alterlab-monarch

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

58|9|Updated Mar 16, 2026

Search Tags:#bioinformatics #hpo #ontologies #monarch #cross-species #phenotypes #disease-genes

Ready to run

npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-monarch

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: alterlab-monarch
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-monarch
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-monarch

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Monarch-based queries unify disease-gene-phenotype data across species, enabling researchers to find candidate genes, map phenotypes to diseases, and explore model organism connections. It integrates data from OMIM, ORPHANET, HPO, ClinVar, and model organism databases to support cross-species disease biology.

Core Features & Use Cases

Monarch API access for multi-source phenotype-to-gene and disease-to-phenotype associations.
Cross-species disease-gene mapping and ortholog exploration to identify model organisms.
HPO term lookup and MONDO-based disease integration to prioritize rare-disease candidates.
Example workflows include phenotype-driven gene prioritization and cross-species model discovery.

Quick Start

Query Monarch with a set of HPO terms to retrieve implicated genes and associated diseases.

Frequently Asked Questions about alterlab-monarch

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

FAQPage Schema

How do I map cross-species phenotypes to disease genes using HPO terms?▼

You can query the Monarch API with a set of HPO terms to retrieve implicated genes, cross-species disease associations, and model organism connections for rare-disease gene prioritization.

What is cross-species disease-gene mapping and how does Monarch handle it?▼

Cross-species disease-gene mapping identifies orthologous genes and model organisms for human diseases. Monarch unifies disease-gene-phenotype data across species by integrating OMIM, ORPHANET, ClinVar, and model organism databases.

Can I use MONDO and OMIM identifiers to find phenotype connections for rare diseases?▼

Yes, querying Monarch with MONDO, OMIM, or ORPHANET disease identifiers retrieves specific disease-phenotype connections and associated candidate genes for rare-disease research.

What's the best way to prioritize rare-disease candidate genes from phenotype data?▼

The best way is phenotype-driven gene prioritization: input a set of HPO terms into Monarch to discover multi-source phenotype-to-gene associations and identify implicated disease genes.

Does the Monarch API require specific access or error handling for large phenotype queries?▼

Yes, querying Monarch for disease-gene-phenotype associations requires API v3 access and robust pagination and error handling to manage large cross-species ontology datasets effectively.

Why use Monarch for cross-species model discovery instead of searching individual databases?▼

Monarch integrates data from OMIM, ORPHANET, HPO, ClinVar, and model organism databases into a single query, providing unified cross-species disease biology and ortholog exploration.