Phenotype¶
Use phenotype commands to rank disease matches from HPO IDs or symptom phrases via the Monarch Initiative similarity search.
Search phenotypes¶
By HPO identifiers (space- or comma-separated):
By one symptom phrase:
By multiple symptom phrases (comma-separated):
Multiple terms with limit:
The positional terms argument accepts:
- canonical HPO IDs, space- or comma-separated
- one symptom phrase
- multiple symptom phrases separated by commas
Free-text symptom phrases are resolved to HPO IDs before the Monarch similarity
search runs. Use --limit and --offset when you need bounded paging.
Get records¶
Phenotype is search-only. There is no get phenotype subcommand.
Request sections¶
Phenotype search rows do not expose extra section names. Use search disease
or get disease <id> phenotypes when you want a normalized disease follow-up.
Helper commands¶
Phenotype is search-only. Start with search phenotype for HPO term sets or
symptom phrases, then switch to disease commands once you have the right
normalized concept. If you want to inspect candidate HPO terms first, run
biomcp discover "<symptom text>" and use the suggested HP: IDs.
Markdown phenotype search results now add a See also: block that reuses the
top-ranked disease match, for example biomcp get disease "Dravet syndrome"
genes phenotypes. biomcp --json search phenotype ... remains a generic
search response and does not add entity-style _meta.next_commands.
JSON mode¶
Practical tips¶
- Use HPO IDs for precise lookups when you know the exact term.
- Use commas to separate multiple symptom phrases in one search.
- Combine multiple HPO IDs in a single query to retrieve a phenotype set.
- Prefer 2-5 high-confidence HPO IDs when you already know them.