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monarch-database

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

1|Updated Mar 12, 2026
Search Tags:#ontology#genetics#phenotype#hpo#monarch initiative#rare disease#gene discovery
One-click install
npx skills add https://github.com/yf8578/clawomics --skill monarch-database-yf8578
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: monarch-database
Source: https://github.com/yf8578/clawomics/tree/main/skills/monarch-database
Command: npx skills add https://github.com/yf8578/clawomics --skill monarch-database-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps researchers and clinicians uncover complex relationships between diseases, genes, and phenotypes across multiple species, accelerating rare disease gene discovery and understanding.

Core Features & Use Cases

  • Phenotype-to-Gene Mapping: Identify candidate genes associated with a set of patient-observed phenotypes (HPO terms).
  • Disease Gene Association: Find all genes linked to a specific disease.
  • Cross-Species Modeling: Discover animal models that share phenotypic similarities with human diseases.
  • HPO Term Lookup: Retrieve detailed information and definitions for Human Phenotype Ontology terms.
  • Use Case: A geneticist suspects a rare neurological disorder. By inputting the patient's HPO terms (e.g., seizures, hypotonia), the skill can query the Monarch database to suggest potential causative genes and relevant model organisms for further study.

Quick Start

Use the monarch-database skill to find genes associated with the HPO terms for seizures and 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 patient HPO terms for rare disease discovery?▼

Phenotype-to-gene mapping identifies candidate genes by querying the Monarch Initiative knowledge graph with patient HPO terms. It integrates OMIM, ORPHANET, and ClinVar data to suggest potential causative genes for rare diseases based on observed phenotypic features.

Can I discover animal models that share phenotypic similarities with human diseases?▼

Cross-species disease modeling finds animal models sharing phenotypic similarities with human diseases. By querying the Monarch knowledge graph, you can identify orthologs and relevant model organism databases for translational research and comparative analysis.

Does this Skill support semantic similarity analysis for comparing rare diseases?▼

Semantic similarity analysis for disease comparison is supported. It leverages the Monarch Initiative knowledge graph to evaluate phenotypic overlap between diseases, facilitating cross-species disease modeling and ortholog identification for translational research.

How do I retrieve detailed definitions for Human Phenotype Ontology terms?▼

HPO term lookup retrieves detailed information and definitions for Human Phenotype Ontology terms. The Skill queries the Monarch database to provide specific semantic details for terms used in phenotype-to-gene mapping and rare disease gene discovery.

What databases are integrated for disease-gene-phenotype association queries?▼

Disease-gene-phenotype association queries integrate data from OMIM, ORPHANET, HPO, ClinVar, and model organism databases. This integration across the Monarch Initiative knowledge graph enables comprehensive gene discovery and cross-species disease modeling.

What do I need to query disease-gene-phenotype links across species?▼

Querying disease-gene-phenotype links requires HPO terms or disease names as input. Using Python with requests and pandas, the Skill queries the Monarch Initiative knowledge graph to output gene associations, orthologs, and model organism data.

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