primekg

Query PrimeKG to retrieve genes, drugs, diseases, and phenotypes.

1|Updated Mar 12, 2026

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

Ready to run

npx skills add https://github.com/yf8578/clawomics --skill primekg-yf8578

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: primekg
Source: https://github.com/yf8578/clawomics/tree/main/skills/primekg
Command: npx skills add https://github.com/yf8578/clawomics --skill primekg-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the Precision Medicine Knowledge Graph (PrimeKG), enabling users to query and analyze complex biological data relationships for drug discovery and disease research.

Core Features & Use Cases

Entity Search: Find genes, drugs, diseases, and phenotypes within the graph.
Relationship Exploration: Retrieve direct associations and neighbors for any given entity.
Contextual Analysis: Summarize the local network around a disease, including related genes, drugs, and phenotypes.
Use Case: Researchers can use this skill to identify potential drug repurposing candidates by finding drugs associated with diseases that share common genetic pathways.

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 knowledge graph for drug discovery and disease relationships?▼

To query a knowledge graph for drug discovery, you can search for genes, drugs, diseases, and phenotypes to retrieve direct associations and explore multiscale biological data relationships.

What is precision medicine knowledge graph data used for in network pharmacology?▼

Precision medicine knowledge graph data is used in network pharmacology to retrieve multiscale biological entities, enabling contextual analysis of local networks around diseases for identifying drug repurposing candidates.

Can I use pandas to retrieve gene-disease associations from a CSV knowledge graph?▼

Yes, you can use pandas to retrieve gene-disease associations from a CSV knowledge graph by running Python scripts that provide programmatic access to query entities and their direct neighbors.

How do I find drugs associated with diseases that share common genetic pathways?▼

To find drugs associated with diseases sharing common genetic pathways, perform neighbor retrieval and contextual analysis on the knowledge graph to summarize related genes, drugs, and phenotypes.

Does this precision medicine Skill support searching for phenotypes and biological entities?▼

Yes, the precision medicine Skill supports entity searching for phenotypes, genes, drugs, and diseases, allowing you to retrieve direct associations and contextual network summaries for research.

What are the limitations of querying a CSV-based knowledge graph for bioinformatics?▼

Querying a CSV-based knowledge graph for bioinformatics relies on Python scripts and pandas, meaning it requires programmatic access and may lack real-time database updates or complex graph database query optimizations.