PubMed-MCP

A Model Context Protocol (MCP) server that provides tools for searching PubMed articles using the NCBI Entrez API.

Author: Emilio Delgado Muñoz

Features

Search PubMed for articles based on queries
Retrieve detailed information including title, authors, abstract, journal, and publication date
Returns results in JSON format
Configurable maximum number of results

Architecture

graph TB A[Usuario] --> B[MCP Server pubmed_search.py] B --> C[Función search_pubmed] C --> D[Entrez.esearch Búsqueda en PubMed] D --> E[Base de datos PubMed NCBI] E --> F[Lista de PMIDs] F --> G[Entrez.efetch Obtener detalles] G --> E G --> H[Registros XML de artículos] H --> I[Procesamiento de datos] I --> J[Extracción de: - Título - Autores - Abstract - Journal - Fecha] J --> K[Lista de artículos en formato JSON] K --> L[Respuesta al usuario] subgraph "Dependencias" M[BioPython requirements.txt] N[FastMCP requirements.txt] end B -.-> M B -.-> N subgraph "Configuración" O[Entrez.email Configurado en código] end C -.-> O style A fill:#e1f5fe style L fill:#c8e6c9 style E fill:#fff3e0

Installation

Clone this repository:
git clone <repository-url> cd PubMed-MCP
Install dependencies:
uv sync
Configure your email in pubmed_search.py:
Entrez.email = 'your-email@example.com' # Replace with your actual email

VS Code Configuration

To use this MCP server locally in VS Code, the project includes a pre-configured .vscode/mcp.json file. This file tells VS Code how to run the MCP server.

The configuration is already set up to use uv for running the server:

{ "servers": { "pubmed-mcp": { "command": "uv", "args": ["run", "${workspaceFolder}/pubmed_search.py"] } } }

Requirements for VS Code Integration

VS Code with MCP extension support
uv package manager installed
Python virtual environment set up

Alternative Configuration

If you prefer to use pip instead of uv, you can modify the .vscode/mcp.json file:

{ "servers": { "pubmed-mcp": { "command": "python", "args": ["${workspaceFolder}/pubmed_search.py"] } } }

Make sure your virtual environment is activated when using this configuration.

Requirements

Python 3.11+
BioPython
FastMCP

Usage

Run the MCP server:

python pubmed_search.py

The server will start and listen for MCP protocol messages on stdin/stdout.

Available Tools

search_pubmed

Searches PubMed for articles matching the given query.

Parameters:

query (string): The search query
max_results (integer, optional): Maximum number of results to return (default: 10)
title (bool, optional): If true (default) search in Title field
abstract (bool, optional): If true (default) search in Abstract field
keywords (bool, optional): If true (default) expand search with Author Keywords ([ot]) and MeSH Headings ([mh])

Field logic:

title=True and abstract=True -> query applied as (your terms)[tiab]
Only title=True -> (your terms)[ti]
Only abstract=True -> (your terms)[ab]
Both false -> no field tag (all fields)
keywords=True -> OR-expanded with (your terms)[ot] OR (your terms)[mh]

Example refined queries:

query = "breast cancer metastasis" title=True, abstract=True, keywords=True -> (breast cancer metastasis)[tiab] OR ((breast cancer metastasis)[ot] OR (breast cancer metastasis)[mh]) title=True, abstract=False, keywords=False -> (breast cancer metastasis)[ti] title=False, abstract=False, keywords=True -> (breast cancer metastasis) OR ((breast cancer metastasis)[ot] OR (breast cancer metastasis)[mh])

Returns: A list of article objects containing:

pmid: PubMed ID
title: Article title
authors: List of author names
abstract: Article abstract
journal: Journal name
publication_year: Year of publication
publication_month: Month of publication
url: PubMed URL

Configuration

Before using the tool, you must set your email address in the Entrez.email variable. This is required by NCBI's Entrez API.

License

This project is open source. Please check the license file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

This server cannot be installed

-

security - not tested

F

license - not found

-

quality - not tested

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Enables searching and retrieving detailed information from PubMed articles using the NCBI Entrez API. Supports configurable search parameters including title/abstract filtering and keyword expansion to find relevant scientific publications.

PubMed MCP Server