Human 1.15 #554

haowang-bioinfo · 2023-05-07T20:48:53Z

Main improvements in this PR:

Fixes (PR fix: sedoheptulose kinase/phosphatase reactions #551)
- remove MAR04568, make MAR04567 irreversible in the direction of ATP consumption, and phosphatase reaction MAR20070, as proposed in Reversibility and GPRs of MAR04567 and MAR04568 #547:
Features/Style (PR docs: add new contribs #550, docs: add Devlin-Moyer as a contributor for bug #542):
- add new contributors
Features (PR feat: add gene symbols to model #549)
- add new field geneShortNames for gene symbols, as discussed in add gene name to Human-GEM #539
Features/Style (PR style: move from lab-based development to community curation #546):
- remove authors, email, and organization fields in code and Yaml file for moving toward community curation on GitHub
Fixes (PR fix: remove orphan mets MAM02662c, MAM02662m, MAM02662x #555, fix: remove duplicate krebs cycle rxns of PDH and OGDH #541, fix: resolve duplicated GCS reactions #538, fix: update GPRs for Cytochrome C Oxidoreductase and remove MAR04456 that is duplicated to MAR04458+MAR04589 #532, Remove Other Glycine Cleavage System Enzymes From GPR of MAR06409 #529, fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism #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
- the implementation plans are discussed in Inaccurate GPRs and Reversibilities for Isocitrate Dehydrogenase Reactions #523, Parallel/Redundant Versions Of Reactions #524, and fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism #525
- fix GPRs for Cytochrome C Oxidoreductase, as discussed in Changes to GPRs for Cytochrome C Oxidoreductase (AKA Complex IV of the Electron Transport Chain) #526
Fixes (PR fix-bug: bug in GPR in #528 #540)
- modify GPRs of MAR01453, MAR11476, MAR11479 AND MAR04281, as introduced in Minor Fixes To Lactate Dehydrogenase Reactions #528
Fixes (PR fix: modify GPRs #537)
- replace ENSG00000137700 with ENSG00000281500, as proposed in feat: remove pseudogenes, read through genes, and ones with only predicted functions #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 Remove Other Glycine Cleavage System Enzymes From GPR of MAR06409 #529
Features (PR feat: Add new reactions annotated for genes related to Glycolysis pathway #535)
- add 87 new mets, 68 new reactions in Glycolysis pathway, as listed in Refine GPR annotation for Glycolysis pathway #507
Fixes (PR fix-remove the duplicate met MAM00077x and corresponding rxns #534)
- remove duplicate met MAM00077x and corresponding rxns MAR03488 and MAR03489, as reported in Duplicate IDs for same mets #519
Fixes (PR Curated names of peptide reactions #533)
- rename mets in tyrosine exchange, transport, and metabolism reactions from XxxtyrYyy to XxxTyrYyy
Fixes (PR fix: refine GPRs in Coenzyme A metabolism #520)
- modify GPRs of CoA metabolism, as proposed by Refine GPRs in CoA metabolism #502
Fixes (PR Fixed the name of MAM02053 #518)
- fix the met name of MAM02053, as discussed in Typo in the name of MAM02053 #491
Fixes (PR Remove wrongly annotated genes for glycolysis pathway and lactate dehydrogenase #517)
- remove wrongly associate genes in glycolysis (Refine GPR annotation for Glycolysis pathway #507) and lactate dehydrogenase (refine GPR for lactate dehydrogenase #516)
Fixes (PR fix: refine GPRs in Pentose phosphate pathway #515)
- refine GPRs in Pentose phosphate pathway, as proposed in Refine GPRs in Pentose phosphate pathway #501
Fixes (PR fix: remove pseudogenes, read through genes, and ones with only predicted functions #513)
- remove 21 pseudogenes, read through genes, and ones with only predicted functions, as proposed in feat: remove pseudogenes, read through genes, and ones with only predicted functions #510.
Fixes (PR fix: refine GPRs for Pyrroline-5-carboxylate reductase #509)
- refine GPRs of Pyrroline-5-carboxylate reductase according to compartment and cofactor annotation reported in GPR refinement of Pyrroline-5-carboxylate reductase #505
Features (PR feat: update Rhea IDs associated from Reactome IDs #508, feat: update Rhea ids #506)
- add/update Rhea master IDs to reacitons.tsv annotation file for a total of 1334 reactions
Fixes (PR fix: refine NADKs GPRs #504)
- assign compartment-specific NAD kinase genes to MAR04268 and MAR04269, and remove MAR04279, based on discussion in Refine GPR for Nicotinate and nicotinamide metabolism #503
Fixes (PR fix: correct TYMP and PNP GPRs #499)
- separate genes TYMP (ENSG00000025708) and PNP (ENSG00000198805) to GPRs of MAR04603, MAR04695, MAR04709, and MAR04485, as reported in TYMP and PNP GPRs #498
Fixes (PR chore: update Docker image of Memote #497)
- update the Docker image used in GH Actions workflow
Fixes (PR fix: correct ARG GPRs #496)
- correct GPRs of Arginases (MAR03816 and MAR08426) by using compartment-specific enzymatic genes, as reported in ARG1 and ARG2 GPRs are incorrect #495
Features/Style (PR fix: consolidate subsystem of coenzyme A metabolism #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 feat: consolidation the subsystems of coenzyme A metabolism #487
Fixes (PR refactor: gh workflow #490)
- refactor the GitHub workflow by using native support for Docker rather than a separate action
Fixes (PR fix: modify GPR rules of mitochondrial complexes II, IV, and V #489)
- fix GPR rules of mitochondrial complexes II, IV, and V, as proposed in Mitochondrial respiratory chain complex II curation #468, Mitochondrial respiratory chain Complex IV curation #469, Mitochondrial proton-transporting ATP synthase curation #470 based on Complex Portal annotation

-Update GPRs for OXPHOS complexes II, IV, V according to Complex Portal annotation

fix: modify GPR rules of mitochondrial complexes II, IV, and V

- This is to address the issue reported in #495

fix: correct TYMP and PNP GPRs

- add Rhea ids to MAR04603, MAR04651, MAR04709, MAR04485, MAR04754

fix: correct ARG GPRs

chore: update Docker image of Memote

refactor: gh workflow

…lism

fix: consolidate subsystem of coenzyme A metabolism

- assign only NADK2 to MAR04268 - assign only NADK to MAR04269 - empty GPR to MAR04279

- removed these fields from Yaml file - disabled them in `importYaml` and `exportYaml` functions

Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>

…uration style: move from lab-based development to community curation

- extract gene symbols from genes.tsv and include to Human-GEM

Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>

fix: sedoheptulose kinase/phosphatase reactions

feat: add gene symbols to model

haowang-bioinfo · 2023-05-07T21:09:50Z

Here's small scale essentiality evaluation of combined Hart2015 datasets (all), by reusing the code of Human1 paper.

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

Overall, the latest model shows good improvements in decreased false positive values and increased true negatives, which actually reversed a little bit after #551 compared to the result #390.

fix: remove orphan mets MAM02662c, MAM02662m, MAM02662x

johan-gson

LGTM

feiranl

LGTM!

haowang-bioinfo · 2023-05-09T07:23:31Z

IMHO, several comments:

forget about perfect, because being the best always delay things from getting better
follow the rule of release early, release often - Eric S. Raymond
therefore avoid too much curations (i.e. limit the number of PRs no more than 20 probably) for each release
welcome critical comments from research community, because given enough eyes, all bugs are shallow

haowang-bioinfo · 2023-05-09T07:39:20Z

#555 is now included to v1.15

haowang-bioinfo and others added 30 commits February 28, 2023 20:23

fix: update GPRs for OXPHOS complexes II, IV, V

a77d9a0

-Update GPRs for OXPHOS complexes II, IV, V according to Complex Portal annotation

fix-gene: update added genes to genes.tsv

c3faf5b

refactor: gh workflow

62404cb

chore: update workflow dependency

0780660

chore: typo

73ace80

fix: worklow needs repo checkout for every job

63d2bcb

Merge pull request #489 from SysBioChalmers/fix/modifyMitoComplexGPR

d6f92a3

fix: modify GPR rules of mitochondrial complexes II, IV, and V

fix: consolidate subsystem of coenzyme A metabolism

be85db2

fix: correct ARG1 and ARG2 GPRs

d42f065

- This is to address the issue reported in #495

feat: update Rhea ids for MAR03816 and MAR08426

5dee342

chore: update Docker image of Memote

e77cd7d

fix: correct TYMP and PNP GPRs

2058020

Merge pull request #499 from juliette-cooke/fix/correctTYMPgprs

a4c4b96

fix: correct TYMP and PNP GPRs

Merge branch 'develop' into fix/correctARGgprs

67ec9e5

feat: update Rhea ids for reactions catalyzed by TYMP and PNP

4248562

- add Rhea ids to MAR04603, MAR04651, MAR04709, MAR04485, MAR04754

Merge pull request #496 from SysBioChalmers/fix/correctARGgprs

ca5dc94

fix: correct ARG GPRs

Merge branch 'develop' into chore/update-memote-image

f88437b

Merge pull request #497 from SysBioChalmers/chore/update-memote-image

6a57017

chore: update Docker image of Memote

Merge branch 'develop' into fix/mergeCoAmetabolism

63a66c3

refactor: combine jobs in workflow

62259e2

Merge branch 'develop' into refactor/gh-workflow

dd51152

feat: update memote image from metabolicatlas

8f736ad

fix: typo

98d2793

Merge branch 'develop' into refactor/gh-workflow

f9cc433

Merge pull request #490 from SysBioChalmers/refactor/gh-workflow

a742f25

refactor: gh workflow

Merge remote-tracking branch 'origin/develop' into fix/mergeCoAmetabo…

48ad302

…lism

Merge pull request #492 from SysBioChalmers/fix/mergeCoAmetabolism

59d45a4

fix: consolidate subsystem of coenzyme A metabolism

fix: refine NADK GPRs

baa413e

- assign only NADK2 to MAR04268 - assign only NADK to MAR04269 - empty GPR to MAR04279

fix-rxn: remove remove MAR04279 from HumanGEM

6719328

doc: update removed rxn to deprecated identifiers

334451b

haowang-bioinfo and others added 18 commits April 30, 2023 10:20

style: removed fields authors, email, and organization

14695c9

- removed these fields from Yaml file - disabled them in `importYaml` and `exportYaml` functions

Update code/io/importYaml.m

a52c2d5

Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>

Update code/io/exportYaml.m

41d9e44

Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>

Merge pull request #546 from SysBioChalmers/style/migrateToCommunityC…

2df1146

…uration style: move from lab-based development to community curation

feat: add gene symbols to model

efe35d9

- extract gene symbols from genes.tsv and include to Human-GEM

feat: enable geneShortNames field for gene symbols

23e088f

fix: remove MAR04568

8141d9d

fix: make MAR04567 irreversible and switch products & reactants

2d1a950

fix: add new reaction MAM02883c + MAM02040c -> MAM02884c + MAM02751c

45c8364

fix: indentation errors in new entry for MAR20070

e146780

Fix: remove empty line at end of deprecatedReactions.tsv

9ed8d58

Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>

Merge pull request #551 from Devlin-Moyer/develop

757585f

fix: sedoheptulose kinase/phosphatase reactions

Merge branch 'develop' into feat/addGeneSymbols

79b628d

chore: add Devlin-Moyer as a contributor (#542)

9396e4c

chore: expand .gitignore

6073f0d

docs: add manas-kohli as contrib

5bf841d

docs: add juliette-cooke as contrib

b760c18

Merge pull request #549 from SysBioChalmers/feat/addGeneSymbols

06ea460

feat: add gene symbols to model

fix: remove orphan mets MAM02662c, MAM02662m, MAM02662x

38fde13

haowang-bioinfo requested review from JonathanRob, mihai-sysbio, feiranl and johan-gson May 8, 2023 10:27

Merge pull request #555 from SysBioChalmers/fix/removeMAM02662

0162a45

fix: remove orphan mets MAM02662c, MAM02662m, MAM02662x

johan-gson approved these changes May 8, 2023

View reviewed changes

feiranl approved these changes May 9, 2023

View reviewed changes

haowang-bioinfo merged commit 30db9d9 into main May 9, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Human 1.15 #554

Human 1.15 #554

haowang-bioinfo commented May 7, 2023 •

edited

Loading

haowang-bioinfo commented May 7, 2023

johan-gson left a comment

feiranl left a comment

haowang-bioinfo commented May 9, 2023 •

edited

Loading

haowang-bioinfo commented May 9, 2023

Human 1.15 #554

Human 1.15 #554

Conversation

haowang-bioinfo commented May 7, 2023 • edited Loading

Main improvements in this PR:

haowang-bioinfo commented May 7, 2023

johan-gson left a comment

Choose a reason for hiding this comment

feiranl left a comment

Choose a reason for hiding this comment

haowang-bioinfo commented May 9, 2023 • edited Loading

haowang-bioinfo commented May 9, 2023

haowang-bioinfo commented May 7, 2023 •

edited

Loading

haowang-bioinfo commented May 9, 2023 •

edited

Loading