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monarch-database

Query Monarch API v3 for disease-gene-phenotype associations across species.

94|11|Updated Mar 26, 2026
Search Tags:#genes#hpo#mondo#monarch#diseases#cross-species#phenotypes
One-click install
npx skills add https://github.com/swaruplab/operon --skill monarch-database-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: monarch-database
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/monarch-database
Command: npx skills add https://github.com/swaruplab/operon --skill monarch-database-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

The Monarch Initiative Database empowers researchers to query across species for disease-gene-phenotype associations by integrating OMIM, ORPHANET, HPO, ClinVar, and model organism data to accelerate rare-disease discovery and translational research.

Core Features & Use Cases

  • Cross-species disease-gene-phenotype mapping to identify candidate genes and model organisms for a given phenotype or disease.
  • HPO term lookup and MONDO ontology integration to harmonize queries across sources.
  • Phenotype-to-disease and gene-to-phenotype associations to support rare-disease gene prioritization and cross-species disease modeling.

Quick Start

Query Monarch API v3 to retrieve genes associated with a given HPO term, or diseases linked to a gene.

Frequently Asked Questions about monarch-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I map human phenotype ontology terms to candidate genes across species?▼

To map HPO terms to candidate genes across species, query the Monarch Initiative knowledge graph to retrieve cross-species disease-gene-phenotype associations using HPO identifiers and orthology data.

What is cross-species disease modeling and when do I need it for rare disease discovery?▼

Cross-species disease modeling integrates model organism data with OMIM, ORPHANET, and ClinVar to identify candidate genes. You need it for rare-disease discovery and translational research when human data is limited.

Can I retrieve disease associations for a specific gene using MONDO identifiers?▼

Yes, you can retrieve disease associations for a specific gene by querying Monarch API v3 endpoints with MONDO identifiers to aggregate cross-ontology relationships and disease-gene-phenotype mappings.

Does the Monarch knowledge graph integrate model organism data with human disease ontologies?▼

Yes, the Monarch knowledge graph integrates model organism data with human disease ontologies by harmonizing HPO and MONDO terms across OMIM, ORPHANET, and ClinVar sources for cross-species queries.

What's the best way to prioritize candidate genes for rare diseases using phenotype-to-gene mapping?▼

The best way to prioritize candidate genes is leveraging phenotype-to-gene associations through the Monarch API v3, querying HPO terms and orthology data to map phenotypes to potential disease-causing genes across species.

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