primekg

# 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. ```python from scripts.query_primekg import search_nodes # Search for Alzheimer's...