Human 1.18

[haowang-bioinfo]

Main improvements in this PR:

• Fixes (PR Remove ACAD10 #740)
  • remove ACAD10 from the GPRs of MAR03212 and MAR03163, as well as from Human-GEM altogether, as explained in ACAD10 #739
• Fixes (PR Fix Oxoadipate Dehydrogenase #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 Duplicate 2-oxoadipate dehydrogenase reactions #719
• Fixes (PR Fix MAR04665 #724)
  • replace inaccurate GPR and reference for MAR04665 with ENSG00000182199 (SHMT2) and "PMID:11087421", as discussed in MAR04665 is probably not an enzyme-catalyzed reaction #720
• Fixes (PR Fix Mitochondrial Glutathione Transport #723)
  • revise mitochondrial Glutathione transport reactions as discussed in Transport of Glutathione into Mitochondria #722, by modifying MAR08771, and removing MAR04940 and MAR06391
• Style (PR add Christoff1993 as a contributor for bug #721)
  • add Christoff1993 as a contributor
• Fixes (PR Fix/hexanoate #717)
  • resolve duplicate chemical speices hexanoate/hexanoic acid by systematically replacing hexanoate (MAM03684c) with hexanoic acid (MAM02120c), as reported by Duplicate species hexanoate/hexanoic acid #716
• Fixes (PR Fix/acot curation #715)
  • curate GPRs and reaction names of 62 cytosolic short- and medium-chain fatty acid hydrolysis reactions, as proposed in Short- and medium-chain fatty acids don't have hydrolysis rxns #689
  • add 4 new hydrolysis reactions
  • add 2 new genes THEM4 (ENSG00000159445) and THEM5 (ENSG00000196407)
• Fixes (PR Fix Representation of LIPT1 #714)
  • refine GPRs involving LIPT1 (ENSG00000144182) gene, as explained in Misrepresentation of Catalytic Activity of LIPT1 #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 Fix DHODH Reactions #713)
  • split formuate dihydroorotate dehydrogenase reaction MAR04575 into two steps by adding new met MAM20019c (FMNH2) and new rxn MAR20167, as advised in Dihydroorotate Dehydrogenase #609
• Fixes (PR Fix/fmn fmnh2 ids #712)
  • update and maintain consistency in the met IDs for FMN and FMNH2 and update their annotations, according to Inconsistent IDs for FMN and FMNH2 #711
• Fixes (PR Fix Duplicate Glycerol-3-Phosphate Dehydrogenase Reactions #710)
  • remove duplicate glycerol-3-phosphate dehydrogenase rxns MAR00478 and MAR00482 and update annotations, as proposed in Proposed fixes to DHAP <=> sn-glycerol-3-phosphate reactions #599
• Fixes (PR Fix/mito nuc trans #709)
  • reorganize nucleotide transport reactions [c]<->[m] by adding genes, reactions, updating GPRs, and removing reactions lack of proper transporters, as listed in Mitochondrial Nucleotide Transporters #694
• Fixes (PR fix: refine Trp metabolism reactions and GPRs #708)
  • revises tryptophan metabolism reactions and GPRs, as outlined in Refine GPR in tryptophan metabolism pathway #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 Merge Duplicate Lipoic Acid Biosynthesis Pathways #707)
  • remove MAR06400 and MAR06401 for being duplicate to MAR06403 and MAR06402, respectively, as illustrated in Duplicate Lipoic Acid Biosynthesis Pathways #682
  • update reaction annotation and remove derived orphan met MAM02397c (lipoyl-[ACP])
• Fixes (PR Fix Duplicate Lipoic Acid Transport Reactions #706)
  • remove lipoic acid transport reactions MAR01483 and MAR06406 that are less accurate duplicates of MAR09608, as notified in Near-Duplicate Lipoic Acid Transport Reactions #679
  • merge annotations of MAR01483 and MAR06406 into MAR09608, update Rhea ids and references
• Fixes (PR style: merge "Heme biosynthesis" subsystem into "Porphyrin metabolism" #703)
  • merge "Heme biosynthesis" subsystem into "Porphyrin metabolism", to address issues raised in Multiple subsystems per reaction #356 and Difference Between YAML and SBML Files #681
• Fixes (PR Remove MAR03940 #702)
  • remove MAR03940 for being redundant with MAR08539+MAR08538, as discovered in Suggested Removal of MAR03940 #632
• Fixes (PR Fix Peroxisomal Cofactor Transport Reactions #701)
  • extensively revise cofactor transport reactions between cytosol <-> peroxisome, as proposed in Transport of Cofactors Across Peroxisomal Membrane #640
• Fixes (PR Fix the NA[c] metabolite in Cellfile metabolic tasks #697)
  • comment-out tasks (37, 38, and 181) with NA[c] metabolite in Cellfile metabolic tasks, as discussed in fix: update name for GAP in CellfieConsensus metabolic tasks #696
• Fixes (PR fix: update name for GAP in CellfieConsensus metabolic tasks #696)
  • update metabolite name from GAP[c] to D-glyceraldehyde 3-phosphate[c] in Cellfile metabolic tasks, by following the change in Change the name of MAM01939 #500
• Fixes (PR feat: add the duplicate rxn check task #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 chore: bump workflow dependency version #512)
  • change the dependency of Yamllint workflow to the repo hosted by metabolicatlas

[haowang-bioinfo]

Updated essentiality evaluation using combined (all) Hart2015 datasets:

version	TP	TN	FP	FN	accuracy	sensitivity	specificity	F1	MCC
v1.12	40	2333	175	77	0.904000000000000	0.341880341880342	0.930223285486443	0.240963855421687	0.204768560393159
v1.13	40	2334	174	77	0.904380952380952	0.341880341880342	0.930622009569378	0.241691842900302	0.205504558241293
v1.14	40	2334	175	77	0.904036557501904	0.341880341880342	0.930251096054205	0.240963855421687	0.204787829413435
v1.15	40	2342	168	77	0.906737723639132	0.341880341880342	0.933067729083665	0.246153846153846	0.210053956889428
v1.16	41	2308	202	76	0.89417587	0.35042735	0.91952191	0.22777778	0.19220101
v1.17	41	2263	237	75	0.880733944954129	0.353448275862069	0.905200000000000	0.208121827411168	0.172768250444715
v1.18	42	2260	245	74	0.878290728729493	0.362068965517241	0.902195608782435	0.208436724565757	0.174052567331894

[mihai-sysbio]

@haowang-bioinfo thank you for updating the essentiality results

I was playing around yesterday with two different solvers on a knockout panel and I got different results, so I am wondering if the same solver has been used in all the evaluations since v1.12.

[mihai-sysbio]

Looks good! I've noticed there two commented-out metabolic tasks. I'm not really fond of having them in that state - I would propose that they are outright removed, or whatever underlying issue there is to be reported and ultimately resolved.

[haowang-bioinfo]

I was playing around yesterday with two different solvers on a knockout panel and I got different results, so I am wondering if the same solver has been used in all the evaluations since v1.12.

good question - for the listed analysis the same solver (gurobi 10) was used except for the results of v1.16, which was copied and I don't know what solver was specifically used

[haowang-bioinfo]

the PR message was just updated with #740 after its merging into v1.18, which should be enough and probably can move on to a new release?

[JonathanRob]

Looks good! I've noticed there two commented-out metabolic tasks. I'm not really fond of having them in that state - I would propose that they are outright removed, or whatever underlying issue there is to be reported and ultimately resolved.

@mihai-sysbio, where are the tasks commented out?

[mihai-sysbio]

@mihai-sysbio, where are the tasks commented out?

It's the Cellfie tasks here, specifically the last two commits. It makes sense for them to be commented out, but I still think it would be good to have an issue to at some point resolve this.

[haowang-bioinfo]

@mihai-sysbio, where are the tasks commented out?

It's the Cellfie tasks here, specifically the last two commits. It makes sense for them to be commented out, but I still think it would be good to have an issue to at some point resolve this.

This most likely refers to the changes made in #697, it was actually discussed but in an atypical way, not via an issue but under a PR (#696)