Skip to content

Human 1.15.0
Compare
Choose a tag to compare
@haowang-bioinfo haowang-bioinfo released this 09 May 08:20
· 660 commits to main since this release
v1.15.0
194ebe5
  • Fixes (PR #555, #541, #538, #532, #529, #525)
    • resolve duplicate krebs cycle reactions catalyzed by aconitase, isocitrate dehydrogenases, pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, as well as glycine cleavage system, by only keeping the highest resolution versions except IDH
    • pinpoint GPRs of above reaction to compartment-specific enzymatic genes, and modify reversibilities when necessary
    • above the implementation plans are discussed in #523, #524, and #525
    • fix GPRs for Cytochrome C Oxidoreductase, as discussed in #526
  • Fixes (PR #551)
    • remove MAR04568, make MAR04567 irreversible in the direction of ATP consumption, and phosphatase reaction MAR20070, as proposed in #547:
  • Features/Style (PR #550, #542):
    • add new contributors
  • Features (PR #549)
    • add new field geneShortNames for gene symbols, as discussed in #539
  • Features/Style (PR #546):
    • remove authors, email, and organization fields in code and Yaml file for moving toward community curation on GitHub
  • Fixes (PR #540)
    • modify GPRs of MAR01453, MAR11476, MAR11479 AND MAR04281, as introduced in #528
  • Fixes (PR #537)
    • replace ENSG00000137700 with ENSG00000281500, as proposed in #510
      • take away GPI (ENSG00000105220) from transport reaction MAR04856
      • complete association to Uniprot ids in genes.tsv
    • remove other GCS genes from GPR of MAR06409, as discussed in #529
  • Features (PR #535)
    • add 87 new mets, 68 new reactions in Glycolysis pathway, as listed in #507
  • Fixes (PR #534)
    • remove duplicate met MAM00077x and corresponding rxns MAR03488 and MAR03489, as reported in #519
  • Fixes (PR #533)
    • rename mets in tyrosine exchange, transport, and metabolism reactions from XxxtyrYyy to XxxTyrYyy
  • Fixes (PR #520)
    • modify GPRs of CoA metabolism, as proposed by #502
  • Fixes (PR #518)
    • fix the met name of MAM02053, as discussed in #491
  • Fixes (PR #517)
    • remove wrongly associate genes in glycolysis (#507) and lactate dehydrogenase (#516)
  • Fixes (PR #515)
    • refine GPRs in Pentose phosphate pathway, as proposed in #501
  • Fixes (PR #513)
    • remove 21 pseudogenes, read through genes, and ones with only predicted functions, as proposed in #510.
  • Fixes (PR #509)
    • refine GPRs of Pyrroline-5-carboxylate reductase according to compartment and cofactor annotation reported in #505
  • Features (PR #508, #506)
    • add/update Rhea master IDs to reacitons.tsv annotation file for a total of 1334 reactions
  • Fixes (PR #504)
    • assign compartment-specific NAD kinase genes to MAR04268 and MAR04269, and remove MAR04279, based on discussion in #503
  • Fixes (PR #499)
    • separate genes TYMP (ENSG00000025708) and PNP (ENSG00000198805) to GPRs of MAR04603, MAR04695, MAR04709, and MAR04485, as reported in #498
  • Fixes (PR #497)
    • update the Docker image used in GH Actions workflow
  • Fixes (PR #496)
    • correct GPRs of Arginases (MAR03816 and MAR08426) by using compartment-specific enzymatic genes, as reported in #495
  • Features/Style (PR #492)
    • re-organize subsystem names by merging Pantothenate and CoA biosynthesis, CoA synthesis, and CoA catabolism into one Pantothenate and CoA metabolism, as proposed in #487
  • Fixes (PR #490)
    • refactor the GitHub workflow by using native support for Docker rather than a separate action
  • Fixes (PR #489)
    • fix GPR rules of mitochondrial complexes II, IV, and V, as proposed in #468, #469, #470 based on Complex Portal annotation
Assets 2
Loading