Human 1.16

[haowang-bioinfo]

Main improvements in this PR:

• Fixes (PR Fix/merge same stoich same gpr rxns #643)
  • remove MAR20015, MAR20014, MAR20052 for being duplicates of MAR04689, MAR06981, MAR00067, repectively, based on Suspected duplicated reactions #630
  • also merge all annotations (E.C. codes, corresponding IDs in other models/databases) from the removed reactions into the kept ones
• Fixes (PR fix-add a error report in the import/export cycle #629)
  • fix Yaml file's bug found in bug identified in development branch #628
• Fixes (PR fix: add GPRs and references for MAR09985 and MAR11307 #623)
  • update GPRs and PMID for 5-aminolevulinate transport reactions MAR09985 and MAR11307
    , as suggested in GPRs for MAR09985 and MAR11307 #588:
• Fixes (PR fix: fatal importYaml bug #619)
  • change metCharges field to int64 type and fix bug in readlines reported in Electron Transport Flavoprotein #608:
    Fixes (PR Fix Representation of ETF #612)
  • reorganize redox reactions catalyzed by electron transfer flavoprotein, as proposed in Electron Transport Flavoprotein #608
    • update GPR of MAR06911
    • remove MAR00562 and MAR00563 for being redundant with MAR06911
    • remove MAM03573m and MAM03574m
• Fixes (PR Fix Reactions Related To CLYBL #606)
  • revise GPRs and modify reactions related to CLYBL (ENSG00000125246), as discussed in Inaccurate Representation of CLYBL #586
    • add CLYBL to the GPR of MAR08666
    • add PMID:24334609 as a reference of MAR08666
    • create new reaction MAR020111 to represent malate synthase activity of CLYBL: MAM02007m + MAM01261m + MAM02040m -> MAM02439m MAM01597m, GPR: ENSG00000125246, reference: PMID:24334609
    • remove MAR05294 and MAR11421 since neither CLYBL nor any other human enzyme catalyzes those reactions
• Fixes (PR Fix Duplicate Malonyl Carnitine Metabolites #605)
  • merge duplicate Malonyl Carnitine metabolites MAR05434 and MAR02599, as reported in Duplicate Metabolites For Malonyl Carnitine #595
    • rename MAM02443c, MAM02443m, MAM02443r, and MAM02443x to "malonyl-carnitine"
    • create new metabolite MAM02443e
    • replace MAM03494c and MAM03494e with MAM02443c and MAM02443e in MAR04886 and MAR11256
    • remove MAR05434 for being redundant with MAR02599
    • remove MAM03494c and MAM03494e for being redundant with MAM02443c and MAM02443e
    • merge old annotations for MAM03494c/e into current annotations for MAM02443c/e in metabolites.tsv
• Fixes (PR Fix GPRs of Carbonic Anhydrase Reactions #602)
  • assign compartment-specifc GPRs to carbonic anhydrase reactions MAR03955 and MAR05407, as detailed in Compartment-Specific GPRs for Carbonic Anhydrase Reactions #597
• Fixes (PR Remove Two-Step Carbonic Anhydrase Reactions & Carbonate Metabolites #601)
  • deal with duplicate carbonic anhydrase reaction sets by removing two-stpe versions and keep one-step reactions, as listed in Duplicate Carbonic Anhydrase Reactions #589
• Fixes (PR Fix/update na pi transport rxn gp rs #600)
  • update NA+/Pi transport reactions GPRs as referenced in Possibly remove Reaction MAR04411 #568
    • remove reaction MAR04411 and MAR05413
    • add ENSG00000143324 (XPR1) to the GPR of MAR02351, add ENSG00000144136 (SLC20A1) and ENSG00000168575 (SLC20A2) to the GPR of MAR04910
• Fixes (PR fix: correct GPR for MAR04372 #596)
  • change the GPR of MAR04372 from ENSG00000172331 to ENSG00000119640 or ENSG00000170634, as discussed in Inaccurate GPR of MAR04372 #587
• Fixes (PR Fix: Add FAHD1 #592)
  • add Acylpyruvase FAHD1 (ENSG00000180185) to Human-GEM and to GPR of MAR20110 and MAR11430, as proposed in FAHD1 Catalyzes MAR11430 #585
• Fixes (PR fix: Add AUH to previously-empty GPRs of MAR05999, MAR08664, and MAR11514 #591)
  • add AUH to previously-empty GPRs of MAR05999, MAR08664, and MAR11514, derived from the discussion in GPR for MAR08664 #590
  • update Rhea Ids and PMID to above reactions
• Fixes (PR Fix Sodium-Dependent Glucose & Galactose Uptake Reactions #581)
  • revise reactions, GPRs, and references for glucose Uptake and Na+/K+ pumps, as detailed in Problems with Glucose Uptake and Sodium/Potassium Pump Reactions #570
    • Remove MAR05295, MAR06894, and MAR06895
    • Remove ENSG00000140675 from MAR05029
    • Copy references from MAR05429 to MAR05295
    • Change MAR01444 to ATP [c] + H2O [c] + K+ [e] + H+ [e] + 2 Na+ [c] ⇒ ADP [c] + Pi [c] + K+ [c] + H+ [c] + 2 Na+ [e], GPR: ENSG00000075673 and ENSG00000186009
• Fixes (PR Fix: Removed ENSG00000268104 from the following reaction GPRs: MAR053… #576)
  • remove chloride-dependent transporter SLC6A14 (ENSG00000268104) from GPRs of 22 reactions without Cl- listed in ENSG00000268104 Should probably be removed from GPRs of reactions without Cl- #567
• Features (PR feat-add new rxn annotations for histidine metabolism #575)
  • add 39 new rxns related to histidine metabolism, as reported in GPR curation for Histidine metabolism #553
• Fixes (PR fix: remove or merge near-duplicate reactions (attempt 2) #573)
  • remove/merge duplicate reactions reported in Suspicious near-duplicate reactions #561
  • adds ENSG00000198099 to the GPR of MAR06644
• Featurs (PR feat: add test for metabolic tasks #564)
  • add GH action check for both essential and basic verification tasks, as mentioned in feat: include an essentiality summary for each release #390
• Featurs (PR feat: add hart2015 essentiality suite #563)
  • add essentiality analysis suite using Hart2015 datasets, as discussed in feat: include an essentiality summary for each release #390
• Features (PR feat-curate GPR for cysteine metabolism #560)
  • curate GPRs for cysteine metabolism reactions, as reported in GPR curation for Cysteine metabolism #552
• Fixes (PR GPR curation for Alanine, Aspartate and Glutamate subsystem #559)
  • curate reactions and GPRs for Alanine, Aspartate and Glutamate subsystem, as proposed in Refine GPRs for Alanine, Aspartate and Glutamate subsystem #548
• Fixes (PR Fix: Make all non-transport/exchange pyrophosphate reactions irreversible #557)
  • make a total of 180 non-transport/exchange pyrophosphate reactions irreversible, based on the report in (d)NTP <-> (d)NMP + PPi Reactions Should Be Irreversible #527
• Features (PR feat: enable sanityCheck.py to check unused mets and genes #556)
  • improve GH actions in sanityCheck.py by enabling detection of unused metabolites, triggered by mistakes found in fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism #525

[feiranl]

LGTM!

[haowang-bioinfo]

now the Hart2015 essentiality suite (#563) is added to this release, with following results:

'cellLine'	'TP'	'TN'	'FP'	'FN'	'accuracy'	'sensitivity'	'specificity'	'F1'	'MCC'	'Penr'	'logPenr'	'PenrAdj'	'logPenrAdj'
'DLD1'	95	2109	143	223	0.85758755	0.29874214	0.93650089	0.34172662	0.26721557	1.04E-30	29.9838919	3.11E-30	29.5067706
'GBM'	85	2081	153	250	0.84312962	0.25373134	0.93151298	0.29668412	0.21515393	1.78E-21	20.7503043	2.67E-21	20.5742131
'HCT116'	113	2137	130	246	0.85681645	0.31476323	0.94265549	0.37541528	0.3051743	3.02E-40	39.519913	1.81E-39	38.7417618
'HELA'	86	2182	157	202	0.86334222	0.29861111	0.9328773	0.32391714	0.24962285	2.74E-27	26.5616613	5.49E-27	26.2606313
'RPE1'	63	2115	175	216	0.8478007	0.22580645	0.92358079	0.24371373	0.16031484	6.69E-13	12.1747792	6.69E-13	12.1747792
'all'	41	2308	202	76	0.89417587	0.35042735	0.91952191	0.22777778	0.19220101	2.19E-15	14.6589606	2.63E-15	14.5797793