pubmedmcp

pubmedmcp is a Python MCP server that provides tools for searching and fetching biomedical articles from PubMed, delegating the actual PubMed operations to the pubmedclient library.

Evaluated Mar 30, 2026 (22d ago)
Repo ↗ Ai Ml mcp pubmed biomedical-search literature-mining python
⚙ Agent Friendliness
44
/ 100
Can an agent use this?
🔒 Security
46
/ 100
Is it safe for agents?
⚡ Reliability
32
/ 100
Does it work consistently?

Score Breakdown

⚙ Agent Friendliness

MCP Quality
45
Documentation
40
Error Messages
0
Auth Simplicity
100
Rate Limits
10

🔒 Security

TLS Enforcement
70
Auth Strength
40
Scope Granularity
0
Dep. Hygiene
55
Secret Handling
70

No auth model is described; if the MCP server makes outbound calls to PubMed/NCBI, security depends on transport (likely HTTPS) and on how the server is deployed. No information is provided about logging practices, secret handling, or how requests are validated.

⚡ Reliability

Uptime/SLA
0
Version Stability
50
Breaking Changes
50
Error Recovery
30
AF Security Reliability

Best When

You want an MCP-compatible tool for PubMed search/fetch that can be called from an AI agent.

Avoid When

You require a documented public REST/GraphQL API, fine-grained access controls, or clearly specified retry/idempotency semantics.

Use Cases

  • • Biomedical literature search for research assistants
  • • Retrieving PubMed records by query for downstream summarization
  • • Building agent workflows that need structured PubMed citations/metadata
  • • On-demand lookup of article metadata in clinical/biomedical projects

Not For

  • • User authentication/authorization use cases
  • • High-volume bulk downloading without rate-limit awareness
  • • Applications requiring a REST/GraphQL/SDK-first integration model
  • • Sensitive data processing environments that require strict audit-ready error handling/guarantees

Interface

REST API
No
GraphQL
No
gRPC
No
MCP Server
Yes
SDK
No
Webhooks
No

Authentication

OAuth: No Scopes: No

No authentication mechanism is described in the provided README/manifest snippet.

Pricing

Free tier: No
Requires CC: No

No pricing information provided (appears to be an open-source/self-hostable component).

Agent Metadata

Pagination
none
Idempotent
False
Retry Guidance
Not documented

Known Gotchas

  • ⚠ README only shows how to launch the MCP server; it does not document available MCP tools, parameters, or output schemas.
  • ⚠ pubmedclient/NCBI endpoints may impose rate limits; retry/pagination behavior is not documented here.

Alternatives

Direct use of pubmedclient in your own code NCBI E-utilities via scripted calls (if appropriate for your workflow) General bibliographic APIs or datasets that provide higher-level indexing

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Scores are editorial opinions as of 2026-03-30.

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