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/
• API v3 base URL: https://api-v3.monarchinitiative.org/v3/api (all endpoints live under /v3/api/...)
• Interactive API docs (Swagger UI): https://api-v3.monarchinitiative.org/v3/docs
• HPO browser: https://hpo.jax.org/

Scripts