SysBioChalmers/Human-GEM: Human 1.8.0

Main improvements in this PR:

• 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