Human 1.9.0

• Style (PR #294):
  • add and reformat citations in README
• Fixes (PR #292):
  • replace deprecated Ensembl gene ids with updated ones, as reported in #278
  • update genes.tsv annotation file using script fetch_ensembl_gene_annotations
• Features (PR #291):
  • adjust sanityCheck script to enable the detection of reusing deprecated MA ids, as discussed in #265
• Fixes (PR #290):
  • fix the ATP hydrolysis stoichiometry in biomass equation MAR13082, as reported in #289.
• Fixes (PR #287):
  • refactor fetch_ensembl_gene_annotations.py script to allow retrieving annotations with empty gene symbols or ENSP ID, and to show the replacement Ensembl IDs for deprecated ones, as proposed in #278
• Features (PR #286):
  • introduces a GH Action for testing the yaml conversion with testYamlConversion.
• Fixes (PR #285):
  • fix: merge duplicated long-chain fatty acyl-CoA mets, as reported in #268, #269
• Style (PR #284):
  • rename default branch (master --> main) as discussed in #226
  • change default branch names in repo documents and code
• Fixes (PR #283):
  • remove cytosolic protons from reaction in other subcellular compartments, as detailed in #282
    • revise MAR05259 by replacing proton with lysosomal version
    • remove MAR04758 that is duplicate to MAR01044
    • remove MAR01459 that is duplicate to MAR02041, whose proton is replaced with the mitochondrial version
• Fixes (PR #281):
  • excluded gene ENSG00000197375 from MAR02590 (carnitine shuttle), due to lack of evidence (#279)
• Style (PR #275):
  • add .gitattributes file to ensure consistent LF line endings as discussed in #264
• Features (PR #274):
  • add rxnNotes field to Human-GEM, as planned in #272
  • adjust importYaml/exportYaml functions to enable handling of rxnNotes field

Human 1.8.0

• 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

Human 1.7.0

• Features (PR #245):
  • a new column metMAID is added to metabolites.tsv, according to the plan proposed in #174
• Features (PR #241):
  • update reactions.tsv by adding associations to Rhea ids that mapped to 590 rxns so far
• Fixes (PR #240):
  • update annotation for mets m01778 and m02646, as suggested in #239:
• Features (PR #237):
  • add new function evalGeneEssentialityPred that can be used to assess gene essentiality predictions made by a GEM
• Features (PR #234):
  • complete the ids of rxnMAID in reactions.tsv by filling blank fields, as agreed in #174
• Fixes (PR #230):
  • remove the extra space at the end of the subsystem and reaction names
• Style (PR #228):
  • rename functions as proposed in #227
    • annotateModel --> annotateGEM
    • importHumanYaml --> importYaml
    • writeHumanYaml --> exportYaml
  • replace branch devel with develop
• Style (PR #223):
  • re-organize files and folders as discussed in #190
    • move files, scripts, and models in data/ and code/ that are no longer maintained or in use to a .deprecated folder
    • add README file for data and code directories

Human 1.6.0

• 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)

Human 1.5.0

• Fixes (PR #206):
  • curate subSystems names as proposed in #205
    • replace 131 Metabolism of xenobiotics by cytochrome P450 with Xenobiotics metabolism
    • change 2 Alkaloids Biosynthesis to Alkaloids biosynthesis
• Fixes (PR #202):
  • Ensembl id mapping file is updated from version 95 to 101
  • remove genes ENSG00000281028 and ENSG00000285441 because they were reported to be retired in Ensembl (#200)
• Fixes (PR #199):
  • correct gene association with reaction HMR_8177, as reported in #198
  • update references and confidence scores for HMR_8171, HMR_8177, HMR_8180, HMR_8181, and HMR_8182
• Features (PR #195):
  • add new functions getModelFromOrthology, extractAllianceGenomeOrthologs, and replaceGrRules, for expanding the applications of Human-GEM

Human 1.4.1

• Style (PR #188, #185):
  • adapt to standard-GEM ver 0.4
    • rename folder from modelFiles to model
    • remove embedded subfolders
    • rename model files from HumanGEM to Human-GEM
• Features (PR #187):
  • implement Python3 and latest pip for cobrapy, add basicCheck script to Yaml-based workflow for routine check
• Fixes (PR #186):
  • remove inactivated reactions from Human-GEM, as described in #183
• Features (PR #182):
  • add dedicated fields of HMR2 reactions (rxnHMR2ID) and metabolites (metHMR2ID) to JSON annotation files for assisting convenient association and tracking

Human 1.4.0

• Features (PR #179):
  • remove the boundary compartment and associated metabolites both in model and metabolite annotation JSON file, as explained in #172
• Style (PR #177):
  • with the consensus reached in #176, authorship and timestamps are completely removed from the code of Human-GEM, given the built-in Github blame feature
• Features (PR #175):
  • add rxnMAID field to reaction annotation JSON file, as discussed in #174
• Features (PR #173):
  • enhancements to Yaml workflow
    • add checks of yamllint and cobrapy model import as GitHub actions
    • address indentation, blank spaces and first line issues raised in #169
• Fixes (PR #171, #178):
  • modify subsystems of HMR_5407, RN0001R, RN0002N and RN0002R, as addressed in #129
  • remove reaction HMR_4362 from model and reaction annotation JSON file, as proposed in #153
• Fixes (PR #170):
  • systematically add double quote to string elements in Yaml, as reported in #169

Human 1.3.2

• Fixes (PR #167):
  • remove dash from model ID Human-GEM when exporting to SMBL format
• Doc (PR #165):
  • update README file with links to new User guide and relevant websites
• Features (PR #163):
  • add gene associations and references to four mitochondrial transport reactions, as proposed in #119
• Fixes (PR #162):
  • standardize EC numbers by reformatting ids and correcting invalid characters, as proposed in #93, #127 and #164
    • modify eccodes field by removing invalid characters, and moving spontaneous and TCDB ids to new fields in annotation file humanGEMRxnAssoc.JSON
    • remove unused metabolites m10018m, m10018p and m10010n from the model and annotation file humanGEMMetAssoc.JSON
    • adjust function annotateModel to adapt to newly added fields
    • rename subfolder ModeFiles to modelFiles

Human 1.3.1

• Fixes (PR #160):
  • modify increaseHumanGemVersion function to adapt with the Yaml-based workflow and enable xlsx format output
• Style (PR #159):
  • reorganize repository directory structure according to standard-GEM template
    • remove deprecated functions docRxnChanges and writeRxnChanges
    • rename folders complementaryData and complementaryScripts to data and code, respectively
    • restructure code subfolder and include a dedicated README
• Fixes (PR #158):
  • adjust getINITModel2 to avoid removing metabolic task-associated metabolites
• Features (PR #156):
  • activate Yaml-based workflow
    • remove MATLAB model file from current and later all other branches except master
    • minor fixes to importHumanYaml and testConversionYaml

Human 1.3.0

• Features (PR #152):
  • feat: enable lossless Mat-Yaml model conversion toward a Yaml-based workflow
    • remove fields compOutside,rxnMiriams and metMiriams from HumanGEM model structure, and modify elements of rxnReferences and rxnConfidenceScores fields
    • importHumanYaml and testYamlConversion functions are adjusted to comply with recent model changes
• Featurs (PR #140):
  • further integration of iHsa model into HumanGEM
    • 1605 InChI strings conflicting with metFormula are removed
    • 67 new reactions
    • 60 new metabolites
    • 688 updated KEGG reaction associations
    • 1 new gene ENSG00000183463
    • modified annotation and model changes are updated to the humanGEMRxn/MetAssoc.JSON and iHsaAdditionalIntegration_modelChanges_mets/rxns.tsv files