// SCAN REPORT

Entrez MCP Server

24 tools. 4 can modify or destroy data without limits.

4 write tools that can modify data. Rate limits recommended.

Last updated: 3 Jul 2026

4 can modify or destroy data

20 read-only

24 tools total

Community server · catalogue entry verified 03/07/2026

How to control Entrez MCP Server ↓

TOOL MAP

What Entrez MCP Server exposes to your agents

Read (20) Write / Execute (4) Destructive / Financial (0)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

High Risk

The most dangerous Entrez MCP Server tools

Execute · Medium blast_submit This tool submits a job to an external service (NCBI BLAST), causing an external operation to execute. Execute · High query_staged_data This tool executes arbitrary SQL queries against a relational database. Write · Low epost The epost tool creates temporary records on NCBI's Entrez History server by uploading UIDs (unique identifiers). Write · Medium efetch_and_stage The tool fetches data (Read) but also parses and writes it into a SQLite database (Write).

4 of Entrez MCP Server's 24 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control Entrez MCP Server

PolicyLayer is an MCP gateway — it sits between your AI agents and Entrez MCP Server, and nothing reaches the server without passing your rules. These are the rules we recommend:

Rate limit write operations

{
  "efetch_and_stage": {
    "limits": [
      {
        "counter": "efetch_and_stage_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations

{
  "blast_get": {
    "limits": [
      {
        "counter": "blast_get_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register Entrez MCP Server — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON ENTREZ →

Instant setup, no code required.

FULL CATALOGUE

All 24 Entrez MCP Server tools

EXECUTE 2 tools

Execute blast_submit Submit sequences for BLAST similarity searching against NCBI databases. Supports all BLAST programs (blastn, b Execute query_staged_data Execute SQL queries against previously staged Entrez datasets. Query the relational database created by efetch

WRITE 2 tools

Write efetch_and_stage Fetches and PARSES data from Entrez databases, then stages it into a relational SQLite database with proper en Write epost Upload UIDs to the Entrez History server for efficient batch processing. Essential for large datasets - upload

READ 20 tools

Read blast_get Retrieve results from a submitted BLAST job using the Request ID. Get detailed sequence alignments, similarity Read egquery Search across all 38+ Entrez databases simultaneously to see hit counts for your query in each database. Globa Read einfo Get comprehensive metadata about NCBI Entrez databases including field statistics, last update dates, and avai Read elink Find UIDs linked between Entrez databases (e.g., SNP records linked to Nucleotide, Domain records linked to Pr Read entrez-capabilities List the available tools, their operations, and guidance for usage. Read entrez-data Stage Entrez payloads and explore them with SQL or smart summaries. Read entrez-external Access PubChem chemistry and PMC article utilities from one entry point. Read entrez-query Compact gateway to Entrez E-utilities with smart defaults and staging hooks. Read esearch Search Entrez databases with text queries to find matching UIDs. Core Entrez function that converts queries in Read espell Get spelling suggestions for search terms in Entrez databases. Helps optimize queries by suggesting correct sp Read esummary Retrieve concise document summaries (DocSums) for UIDs from any Entrez database. Essential for getting key met Read get_staged_schema Get comprehensive schema information for staged datasets including table structures, column descriptions, comm Read pmc_citation_exporter Export properly formatted citations for PMC articles in various bibliographic formats including RIS, NBIB, MED Read pmc_id_converter Convert between different PMC article identifiers including PMC IDs, PubMed IDs (PMID), DOIs, and Manuscript I Read pmc_oa_service Check if a PMC article is available in the Open Access subset and get download links for full-text content. Wo Read pubchem_bioassay Get bioassay information from PubChem including assay descriptions, targets, and activity data. Search by AID, Read pubchem_compound Get detailed compound information from PubChem including chemical properties, synonyms, and classifications. S Read pubchem_structure_search Perform structure-based searches in PubChem including identity, substructure, superstructure, and similarity s Read pubchem_substance Get substance information from PubChem including substance records, synonyms, and cross-references. Search by Read system-api-key-status Report NCBI API key presence and summarise the effective rate limits.

FAQ

Questions about Entrez MCP Server

How do I prevent bulk modifications through Entrez MCP Server? +

The Entrez MCP Server server has 2 write tools including efetch_and_stage, epost. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach Entrez MCP Server.

How many tools does the Entrez MCP Server MCP server expose? +

24 tools across 2 categories: Read, Write. 20 are read-only. 4 can modify, create, or delete data.

How do I enforce a policy on Entrez MCP Server? +

Register the Entrez MCP Server MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every Entrez MCP Server tool call.

Deterministic rules across all 24 Entrez MCP Server tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON ENTREZ →

Instant setup, no code required.

24 Entrez MCP Server tools catalogued and risk-classified — across an index of 43,000+ MCP servers.