gene_set_enrichment

THE RISK

Low Risk

Why gene_set_enrichment needs a policy

This tool queries external databases (Enrichr, MSigDB, GO, KEGG) to retrieve and analyze pathway enrichment data for a given gene list. It is a read/query operation with no side effects — it retrieves biological annotations and statistical enrichment results without creating, modifying, or deleting any data.

From the tool's definition Perform gene set enrichment analysis on a list of genes. Queries Enrichr or GSEA against MSigDB, GO, KEGG pathways to identify enriched biological processes.

Documented attack patterns abuse exactly the kind of access gene_set_enrichment gives an agent:

POLICY

How to control gene_set_enrichment

PolicyLayer is an MCP gateway — it sits between your AI agents and MedSci Agent, and nothing reaches the server without passing your rules. This is the rule we recommend for gene_set_enrichment:

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "gene_set_enrichment": {}
  }
}

gene_set_enrichment is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.

Create a free account and register MedSci Agent — nothing to install.
Add this policy — paste it, or build it visually.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

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EXPLORE

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Go deeper

The MCP Attack Database → Documented attack patterns against MCP deployments — and the policies that stop them.
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FAQ

Questions about gene_set_enrichment

What does the gene_set_enrichment tool do? +

Perform gene set enrichment analysis on a list of genes. Queries Enrichr or GSEA against MSigDB, GO, KEGG pathways to identify enriched biological processes. It is categorised as a Read tool in the MedSci Agent MCP Server, which means it retrieves data without modifying state.

How do I enforce a policy on gene_set_enrichment? +

Register the MedSci Agent MCP server in PolicyLayer and add a rule for gene_set_enrichment: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches MedSci Agent. Nothing to install.

What risk level is gene_set_enrichment? +

gene_set_enrichment is a Read tool with low risk. Read-only tools are generally safe to allow by default.

Can I rate-limit gene_set_enrichment? +

Yes. Add a rate_limit block to the gene_set_enrichment rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block gene_set_enrichment completely? +

Set action: deny in the PolicyLayer policy for gene_set_enrichment. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides gene_set_enrichment? +

gene_set_enrichment is provided by the MedSci Agent MCP server (omar-a-hassan/medsci-agent). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

Enforce policy on every MedSci Agent tool call.

Start from MedSci Agent, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

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