primekg

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

1|1|Updated Mar 13, 2026

Search Tags:#knowledge graph #bioinformatics #drug discovery #drug repurposing #precision medicine #gene-disease association

Ready to run

npx skills add https://github.com/youyinnn/skills-collection --skill primekg

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: primekg
Source: https://github.com/youyinnn/skills-collection/tree/main/plugins/model-development-and-experiments/skills/primekg
Command: npx skills add https://github.com/youyinnn/skills-collection --skill primekg

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill addresses the challenge of navigating and extracting complex biological and medical data by providing programmatic access to the Precision Medicine Knowledge Graph (PrimeKG).

Core Features & Use Cases

Entity Search: Find nodes for genes, drugs, diseases, and phenotypes.
Relationship Exploration: Retrieve direct associations and neighbors for any given node.
Disease Context Analysis: Summarize key associated genes, drugs, and phenotypes for a disease.
Pathfinding: Identify potential drug repurposing opportunities by finding paths between drugs and diseases.
Use Case: Researchers can use this Skill to discover potential drug targets for a specific disease by querying for genes associated with that disease and then finding drugs that interact with those genes.

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 genes associated with a specific disease?▼

To query a precision medicine knowledge graph for disease-associated genes, you can use programmatic Python scripts to search for the disease node and retrieve its direct gene neighbors. This allows you to extract multiscale biological data for target discovery.

What is the best way to find drug repurposing opportunities using a bioinformatics knowledge graph?▼

Finding drug repurposing opportunities with a bioinformatics knowledge graph involves using pathfinding scripts to identify paths between drugs and diseases. You can also retrieve drugs that interact with genes associated with the target disease.

Can I retrieve direct drug and phenotype associations for a disease without manual database searches?▼

Yes, you can retrieve direct drug and phenotype associations for a disease programmatically. By querying the knowledge graph for disease context analysis, you can summarize key associated genes, drugs, and phenotypes automatically without manual database searches.

Does the PrimeKG skill support programmatic access for node searching and neighbor retrieval?▼

Yes, the PrimeKG skill supports programmatic access via Python scripts for node searching and neighbor retrieval. It allows you to find nodes for genes, drugs, diseases, and phenotypes, and retrieve their direct associations.

What data sources are integrated into this precision medicine knowledge graph?▼

This precision medicine knowledge graph integrates multiscale biological data from over 20 primary databases and scientific literature. It consolidates data on genes, drugs, diseases, and phenotypes to facilitate knowledge-based drug discovery.

Are there limitations to using a knowledge graph for phenotype analysis and gene-disease association mapping?▼

Limitations of using this knowledge graph for phenotype analysis include relying on pre-integrated data from primary databases and scientific literature, which may restrict real-time updates or novel, unindexed gene-disease associations not yet present in the graph.