primekg
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
npx skills add BioTender-max/awesome-bio-agent-skills --skill primekg --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 outco
- Overview
- When to Use This Skill
- Core Workflow
- 1. Search for Entities
- 2. Get Neighbors (Direct Associations)
- 3. Analyze Disease Context
- Relationship Types in PrimeKG
- Best Practices
- Resources
- Scripts
- Data Path
What does the primekg skill do?
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill primekg --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.