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@haowang-bioinfo haowang-bioinfo released this 30 Sep 16:52
· 298 commits to main since this release
v1.17.0
ca9745d
  • Fixes (PR #696)
    • update name for GAP in Cellfie Consensus metabolic tasks
  • Features (PR #692)
    • sync geneShortNames field (introduced by #539) by padding with empty elements in function addMetabolicNetwork
    • enable updateAnimalGEM with option of reusing Human-GEM biomass equation
  • Fixes (PR #678)
    • remove 9 reactions involving MAM01268 or MAM02757 in all compartments, and 10 metabolites and 22 genes that only participated in these reactions, as discussed in the comments on #580
  • Fixes (PR #677)
    • remove MAR01515, MAR00039, MAR00096, MAR02027, MAR02006 that are duplicates of MAR08529, MAR07992, MAR04819, MAR04302, MAR03873, respectively, as proposed in #665
    • merge references from removed reactions into kept ones
  • Fixes (PR #676)
    • convert MAR04145, the citrate synthase reaction, irreversible, as proposed in #673
    • swap the products and reactants to have non-negative fluxes, and add textbook reference to rxnNotes
  • Features/Fixes (PR #672, #635)
    • fix GH workflow test of the import-export cycle for resolving #628
    • introduce basic MEMOTE tests in the yaml-validation workflow, including checks for duplicate reactions and ensure all reactions have at least one metabolite
  • Fixes (PR #670)
    • remove MAR00059 for being a less accurate version of MAR01706, as discussed in #639
    • change the GPR of MAR01706 to "ENSG00000113790 or ENSG00000133835" and add PMID:19357427 as reference
    • remove MAR01639, MAR03301, MAR03306, MAR03311, MAR04966, MAR03364, MAR03369 that are duplicates of MAR01638, MAR02804, MAR02808, MAR02810, MAR02818, MAR03276, MAR03289, respectively
    • create new reaction MAR20114 to represent reduction of O2 by FADH2: MAM02630x + MAM01803x -> MAM02041x + MAM01802x, GPR: ENSG00000161533 or ENSG00000168306 or ENSG00000087008 or ENSG00000110887 or ENSG00000203797 or ENSG00000007171 or ENSG00000148832 or ENSG00000179761 or ENSG00000158125, with reference: PMID:30378035
    • replace MAM02630x (O2) with MAM01802x (FAD) and MAM02041x (H2O2) with MAM01803x (FADH2) in a total of 120 reactions, as detailed in #639
  • Fixes (PR #669)
    • remove implausible mitochondrial version Bile Acid Synthesis pathway (13 reactions and 8 metabolites), as outlined in #637
  • Fixes (PR #667)
    • merge MAM03231 into MAM03232, as reported in #627
    • update ChEBI ID for MAM02679, MAM02579, MAM02043, MAM03887
  • Features/Fixes (PR #666)
    • improves documentation of deprecated reactions in #613 by adding them to corresponding rows "rxnRetired" column in reactions.tsv, as a tentative implementation according to the discussion in #615
  • Fixes (PR #664)
    • update GPR of reversible transport reaction MAR01527 of sodium across cell membrane by expanding 19 transporter genes based on TCDB and literature, as discussed in #583
  • Fixes (PR #663)
    • remove mets MAM03318 and MAM03325 for being duplicates of MAM01435 and MAM00684, respectively, as discussed in #617
    • remove rxns MAR02276, MAR02277, MAR02384, MAR02390, MAR02392, MAR02394, MAR04144 and MAR10447 for being affected by duplicate mets
    • change HMDB ID annotations for MAM02679 and MAM01090
  • Fixes (PR #662)
    • remove met MAM03540, for being duplicate of MAM01729, and rxn MAR04506, as discussed in #622
    • change KEGG ID annotations for MAM01230, MAM02676, MAM02647, MAM03021, MAM00531, MAM02678, MAM02679
  • Fixes (PR #661)
    • remove mets MAM00591 and MAM03162 for being duplicates of MAM0270 and MAM1739, respectively, as discussed in #621
    • remove rxns MAR00941, MAR06142, MAR06143, MAR06144, MAR06220, MAR06252, MAR10025, MAR09733, MAR09734 for being affected by duplicate mets
    • update annotation for MAM01322, MAM02043, MAM02579, MAM02679
  • Fixes (PR #660)
    • remove MAR03767 for being duplicate of MAR06421+MAR06422, as proposed in #633
    • update duplication info to "rxnRetired" column in reactions.tsv
  • Fixes (PR #658)
    • remove lipid droplet reaction MAR00032 and associated non-metabolic genes ENSG00000072062, ENSG00000142875, ENSG00000165059, ENSG00000172531, ENSG00000186298, and ENSG00000213639, as proposed in #631
  • Fixes (PR #657)
    • remove MAR02358, MAR20066, MAR20020, MAR20002, MAR00030 that are duplicates of MAR08482, MAR03984, MAR04521, MAR06631, MAR00025, respectively, as reported in #580 and #630
    • update the pairing info to "rxnRetired" column for kept reactions in reactions.tsv
    • merge annotations, references, E.C. codes, etc. from removed reactions into kept reactions
    • make MAR08482 reversible
    • revise compartment-specific GPRs for MAR08482 and MAR03931
  • Fixes (PR #655)
    • remove MAR05310 for being partially duplicate to MAR06380, and merge its annotation into that of MAR06380, as proposed in #569
    • revise GPR of MAR06380 to ENSG00000017483 or ENSG00000188338
    • convert MAR06380 to reversible
    • removes MAR09887 for being partially duplicate to MAR06896
  • Fixes (PR #650)
    • remove met MAM00759 for being duplicates of MAM01314, as investigated in #620
    • update LipidMaps ID annotation for MAM00892, MAM00895, MAM00057, MAM02647
  • Fixes (PR #649)
    • remove mets MAM03354, MAM03332, MAM00029, MAM03368, MAM00902 for being duplicates of MAM00131, MAM01696, MAM00028, MAM00748, and MAM00853, respectively, as discovered in #616
    • remove rxns MAR03441, MAR02588, MAR10164, MAR10433 for being affected by duplicate mets
    • change EHMN ID annotations for MAM01123
  • Fixes (PR #646)
    • remove mets MAM03226, MAM03884, MAM03554 for being duplicates of MAM00785, MAM02746, and MAM00933, respectively, as discussed in #610
    • remove rxns MAR00042, MAR01617, MAR00740, MAR00659, MAR05323, MAR01709 for being affected by duplicate mets
    • change BiGG ID annotations for MAM01746, MAM00078, MAM02328, MAM02008
  • Fixes (PR #641)
    • convert pyrophosphate-producing MAR02786, MAR02802, MAR03388, MAR03390, MAR09508, MAR01845, MAR09523, and MAR09546 irreversible, as mentioned in #527
  • Fixes (PR #625)
    • merge 31 pairs of irreversible transport reactions, reported in #562, into single reversible reactions
  • Fixes (PR #624)
    • tidy up acetyl-CoA carboxylase reactions, as proposed in #593:
  • Fixes (PR #613)
    • remove 15 FAD/Ubiquinone duplicate reactions, as detailed in #607
  • Fixes (PR #494)
    • modify simplifyGrRules function to fix compatibility with Matlab "children" function, which has been changed since 2020b, to resolve issue described in #493
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