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Discover

Use biomcp discover to resolve free-text biomedical phrases into the right BioMCP follow-up commands. It is primarily a single-entity resolver for aliases, brands, symptoms, and close concept names. Run it when you know the 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. Relational or multi-entity questions may redirect to biomcp search all --keyword "<query>" instead of surfacing weak collocation matches as if they were a good discover answer.

Examples

biomcp discover BRCA1
biomcp discover dabigatran
biomcp discover ERBB1
biomcp discover Keytruda
biomcp discover "chest pain"
biomcp discover "developmental delay"
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.
  • Suggests biomcp search phenotype "HP:..." first when symptom concepts resolve to HPO-backed IDs.
  • Keeps the existing discover-specific routed flows for symptom-of-disease, HPO symptom, treatment, gene+disease, and unambiguous gene-plus-topic prompts.
  • Relational or multi-entity questions may redirect to biomcp search all --keyword "<query>" through notes and _meta.next_commands when only weak single-entity residue remains.
  • If no entities resolve, suggests biomcp search article -k "<query>" --type review --limit 5.
  • If only low-confidence concepts resolve, adds a broader-results article-search hint.
  • Returns suggested BioMCP follow-up commands without auto-executing them.

Output

Markdown groups concepts by type, shows notes, and lists suggested commands.

For symptom-first queries such as biomcp discover "developmental delay", discover can surface HP: identifiers directly in the concept list and suggest biomcp search phenotype "HP:..." as the next command. Disease-specific queries like biomcp discover "symptoms of Marfan syndrome" still route to biomcp get disease ... phenotypes. Treatment prompts, gene+disease orientation, and unambiguous gene-plus-topic follow-ups stay supported as existing discover exceptions.

JSON preserves the same concepts, keeps the same guidance in notes, and adds:

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

notes is the user-visible guidance channel in both markdown and JSON. _meta.next_commands remains the machine-actionable command list, including the relational redirect to biomcp search all --keyword "<query>" when discover declines to answer a multi-entity question directly.

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 supplemental 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.