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Human 1.8.0
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@haowang-bioinfo haowang-bioinfo released this 23 Jun 15:07
v1.8.0
fb2632e
  • Style/Features (PR #270):
    • replace rxns and mets fields in Human-GEM and annotation tsv files with respective MA ids, as planned in #265
    • regenerate metsNoComp column from MA met ids
  • Fixes (PR #263):
    • fix bug reported in #262, by removing quotes from spontaneous column in reactions.tsv
    • add structure information of annotation tsv files to README
    • Add test to the type of spontaneous in sanityCheck
  • Fixes (PR #261):
    • modify the subsystem annotation for the exchange reactions found in #255, by changing from Miscellaneous to Exchange/demand reactions
  • Features (PR #258):
    • add new reaction HMR_10133 of taurine synthesis from oxygenation of hypotaurine, as discussed in #257
    • the existing HMR_8759 and HMR_3911 appear to be infeasible and therefore are blocked (ub = lb = 0).
  • Fixes (PR #254):
    • reformat field rxnReferences by consistently using pmids:
      • remove uniprot ids
      • remove omim ids
      • remove hmdb ids
      • use only pmids
      • format the field as PMID:\d+ and separate multiple values by ;
      • highlight broken references by having the field start with ??
  • Features (PR #251):
    • update fetch_ensembl_gene_annotations.py script so that gene annotationgenes.tsv file can be directly generated as defined in #157
  • Features (PR #244):
    • add more annotation features geneNames and geneAliases for genes
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