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monarch-database

Query cross-species disease-gene-phenotype associations via the Monarch Initiative API.

21|1|Updated Mar 19, 2026
Search Tags:#api#disease#orthologs#phenotype#gene#monarch#cross-species
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill monarch-database-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: monarch-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/monarch-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill monarch-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Monarch Initiative data across species to connect genes, diseases, and phenotypes for rare disease research and cross-species analysis.

Core Features & Use Cases

  • Monarch API v3 access for gene-disease-phenotype queries.
  • Cross-species ortholog mapping and model organism phenotype associations.
  • Phenotype-to-gene and disease-to-gene retrieval to prioritize candidate genes.

Quick Start

Provide your list of HPO terms and MONDO disease IDs, and the tool will return related genes, diseases, and prioritized candidates.

Frequently Asked Questions about monarch-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query cross-species disease-gene-phenotype associations using the Monarch Initiative API?▼

You can query cross-species disease-gene-phenotype associations by providing HPO terms and MONDO disease IDs to retrieve related genes, diseases, and prioritized candidate genes via Monarch API v3 endpoints.

Can I retrieve model organism phenotypes and ortholog mapping for rare disease research?▼

Yes, cross-species ortholog mapping and model organism phenotype associations are supported, enabling you to connect genes, diseases, and phenotypes across species for rare disease analysis.

How does the Monarch API handle large result sets for gene-disease-phenotype retrieval?▼

Monarch API v3 endpoints support pagination to handle large result sets when retrieving gene-disease-phenotype associations, ensuring comprehensive data extraction without overwhelming the query response.

What input formats do I need to prioritize candidate genes for cross-species analysis?▼

You need to provide a list of HPO terms and MONDO disease IDs as input formats, which the tool then uses to return related genes, diseases, and prioritized candidate genes for cross-species analysis.

Are there limitations when using Monarch API v3 endpoints for entity and association searches?▼

Limitations include relying strictly on Monarch API v3 endpoints (association, entity, search, semsim) for data retrieval, meaning any upstream API downtime or rate limits will directly impact query execution.

Does this tool work with phenotype-to-gene and disease-to-gene retrieval workflows?▼

Yes, phenotype-to-gene and disease-to-gene retrieval workflows are natively supported, allowing researchers to prioritize candidate genes by mapping specific HPO terms and MONDO disease IDs.

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