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Remove inaccurate mitochondrial nucleotide transport reactions #944

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Remove inaccurate mitochondrial nucleotide transport reactions #944

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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
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55 changes: 55 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -302,3 +302,58 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR07799" "" "ATPasel" "" "" "" "" "MNXR96136" "HMR_7799" "RCR20334" "" 0 "" "" "HMR_7799"
"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180"
"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m"
"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"
2 changes: 1 addition & 1 deletion data/testResults/README.md
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Expand Up @@ -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 #830** (MACAW)
- **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
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Expand Up @@ -5264,7 +5264,6 @@ 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 @@ -5930,7 +5929,7 @@ 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 @@ -6815,18 +6814,6 @@ 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 @@ -6851,48 +6838,6 @@ 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
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4 changes: 2 additions & 2 deletions data/testResults/macaw_summary.md
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Expand Up @@ -4,7 +4,7 @@ Starting dead-end test...
- Found 1975 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 447 reactions that were some type of duplicate:
- Found 445 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.
- 447 involve the same metabolites but with different coefficients as at least one other reaction.
- 445 involve the same metabolites but with different coefficients as at least one other reaction.
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