Individual skill

monarch-database

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.

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Repository last updated: Oct 30, 2026
License: Apache-2.0

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# 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.

## Core Capabilities

The skill provides REST API v3 access for:

1. **Phenotype-to-gene mapping** - Find genes associated with human phenotype terms
2. **Disease-to-gene associations** - Discover disease-causing genes using MONDO disease identifiers
3. **Cross-species ortholog discovery** - Identify model organism orthologs for human genes
4. **HPO semantic similarity** - Compare phenotype profiles between individuals/organisms