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Pathway

Use pathway commands to move from pathway names or IDs to genes, events, enrichment, and drug pivots.

Key boundaries:

  • Search is multi-source across Reactome, KEGG, and WikiPathways.
  • Exact title matches surface first across sources.
  • KEGG base cards stay summary-only unless you explicitly request genes.
  • events and pathway enrichment are Reactome-only.
  • all means all sections available for the resolved pathway source.

Search pathways

QUERY is required for normal pathway search. --top-level is the only queryless search mode.

biomcp search pathway "MAPK signaling" --limit 5
biomcp search pathway -q "Pathways in cancer" --limit 5
biomcp search pathway --top-level --limit 5

Get pathway records

biomcp get pathway R-HSA-5673001
biomcp get pathway hsa05200

Request pathway sections

Genes:

biomcp get pathway R-HSA-5673001 genes
biomcp get pathway hsa05200 genes

Contained events (Reactome only):

biomcp get pathway R-HSA-5673001 events

Gene-set enrichment (Reactome only):

biomcp get pathway R-HSA-5673001 enrichment

All supported sections for the resolved source:

biomcp get pathway R-HSA-5673001 all
biomcp get pathway hsa05200 all

Helper commands

biomcp pathway drugs R-HSA-5673001 --limit 5
biomcp pathway drugs hsa05200 --limit 5
biomcp pathway articles R-HSA-5673001
biomcp pathway trials R-HSA-5673001

JSON mode

biomcp --json get pathway R-HSA-5673001 genes
biomcp --json get pathway hsa05200 genes

Practical tips

  • Use search pathway when you know the label but not the stable ID.
  • Reach for Reactome IDs when you need events or pathway enrichment.
  • Use the helper commands when the next step is drug, article, or trial context rather than more pathway detail.