monarch-database

Monarch Initiative Database

Overview

The Monarch Initiative (https://monarchinitiative.org/) is a multi-species integrated knowledgebase that links genes, diseases, and phenotypes across humans and model organisms. It integrates data from over 40 sources including OMIM, ORPHANET, HPO (Human Phenotype Ontology), ClinVar, MGI (Mouse Genome Informatics), ZFIN (Zebrafish), RGD (Rat), FlyBase, and WormBase.

Monarch enables:

• Mapping phenotypes across species to identify candidate disease genes
• Finding all genes associated with a disease or phenotype
• Discovering model organisms for human diseases
• Navigating the HPO hierarchy for phenotype ontology queries

Key resources:

• Monarch portal: https://monarchinitiative.org/
• Monarch API v3: https://api-v3.monarchinitiative.org/v3/
• API docs: https://api-v3.monarchinitiative.org/v3/docs
• HPO browser: https://hpo.jax.org/

When to Use This Skill

Use Monarch when:

• 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

Core Capabilities

1. Monarch API v3

Base URL: https://api-v3.monarchinitiative.org/v3/

import requests

BASE_URL = "https://api-v3.monarchinitiative.org/v3"

def monarch_get(endpoint, params=None):
    """Make a GET request to the Monarch API."""
    url = f"{BASE_URL}/{endpoint}"
    response = requests.get(url, params=params, headers={"Accept": "application/json"})
    response.raise_for_status()
    return response.json()