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PrimeKG Precision Medicine Knowledge Graph

Lets Claude query PrimeKG to explore links between genes, drugs, diseases and phenotypes.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 6/10Last updated: Aug 9, 2026

What it does

Wires Claude Code into PrimeKG, Harvard's precision-medicine knowledge graph (~129K nodes, 4M edges, 29 relation types), through a small Python query layer.

  • search_nodes: resolve gene, protein, drug, disease or phenotype names to graph IDs
  • get_neighbors: pull direct associations (drug-target, disease-gene, GWAS, contraindications...)
  • get_disease_context: one-call summary of genes, drugs and phenotypes tied to a disease
  • relation_type filtering to isolate a single evidence type

Who it's for

  • Drug discovery researchers hunting for targets or repurposing hypotheses
  • Bioinformatics and translational scientists mapping symptoms to diseases and genes
  • Grad students and analysts doing network pharmacology or multiscale biology work

Example uses

  1. "Summarize genes and approved drugs linked to Alzheimer's disease in PrimeKG" → runs get_disease_context and tabulates the result
  2. "List metformin's protein targets, then find other diseases tied to those proteins" → drug_protein filter plus a 2-hop expansion to surface repurposing candidates
  3. "Given this phenotype list, rank the best-matching rare diseases" → overlap analysis over disease_phenotype edges

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/primekg folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/primekg/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/primekg ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Copy the skill into Claude's skills folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/primekg ~/.claude/skills/
  3. Install the Python dependency: pip install pandas
  4. Download kg.csv from the PrimeKG Harvard Dataverse — it is a large file, so allow disk space and time
  5. Point the scripts at your copy: export PRIMEKG_DATA=/path/to/kg.csv (ignore the leftover Windows path in the skill docs)
  6. Restart Claude Code and try a prompt such as "Find Alzheimer-associated genes in PrimeKG".
View source on GitHub ↗License: MIT