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 |
Semantic-similarity disease candidates plus exact direct-association checks for the returned slice | Similarity is not direct phenotype evidence |
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 HPO-resolved semantic-similarity candidates and an ordered direct-support state for every disease/HPO pair.
supported means an exact positive
direct association was returned. not_supported is used only when the fixed
association lookup is complete; it means no association was found in that
lookup, not that the disease cannot have the phenotype. indeterminate marks
an incomplete or inconsistent lookup, while unavailable preserves the
similarity page when enrichment fails.
BioMCP suggests a disease follow-up only when one returned candidate is
supported for every resolved HPO term. Otherwise it explains why the
follow-up was suppressed.
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.