Releases · SysBioChalmers/Human-GEM

08 Dec 14:29

haowang-bioinfo

v1.18.0

104f22b

Human 1.18.0 Latest

Latest

Fixes (PR #740)
- remove ACAD10 from the GPRs of MAR03212 and MAR03163, as well as from Human-GEM altogether, as explained in #739
Fixes (PR #725)
- remove duplicate 2-oxoadipate dehydrogenase reaction MAR04239, modify GPRs of MAR04599, MAR04209, and MAR06413, remove ENSG00000197444 (OGDHL) gene, as well as incoporate other miscellaneous curations, based on investigation results presented in #719
Fixes (PR #724)
- replace inaccurate GPR and reference for MAR04665 with ENSG00000182199 (SHMT2) and "PMID:11087421", as discussed in #720
Fixes (PR #723)
- revise mitochondrial Glutathione transport reactions as discussed in #722, by modifying MAR08771, and removing MAR04940 and MAR06391
Style (PR #721)
- add Christoff1993 as a contributor
Fixes (PR #717)
- resolve duplicate chemical speices hexanoate/hexanoic acid by systematically replacing hexanoate (MAM03684c) with hexanoic acid (MAM02120c), as reported by #716
Fixes (PR #715)
- curate GPRs and reaction names of 62 cytosolic short- and medium-chain fatty acid hydrolysis reactions, as proposed in #689
- add 4 new hydrolysis reactions
- add 2 new genes THEM4 (ENSG00000159445) and THEM5 (ENSG00000196407)
Fixes (PR #714)
- refine GPRs involving LIPT1 (ENSG00000144182) gene, as explained in #683
  - remove LIPT1 (ENSG00000144182) from the GPRs of MAR01088 and MAR01091
  - remove MAR06398, MAR06399, and MAM02398c (lipoyl-AMP), MAR06408, and MAM01701c
  - replace MAM02393m with MAM00209c in MAR08433, MAM01701m with MAM00208c in MAR08434
  - remove MAM02039c and MAM02039e from MAR11346
  - remove MAM02039i and MAM02039m from MAR11361
  - make MAR11361 reversible
Fixes (PR #713)
- split formuate dihydroorotate dehydrogenase reaction MAR04575 into two steps by adding new met MAM20019c (FMNH2) and new rxn MAR20167, as advised in #609
Fixes (PR #712)
- update and maintain consistency in the met IDs for FMN and FMNH2 and update their annotations, according to #711
Fixes (PR #710)
- remove duplicate glycerol-3-phosphate dehydrogenase rxns MAR00478 and MAR00482 and update annotations, as proposed in #599
Fixes (PR #709)
- reorganize nucleotide transport reactions [c]<->[m] by adding genes, reactions, updating GPRs, and removing reactions lack of proper transporters, as listed in #694
Fixes (PR #708)
- revises tryptophan metabolism reactions and GPRs, as outlined in #545
  - remove ENSG00000159423 (ALDH4A1) from MAR00051
  - remove MAR08564+MAR08565 that are duplicate to MAR04222
  - merge annotations for MAR08564+MAR08565 to that of MAR04222
  - remove derived orhpan met MAM00926c (4-(2-aminophenyl)-2,4-dioxobutanoate)
Fixes (PR #707)
- remove MAR06400 and MAR06401 for being duplicate to MAR06403 and MAR06402, respectively, as illustrated in #682
- update reaction annotation and remove derived orphan met MAM02397c (lipoyl-[ACP])
Fixes (PR #706)
- remove lipoic acid transport reactions MAR01483 and MAR06406 that are less accurate duplicates of MAR09608, as notified in #679
- merge annotations of MAR01483 and MAR06406 into MAR09608, update Rhea ids and references
Fixes (PR #703)
- merge "Heme biosynthesis" subsystem into "Porphyrin metabolism", to address issues raised in #356 and #681
Fixes (PR #702)
- remove MAR03940 for being redundant with MAR08539+MAR08538, as discovered in #632
Fixes (PR #701)
- extensively revise cofactor transport reactions between cytosol <-> peroxisome, as proposed in #640
Fixes (PR #697)
- comment-out tasks (37, 38, and 181) with NA[c] metabolite in Cellfile metabolic tasks, as discussed in #696
Fixes (PR #696)
- update metabolite name from GAP[c] to D-glyceraldehyde 3-phosphate[c] in Cellfile metabolic tasks, by following the change in #500
Fixes (PR #582)
- enable GitHub action check for detecting duplicate reactions by enabling sanityCheck to report reactions with identical metabolite IDs
- remove MAR20012 and MAR20089 that are duplicate to MAR06646 and MAR04545, respectively
Fixes (PR #512)
- change the dependency of Yamllint workflow to the repo hosted by metabolicatlas

Assets 2

30 Sep 16:52

haowang-bioinfo

v1.17.0

ca9745d

Human 1.17.0

Fixes (PR #696)
- update name for GAP in Cellfie Consensus metabolic tasks
Features (PR #692)
- sync geneShortNames field (introduced by #539) by padding with empty elements in function addMetabolicNetwork
- enable updateAnimalGEM with option of reusing Human-GEM biomass equation
Fixes (PR #678)
- remove 9 reactions involving MAM01268 or MAM02757 in all compartments, and 10 metabolites and 22 genes that only participated in these reactions, as discussed in the comments on #580
Fixes (PR #677)
- remove MAR01515, MAR00039, MAR00096, MAR02027, MAR02006 that are duplicates of MAR08529, MAR07992, MAR04819, MAR04302, MAR03873, respectively, as proposed in #665
- merge references from removed reactions into kept ones
Fixes (PR #676)
- convert MAR04145, the citrate synthase reaction, irreversible, as proposed in #673
- swap the products and reactants to have non-negative fluxes, and add textbook reference to rxnNotes
Features/Fixes (PR #672, #635)
- fix GH workflow test of the import-export cycle for resolving #628
- introduce basic MEMOTE tests in the yaml-validation workflow, including checks for duplicate reactions and ensure all reactions have at least one metabolite
Fixes (PR #670)
- remove MAR00059 for being a less accurate version of MAR01706, as discussed in #639
- change the GPR of MAR01706 to "ENSG00000113790 or ENSG00000133835" and add PMID:19357427 as reference
- remove MAR01639, MAR03301, MAR03306, MAR03311, MAR04966, MAR03364, MAR03369 that are duplicates of MAR01638, MAR02804, MAR02808, MAR02810, MAR02818, MAR03276, MAR03289, respectively
- create new reaction MAR20114 to represent reduction of O2 by FADH2: MAM02630x + MAM01803x -> MAM02041x + MAM01802x, GPR: ENSG00000161533 or ENSG00000168306 or ENSG00000087008 or ENSG00000110887 or ENSG00000203797 or ENSG00000007171 or ENSG00000148832 or ENSG00000179761 or ENSG00000158125, with reference: PMID:30378035
- replace MAM02630x (O2) with MAM01802x (FAD) and MAM02041x (H2O2) with MAM01803x (FADH2) in a total of 120 reactions, as detailed in #639
Fixes (PR #669)
- remove implausible mitochondrial version Bile Acid Synthesis pathway (13 reactions and 8 metabolites), as outlined in #637
Fixes (PR #667)
- merge MAM03231 into MAM03232, as reported in #627
- update ChEBI ID for MAM02679, MAM02579, MAM02043, MAM03887
Features/Fixes (PR #666)
- improves documentation of deprecated reactions in #613 by adding them to corresponding rows "rxnRetired" column in reactions.tsv, as a tentative implementation according to the discussion in #615
Fixes (PR #664)
- update GPR of reversible transport reaction MAR01527 of sodium across cell membrane by expanding 19 transporter genes based on TCDB and literature, as discussed in #583
Fixes (PR #663)
- remove mets MAM03318 and MAM03325 for being duplicates of MAM01435 and MAM00684, respectively, as discussed in #617
- remove rxns MAR02276, MAR02277, MAR02384, MAR02390, MAR02392, MAR02394, MAR04144 and MAR10447 for being affected by duplicate mets
- change HMDB ID annotations for MAM02679 and MAM01090
Fixes (PR #662)
- remove met MAM03540, for being duplicate of MAM01729, and rxn MAR04506, as discussed in #622
- change KEGG ID annotations for MAM01230, MAM02676, MAM02647, MAM03021, MAM00531, MAM02678, MAM02679
Fixes (PR #661)
- remove mets MAM00591 and MAM03162 for being duplicates of MAM0270 and MAM1739, respectively, as discussed in #621
- remove rxns MAR00941, MAR06142, MAR06143, MAR06144, MAR06220, MAR06252, MAR10025, MAR09733, MAR09734 for being affected by duplicate mets
- update annotation for MAM01322, MAM02043, MAM02579, MAM02679
Fixes (PR #660)
- remove MAR03767 for being duplicate of MAR06421+MAR06422, as proposed in #633
- update duplication info to "rxnRetired" column in reactions.tsv
Fixes (PR #658)
- remove lipid droplet reaction MAR00032 and associated non-metabolic genes ENSG00000072062, ENSG00000142875, ENSG00000165059, ENSG00000172531, ENSG00000186298, and ENSG00000213639, as proposed in #631
Fixes (PR #657)
- remove MAR02358, MAR20066, MAR20020, MAR20002, MAR00030 that are duplicates of MAR08482, MAR03984, MAR04521, MAR06631, MAR00025, respectively, as reported in #580 and #630
- update the pairing info to "rxnRetired" column for kept reactions in reactions.tsv
- merge annotations, references, E.C. codes, etc. from removed reactions into kept reactions
- make MAR08482 reversible
- revise compartment-specific GPRs for MAR08482 and MAR03931
Fixes (PR #655)
- remove MAR05310 for being partially duplicate to MAR06380, and merge its annotation into that of MAR06380, as proposed in #569
- revise GPR of MAR06380 to ENSG00000017483 or ENSG00000188338
- convert MAR06380 to reversible
- removes MAR09887 for being partially duplicate to MAR06896
Fixes (PR #650)
- remove met MAM00759 for being duplicates of MAM01314, as investigated in #620
- update LipidMaps ID annotation for MAM00892, MAM00895, MAM00057, MAM02647
Fixes (PR #649)
- remove mets MAM03354, MAM03332, MAM00029, MAM03368, MAM00902 for being duplicates of MAM00131, MAM01696, MAM00028, MAM00748, and MAM00853, respectively, as discovered in #616
- remove rxns MAR03441, MAR02588, MAR10164, MAR10433 for being affected by duplicate mets
- change EHMN ID annotations for MAM01123
Fixes (PR #646)
- remove mets MAM03226, MAM03884, MAM03554 for being duplicates of MAM00785, MAM02746, and MAM00933, respectively, as discussed in #610
- remove rxns MAR00042, MAR01617, MAR00740, MAR00659, MAR05323, MAR01709 for being affected by duplicate mets
- change BiGG ID annotations for MAM01746, MAM00078, MAM02328, MAM02008
Fixes (PR #641)
- convert pyrophosphate-producing MAR02786, MAR02802, MAR03388, MAR03390, MAR09508, MAR01845, MAR09523, and MAR09546 irreversible, as mentioned in #527
Fixes (PR #625)
- merge 31 pairs of irreversible transport reactions, reported in #562, into single reversible reactions
Fixes (PR #624)
- tidy up acetyl-CoA carboxylase reactions, as proposed in #593:
Fixes (PR #613)
- remove 15 FAD/Ubiquinone duplicate reactions, as detailed in #607
Fixes (PR #494)
- modify simplifyGrRules function to fix compatibility with Matlab "children" function, which has been changed since 2020b, to resolve issue described in #493

Assets 2

19 Jun 09:18

haowang-bioinfo

v1.16.0

07ec978

Human 1.16.0

Fixes (PR #643)
- remove MAR20015, MAR20014, MAR20052 for being duplicates of MAR04689, MAR06981, MAR00067, repectively, based on #630
- also merge all annotations (E.C. codes, corresponding IDs in other models/databases) from the removed reactions into the kept ones
Fixes (PR #629)
- fix Yaml file's bug found in #628
Fixes (PR #623)
- update GPRs and PMID for 5-aminolevulinate transport reactions MAR09985 and MAR11307
  , as suggested in #588:
Fixes (PR #619)
- change metCharges field to int64 type and fix bug in readlines reported in #608:
  Fixes (PR #612)
- reorganize redox reactions catalyzed by electron transfer flavoprotein, as proposed in #608
  - update GPR of MAR06911
  - remove MAR00562 and MAR00563 for being redundant with MAR06911
  - remove MAM03573m and MAM03574m
Fixes (PR #606)
- revise GPRs and modify reactions related to CLYBL (ENSG00000125246), as discussed in #586
  - add CLYBL to the GPR of MAR08666
  - add PMID:24334609 as a reference of MAR08666
  - create new reaction MAR020111 to represent malate synthase activity of CLYBL: MAM02007m + MAM01261m + MAM02040m -> MAM02439m MAM01597m, GPR: ENSG00000125246, reference: PMID:24334609
  - remove MAR05294 and MAR11421 since neither CLYBL nor any other human enzyme catalyzes those reactions
Fixes (PR #605)
- merge duplicate Malonyl Carnitine metabolites MAR05434 and MAR02599, as reported in #595
  - rename MAM02443c, MAM02443m, MAM02443r, and MAM02443x to "malonyl-carnitine"
  - create new metabolite MAM02443e
  - replace MAM03494c and MAM03494e with MAM02443c and MAM02443e in MAR04886 and MAR11256
  - remove MAR05434 for being redundant with MAR02599
  - remove MAM03494c and MAM03494e for being redundant with MAM02443c and MAM02443e
  - merge old annotations for MAM03494c/e into current annotations for MAM02443c/e in metabolites.tsv
Fixes (PR #602)
- assign compartment-specifc GPRs to carbonic anhydrase reactions MAR03955 and MAR05407, as detailed in #597
Fixes (PR #601)
- deal with duplicate carbonic anhydrase reaction sets by removing two-stpe versions and keep one-step reactions, as listed in #589
Fixes (PR #600)
- update NA+/Pi transport reactions GPRs as referenced in #568
  - remove reaction MAR04411 and MAR05413
  - add ENSG00000143324 (XPR1) to the GPR of MAR02351, add ENSG00000144136 (SLC20A1) and ENSG00000168575 (SLC20A2) to the GPR of MAR04910
Fixes (PR #596)
- change the GPR of MAR04372 from ENSG00000172331 to ENSG00000119640 or ENSG00000170634, as discussed in #587
Fixes (PR #592)
- add Acylpyruvase FAHD1 (ENSG00000180185) to Human-GEM and to GPR of MAR20110 and MAR11430, as proposed in #585
Fixes (PR #591)
- add AUH to previously-empty GPRs of MAR05999, MAR08664, and MAR11514, derived from the discussion in #590
- update Rhea Ids and PMID to above reactions
Fixes (PR #581)
- revise reactions, GPRs, and references for glucose Uptake and Na+/K+ pumps, as detailed in #570
  - Remove MAR05295, MAR06894, and MAR06895
  - Remove ENSG00000140675 from MAR05029
  - Copy references from MAR05429 to MAR05295
  - Change MAR01444 to ATP [c] + H2O [c] + K+ [e] + H+ [e] + 2 Na+ [c] ⇒ ADP [c] + Pi [c] + K+ [c] + H+ [c] + 2 Na+ [e], GPR: ENSG00000075673 and ENSG00000186009
Fixes (PR #576)
- remove chloride-dependent transporter SLC6A14 (ENSG00000268104) from GPRs of 22 reactions without Cl- listed in #567
Features (PR #575)
- add 39 new rxns related to histidine metabolism, as reported in #553
Fixes (PR #573)
- remove/merge duplicate reactions reported in #561
- adds ENSG00000198099 to the GPR of MAR06644
Featurs (PR #564)
- add GH action check for both essential and basic verification tasks, as mentioned in #390
Featurs (PR #563)
- add essentiality analysis suite using Hart2015 datasets, as discussed in #390
Features (PR #560)
- curate GPRs for cysteine metabolism reactions, as reported in #552
Fixes (PR #559)
- curate reactions and GPRs for Alanine, Aspartate and Glutamate subsystem, as proposed in #548
Fixes (PR #557)
- make a total of 180 non-transport/exchange pyrophosphate reactions irreversible, based on the report in #527
Features (PR #556)
- improve GH actions in sanityCheck.py by enabling detection of unused metabolites, triggered by mistakes found in #525

Assets 2

09 May 08:20

haowang-bioinfo

v1.15.0

194ebe5

Human 1.15.0

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

25 Feb 16:46

haowang-bioinfo

v1.14.0

8ba6b21

Human 1.14.0

Fix: remove 149 non-metabolic genes, that are discovered using the GPT-3 language model, from following subsystems:
- #485 remove non-metabolic Isolated (#481), and Glycosphingolipid metabolism related genes (#484)
- #480 remove non-metabolic genes from Protein assembly and degradation (#476), Glycerophospholipid metabolism (#477), Cholesterol biosynthesis pathway (#478)
- #474 remove two rxns wrongly annotated with Phe metabolismand #472 and remove non metabolic gene from aromatic amino acid metabolism (#471)
- #467 remove non-metabolic genes from amino acid metabolism (#463), (#464), (#465), (#466)
- #461 remove non-metabolic genes from Fructose and mannose metabolism (#457)
- #455 remove non-metabolic genes from Inositol phosphate metabolism (#452)
- #453 remove non-metabolic genes from Nucleotide metabolism pathway (#449)
- #451 remove ST20 from Pentose phosphate pathway (#447)
- #450 remove non-transporter genes from transport reactions (#444)
- #445 remove non-metabolic genes from glycolysis pathway (#443)
- #442 removal of MEIKIN from fatty acid activation reactions (#426)
Feature (PR #482):
- refactor extractAllianceGenomeOrthologs from reading JSON to TSV file, as discussed in #15 of Mouse-GEM
Feature/Style (PR #479):
- add @feiranl as a contributor
Feature (PR #475):
- improve issue and PR templates
Fix(PR #462):
- add subunit NDUFA7 to complex I, as explained in #446
Fix (PR #460):
- correct wrongly associated CHEBI annotation to MAM03882, as reported in Mouse-GEM issue #21
Fix (PR #459):
- changed subsystems for 2 exchange rxns, modified name 7 transport rxns, as discussed in #456

Contributors

feiranl

Assets 2

23 Dec 16:03

haowang-bioinfo

v1.13.0

20dcd0c

Human 1.13.0

Features (PR #440, #437):
- add compartment information to genes.tsv based on SwissProt annotation, Cell Atlas, and deeploc2 prediction, as discussed in #436
Fixes (PR #435):
- update HMDB IDs to version 4 format and fix ID for MAM03055r, as suggested #434
Fixes (PR #432):
- remove the reaction MAR02517 and 4 metabolites (MAM02444l, MAM02678l, MAM00890l, and MAM01596l) that were involved in no other reactions, to address issue #381
Fixes (PR #431, #428):
- systematically format PMIDs, to resolve inconsistency reported in #430, #427
Features (PR #429):
- add cis-aconitate decarboxylase reaction according to Mouse-GEM issue #20, and change reversibility for MAR09498, as reported in #425
Features (PR #423):
- add an install script to resolve #136
Features (PR #422):
- allow prepHumanModelForftINIT to take the paths to reactions.tsv and essential tasks as optional parameters, as proposed in #401
Fixes (PR #420):
- enables importYaml to get rid of empty and non-essential fields
Fixes (PR #419):
- curate GPR rule for MAR04926, as discussed in #417
Fixes (PR #415):
- set MAR05998 to be reversible, as proposed in #412
Fixes (PR #405, #403):
- evaluate and remove duplicated reactions, to address the issue discussed in #345

Assets 2

21 Jun 05:38

haowang-bioinfo

v1.12.0

4a2e260

Human 1.12.0

Features (PR #393):
- speed up importYaml in loading model fields
Features (PR #392):
- turn importYaml into a more generic function
Features (PR #388):
- add help functions that are used together with ftINIT in RAVEN
Fixes (PR #382):
- change metabolic task file format from xlsx to txt
- inactivate human biomass reaction (MAR13082), as suggested in Mouse-GEM PR #11
- add proper LB and UB values to annotation field, as reported in Mouse-GEM PR #12
- turn annotateGEM into a more generic function, as discussed in Convert annotateGEM into a more generic function #380
Fixes (PR #379):
- flag reactions MAR05127, MAR08749, MAR08750 as spontaneous, as identified in #349
Style (PR #374):
- doc: tINIT rename 'exchange metabolites' to 'boundary metabolites in getINITModel2
Features (PR #367):
- add reaction names from KEGG, to address #181
Fixes (PR #365):
- merge MAR08973 into MAR04474, as suggested in #346
Fixes (PR #362):
- resolves #342 by applying the suggestion to remove the gene (and thus the GPR) and mark MAR04840 as spontaneous
Fixes (PR #358):
- correct CHEBI associations to avoid conflict during MNXref conversion

Assets 2

07 Feb 07:25

haowang-bioinfo

v1.11.0

26a83e9

Human 1.11.0

Fixes (PR #351):
- remove duplicated reactions, as reported in #344
Fixes (PR #343):
- sync met ids with new comp abbreviations in metabolites.tsv to resolve branch conflict while merging #341
Features (PR #341):
- modify compartment abbreviations (Extracellular: s->e, Boundary: x->b, Peroxisome: p->x), as discussed in #314
Style (PR #340):
- refine README
Features (PR #339):
- continue on improving metabolite annotation with CHEBI ids
Features (PR #338):
- refactor exportTsvFile function with options of .txt output format and double-quote free mode
Features (PR #337):
- remove generic (de)phosphorylation reactions and 558 associated genes, as suggested by #336
Fixes (PR #334):
- clean reaction name field, according to discussions in #181, #333
Features (PR #332):
- refactor GitHub actions with more robust and reproducible setup, by replacing the direct usage of Python and installation of packages with the opencobra/memote container from DockerHub
Features/Fixes (PR #331):
- reformat metabolic task files
  - change all metabolic task .xlsx files in /data/metabolicTasks to .txt format
  - correct the compartment of NEFA blood pool in from Boundary to Extracellular ([x] to [s]) for addressing #311
Features (PR #329):
- add CHEBI:53019 'glycan G00008' to MAM00154r, as clarified in #328
Fixes (PR #327):
- empty Should Fail column to Cellfie metabolic tasks, this was mentioned in #280
Fixes (PR #325):
- correct metabolite annotations according to discussions in #297, #299, and #308
Fixes (PR #296):
- standardize references field by systematically implementing PMID and separating entries by semicolon, as proposed in #259

Assets 2

14 Sep 08:35

haowang-bioinfo

v1.10.0

26005b7

Human 1.10.0

Fixes (commit 339ff64):
- revise workflow to avoid duplicated checks
Fixes (PR #324):
- force cache refreshing by using commit SHA as key, to address random GH action failures
Style (PR #320):
- simplify contributing guidelines to adapt with yaml workflow
Features (PR #315):
- expand to cover all participants who have constructively contributed to Human-GEM, as claimed in #288
Fixes (PR #313):
- removed beta-D-glucose detour, based on the discussion in #307
  - MAM01389c, MAR07746, MAR07748, MAR07749 are removed
  - MAR07747 changed stoichiometry from beta- form to generic
Fixes (PR #312):
- remove KEGG annotation to MAM03165c, as proposed in #310
Features (PR #305):
- Include Cellfie's metabolic tasks, as discussed in #280
  - all metabolite ids are adjusted for Human-GEM except Try_ggn
  - change compartment [x] into [s]
  - metes that are both in IN and OUT columns (e.g. H20) are removed from OUT
Fixes (PR #302):
- removed ChEBI annotation 71980 to MAM00535c, as suggested in #273
Features (PR #298):
- adopt all-contributors to recognize those who contributed and improve their visibility

Assets 2

12 Aug 11:09

haowang-bioinfo

v1.9.0

8580072

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

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Releases: SysBioChalmers/Human-GEM

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