SKILL.md
PrimeKG Knowledge Graph Skill
Overview
PrimeKG is a precision medicine knowledge graph that integrates over 20 primary databases and high-quality scientific literature into a single resource. It contains over 100,000 nodes and 4 million edges across 29 relationship types, including drug-target, disease-gene, and phenotype-disease associations.
Key capabilities:
- Search for nodes (genes, proteins, drugs, diseases, phenotypes)
- Retrieve direct neighbors (associated entities and clinical evidence)
- Analyze local disease context (related genes, drugs, phenotypes)
- Identify drug-disease paths (potential repurposing opportunities)
Data access: Programmatic access via query_primekg.py. Data is stored at C:\Users\eamon\Documents\Data\PrimeKG\kg.csv.
When to Use This Skill
This skill should be used when:
- Knowledge-based drug discovery: Identifying targets and mechanisms for diseases.
- Drug repurposing: Finding existing drugs that might have evidence for new indications.
- Phenotype analysis: Understanding how symptoms/phenotypes relate to diseases and genes.
- Multiscale biology: Bridging the gap between molecular targets (genes) and clinical outcomes (diseases).
- Network pharmacology: Investigating the broader network effects of drug-target interactions.
Core Workflow
1. Search for Entities
Find identifiers for genes, drugs, or diseases.
from scripts.query_primekg import search_nodes
# Search for Alzheimer's disease nodes
results = search_nodes("Alzheimer", node_type="disease")
# Returns: [{"id": "EFO_0000249", "type": "disease", "name": "Alzheimer's disease", ...}]