monarch-database

To find candidate genes for rare disease, query the Monarch knowledge graph with a set of patient HPO terms to retrieve and prioritize overlapping phenotype-to-gene associations. The Skill maps HPO term sets to ranked candidate genes using Monarch API v3 association endpoints.

Disease semantic comparison is performed by executing a semsim compare operation through the Monarch API v3 endpoints. This calculates phenotype-profile semantic similarity between two diseases to support differential diagnosis workflows.

Yes, HPO term lookup and ontology navigation are supported through Monarch API v3 entity lookup endpoints. You can search for specific HPO terms, fetch their definitions, and retrieve hierarchy context for clinical phenotype annotation.

Cross-species ortholog discovery is supported by querying the Monarch knowledge graph for ortholog-phenotype relationships and model organism connections. The Skill retrieves disease–gene–phenotype associations across species using Monarch API v3 endpoints with properly formed identifier prefixes.

Disease-to-gene and gene-to-phenotype associations are retrieved by querying Monarch API v3 association endpoints with correctly formed identifier prefixes and pagination-aware parameters. The Skill handles entity lookups and association retrieval for bidirectional exploration of the biomedical knowledge graph.

Monarch API v3 queries require properly formed identifier prefixes for all entity, HPO, and association lookups. Pagination-aware query parameters must also be included to ensure complete retrieval of disease–gene–phenotype associations across the multi-species knowledge graph.