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Discover

biomcp discover <query> is the free-text entrypoint for concept resolution. Use it when you know the biomedical phrase but do not yet know whether the next step should be get gene, search disease, search pathway, or another typed command.

Use search all after you already have typed slots such as --gene, --disease, --drug, --variant, or --keyword. discover resolves free text into concepts first; search all fans out from the typed slots you already trust.

Examples

biomcp discover ERBB1
biomcp discover Keytruda
biomcp discover "chest pain"
biomcp --json discover diabetes

What it does

  • Queries OLS4 for structured ontology-backed matches.
  • Adds optional UMLS crosswalks when UMLS_API_KEY is set.
  • Adds MedlinePlus plain-language context for disease and symptom queries.
  • Returns suggested BioMCP follow-up commands without auto-executing them.

Output

Markdown groups concepts by type and shows suggested commands.

JSON preserves the same concepts and adds:

  • _meta.next_commands
  • _meta.section_sources
  • _meta.discovery_sources
  • _meta.evidence_urls

Notes

  • OLS4 is required; if it fails, discover fails.
  • UMLS is optional. Without UMLS_API_KEY, discover still works and reports that clinical crosswalk enrichment is unavailable.
  • MedlinePlus is best-effort and only shown for disease or symptom flows.
  • Queries are sent to third-party biomedical APIs. Do not send PHI or other patient-identifying text.