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PrimeKG Precision Medicine Knowledge Graph

Query the PrimeKG biomedical knowledge graph — genes, drugs, diseases, phenotypes — straight from Claude Code.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Gives Claude programmatic access to PrimeKG, Harvard's precision medicine knowledge graph (~129K nodes, ~4M edges, 29 relation types).

  • search_nodes() to find genes, proteins, drugs, diseases, phenotypes
  • get_neighbors() to pull direct associations, filterable by relation type
  • get_disease_context() for a one-shot summary of a disease's genes, drugs and phenotypes
  • Reference list of key edge types: drug_protein, disease_gene, disease_phenotype, gwas, protein_protein

Who it's for

  • Researchers hunting for drug targets or drug-repurposing hypotheses
  • Biomedical data analysts linking symptoms to diseases and genes
  • Grad students and labs working on network pharmacology or multiscale biology

Example uses

  1. "Summarize the genes and approved drugs associated with Alzheimer's disease" → get_disease_context("Alzheimer's disease")
  2. "List only the protein targets of this drug" → get_neighbors(drug_id, relation_type="drug_protein")
  3. "Find diseases sharing phenotypes with X" → traverse phenotype neighbors to surface repurposing paths

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/primekg/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

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. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Copy the skill into your 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 C:\Users\eamon\... path in the doc).
  6. Restart Claude Code and try: "Use PrimeKG to find genes associated with Alzheimer's disease."
View source on GitHub ↗License: MIT