omicverse.metabol.load_pathways

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omicverse.metabol.load_pathways#

omicverse.metabol.load_pathways(path=None, *, organism=None)[source]#

Return {pathway_name: [kegg_id, ...]} — the pathway database used by msea_ora() / msea_gsea() / mummichog_basic().

The default is the full KEGG pathway database fetched from the public KEGG REST endpoint (cached under ~/.cache/omicverse/metabol/; ~550 pathways). First call needs network; subsequent calls are free.

Parameters:

  • path (Optional[Path] (default: None)) – Override with your own pathway CSV (columns: pathway_name, kegg_compounds — the latter a ;-joined list of KEGG IDs). Useful for domain-specific pathway collections (e.g. SMPDB, Reactome-metabolite, or a curated clinical panel). Skips the network entirely.

  • organism (Optional[str] (default: None)) – KEGG organism code for species-specific pathways ("hsa" human, "mmu" mouse, …). Default None → species-agnostic map##### reference metabolic pathways, which is what enrichment papers usually use.

Return type:

dict[str, list[str]]

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