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monarch-database

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Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.

When to use

• **Rare disease gene discovery**: What genes are associated with my patient's phenotypes (HPO terms)?
• **Phenotype similarity**: Are two diseases similar based on their phenotypic profiles?
• **Cross-species modeling**: Are there mouse/zebrafish models for my disease of interest?
• **HPO term lookup**: Retrieve HPO term names, definitions, and ontology hierarchy
• **Disease-phenotype mapping**: List all HPO terms associated with a specific disease
• **Gene-phenotype associations**: What phenotypes are caused by variants in a gene?
• **Ortholog-phenotype mapping**: Use animal model phenotypes to infer human gene function

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