Releases · SysBioChalmers/Human-GEM

24 Jun 23:09

edkerk

v1.19.0

022ed5c

Human 1.19.0 Latest

Latest

Main improvements in this PR:

Fixes (PR #818)
- resolve the Node 16 warning as discussed in #817
Fixes (PR #816)
- Refine unbalance reactipns as discussed in #814 and #813
  - change the charge of mets MAM20004n, MAM20006c, MAM20018r, MAM20021i, MAM20024r, MAM20025i, MAM20026r, MAM20027i, MAM20028r, MAM20029i, MAM20030r, MAM20031i, MAM20041r, MAM20042c, MAM20043r, MAM20044c, MAM20056r, MAM20057c from 0 to -1
  - remove MAM02039e in MAR01444; remove MAM02039i in MAR20022, MAR20024, MAR20026, MAR20028 and MAR20030; remove MAM02039r in MAR20023, MAR20025, MAR20027, MAR20029 and MAR20021;
  - add MAM02039m in MAR20111 as a product; add MAM01422m in MAR20112 as a product; and add MAM02039c in MAR03481 as a product;
  - replace the formula of MAM01657r to "C40H65O7P2"; replace the formula of MAM20082m from None to "C11H23N1O2S2"; replace MAM02041x with MAM01803x in MAR08415; replace MAM02630x with MAM01802x in MAR08415; replace MAM02041x with MAM01803x in MAR03984; replace MAM02630x with MAM01802x in MAR03984; replace MAM02041x with MAM01803x in MAR12372; replace MAM02630x with MAM01802x in MAR12372
Fixes (PR #815)
- Fixes the transport of thiamine Di- and Monophosphate between cytosol and mitochondria as discussed in #783
  - Created MAR20181 with ENSG00000125454 as GPR;
  - Created MAR20182 with ENSG00000125454 as GPR;
  - Created MAR20813 with ENSG00000125454 as GPR;
  - Removed MAR01788, MAR01789, MAR04205, MAR08745, and MAR08747 for lacking evidence and being redundant with the three new reactions above.
Fixes (PR #811）
- Standardize all names of exchange reactions as discussed in #181
Fixes (PR #808)
- Refine GPRs of Mitochondrial 2-enoyl-CoA Hydration Reactions as explained in #808
  - Set GPRs of MAR01163, MAR01177, MAR01182, MAR01206, MAR01219, MAR01224, MAR01255, MAR01272, MAR03108, MAR03112, MAR03116, MAR03122, MAR03129, MAR03171, MAR03175, MAR03179, MAR03183, MAR03187, MAR03219, MAR03223, MAR03227, MAR03231, MAR03235, MAR03241, MAR03245, MAR03252, MAR03260, MAR03277, MAR03281, MAR03285, MAR03449, and MAR03453 to ENSG00000084754 (HADHA)
  - Set GPRs of MAR03136, MAR03143, MAR03150, MAR03157, MAR03191, MAR03195, MAR03199, MAR03290, MAR03523, and MAR03528 to ENSG00000084754 or ENSG00000127884 (HADHA or ECHS1)
  - Set GPRs of MAR03164, MAR03203, MAR03532, MAR03753, MAR03785, and MAR04735 to ENSG00000127884 (ECHS1)
Fixes (PR #807)
- Removes MAR04774, MAR04775, and MAR02955c as they seem could not occur in human cells;
- Updates the references of MAR09417, MAR08760, MAR01472, MAR01038, MAR08761 and MAR08762 as discussed in #754
Fixes (PR #805)
- Curate stereochemistry of phytanic acid metabolism as discussed in #773
  - Rename MAM02746e, MAM02746c and MAM02746x to "(3R)-phytanic acid" and MAM02747c and MAM02747x to "(3R)-phytanoyl-CoA"
  - Brought back previously-deprecated MAM03884e, MAM03884c and MAM03884x and renamed them to "(3S)-phytanic acid"
  - Brought back previously-deprecated MAR00659 and MAR01617 (transport reactions for MAM03884)
  - Replace MAM02746c with MAM03884c in MAR03388
  - Change MAR03481 to be MAM02747c + MAM01371c + 2 MAM02040c -> MAM02746x + MAM01597c + MAM02039c + MAM01285c + MAM02751c, GPR: ENSG00000117528, references: PMID:24333844;PMID:33500543
  - Change MAR06779 to be MAM03362c + MAM01371c + 2 MAM02040c -> MAM03384x + MAM01597c + MAM02039c + MAM01285c + MAM02751c, GPR: ENSG00000117528, references: PMID:24333844;PMID:33500543
  - Replace MAM02746x with MAM03884x in MAR03389
  - Rename MAM00655x to "(3R)-2-hydroxyphytanoyl-CoA"
  - Create MAM20083x to represent peroxisomal (2R)-pristanal, and replace MAM00564x ((2S)-pristanal) with MAM20083x in MAR03486
  - Rename MAM02766e, MAM02766c, and MAM02766x to "(2S)-pristanic acid"
  - Brought back previously-deprecated MAR03488 and MAM00077x
  - Replace MAM00564x with MAM20083x in MAR03488, and replace MAM02766x with MAM00077x in MAR03493
  - Create MAM00077c and MAM00077e to represent cytosolic and extracellular (2R)-pristanic acid, and create MAR20179 to represent export of (2R)-pristanic acid from cytosol to extracellular environment
  - Replace MAM02766c with MAM00077c in MAR03390
  - Create MAR20180 to represent exchange of (2R)-pristanic acid
Fixes (PR #794)
- Removes MAR00965 and fixes the gpr of MAR00970 as explained in #748
Fixes (PR #793)
- Curate duplicate Beta-oxidation pathways for Linoleoyl- and gamma-Linolenoyl-CoA as explained in #793
  - Removes MAR05358 for being a duplicate of MAR03452 + MAR03453 + MAR03454 + MAR03455
  - Removes MAR05195 for being a duplicate of MAR03456
  - Removes MAR05302 for being a duplicate of MAR03457
  - Removes MAR05229 for being a duplicate of MAR03458
  - Removes MAR05208 for being a duplicate of MAR03281 + MAR03282 + MAR03283
  - Removes MAR05356 for being a duplicate of MAR03275 + MAR03277 + MAR03278 + MAR03279
  - Removes MAR05191 for being a duplicate of MAR03280 + MAR03281 + MAR03282 + MAR03283
  - Removes MAR05123 for being a duplicate of MAR03284 + MAR03285 + MAR03286 + MAR03287
  - Removes MAR05075 for being a duplicate of MAR03288
  - Removes MAR05072 for being a duplicate of MAR03290 + MAR03292 + MAR03293
  - Replaces MAM03274m with MAM00091m in MAR05360
  - Removes MAM03274m for being a duplicate of MAM00091m
  - Removes MAM03653m for being a duplicate of MAM00072m
  - Removes MAM03221m for being a duplicate of MAM00089m
  - Removes MAM03182m for being a duplicate of MAM03009m
  - Removes MAM03978m for being a duplicate of MAM01576m
  - Removes MAM03203m for being a duplicate of MAM01575m
  - Removes MAM02698m for being a duplicate of MAM03021m
  - Removes MAM03650m for being a duplicate of MAM01577m
Fixes (PR #792)
- Removes MAR05187 for being a duplicate of MAR03486 + MAR03386;
- Removes MAR05186 for being a misrepresentation of ALDH3A2;
- Set GPR of MAR03386 to ENSG00000072210;
- Removes ENSG00000182591 from the GPR of MAR03486 and remove it from Human-GEM. All these are explained in #775
Fixes (PR #790)
- removes EHHADH (ENSG00000113790) from the GPR of MAR03288 as discussed in #756
Fixes (PR #789)
- Removes MAR05019 for being a duplicate of MAR03142 + MAR03143;
- Removes MAR04967 for being a duplicate of MAR03143 + MAR03144 + MAR03146;
- Removes MAR05024 for being a duplicate of MAR03142 + MAR03143 + MAR03144 + MAR03146. All these are discussed in #745
Fixes (PR #788)
- Remove MAR03322 and MAR03296 due to cofactor mismatch and remove MAR04005, and associated MAM00678c and MAM03035c, due to compartment mismatch as reported in #736;
- Set the GPRs of MAR01176, MAR01181, MAR01218, MAR01222, MAR03446, and MAR03457 to ENSG00000104325 and set the GPRs of MAR01297, MAR03461, and MAR03471 to ENSG00000242612 as reported in #755
Fixes (PR #770)
- Remove ENSG00000115425 from MAR02028, MAR02148, MAR02149, MAR02183, MAR02187 and MAR02207 as explained in #767
Fixes (PR #768)
- remove inaccurate reaction MAR00789 and duplicate reaction MAR03426 of beta-oxidation of linolenoyl-CoA as explained in #765
Fixes (PR #760)
- Refine GPR of MAR03269 and MAR03380 to ENSG00000084754 or ENSG00000072506 genes, as discussed in #758
Fixes (PR #753)
- revise inconsistent representation of Thiamine in 2-Oxoacid Dehydrogenase Complexes as explained in #744
  - Creates MAM20077m to represent 2-(4-carboxy-1-hydroxybutyl)thiamine diphosphate and MAR20173 with ENSG00000105953 or ENSG00000181192 as GPR
  - Replaces MAM00670m with MAM20077m, replaces MAM01596m with MAM02984m, and removes MAM02039m in MAR04599
  - Creates MAM20078m to represent 2-(2-methyl-1-hydroxypropyl)thiamine diphosphate and MAR20174 with ENSG00000248098 and ENSG00000083123 as GPR
  - Replaces MAM00824m with MAM20078m, replaces MAM01596m with MAM02984m, and removes MAM02039m in MAR06416
  - Creates MAM20079m to represent 2-(2-methyl-1-hydroxybutyl)thiamine diphosphate and MAR20175 with ENSG00000248098 and ENSG00000083123 as GPR
  - Replaces MAM00669m with MAM20079m, replaces MAM01596m with MAM02984m, and removes MAM02039m in MAR06419
  - Creates MAM20080m to represent 2-(3-methyl-1-hydroxybutyl)thiamine diphosphate and MAR02176 with ENSG00000248098 and ENSG00000083123 as GPR
  - Replaces MAM01013m with MAM20080m, replaces MAM01596m with MAM02984m, and removes MAR02039m in MAR06421
  - Creates MAM20081m to represent 2-(1-hydroxypropyl)thiamine diphosphate and MAM20082m to represent S-propanoyldihydrolipoamide
  - Changes MAR03800 to: MAM00671m + MAM02984m + MAM02039m -> MAM20081m + MAM01596m, GPR: ENSG00000248098 and ENSG00000083123
  - Creates MAR20177 with ENSG00000248098 and ENSG00000083123 as GPR and MAR20178 with ENSG00000137992 as GPR.
Fixes (PR #752)
- Remove duplicate Beta-oxidation reaction MAR03422 as explained in #746
Fixes (PR #751)
- Remove duplicate octanoyl-CoA Beta-oxidation reactions, include MAR06329, MAR06283, MAR06279, MAR05449 and MAR01009 as explained in #747
Fixes (PR #750)
- Refine gpr involving BCKDHA (ENSG00000248098), BCKDHB (ENSG00000083123), and TMEM91 (ENSG00000142046) genes, as explained in #742
  - Remove MAR02532 and MAR02534;
  - Remove MAM02158m, MAM02158n, and MAM02986n;
  - Remove ENSG00000130508 and ENSG00000117592 from the GPR of MAR06523;
  - Add ENSG00000137992 to the GPRs of MAR06416, MAR06419, and MAR06421;
  - Add PMID:11013238 and PMID:31989833 to the references of MAR06523;
  - Removes ENSG00000142046 from the GPRs of MAR06416, MAR06419, MAR06421, and MAR06523 as well as the list of genes in Human-GEM
Fixes (PR #743)
- Remove duplicate branched-chain alpha-ketoacid dehydrogenase reaction MAR03748 and MAR03780 as explained in #741
Features (PR #731)
- Add SMILES and InChI of metabolites in Human-GEM as discuss...

Assets 2

08 Dec 14:29

haowang-bioinfo

v1.18.0

104f22b

Human 1.18.0

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

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