Eduard Kerkhoven

feat: standardize and simplify curation of yeast-GEM

9

### Description of the issue: Currently, `code/` and `data/` contain various scripts and datasets in a variety of formats, which have previously been used to curate yeast-GEM. However, this is...

yeast 8.6.1

1

### Main improvements in this PR: - Fixes: - Manual curation of gene associations of transport reactions, based on various databases. (PR #306, closes #160) - Correct annotation of gene...

feat: Uniprot annotations for all genes

4

### Description of the issue: Add Uniprot annotations in `model.geneMiriams` (see [identifiers.org](https://registry.identifiers.org/registry/uniprot)) for all genes. Use the S288c reference [proteome](https://www.uniprot.org/proteomes/UP000002311) as source, providing one Uniprot ID per gene. **I hereby...

feat: single ec-code annotation per reaction

5

### Description of the issue: Many reactions do not have any ec-code, or are annotated with multiple ec-codes. Instead, each reaction should be annotated with one ec-code, and if not...

refactor: reduce dependencies modelTests

1

### Description of the issue: Currently, `code/modelTests/` still has some COBRA Toolbox dependencies ([1](https://github.com/SysBioChalmers/yeast-GEM/pull/301#discussion_r826050818), [2](https://github.com/SysBioChalmers/yeast-GEM/pull/301#discussion_r826055614), possibly more), that are not necessary given the aim of #301. #### Expected feature/value/output: Use...

feat: metSMILES annotation

1

### Description of the issue: This information is already retained in COBRA-style models, and would be valuable to also be kept here (and have RAVEN support the I/O of this...

### Description of the issue: With single subSystem assignments (#11), that do no necessarily match KEGG pathways (#307), and multiple KEGG pathways that can match one reaction, there should be...

### Description of the issue: [GPRuler](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009550) has corrected grRules for 889 reactions ([S5 File](https://doi.org/10.1371/journal.pcbi.1009550.s005)). Overall, the essential gene analysis was improved:  (where "V" stands for viable and "N" for...

bug: unnecessary invalid BiGG identifiers suggested

1

### Description of the issue: The list of replacement BiGG identifiers ([rxns](https://github.com/SysBioChalmers/yeast-GEM/blob/main/data/databases/BiGGrxnDictionary_newIDs.csv), [mets](https://github.com/SysBioChalmers/yeast-GEM/blob/main/data/databases/BiGGmetDictionary_newIDs.csv)) contain new BiGG-style identifiers when no official BiGG identifier could be found. However, these files contain entries...

### Description of the issue: While there are benefits in having [SLIME reactions](https://github.com/SysBioChalmers/SLIMEr), they can also be a nuisance. An example is when `yeast-GEM` is used as template model for...