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monarch-database

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations.

Updated Mar 10, 2026
Search Tags:#knowledge graph#genetics#phenotype#hpo#monarch initiative#rare disease#gene discovery
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill monarch-database-felixboehm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: monarch-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/monarch-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill monarch-database-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to the Monarch Initiative knowledge graph, enabling users to query complex relationships between diseases, genes, and phenotypes across multiple species, facilitating rare disease gene discovery and cross-species disease modeling.

Core Features & Use Cases

  • Phenotype-to-Gene Mapping: Identify candidate genes associated with a set of patient phenotypes (HPO terms).
  • Disease-Gene Association: Retrieve genes linked to specific human diseases (using MONDO, OMIM, ORPHANET IDs).
  • Cross-Species Comparison: Find orthologous genes and model organisms for human diseases.
  • HPO Term Lookup: Search and retrieve information about Human Phenotype Ontology terms.
  • Use Case: A researcher investigating a rare neurological disorder can input the patient's HPO terms to find potential causative genes and identify relevant animal models for further study.

Quick Start

Use the monarch-database skill to find genes associated with the HPO terms 'HP:0001250' (Seizures) and 'HP:0004322' (Short stature).

Frequently Asked Questions about monarch-database

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

FAQPage Schema
How do I find candidate genes from a list of HPO phenotype terms?▼

Phenotype-to-gene mapping uses HPO terms like 'HP:0001250' to query the Monarch Initiative knowledge graph, identifying candidate genes associated with the input patient phenotypes for rare disease discovery.

Can I retrieve disease-gene associations using OMIM or ORPHANET identifiers?▼

Disease-gene association queries accept MONDO, OMIM, and ORPHANET IDs to retrieve genes linked to specific human diseases from the integrated knowledge graph database.

How do I find orthologous genes and animal models for a human disease?▼

Cross-species comparison queries the knowledge graph to find orthologous genes and identify relevant model organisms for human diseases, facilitating cross-species disease modeling.

What is the best way to search for Human Phenotype Ontology term information?▼

HPO term lookup searches the Monarch Initiative knowledge graph to retrieve detailed information about Human Phenotype Ontology terms integrated with ClinVar and model organism databases.

Does this rare disease knowledge graph integrate ClinVar and model organism databases?▼

The knowledge graph integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases via a Python API client to query disease-gene-phenotype associations across species.

What do I need to query the Monarch Initiative knowledge graph for rare disease gene discovery?▼

You need Python with the requests and pandas libraries to run the API client scripts that query the knowledge graph for disease-gene-phenotype associations and rare disease gene discovery.

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