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fix: update HMDB IDs to version 4 #435

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merged 7 commits into from
Dec 10, 2022
Merged

fix: update HMDB IDs to version 4 #435

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49136b1
fix: update HMDB ID format to version 4
haowang-bioinfo Nov 18, 2022
e03eb8c
fix: update HMDB ID for MAM03055r
haowang-bioinfo Nov 18, 2022
a6f7f92
fix-met: revert unnecessary inserting of zeros
haowang-bioinfo Nov 20, 2022
995fe24
fix-met: remove deprecated HMDB ids
haowang-bioinfo Nov 20, 2022
6b171ed
fix-met: replace old ids with updated ones
haowang-bioinfo Nov 20, 2022
4e99f62
Merge branch 'develop' into fix/HMDB_ids_issue434
haowang-bioinfo Dec 8, 2022
c3b720f
doc: update README files
haowang-bioinfo Dec 10, 2022
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2 changes: 1 addition & 1 deletion code/modelCuration/README.md
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This directory contains curation-related scripts and functions used to make changes to the Human-GEM repository. These curation scripts help to improve transparency of changes made to the model when the number of changes is too large to view practically.


- `getCompFromUniprotCellAtlas.py`: Code for collecting subcellular localization information for existing metabolic enzymes from **Swissprot** and **Cell Atlas** ([HPA](https://www.proteinatlas.org/search/has_protein_data_in%3ACell)), and then incorporating the compartment info from both sources into `genes.tsv`.
5 changes: 4 additions & 1 deletion data/modelCuration/README.md
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This directory contains curation-related data files used for making changes to the Human-GEM model. These model curation data files help to improve transparency of changes made to the model.

* #241: `rhea_reaction_association.tsv` includes Rhea reaction ids that are associated with Human-GEM reactions by equation mapping method and/or via UniProt id. `metabolite_name_synonyms.tsv` stores mapped synonymous metabolite names used in Human-GEM and other databases.
- #241: `rhea_reaction_association.tsv` includes Rhea reaction ids that are associated with Human-GEM reactions by equation mapping method and/or via UniProt id.
- `metabolite_name_synonyms.tsv` stores mapped synonymous metabolite names used in Human-GEM and other databases.
- `Swissprot_compartments.tsv`: Subcellular location annotations extracted from SwissProt on 2022-11-15.
- `CellAtlasCompartments_science_2017.tsv`: Experimentally [validated](https://www.science.org/doi/10.1126/science.aal3321) subcellular location information downloaded from [Cell Atlas](https://www.proteinatlas.org/search/has_protein_data_in%3ACell).
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