Merge pull request #435 from SysBioChalmers/fix/HMDB_ids_issue434

fix: update HMDB IDs to version 4
SysBioChalmers · Dec 10, 2022 · 315d2c7 · 315d2c7
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diff --git a/code/modelCuration/README.md b/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.
 
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+- `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`.
diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md
@@ -2,4 +2,7 @@
 
 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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		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`.