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primekg

Query PrimeKG CSV data to retrieve disease-related genes, drugs, and phenotypes.

22|4|Updated May 25, 2026
Search Tags:#knowledge-graph#drug-discovery#primekg#biomedical-graph#network-pharmacology#gene-drug-disease
One-click install
npx skills add https://github.com/crazymsn/academic-skills --skill primekg-crazymsn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: primekg
Source: https://github.com/crazymsn/academic-skills/tree/main/academic-skills/primekg
Command: npx skills add https://github.com/crazymsn/academic-skills --skill primekg-crazymsn

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

PrimeKG provides an integrated knowledge graph that connects genes, drugs, diseases, and phenotypes from multiple sources, enabling researchers to access comprehensive biological relationships from a single API.

Core Features & Use Cases

  • Search for nodes (genes, proteins, drugs, diseases, phenotypes) by name or ID.
  • Retrieve direct neighbors and evidence across relationship types to map biological connections.
  • Analyze local disease context by summarizing associated genes, drugs, and phenotypes.
  • Identify drug-disease paths for potential repurposing.
  • Programmatic access via query_primekg.py; data stored as PrimeKG CSV at the specified path.

Quick Start

Query PrimeKG to identify a disease of interest and retrieve its immediate network of genes, drugs, and phenotypes.

Frequently Asked Questions about primekg

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

FAQPage Schema
How do I query a biomedical knowledge graph for drug-disease connections?▼

To map gene-drug-disease relationships, use the query_primekg.py script to search nodes by name or ID and retrieve direct neighbors across relationship types from the local PrimeKG CSV dataset.

What is the best way to find drug repurposing candidates using biomedical graph data?▼

Finding drug repurposing candidates involves analyzing local disease context by retrieving direct neighbors and identifying drug-disease paths within the PrimeKG knowledge graph to reveal potential new treatments.

Do I need a local CSV dataset to explore genes, drugs, and diseases in PrimeKG?▼

Yes, exploring PrimeKG requires a local PrimeKG CSV dataset and the query_primekg.py script to search for genes, drugs, diseases, and phenotypes and retrieve their biological connections.

Can I use pandas to analyze multiscale biology relationships in a knowledge graph?▼

Yes, pandas is a required dependency for querying the PrimeKG CSV dataset to perform multiscale biology analyses and retrieve biological connections across genes, drugs, diseases, and phenotypes.

How does retrieving direct neighbors help with network pharmacology analysis?▼

Retrieving direct neighbors maps biological connections and evidence across relationship types, allowing you to summarize local disease context for network pharmacology analysis and identify potential drug-disease paths.

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