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scientific-monarch-ontology

Retrieve disease-phenotype-gene associations and compute ontology-based relations via the Monarch Initiative API.

3|1|Updated Feb 11, 2026
Search Tags:#ontology#disease#association#phenotype#gene#hpo#monarch
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-monarch-ontology
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-monarch-ontology
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-monarch-ontology
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-monarch-ontology

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Monarch Initiative exposes disease-gene-phenotype associations and ontology-based analyses; this skill enables programmatic retrieval and systematic interpretation of disease, gene, and HPO data to accelerate biomedical research.

Core Features & Use Cases

  • Retrieve disease-gene-phenotype associations via the Monarch API for research queries.
  • Support inverse lookups (gene to disease) and phenotype-based querying, including HPO-term typing and semantic similarity estimation.
  • Provide a deterministic pipeline for integrating disease-genes-phenotypes into downstream analyses and pipelines.

Quick Start

Run monarch_pipeline on a disease query to generate results and outputs.

Frequently Asked Questions about scientific-monarch-ontology

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

FAQPage Schema
How do I retrieve disease-gene-phenotype associations using the Monarch API?▼

You retrieve disease-gene-phenotype associations by running the monarch_pipeline on a disease query, which fetches and aggregates related genes and HPO terms via the Monarch Initiative API.

Can I perform a reverse lookup from a gene to its associated diseases?▼

Yes, you can perform inverse lookups from a gene to disease, along with phenotype-based querying and HPO-term typing, using the Monarch Initiative API integration.

How do I calculate semantic similarity for HPO terms in disease queries?▼

The skill computes ontology-based relations and estimates semantic similarity for HPO terms by systematically processing disease, gene, and phenotype data retrieved from the Monarch API.

What is the best way to integrate ontology-based disease data into downstream pipelines?▼

The best way is to use the skill's deterministic, scriptable pipeline, which systematically interprets disease, gene, and HPO data to generate structured outputs for downstream analyses.

Can I use this approach for phenotype typing across diseases with related genes?▼

Yes, the skill supports phenotype typing across diseases with related genes by leveraging ontology-based search workflows and Monarch API data aggregation.

Do I need any external dependencies to run the monarch_pipeline?▼

No, you do not need any external dependencies to run the monarch_pipeline, as the skill operates independently to retrieve and compute ontology-based relations from the Monarch API.

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