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edkerk merged 15 commits into from
Sep 28, 2026
Merged

fix: corrections to curation since v2.0.1 from an evidence review #1105

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61a012a
fix: corrections to #1039, #1041, #1040, #1090, #1028, #1099 and #103…
edkerk Sep 26, 2026
e0ca5d4
fix: corrections to #1101, #1103, #1084, #1086 and #1087 from the cur…
edkerk Sep 26, 2026
6dc6076
fix: remaining corrections from the curation review (deprecated rows,…
edkerk Sep 26, 2026
82d6a18
fix: remaining low-priority corrections from the curation review
edkerk Sep 26, 2026
3f534a3
chore: update model QC results [skip ci]
edkerk Sep 26, 2026
d4d832a
Merge develop into fix/review-v2.0.1-curation
edkerk Sep 28, 2026
ecc9291
chore: update model QC results [skip ci]
edkerk Sep 28, 2026
4ef6e6d
fix: corrections to #1043, #1088, #1093-#1096 from an evidence review
edkerk Sep 28, 2026
01b0519
fix: corrections to #1044 and #1089 from an evidence review
edkerk Sep 28, 2026
e2e4956
chore: update model QC results [skip ci]
edkerk Sep 28, 2026
5d8a854
feat: add CYP26C1 to the retinoate 4-hydroxylation and 4-oxo reactions
edkerk Sep 28, 2026
26ee53a
Merge remote-tracking branch 'origin/develop' into HEAD
edkerk Sep 28, 2026
e9617ab
chore: update model QC results [skip ci]
edkerk Sep 28, 2026
29a05ef
chore: add gene essentiality test result [skip ci]
github-actions[bot] Sep 28, 2026
e03cdd7
chore: add gene essentiality test result [skip ci]
github-actions[bot] Sep 28, 2026
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8 changes: 7 additions & 1 deletion data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2272,7 +2272,7 @@ 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
MAM01690m MAM01690 dhap C00111 CHEBI:16108 668 HC00109 dhap MNXM77 m01690m m01690m
MAM01690m MAM01690 dhap C00111 HMDB0001473 CHEBI:16108 668 HC00109 dhap MNXM77 m01690m m01690m
MAM03971e MAM03971 Temp001 temp001s
MAM20005c MAM20005 CHEBI:76645 72551583 MNXM145653
MAM20006c MAM20006 CHEBI:76647 6437827 LMFA01170034 MNXM23130
Expand Down Expand Up @@ -2378,3 +2378,9 @@ MAM03652c MAM03652 hexdeceeth HMDB0013648 CHEBI:71465 9835868 LMFA08040043 M
MAM20077m MAM20077 C22667 CHEBI:29144 5460642 MNXM37367
MAM20017n MAM20017 C04671 HMDB0002776 CHEBI:57402 5280711 LMFA03010031 MNXM733372
MAM03322c MAM03322 C06453 C06453 CHEBI:28115 C06453 MNXM90852 C06453_c
MAM03270c MAM03270 4glu56dihdind 102068183 4glu56dihdind MNXM744448 4glu56dihdind_c
MAM03270e MAM03270 4glu56dihdind 102068183 4glu56dihdind MNXM744448 4glu56dihdind_s
MAM01739x MAM01739 CE4888 C05578 HMDB0004058 CHEBI:27404 114683 CE4888 CE4888 MNXM730705 m01739p
MAM01136x MAM01136 CE5545 HMDB0060086 131769818 CE5545 CE5545 MNXM151428 m01136p
MAM02043c MAM02043 HC01501 C05529 HMDB0000257 CHEBI:5587 24478 HC01501 HC01501 MNXM1094289 m02043c m02043c
MAM03584g MAM03584 galacglcgalacglcgal14acglcgalgluside_hs galacglcgalacglcgal14acglcgalgluside_hs MNXM11849 galacglcgalacglcgal14acglcgalgluside_hs_g
40 changes: 25 additions & 15 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -245,7 +245,7 @@ MAR07926 DGTPtm DGTPtm MNXR97327 0 DGTPtm
MAR01483 LIPOti LIPOti MNXR101093 0 LIPOti
MAR06406 LIPOti RT1089 MNXR101093 HMR_6406 RCR41534 0 HMR_6406
MAR00478 R00844 R-HSA-75889 HMR_0478 MNXR99876 HMR_0478 RCR14575 0 RHEA:11098 RHEA:11096 HMR_0478
MAR00482 R00848;R00849 G3PD2m R00848C r0205 HMR_0482;r0205 MNXR99875;MNXR106713 HMR_0482;HMR_0483 RCR14578;RCR21050 0 RHEA:31283;RHEA:18977 HMR_0482;HMR_0483;MAR00483
MAR00482 R00848;R00849 G3PD2m R00848C r0205 HMR_0482;r0205 MNXR99875;MNXR106713 HMR_0482 RCR14578;RCR21050 0 RHEA:31283;RHEA:18977 HMR_0482
MAR20012 R02123 HMR_6647;RADH;R_HMR_6647;R_RADH MNXR146215 0 RHEA:42080
MAR20089 R02701 MNXR151808 0 RHEA:18533
MAR06398 R07770 R07770C RE1944C MNXR101081 HMR_6398 RCR14489 0 RHEA:12913 HMR_6398
Expand Down Expand Up @@ -399,10 +399,10 @@ 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
MAR08611 R10507 PROD2m r1453 PROD2m MNXR103187 HMR_8611;HMR_3838 RCR11294;RCR14286 0 HMR_8611;HMR_3838;MAR03838
MAR08610 HMR_8610 0 HMR_8610
MAR00449 R00848;R00849 r0205 R-HSA-188467 GLYC3PFADm;r0205 MNXR99875;MNXR106713 HMR_0449;HMR_0483 RCR12494;RCR21050 0 RHEA:31283;RHEA:18977 HMR_0449;HMR_0483
MAR01169 R00849;R00848 G3PD2m R00848C r0205 G3PD2m;r0205;HMR_0482 MNXR99878;MNXR106713;MNXR192664 HMR_0483;HMR_0482 RCR21050;RCR14578 0 RHEA:18977 G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483
MAR08611 R10507 PROD2m r1453 PROD2m MNXR103187 HMR_8611 RCR11294;RCR14286 0 HMR_8611
MAR08610 R10507 PROD2 PROD2 MNXR192607 HMR_8610 RCR10316 0 HMR_8610
MAR00449 R00848;R00849 G3PD r0205 R-HSA-188467 GLYC3PFADm;r0205 MNXR192664 HMR_0449 RCR12494;RCR21050 0 RHEA:31283 RHEA:31283;RHEA:18977 HMR_0449
MAR01169 R00849;R00848 G3PD2m R00848C r0205 G3PD2m;r0205;HMR_0482 MNXR99878;MNXR106713;MNXR192664 HMR_0482 RCR21050;RCR14578 0 RHEA:18977 G3PD2m;HMR_0482;MAR00482
MAR08111 DHAPtm DHAPtc MNXR97366 0 DHAPtc
MAR08543 R03973 IDHPOXOX2b IDHPOXOX2b MNXR138528 HMR_8543 RCR14343 0 HMR_8543
MAR08544 R03539 IDHPOXOXb IDHPOXOXb MNXR138529 HMR_8544 RCR14344 0 HMR_8544
Expand Down Expand Up @@ -443,17 +443,7 @@ MAR01355 RE3455C MNXR171967 HMR_1355 RCR13335 0 RHEA:63284 HMR_1355
MAR01358 RE3449C HMR_1358 RCR13338 0 HMR_1358
MAR01361 RE3458C HMR_1361 RCR13341 0 HMR_1361
MAR01405 RE2852C HMR_1405 HMR_1405 RCR13691 0 HMR_1405
MAR07633 HISTAVESSEC MNXR100640 HMR_7633 RCR40283 0 HMR_7633
MAR07634 5HTRPVESSEC MNXR95084 HMR_7634 RCR40739 0 HMR_7634
MAR07635 ADRNLPVESSEC MNXR95488 HMR_7635 RCR40284 0 HMR_7635
MAR07636 DOPAVESSEC MNXR97756 HMR_7636 RCR41548 0 HMR_7636
MAR07637 NRPPHRVESSEC MNXR102017 HMR_7637 RCR40285 0 HMR_7637
MAR07667 BTNt3i BTNt3ile MNXR96336 HMR_7667 RCR41553 0 HMR_7667
MAR07681 ACHVESSEC MNXR95266 HMR_7681 RCR40287 0 HMR_7681
MAR07736 BALAVECSEC MNXR96211 HMR_7736 RCR40289 0 HMR_7736
MAR07737 GLYVESSEC MNXR100366 HMR_7737 RCR40290 0 HMR_7737
MAR07738 GABAVESSEC MNXR99916 HMR_7738 RCR40291 0 HMR_7738
MAR08922 MEPIVESSte MNXR101465 HMR_8922 RCR40876 0 HMR_8922
MAR08930 PNTOt5 PNTOt5le MNXR103055 HMR_8930 RCR41594 0 HMR_8930
MAR09603 HMR_9603 HMR_9603 RCR41619 0 HMR_9603
MAR09604 HMR_9604 HMR_9604 RCR41620 0 HMR_9604
Expand Down Expand Up @@ -490,3 +480,23 @@ MAR06466 RE2398C RE2398C RE2398C MNXR103666 HMR_6466 RCR14004 0 HMR_6466
MAR06476 RE2387C RE2387C RE2387C MNXR146285 HMR_6476 RCR14010 0 HMR_6476
MAR06478 RE2383C RE2383C RE2383C MNXR103662 HMR_6478 RCR14012 0 HMR_6478
MAR03138 RE2493C RE2493C MNXR103686 0 RE2493C
MAR01442 HISTAVESSEC HISTAVESSEC MNXR158225 0 HISTAVESSEC
MAR00052 5HTRPVESSEC 5HTRPVESSEC MNXR154062 0 5HTRPVESSEC
MAR00065 ADRNLPVESSEC ADRNLPVESSEC MNXR154425 0 ADRNLPVESSEC
MAR00334 DOPAVESSEC DOPAVESSEC MNXR156001 0 DOPAVESSEC
MAR01555 NRPPHRVESSEC NRPPHRVESSEC MNXR159802 0 NRPPHRVESSEC
MAR00058 ACHVESSEC ACHVESSEC MNXR154202 0 ACHVESSEC
MAR00087 BALAVECSEC BALAVECSEC MNXR154853 0 BALAVECSEC
MAR01396 GLYVESSEC GLYVESSEC MNXR100367 0 GLYVESSEC
MAR01314 GABAVESSEC GABAVESSEC MNXR99916 0 GABAVESSEC
MAR01518 MEPIVESSte MEPIVESSte MNXR101465 0 MEPIVESSte
MAR01857 r1017 MNXR104744 HMR_1857 RCR40318 0 HMR_1857
MAR01861 r1029 MNXR105431 HMR_1861 RCR40147 0 HMR_1861
MAR00751 FAOXC11 FAOXC11 MNXR99270 0 FAOXC11
MAR06817 RE2526C RE2526C RE2526C MNXR103695 HMR_6817 RCR11448 0 HMR_6817
MAR06815 RE2525C RE2525C RE2525C MNXR103694 HMR_6815 RCR11447 0 HMR_6815
MAR03161 RE2525X RE2525X MNXR103694 0 RE2525X
MAR04840 r0795 r0795 r0795 MNXR105387 HMR_4840 RCR11650 1 HMR_4840
MAR03928 R03105 HMR_6515;r0595 R03105C r0595 r0595 MNXR146789 HMR_3928 RCR14400 0 RHEA:21740 HMR_3928
MAR08365 ACETONEt2m MNXR95230 HMR_8365 RCR20655 1.D.6.1.1 0 HMR_8365
MAR08317 B3GNT314g MNXR96181 HMR_8317 RCR20529 0 HMR_8317
12 changes: 6 additions & 6 deletions data/testResults/README.md
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Expand Up @@ -21,12 +21,12 @@ own files. The pull request in each row is the one whose run last wrote those fi

| Result file(s) | Produced by | Last updated by |
| --- | --- | --- |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1104** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1104** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1104** (model QC checks) |
| `macaw_results.tsv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1104** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1104** (MEMOTE) |
| `gene-essential.csv`, `gene-essential_summary.md` | `gradedEssentiality.py` via `/run gene-essentiality` | **PR #1104** (gene essentiality) |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1105** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1105** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1105** (model QC checks) |
| `macaw_results.tsv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1105** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1105** (MEMOTE) |
| `gene-essential.csv`, `gene-essential_summary.md` | `gradedEssentiality.py` via `/run gene-essentiality` | **PR #1105** (gene essentiality) |

## 2. What each check means

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6 changes: 1 addition & 5 deletions data/testResults/balance_results.csv
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Expand Up @@ -9,7 +9,7 @@ MAR00031,lipid droplet formation,C:-13.4364;H:-19.2074;N:-0.0188;O:-4.4474;P:-0.
MAR00033,"24-oxo-1alpha,23,25-trihydroxyvitamin D3 to vitamin D derivatives conversion",C:-108;H:-164;O:-18;X:1,
MAR00034,3-carboxy-alpha-chromanol to vitamin E derivatives conversion,C:-37;H:-48;O:-14;X:1,2
MAR00035,"(1aalpha,2beta,3alpha,11calpha)... to xenobiotics conversion",Br:-6;C:-588;Cl:-12;H:-621;N:-66;O:-209;S:-15,11
MAR00036,(11R)-HPETE to arachidonate derivatives conversion,C:-3170;H:-4889;N:-76;O:-823;P:-15;S:-23,180
MAR00036,(11R)-HPETE to arachidonate derivatives conversion,C:-3150;H:-4860;N:-76;O:-819;P:-15;S:-23,179
MAR00037,16alpha-hydroxyestrone to steroids conversion,C:-1116;H:-1488;I:-1;N:-81;O:-299;S:-24;Se:-1,24
MAR00477,phospholipids extracellular pool formation,C:-32;H:-61;N:-4;O:-24;P:-3;R:-5,-1
MAR00545,acyl-CoA-CL pool (liver tissue) formation,C:-16.6164;H:-31.9336;R:1,
Expand All @@ -36,7 +36,6 @@ MAR00689,(10Z)-heptadecenoic acid formation,C:17.4164;H:31.8982;R:-1,
MAR00690,(10Z)-heptadecenoic acid formation,C:17.993;H:33.083;R:-1,
MAR00691,(10Z)-heptadecenoic acid formation,C:17.595;H:32.8888;R:-1,
MAR00692,(10Z)-heptadecenoic acid formation,C:16.0152;H:32.0204;R:-1,
MAR00751,Beta Oxidation of Long Chain Fatty Acid,,2
MAR00961,"arachidonate 12-lipoxygenase, 12S type (5(S)-HETE)",,-2
MAR00964,"arachidonate 12-lipoxygenase, 12S type (5(S)-HETE)",,-2
MAR00967,"arachidonate 12-lipoxygenase, 12S type (5(S)-HETE)",,-2
Expand All @@ -56,14 +55,11 @@ MAR01227,(2E)-dodecenoyl-CoA formation,,2
MAR01301,acetyl-CoA C-acyltransferase (16e-18-oxo-18-CoA-dinor-LTE4),,5
MAR01302,choloyl-CoA hydrolase (omega-COOH-tetranor-LTE3-CoA),,-3
MAR01303,acyl-CoA oxidase (omega-COOH-tetranor-LTE3-CoA),,-3
MAR01307,prostaglandin-endoperoxide synthase (prostaglandin G2),,-2
MAR01337,"13,14-dihydro-15-keto-PGD2 to 15-dehydro-prostaglandin D2 conversion",,2
MAR01363,"9,11,15-trihydroxyprosta-(5Z,13E)-dien-1-oate hydrolysis",,4
MAR01366,"11,15-cyclo-12,14-cycloperoxy... to 11,15-cyclo-8,12,14-trihydroxy... conversion",,-4
MAR01383,9-deoxy-delta12-PGD2 hydrolysis,,2
MAR01389,15(S)-HETrE hydrolysis,,2
MAR01392,prostaglandin-endoperoxide synthase (prostaglandin G1),,-2
MAR01393,prostaglandin-endoperoxide synthase (prostaglandin G1),,-2
MAR01403,7-peroxy-docosahexaenoate to DHA conversion,,-2
MAR01404,8-peroxy-docosahexaenoate to DHA conversion,,-2
MAR01406,11-peroxy-docosahexaenoate to DHA conversion,,-2
Expand Down
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