Skip to content

Remove inaccurate mitochondrial nucleotide transport reactions #944

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
edkerk merged 9 commits into from
Mar 24, 2026
Merged

Remove inaccurate mitochondrial nucleotide transport reactions #944

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
09ce67d
fix: remove SLC15A19 from GPR of MAR05047
Devlin-Moyer Dec 23, 2024
2431f57
fix: removed MAR04933 for being less accurate duplicate of MAR05992
Devlin-Moyer Dec 23, 2024
3958951
fix: removed MAR06332-MAR06343 for misrepresenting transport of (d)NT…
Devlin-Moyer Dec 23, 2024
8feea60
fix: removed MAR07804-MAR07854 for misrepresenting transport of (d)NT…
Devlin-Moyer Dec 23, 2024
e1901bc
chore: add macaw test result
Devlin-Moyer Dec 23, 2024
8f3dd48
chore: tsv style
edkerk Mar 20, 2026
22f5767
Merge remote-tracking branch 'origin/develop' into fix/SLC15A19
edkerk Mar 20, 2026
15205f9
chore: add macaw test result
edkerk Mar 20, 2026
536fccf
Merge branch 'develop' into fix/SLC15A19
edkerk Mar 24, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
55 changes: 55 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -346,3 +346,58 @@ MAR05794 r1879 r1879 MNXR105791 HMR_5794 RCR41296 0 HMR_5794
MAR05759 r1844 r1844 MNXR105763 HMR_5759 RCR41261 0 HMR_5759
MAR03102 HMR_3102 HMR_3102 RCR12543 0 HMR_3102
MAR03103 R03026 ECOAH1x HMR_3103 RCR12544 0 RHEA:26558 HMR_3103
MAR04933 r0879 r0879 MNXR95660 HMR_4933 RCR40980 2.A.29.2.4;2.A.29.16.1 0 HMR_4933
MAR06332 DNDPt13m r2421 DNDPt13m MNXR97631 HMR_6332 RCR20118 2.A.29.16.1 0 HMR_6332
MAR06333 DNDPt32m r2422 DNDPt32m MNXR97648 HMR_6333 RCR20179 2.A.29.16.1 0 HMR_6333
MAR06334 DNDPt19m r2423 DNDPt19m MNXR97637 HMR_6334 RCR20614 2.A.29.16.1 0 HMR_6334
MAR06335 DNDPt12m r2424 DNDPt12m MNXR97630 HMR_6335 RCR20119 2.A.29.16.1 0 HMR_6335
MAR06336 r2425 r2425 MNXR106294 HMR_6336 RCR20180 2.A.29.16.1 0 HMR_6336
MAR06337 DNDPt18m r2426 DNDPt18m MNXR97636 HMR_6337 RCR20615 2.A.29.16.1 0 HMR_6337
MAR06338 DNDPt2m r2427 DNDPt2m MNXR97645 HMR_6338 RCR20077 2.A.29.16.1 0 HMR_6338
MAR06339 DNDPt57m r2428 DNDPt57m MNXR97670 HMR_6339 RCR20139 2.A.29.16.1 0 HMR_6339
MAR06340 DNDPt43m r2429 DNDPt43m MNXR97656 HMR_6340 RCR20275 2.A.29.16.1 0 HMR_6340
MAR06341 DNDPt1m r2430 DNDPt1m MNXR97638 HMR_6341 RCR20078 2.A.29.16.1 0 HMR_6341
MAR06342 DNDPt58m r2431 DNDPt58m MNXR97671 HMR_6342 RCR20140 2.A.29.16.1 0 HMR_6342
MAR06343 DNDPt42m r2432 DNDPt42m MNXR97655 HMR_6343 RCR20276 2.A.29.16.1 0 HMR_6343
MAR07804 DNDPt29m DNDPt29m;DNDPt10m MNXR97628 HMR_7804 RCR20121 0 HMR_7804
MAR07806 DNDPt35m DNDPt35m;DNDPt11m MNXR97629 HMR_7806 RCR20183 0 HMR_7806
MAR07808 DNDPt22m DNDPt22m;DNDPt14m MNXR97632 HMR_7808 RCR20635 0 HMR_7808
MAR07810 DNDPt33m DNDPt33m;DNDPt15m MNXR97633 HMR_7810 RCR20636 0 HMR_7810
MAR07812 DNDPt8m DNDPt8m;DNDPt16m MNXR97634 HMR_7812 RCR20637 0 HMR_7812
MAR07814 DNDPt26m DNDPt26m;DNDPt17m MNXR97635 HMR_7814 RCR20638 0 HMR_7814
MAR07815 DNDPt20m DNDPt20m MNXR97639 HMR_7815 RCR20184 0 HMR_7815
MAR07816 DNDPt21m DNDPt21m MNXR97640 HMR_7816 RCR20185 0 HMR_7816
MAR07818 DNDPt34m DNDPt34m;DNDPt23m MNXR97641 HMR_7818 RCR20186 0 HMR_7818
MAR07820 DNDPt9m DNDPt9m;DNDPt24m MNXR97642 HMR_7820 RCR20187 0 HMR_7820
MAR07822 DNDPt27m DNDPt27m;DNDPt25m MNXR97643 HMR_7822 RCR20188 0 HMR_7822
MAR07824 DNDPt36m DNDPt36m;DNDPt28m MNXR97644 HMR_7824 RCR20189 0 HMR_7824
MAR07825 DNDPt30m DNDPt30m MNXR97646 HMR_7825 RCR20057 0 HMR_7825
MAR07826 DNDPt31m DNDPt31m MNXR97647 HMR_7826 RCR20058 0 HMR_7826
MAR07827 DNDPt37m DNDPt37m MNXR97649 HMR_7827 RCR20278 0 HMR_7827
MAR07828 DNDPt38m DNDPt38m MNXR97650 HMR_7828 RCR20639 0 HMR_7828
MAR07829 DNDPt39m DNDPt39m MNXR97651 HMR_7829 RCR20279 0 HMR_7829
MAR07830 DNDPt3m DNDPt3m MNXR97652 HMR_7830 RCR20079 0 HMR_7830
MAR07831 DNDPt40m DNDPt40m MNXR97653 HMR_7831 RCR20280 0 HMR_7831
MAR07832 DNDPt41m DNDPt41m MNXR97654 HMR_7832 RCR20281 0 HMR_7832
MAR07833 DNDPt44m DNDPt44m MNXR97657 HMR_7833 RCR20282 0 HMR_7833
MAR07834 DNDPt45m DNDPt45m MNXR97658 HMR_7834 RCR20283 0 HMR_7834
MAR07835 DNDPt46m DNDPt46m MNXR97659 HMR_7835 RCR20640 0 HMR_7835
MAR07836 DNDPt47m DNDPt47m MNXR97660 HMR_7836 RCR20284 0 HMR_7836
MAR07837 DNDPt48m DNDPt48m MNXR97661 HMR_7837 RCR20285 0 HMR_7837
MAR07838 DNDPt49m DNDPt49m MNXR97662 HMR_7838 RCR20286 0 HMR_7838
MAR07839 DNDPt4m DNDPt4m MNXR97663 HMR_7839 RCR20641 0 HMR_7839
MAR07840 DNDPt50m DNDPt50m MNXR97664 HMR_7840 RCR20287 0 HMR_7840
MAR07841 DNDPt51m DNDPt51m MNXR97204 HMR_7841 RCR20141 0 HMR_7841
MAR07842 DNDPt52m DNDPt52m MNXR97665 HMR_7842 RCR20642 0 HMR_7842
MAR07843 DNDPt53m DNDPt53m MNXR97666 HMR_7843 RCR20190 0 HMR_7843
MAR07844 DNDPt54m DNDPt54m MNXR97667 HMR_7844 RCR20142 0 HMR_7844
MAR07845 DNDPt55m DNDPt55m MNXR97668 HMR_7845 RCR20143 0 HMR_7845
MAR07846 DNDPt56m DNDPt56m MNXR97669 HMR_7846 RCR20144 0 HMR_7846
MAR07847 DNDPt59m DNDPt59m MNXR97672 HMR_7847 RCR20145 0 HMR_7847
MAR07848 DNDPt5m DNDPt5m MNXR97673 HMR_7848 RCR20191 0 HMR_7848
MAR07849 DNDPt60m DNDPt60m MNXR97674 HMR_7849 RCR20643 0 HMR_7849
MAR07850 DNDPt61m DNDPt61m MNXR97675 HMR_7850 RCR20192 0 HMR_7850
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
4 changes: 2 additions & 2 deletions data/testResults/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/

The test results shown in this folder were last modified by the GitHub Actions run in:

- **PR #943** (MACAW)
- **PR #929** (gene essentiality)
- **PR #944** (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.

Expand Down
57 changes: 1 addition & 56 deletions data/testResults/macaw_results.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5262,7 +5262,6 @@ MAR04919,MAM01596c <=> MAM01596e,ok,ok,ok,ok,N/A
MAR04928,MAM02039e + MAM02819e --> MAM02039c + MAM02819c,ok,ok,ok,ok,N/A
MAR04931,MAM01629e + MAM01974c --> MAM01629c + MAM01974e,ok,ok,ok,ok,N/A
MAR04932,MAM01974e + MAM02039e + MAM02200c + 3 MAM02519e --> MAM01974c + MAM02039c + MAM02200e + 3 MAM02519c,ok,ok,ok,ok,N/A
MAR04933,MAM01306e + MAM02519e --> MAM01306c + MAM02519c,ok,ok,ok,MAR05992,N/A
MAR04934,MAM01252e + MAM02519e --> MAM01252c + MAM02519c,ok,ok,ok,ok,N/A
MAR04935,MAM01252e + MAM02039e --> MAM01252c + MAM02039c,ok,ok,ok,ok,N/A
MAR04938,3 MAM02519e + MAM02943e --> 3 MAM02519c + MAM02943c,ok,ok,ok,MAR04939;MAR09610,N/A
Expand Down Expand Up @@ -5888,7 +5887,7 @@ MAR05986,MAM01588e + MAM02184c --> MAM01588c + MAM02184e,ok,ok,ok,ok,N/A
MAR05987,MAM01821e + MAM02039e --> MAM01821c + MAM02039c,ok,ok,ok,ok,N/A
MAR05989,MAM02039e + MAM03157e --> MAM02039c + MAM03157c,ok,ok,ok,ok,N/A
MAR05990,MAM01442c + MAM02200c --> MAM01442e + MAM02200e,ok,ok,ok,ok,N/A
MAR05992,MAM01306e + 3 MAM02519e --> MAM01306c + 3 MAM02519c,ok,ok,ok,MAR04933,N/A
MAR05992,MAM01306e + 3 MAM02519e --> MAM01306c + 3 MAM02519c,ok,ok,ok,ok,N/A
MAR05993,MAM01587e + MAM02039e --> MAM01587c + MAM02039c,ok,ok,ok,ok,N/A
MAR05994,MAM01587e + MAM02519e --> MAM01587c + MAM02519c,ok,ok,ok,MAR05995;MAR05996;MAR05997,N/A
MAR05995,MAM01587e + 2 MAM02519e --> MAM01587c + 2 MAM02519c,ok,ok,ok,MAR05994;MAR05996;MAR05997,N/A
Expand Down Expand Up @@ -6771,18 +6770,6 @@ MAR06327,MAM01588m + MAM02039i --> MAM01588c + MAM02039m,ok,ok,ok,ok,N/A
MAR06328,MAM01285c + MAM01371m <=> MAM01285m + MAM01371c,ok,ok,ok,ok,N/A
MAR06330,MAM01306c + MAM02751m --> MAM01306m + MAM02751c,ok,ok,ok,ok,N/A
MAR06331,MAM02661c + MAM02751m --> MAM02661m + MAM02751c,ok,ok,ok,ok,N/A
MAR06332,MAM01371m + MAM01637c --> MAM01371c + MAM01637m,ok,ok,ok,ok,N/A
MAR06333,MAM01371m + MAM01680c --> MAM01371c + MAM01680m,ok,ok,ok,ok,N/A
MAR06334,MAM01371m + MAM01754c --> MAM01371c + MAM01754m,ok,ok,ok,ok,N/A
MAR06335,MAM01285m + MAM01637c --> MAM01285c + MAM01637m,ok,ok,ok,ok,N/A
MAR06336,MAM01285m + MAM01680c --> MAM01285c + MAM01680m,ok,ok,ok,ok,N/A
MAR06337,MAM01285m + MAM01754c --> MAM01285c + MAM01754m,ok,ok,ok,ok,N/A
MAR06338,MAM01371m + MAM01642c --> MAM01371c + MAM01642m,ok,ok,ok,ok,N/A
MAR06339,MAM01371m + MAM01688c --> MAM01371c + MAM01688m,ok,ok,ok,ok,N/A
MAR06340,MAM01371m + MAM01756c --> MAM01371c + MAM01756m,ok,ok,ok,ok,N/A
MAR06341,MAM01285m + MAM01642c --> MAM01285c + MAM01642m,ok,ok,ok,ok,N/A
MAR06342,MAM01285m + MAM01688c --> MAM01285c + MAM01688m,ok,ok,ok,ok,N/A
MAR06343,MAM01285m + MAM01756c --> MAM01285c + MAM01756m,ok,ok,ok,ok,N/A
MAR06389,MAM02751m + MAM02914c --> MAM02751c + MAM02914m,ok,ok,ok,ok,N/A
MAR06431,MAM00345c --> MAM00345m,ok,ok,ok,ok,N/A
MAR06438,MAM00766c <=> MAM00766m,only when going forwards,ok,ok,ok,N/A
Expand All @@ -6807,48 +6794,6 @@ MAR07723,MAM01630c <=> MAM01630m,only when going backwards,ok,ok,ok,N/A
MAR07757,MAM02039i + MAM02944c --> MAM02039m + MAM02944m,ok,ok,ok,ok,N/A
MAR07760,MAM01736c + MAM02039i --> MAM01736m + MAM02039m,MAM01736m,ok,ok,ok,N/A
MAR07769,MAM02871c + MAM02877m <=> MAM02871m + MAM02877c,ok,ok,ok,ok,N/A
MAR07804,MAM01637m + MAM01643c <=> MAM01637c + MAM01643m,ok,ok,ok,ok,N/A
MAR07806,MAM01637m + MAM01680c <=> MAM01637c + MAM01680m,ok,ok,ok,ok,N/A
MAR07808,MAM01747c + MAM01754m <=> MAM01747m + MAM01754c,ok,ok,ok,ok,N/A
MAR07810,MAM01680c + MAM01754m <=> MAM01680m + MAM01754c,ok,ok,ok,ok,N/A
MAR07812,MAM01637c + MAM01754m <=> MAM01637m + MAM01754c,ok,ok,ok,ok,N/A
MAR07814,MAM01643c + MAM01754m <=> MAM01643m + MAM01754c,ok,ok,ok,ok,N/A
MAR07815,MAM01371m + MAM01747c --> MAM01371c + MAM01747m,ok,ok,ok,ok,N/A
MAR07816,MAM01285m + MAM01747c --> MAM01285c + MAM01747m,ok,ok,ok,ok,N/A
MAR07818,MAM01680c + MAM01747m <=> MAM01680m + MAM01747c,ok,ok,ok,ok,N/A
MAR07820,MAM01637c + MAM01747m <=> MAM01637m + MAM01747c,ok,ok,ok,ok,N/A
MAR07822,MAM01643c + MAM01747m <=> MAM01643m + MAM01747c,ok,ok,ok,ok,N/A
MAR07824,MAM01643m + MAM01680c <=> MAM01643c + MAM01680m,ok,ok,ok,ok,N/A
MAR07825,MAM01285m + MAM01643c --> MAM01285c + MAM01643m,ok,ok,ok,ok,N/A
MAR07826,MAM01371m + MAM01643c --> MAM01371c + MAM01643m,ok,ok,ok,ok,N/A
MAR07827,MAM01747m + MAM01756c --> MAM01747c + MAM01756m,ok,ok,ok,ok,N/A
MAR07828,MAM01754m + MAM01756c --> MAM01754c + MAM01756m,ok,ok,ok,ok,N/A
MAR07829,MAM01680m + MAM01756c --> MAM01680c + MAM01756m,ok,ok,ok,ok,N/A
MAR07830,MAM01642c + MAM01643m --> MAM01642m + MAM01643c,ok,ok,ok,ok,N/A
MAR07831,MAM01637m + MAM01756c --> MAM01637c + MAM01756m,ok,ok,ok,ok,N/A
MAR07832,MAM01643m + MAM01756c --> MAM01643c + MAM01756m,ok,ok,ok,ok,N/A
MAR07833,MAM01371m + MAM01753c --> MAM01371c + MAM01753m,ok,ok,ok,ok,N/A
MAR07834,MAM01285m + MAM01753c --> MAM01285c + MAM01753m,ok,ok,ok,ok,N/A
MAR07835,MAM01753c + MAM01754m --> MAM01753m + MAM01754c,ok,ok,ok,ok,N/A
MAR07836,MAM01747m + MAM01753c --> MAM01747c + MAM01753m,ok,ok,ok,ok,N/A
MAR07837,MAM01680m + MAM01753c --> MAM01680c + MAM01753m,ok,ok,ok,ok,N/A
MAR07838,MAM01637m + MAM01753c --> MAM01637c + MAM01753m,ok,ok,ok,ok,N/A
MAR07839,MAM01642c + MAM01754m --> MAM01642m + MAM01754c,ok,ok,ok,ok,N/A
MAR07840,MAM01643m + MAM01753c --> MAM01643c + MAM01753m,ok,ok,ok,ok,N/A
MAR07841,MAM01643m + MAM01645c --> MAM01643c + MAM01645m,ok,ok,ok,ok,N/A
MAR07842,MAM01645c + MAM01754m --> MAM01645m + MAM01754c,ok,ok,ok,ok,N/A
MAR07843,MAM01645c + MAM01680m --> MAM01645m + MAM01680c,ok,ok,ok,ok,N/A
MAR07844,MAM01637m + MAM01645c --> MAM01637c + MAM01645m,ok,ok,ok,ok,N/A
MAR07845,MAM01285m + MAM01645c --> MAM01285c + MAM01645m,ok,ok,ok,ok,N/A
MAR07846,MAM01371m + MAM01645c --> MAM01371c + MAM01645m,ok,ok,ok,ok,N/A
MAR07847,MAM01637m + MAM01688c --> MAM01637c + MAM01688m,ok,ok,ok,ok,N/A
MAR07848,MAM01642c + MAM01747m --> MAM01642m + MAM01747c,ok,ok,ok,ok,N/A
MAR07849,MAM01688c + MAM01754m --> MAM01688m + MAM01754c,ok,ok,ok,ok,N/A
MAR07850,MAM01688c + MAM01747m --> MAM01688m + MAM01747c,ok,ok,ok,ok,N/A
MAR07851,MAM01680m + MAM01688c --> MAM01680c + MAM01688m,ok,ok,ok,ok,N/A
MAR07852,MAM01643m + MAM01688c --> MAM01643c + MAM01688m,ok,ok,ok,ok,N/A
MAR07853,MAM01642c + MAM01680m --> MAM01642m + MAM01680c,ok,ok,ok,ok,N/A
MAR07854,MAM01637m + MAM01642c --> MAM01637c + MAM01642m,ok,ok,ok,ok,N/A
MAR07897,MAM02193c <=> MAM02193m,ok,ok,ok,ok,N/A
MAR07899,MAM01714c <=> MAM01714m,MAM01714m,ok,ok,ok,N/A
MAR07914,MAM00267m --> MAM00267c,ok,ok,ok,ok,N/A
Expand Down
4 changes: 2 additions & 2 deletions data/testResults/macaw_summary.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ Starting dead-end test...
- Found 1368 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.
- Found 379 reactions that were some type of duplicate:
- Found 377 reactions that were some type of duplicate:
- 0 were completely identical to at least one other reaction.
- 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
- 379 involve the same metabolites but with different coefficients as at least one other reaction.
- 377 involve the same metabolites but with different coefficients as at least one other reaction.
Loading
Loading