!omap - id: "MAM00350n" - name: "13-cis-retinoate" @@ -39458,7 +39444,7 @@ - metFrom: "Recon3D" - !!omap - id: "MAM01026n" - - name: "4-oxo-13-cis-retinoate" + - name: "4-hydroxy-13-cis-retinoate" - compartment: "n" - formula: "C20H27O3" - charge: -1 @@ -134283,7 +134269,7 @@ - !!omap - id: "MAR08703" - metabolites: !!omap - - MAM01026c: 2 + - MAM00993c: 2 - MAM02630c: -1 - MAM02833c: -2 - lower_bound: 0 @@ -134291,21 +134277,11 @@ - rxnFrom: "HMRdatabase" - subsystem: "Retinol metabolism" - confidence_score: 0 - - !!omap - - id: "MAR08704" - - metabolites: !!omap - - MAM00348c: -1 - - MAM01026c: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - subsystem: "Retinol metabolism" - - confidence_score: 0 - !!omap - id: "MAR08706" - metabolites: !!omap - - MAM00348c: 2 - MAM00350c: -2 + - MAM01026c: 2 - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 @@ -183606,18 +183582,6 @@ - references: "PMID:1503811" - subsystem: "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR01564" - - name: "13-Cis-4-Oxo-Retinoic Acid Transport, Nuclear" - - metabolites: !!omap - - MAM00348c: -1 - - MAM00348n: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - rxnFrom: "Recon3D" - - references: "PMID:1503811" - - subsystem: "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR01566" - name: "Oxalate Transport Out of Peroxisome" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 928d9f09..8089d836 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -639,7 +639,6 @@ MAM00346r MAM00346 53481463 CE4898 CE4898 MNXM164055 m00346r m00346r MAM00347c MAM00347 53481464 CE7072 CE7072 MNXM164056 m00347c m00347c MAM00347m MAM00347 53481464 CE7072 CE7072 MNXM164056 m00347m m00347m MAM00347r MAM00347 53481464 CE7072 CE7072 MNXM164056 m00347r m00347r -MAM00348c MAM00348 13_cis_oretn 13_cis_oretn MNXM146866 m00348c m00348c MAM00349c MAM00349 retinal_cis_13 HMDB0006220 CHEBI:45487 6436079 LMPR01090018 retinal_cis_13 MNXM425;MNXM6641 m00349c m00349c MAM00349r MAM00349 retinal_cis_13 HMDB0006220 CHEBI:45487 6436079 LMPR01090018 retinal_cis_13 MNXM425;MNXM6641 m00349r m00349r MAM00350c MAM00350 13_cis_retn D00348 HMDB0006219 CHEBI:6067 5282379 LMPR01090021 13_cis_retn MNXM521;MNXM58377 m00350c m00350c @@ -1601,8 +1600,8 @@ MAM01023r MAM01023 CE5592 CE5592 MNXM164317 m01023r m01023r MAM01024c MAM01024 14015984 CE5593 CE5593 MNXM37693 m01024c m01024c MAM01024r MAM01024 14015984 CE5593 CE5593 MNXM37693 m01024r m01024r MAM01025c MAM01025 C19567 M01025 MNXM10233 m01025c m01025c -MAM01026c MAM01026 oretn 104857 CE5654 CE5654;oretn MNXM37697;MNXM6902 m01026c m01026c -MAM01026r MAM01026 oretn 104857 CE5654 CE5654;oretn MNXM37697;MNXM6902 m01026r m01026r +MAM01026c MAM01026 oretn 104857 CE5654 CE5654;oretn m01026c m01026c;MAM00348 +MAM01026r MAM01026 oretn 104857 CE5654 CE5654;oretn m01026r m01026r;MAM00348 MAM01027c MAM01027 CHEBI:58972 216297 CE2577 CE2577 MNXM7935 m01027c m01027c MAM01028c MAM01028 CE5652 CE5652 m01028c m01028c MAM01028r MAM01028 CE5652 CE5652 m01028r m01028r @@ -5576,11 +5575,10 @@ MAM01066r MAM01066 chlstol C05439 CHEBI:16290 HC01452 chlstol MNXM162749;MNX MAM02343r MAM02343 lthstrl C01189 HMDB0001170 CHEBI:17168 65728 LMST01010089 HC00706 lthstrl MNXM162760;MNXM810 m02343r MAM01675r MAM01675 dsmsterol C01802 HMDB0002719 CHEBI:17737 439577 LMST01010016 HC00847 dsmsterol MNXM162959;MNXM695 m01675r MAM01189r MAM01189 ddsmsterol C05107 HMDB0003896 CHEBI:27910 440558 LMST01010121 CE2321 HC01373 ddsmsterol MNXM162832;MNXM941 m01189r -MAM00348n MAM00348 13_cis_oretn 13_cis_oretn MNXM146866 m00348n MAM00350n MAM00350 13_cis_retn D00348 HMDB0006219 CHEBI:6067 5282379 LMPR01090021 13_cis_retn MNXM521;MNXM58377 m00350n MAM01006n MAM01006 hretn C16677 HMDB0006254 CHEBI:63795 6438629 hretn MNXM8133 m01006n MAM03758c MAM03758 melanin melanin MNXM92454 melanin_c -MAM01026n MAM01026 oretn 104857 CE5654 CE5654;oretn MNXM37697;MNXM6902 m01026n +MAM01026n MAM01026 oretn 104857 CE5654 CE5654;oretn m01026n;MAM00348 MAM03395l MAM03395 Ser_Thr Ser_Thr MNXM147296 Ser_Thr_l MAM01706x MAM01706 dmpp C00235 HMDB0001120 CHEBI:16057 647 LMPR01010001 HC00213 dmpp MNXM132 m01706p MAM01953x MAM01953 grdp C00341 CHEBI:17211 445995 HC00288 grdp MNXM100 m01953p diff --git a/model/reactions.tsv b/model/reactions.tsv index e5b1099e..3c48f883 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -4627,7 +4627,6 @@ MAR08699 RADH4 RADH4 MNXR103415 HMR_8699 RCR13920 0 HMR_8699 MAR08700 R08392 RAHY RAHY MNXR103421 HMR_8700 RCR13921 0 HMR_8700 MAR08702 RAI2 RAI2 MNXR103423 HMR_8702 RCR10991 0 HMR_8702 MAR08703 ORETNF ORETNF MNXR102210 HMR_8703 RCR10992 0 HMR_8703 -MAR08704 RAI4 RAI4 MNXR103425 HMR_8704 RCR13922 0 HMR_8704 MAR08706 ORETNF2 ORETNF2 MNXR102211 HMR_8706 RCR13923 0 HMR_8706 MAR08709 R08380 RDH3a RDH3a MNXR96890 HMR_8709 RCR13924 0 RHEA:54915 RHEA:54912 HMR_8709 MAR08710 RDH4 RDH4 MNXR103443 HMR_8710 RCR13925 0 RHEA:42059 RHEA:42056 HMR_8710 @@ -8289,7 +8288,6 @@ MAR01560 O16G1e O16G1e MNXR102083 0 O16G1e MAR01561 OCCOAtx OCCOAtx MNXR102138 0 OCCOAtx MAR01562 ODECOAtx ODECOAtx MNXR102156 0 ODECOAtx MAR01563 ORETNtn ORETNtn MNXR102214 0 ORETNtn -MAR01564 ORETNtn2 ORETNtn2 MNXR102215 0 ORETNtn2 MAR01566 OXAtp OXAtp MNXR102238 0 OXAtp MAR01567 P45027A15m P45027A15m MNXR102269 0 P45027A15m MAR01569 P45039A1r P45039A1r MNXR102283 0 P45039A1r