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Human 1.6.0

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@haowang-bioinfo haowang-bioinfo released this 25 Jan 12:05
  • Fixes (PR #222, #216):
    • revise GPR for HMR_4137 as suggested by #214
      • add PDHA2 gene as an isoenzyme of PDHA1, and the supporting reference
  • Fixes (PR #221):
    • fix InChI strings as proposed in #220:
      • add InChI= prefix to all InChI strings
      • 338 missing InChI strings were filled by retrieving values from the same some metabolites in other compartments
      • 2 different mets but having identical InChI strings were corrected
      • 2 inconsistent formulas between inchi formula and metFormulas were fixed
  • Features (PR #218, #210):
    • add new functions
      • addMetabolicNetwork allows efficient integrating new reactions and metabolites into a model
      • gapfill4EssentialTasks conducts gap-filling so that the resulting model can undertake all essential tasks defined by Human-GEM
  • Features (PR #217):
    • add new metabolic task for vitamin C biosynthesis
  • Fixes (PR #215):
    • remove GPR association to HMR_4740, as explained in #149
  • Fixes/Features (PR #213):
    • remove 16 duplicated mets, which were reported in #184, and derived duplicated rxns
    • remove others reaction, as agreed in #197
    • move tsv format annotation files from data/annotation to model/
  • Features (PR #212)
    • a tsv-based annotation scheme was implemented, as proposed in #203
      • JSON format annotation files for rxns, mets and genes were replaced with tsv format ones
      • dedicated functions importTsvFile and exportTsvFile for handling tsv files were provided
      • functions annotateModel, exportHumanGEM, sanityCheck and files README, CONTRIBUTING were updated accordingly
  • Fixes (PR #211):
    • add glpk, which is dependent by swiglpk, to GH Actions workflow
  • Features (PR #208):
    • tag Human-GEM releases to Zenodo (#194)