Phenotype¶
Use phenotype commands to search HPO terms and phenotype-gene associations from the Monarch Initiative.
Search phenotypes¶
By HPO identifiers (space-separated):
By name or keyword:
Multiple terms with limit:
The positional terms argument accepts HPO IDs or keywords, space-separated or
comma-separated. 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
keyword discovery, then switch to disease commands once you have the right
normalized concept.
JSON mode¶
Practical tips¶
- Use HPO IDs for precise lookups when you know the exact term.
- Use plain-text keywords for exploratory searches across phenotype names.
- Combine multiple HPO IDs in a single query to retrieve a phenotype set.