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.
npx skills add LeonChaoX/qinyan-academic-skills --skill monarch-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 dise
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Monarch API v3
- 2. Phenotype-to-Gene Association (Pheno2Gene)
- 3. Disease-to-Gene Associations
- 4. Gene-to-Phenotype and Disease
- 5. HPO Term Lookup
- 6. Semantic Similarity (Disease Comparison)
- 7. Cross-Species Orthologs
- 8. Full Workflow: Rare Disease Gene Prioritization
- Query Workflows
- Workflow 1: HPO-Based Differential Diagnosis
- Workflow 2: Disease Model Discovery
What does the monarch-database skill do?
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.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill monarch-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.