monarch-database

monarch-database

Overview

The Monarch Initiative integrates disease-phenotype-gene relationships from 30+ biomedical databases (OMIM, Orphanet, ClinVar, MGI, ZFIN, Reactome) into a unified knowledge graph. The REST API at https://api.monarchinitiative.org/v3/api provides access to associations between genes, diseases, and phenotypes using MONDO disease IDs, Human Phenotype Ontology (HPO) terms, and standard gene identifiers. No authentication is required; the service is free for academic use.

When to Use

• Mapping a disease (MONDO ID) to all associated causal genes and their evidence sources
• Retrieving phenotype profiles (HP terms) for a disease to build phenotypic similarity models
• Ranking candidate genes by phenotypic similarity to a patient's HPO symptom list
• Querying cross-species gene-phenotype associations (mouse, zebrafish, fly) for model organism comparisons
• Exploring rare disease gene-phenotype networks for diagnostic candidate generation
• Resolving entity metadata (gene symbol, disease name, phenotype label) from a MONDO/HP/HGNC ID
• Use opentargets-database instead when you need drug-target evidence scores or tractability data alongside disease associations
• Use clinvar-database when you need clinical pathogenicity classifications with submitter review status

Prerequisites

• Python packages: requests, pandas, matplotlib
• Data requirements: MONDO IDs (e.g., MONDO:0007374), HP term IDs (e.g., HP:0001250), or gene symbols/HGNC IDs
• Environment: internet connection; no API key required
• Rate limits: no published rate limit; use time.sleep(0.3) between batch requests; avoid bursts over 10 requests/second

pip install requests pandas matplotlib

Quick Start

import requests

MONARCH_API = "https://api.monarchinitiative.org/v3/api"

def monarch_get(endpoint: str, params: dict = None) -> dict:
    """GET request to Monarch API; raises on HTTP errors."""
    r = requests.get(f"{MONARCH_API}{endpoint}", params=params, timeout=30)
    r.raise_for_status()
    return r.json()