omicverse.metabol.fetch_kegg_pathways

omicverse.metabol.fetch_kegg_pathways#

omicverse.metabol.fetch_kegg_pathways(organism=None, *, cache=True, refresh=False)[source]#

Fetch the full KEGG compound→pathway map via KEGG REST.

Parameters:

  • organism (Optional[str] (default: None)) – KEGG organism code ("hsa" human, "mmu" mouse, …). When None, the reference pathway namespace (map#####, species- agnostic metabolic pathways) is used. For metabolomics enrichment this is almost always what you want.

  • cache (bool (default: True)) – Read/write a TSV cache at ~/.cache/omicverse/metabol/kegg_<org>.tsv.

  • refresh (bool (default: False)) – Ignore the cache and re-fetch.

Returns:

{pathway_name: [kegg_compound_id, ...]} — the same shape load_pathways() returns for the shipped subset, so msea_ora() / msea_gsea() accept it directly.

Return type:

dict[str, list[str]]

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