Releases v1.16.0
Fixes (PR #643 )
remove MAR20015, MAR20014, MAR20052 for being duplicates of MAR04689, MAR06981, MAR00067, repectively, based on #630
also merge all annotations (E.C. codes, corresponding IDs in other models/databases) from the removed reactions into the kept ones
Fixes (PR #629 )
fix Yaml file's bug found in #628
Fixes (PR #623 )
update GPRs and PMID for 5-aminolevulinate transport reactions MAR09985 and MAR11307#588 :
Fixes (PR #619 )
change metCharges field to int64 type and fix bug in readlines reported in #608 :#612 )
reorganize redox reactions catalyzed by electron transfer flavoprotein, as proposed in #608
update GPR of MAR06911
remove MAR00562 and MAR00563 for being redundant with MAR06911
remove MAM03573m and MAM03574m
Fixes (PR #606 )
revise GPRs and modify reactions related to CLYBL (ENSG00000125246), as discussed in #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 #605 )
merge duplicate Malonyl Carnitine metabolites MAR05434 and MAR02599, as reported in #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 #602 )
assign compartment-specifc GPRs to carbonic anhydrase reactions MAR03955 and MAR05407, as detailed in #597
Fixes (PR #601 )
deal with duplicate carbonic anhydrase reaction sets by removing two-stpe versions and keep one-step reactions, as listed in #589
Fixes (PR #600 )
update NA+/Pi transport reactions GPRs as referenced in #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 #596 )
change the GPR of MAR04372 from ENSG00000172331 to ENSG00000119640 or ENSG00000170634, as discussed in #587
Fixes (PR #592 )
add Acylpyruvase FAHD1 (ENSG00000180185) to Human-GEM and to GPR of MAR20110 and MAR11430, as proposed in #585
Fixes (PR #591 )
add AUH to previously-empty GPRs of MAR05999, MAR08664, and MAR11514, derived from the discussion in #590
update Rhea Ids and PMID to above reactions
Fixes (PR #581 )
revise reactions, GPRs, and references for glucose Uptake and Na+/K+ pumps, as detailed in #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 #576 )
remove chloride-dependent transporter SLC6A14 (ENSG00000268104) from GPRs of 22 reactions without Cl- listed in #567
Features (PR #575 )
add 39 new rxns related to histidine metabolism, as reported in #553
Fixes (PR #573 )
remove/merge duplicate reactions reported in #561
adds ENSG00000198099 to the GPR of MAR06644
Featurs (PR #564 )
add GH action check for both essential and basic verification tasks, as mentioned in #390
Featurs (PR #563 )
add essentiality analysis suite using Hart2015 datasets, as discussed in #390
Features (PR #560 )
curate GPRs for cysteine metabolism reactions, as reported in #552
Fixes (PR #559 )
curate reactions and GPRs for Alanine, Aspartate and Glutamate subsystem, as proposed in #548
Fixes (PR #557 )
make a total of 180 non-transport/exchange pyrophosphate reactions irreversible, based on the report in #527
Features (PR #556 )
improve GH actions in sanityCheck.py by enabling detection of unused metabolites, triggered by mistakes found in #525
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