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primekg

Query PrimeKG for genes, drugs, diseases, and phenotypes via Python scripts.

Updated Mar 10, 2026
Search Tags:#knowledge graph#genomics#drug discovery#cheminformatics#precision medicine#disease analysis
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill primekg-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: primekg
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/primekg
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill primekg-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

This Skill provides programmatic access to the Precision Medicine Knowledge Graph (PrimeKG), enabling users to query vast amounts of multiscale biological data and discover relationships between genes, drugs, diseases, and phenotypes.

Core Features & Use Cases

  • Entity Search: Find genes, drugs, diseases, and phenotypes within the knowledge graph.
  • Relationship Discovery: Retrieve direct associations and neighbors for any given entity.
  • Disease Context Analysis: Summarize key associated genes, drugs, and phenotypes for a specific disease.
  • Pathfinding: Identify potential drug repurposing opportunities by finding paths between drugs and diseases.
  • Use Case: A researcher can use this Skill to find all known drugs associated with a specific gene implicated in a rare disease, or to explore potential drug targets for a newly identified disease.

Quick Start

Use the primekg skill to find all genes associated with Alzheimer's disease.

Frequently Asked Questions about primekg

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

FAQPage Schema
How do I query a precision medicine knowledge graph for drug discovery and disease analysis?▼

Query a precision medicine knowledge graph using Python scripts to access multiscale biological data, retrieving genes, drugs, diseases, and phenotypes for drug discovery and disease analysis. This integration of over 20 databases enables knowledge-based drug repurposing.

What is the best way to retrieve associated genes and phenotypes for a specific disease?▼

Retrieve associated genes and phenotypes for a specific disease by performing disease context analysis. This summarizes key biological relationships within the precision medicine knowledge graph for conditions like Alzheimer's.

Can I search for specific genes and drugs within a multiscale biological knowledge graph?▼

Search for specific genes and drugs within the multiscale biological knowledge graph using programmatic Python scripts. Entity search functions return direct associations and neighbor relationships for any queried biological entity.

Does this knowledge graph tool support cheminformatics and phenotype analysis?▼

The knowledge graph tool supports cheminformatics and phenotype analysis by integrating data from over 20 databases and scientific literature. This enables comprehensive entity searching and relationship discovery across multiscale biological datasets.

How do I discover direct associations and neighbors for a given biological entity?▼

Discover direct associations and neighbors for a biological entity by executing neighbor retrieval scripts. The query returns all directly connected nodes, mapping relationships between genes, drugs, diseases, and phenotypes.

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