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Human 1.15 #554
Human 1.15 #554
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-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
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>
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
Here's small scale essentiality evaluation of combined Hart2015 datasets (
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
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LGTM
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LGTM!
IMHO, several comments:
|
#555 is now included to v1.15 |
Main improvements in this PR:
geneShortNames
for gene symbols, as discussed in add gene name to Human-GEM #539authors
,email
, andorganization
fields in code and Yaml file for moving toward community curation on GitHubgenes.tsv
XxxtyrYyy
toXxxTyrYyy
reacitons.tsv
annotation file for a total of 1334 reactionsPantothenate and CoA biosynthesis
,CoA synthesis
, andCoA catabolism
into onePantothenate and CoA metabolism
, as proposed in feat: consolidation the subsystems of coenzyme A metabolism #487