Monarch Initiative¶
Monarch Initiative matters when a disease workflow depends on phenotype evidence, cross-species model context, or phenotype-to-disease matching instead of a single disease identifier lookup. It is particularly useful when you need a phenotype-first starting point and then want to pivot into disease records with supporting evidence.
In BioMCP, Monarch is visible in the disease genes section, the disease models section, and search phenotype for ranked HPO-set matching. There is no get phenotype subcommand, so phenotype work begins with search and then pivots back into disease records and sections.
What BioMCP exposes¶
| Command | What BioMCP gets from this source | Integration note |
|---|---|---|
get disease <id> genes |
Disease-gene associations with relationship and provenance context | Monarch-backed disease section that can be augmented with other source scores |
get disease <id> phenotypes |
Phenotype associations for a disease | Monarch-backed disease section |
get disease <id> models |
Model-organism evidence for a disease | Monarch-backed disease section |
search phenotype |
Ranked disease matches from phenotype terms | Search-first phenotype workflow |
Example commands¶
Returns disease-associated genes with Monarch-backed evidence context.
Returns disease phenotypes and qualifiers for the requested disease.
Returns model-organism evidence for the requested disease.
Returns ranked disease matches from the supplied HPO term set.
API access¶
No BioMCP API key required.
Official source¶
Monarch Initiative is the official integrated phenotype and disease platform behind BioMCP's Monarch-backed disease and phenotype workflows.