Human 1.13

[haowang-bioinfo]

Main improvements in this PR:

• Features (PR feat: add compartment info from deeploc2 prediction #440, feat: add compartment information to genes.tsv #437):
  • add compartment information to genes.tsv based on SwissProt annotation, Cell Atlas, and deeploc2 prediction, as discussed in tabulate sub-cellular localizations for metabolic enzymes #436
• Fixes (PR fix: update HMDB IDs to version 4  #435):
  • update HMDB IDs to version 4 format and fix ID for MAM03055r, as suggested Issues with the HMDB IDs of metabolites #434
• Fixes (PR Fix: Remove reaction MAR02517 #432):
  • remove the reaction MAR02517 and 4 metabolites (MAM02444l, MAM02678l, MAM00890l, and MAM01596l) that were involved in no other reactions, to address issue MAR02517 should not be associated with the CTSA gene #381
• Fixes (PR fix: make sure pmid is followed by colon #431, fix: add missing PMID prefix for references #428):
  • systematically format PMIDs, to resolve inconsistency reported in Inconsistency of PMID in the REFERENCE field for several reactions #430, reaction MAR03099 is missing a PMID prefix #427
• Features (PR feat: add cis-aconitate decarboxylase reaction and change reversibility for MAR09498 #429):
  • add cis-aconitate decarboxylase reaction according to Mouse-GEM issue #20, and change reversibility for MAR09498, as reported in MAR09498 (catalyzed by MGMT) should be irreversible #425
• Features (PR feat: add an install script like in GECKO3 #423):
  • add an install script to resolve Create an "install" function for easy repo installation #136
• Features (PR feat: prepHumanModelForftINIT with paths #422):
  • allow prepHumanModelForftINIT to take the paths to reactions.tsv and essential tasks as optional parameters, as proposed in prepHumanModelForftINIT should take the paths to reactions.tsv and essential tasks as optional params #401
• Fixes (PR fix: remove some empty fields from imported yaml model #420):
  • enables importYaml to get rid of empty and non-essential fields
• Fixes (PR fix: curate GPR rule for MAR04926 #419):
  • curate GPR rule for MAR04926, as discussed in GPR curation for MAR04926 #417
• Fixes (PR fix: set MAR05998 to be reversible #415):
  • set MAR05998 to be reversible, as proposed in Reaction MAR05998 should be listed as reversible #412
• Fixes (PR Fix: Amend #403 by merging additional model fields from duplicated rxns #405, Fix: Remove duplicate reactions (addresses Issue 345) #403):
  • evaluate and remove duplicated reactions, to address the issue discussed in Remove duplicates - identical except that one is unidirectional, the other reversible #345

[feiranl]

Looks good!