MCP Servers

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P
Pubmed MCP
by @Morii0603
GitHub Repo(1 stars)

A PubMed MCP server implemented by Golang.

Created 1/25/2026
Updated 3 days ago
README
View Source
Repository documentation and setup instructions

PubMed MCP Server (SSE)

English | 简体中文

An MCP server for biomedical researchers that searches the PubMed literature database using SSE (Server-Sent Events) transport.

Features

  • PubMed search: Query the world's largest biomedical literature database
  • SSE transport: Uses Server-Sent Events over HTTP

Getting Started

Configure API key

  • PubMed API Key (obtain from https://account.ncbi.nlm.nih.gov/settings/)

Set environment variables

Create a .env file:

PUBMED_API_KEY=your_actual_api_key_here
PORT=8080

Run the SSE server

# Run the prebuilt binary (Windows and Linux builds provided)
./pubmed-mcp

The server listens on the configured port:

  • SSE endpoint: http://localhost:8080/sse
  • Message endpoint: http://localhost:8080/message

Configure Claude Desktop or Cherry Studio

Add this snippet to your MCP client config:

{
  "mcpServers": {
    "pubmed-mcp-sse": {
      "url": "http://localhost:8080/sse",
      "transport": "sse"
    }
  }
}

Build from source

  1. Clone the project
git clone https://github.com/Morii0603/PubMed-MCP.git
cd PubMed-MCP
  1. Install dependencies
go mod download
  1. Build
go build -o pubmed-mcp

Available tools

1. pubmed_search

Search the PubMed database with advanced filtering options.

Parameters:

  • query (required): Search keywords, supports boolean operators (AND, OR, NOT) and field tags, e.g., "cancer AND immunotherapy", "diabetes[ti] AND treatment[tiab]"
  • max_results (optional): Number of results, default 10, max 100
  • date_from (optional): Start date in YYYY/MM/DD or YYYY format, e.g., "2020/01/01"
  • date_to (optional): End date in YYYY/MM/DD or YYYY format, e.g., "2024/12/31"
  • date_type (optional): Date type - "pdat" (publication date, default), "edat" (Entrez date), "mdat" (modification date)
  • text_availability (optional): Filter by text availability:
    • abstract - has abstract
    • free_full_text - free full text available
    • full_text - full text available
  • article_attribute (optional): Filter by article attributes:
    • has_abstract - has abstract
    • has_associated_data - has associated data
  • article_type (optional): Filter by article type (comma-separated):
    • clinical_trial, meta_analysis, randomized_controlled_trial, review, systematic_review, case_reports, editorial, letter, practice_guideline, observational_study, comparative_study
  • language (optional): Filter by language (comma-separated):
    • english, chinese, french, german, japanese, spanish, russian, italian, korean, portuguese
  • species (optional): Filter by species: humans, animals, other
  • sex (optional): Filter by sex: male, female
  • age (optional): Filter by age group (comma-separated):
    • infant (0-23 months), child (0-18 years), preschool_child (2-5 years), adolescent (13-18 years), adult (19+ years), young_adult (19-24 years), middle_aged (45-64 years), aged (65+ years), aged_80_over (80+ years)
  • exclude_preprints (optional): Set to true to exclude preprint articles
  • journal (optional): Filter by journal name or ISSN
  • sort (optional): Sort by: relevance (default), pub_date (newest first), first_author, journal

Example prompt:

Search PubMed for "heart failure treatment" with max 20 results, randomized controlled trials only, from 2020 to now, English language, human studies, adult patients, exclude preprints

Response format:

{
  "count": 150,
  "query": "cancer immunotherapy",
  "results": [
    {
      "title": "Advances in cancer immunotherapy",
      "authors": ["Smith J", "Johnson A", "Brown R"],
      "journal": "New England Journal of Medicine",
      "pub_date": "2024 Jan",
      "pmid": "12345678",
      "url": "https://pubmed.ncbi.nlm.nih.gov/12345678/",
      "abstract": "This article discusses..."
    }
  ]
}

2. pubmed_advanced_search

Execute advanced PubMed search using native query syntax with full support for field tags and boolean operators.

Parameters:

  • query (required): PubMed native query with field tags and boolean operators
  • max_results (optional): Number of results, default 10, max 100
  • sort (optional): Sort order

Field Tags Reference: | Tag | Description | Example | |-----|-------------|---------| | [ti] | Title | cancer[ti] | | [tiab] | Title/Abstract | diabetes[tiab] | | [au] | Author | Smith J[au] | | [1au] | First Author | Wang Y[1au] | | [lastau] | Last Author | Zhang L[lastau] | | [ad] | Affiliation | Harvard[ad] | | [mh] | MeSH Terms | breast neoplasms[mh] | | [majr] | MeSH Major Topic | diabetes mellitus[majr] | | [pt] | Publication Type | Meta-Analysis[pt] | | [ta] | Journal Abbreviation | N Engl J Med[ta] | | [journal] | Full Journal Name | Nature[journal] | | [la] | Language | english[la] | | [pdat] | Publication Date | 2020/01/01:2024/12/31[pdat] | | [sb] | Subset | free full text[sb] | | [doi] | DOI | 10.1056/NEJMoa2401234[doi] |

Advanced Search Examples:

# 1. Author + Title combination
Smith J[1au] AND cancer[ti]

# 2. MeSH term search
breast neoplasms[mh] AND tamoxifen[mh]

# 3. Date range
("2020/01/01"[pdat] : "2024/12/31"[pdat]) AND covid-19[tiab]

# 4. Complex combined search
(diabetes[mh] OR diabetes mellitus[tiab]) AND (meta-analysis[pt] OR systematic review[pt]) AND english[la]

# 5. Exclude preprints
cancer immunotherapy NOT preprint[pt]

3. pubmed_fetch

Fetch detailed article information from PubMed using EFetch API. Returns comprehensive metadata including full abstract, complete author names, journal details, DOI, PMCID, etc.

Parameters:

  • pmids (required): One or more PubMed IDs (PMIDs) separated by commas, e.g., "12345678" or "12345678,87654321"

Example prompt:

Fetch detailed information for PubMed articles 12345678 and 87654321

Response format:

{
  "articles": [
    {
      "pmid": "12345678",
      "title": "Advances in cancer immunotherapy",
      "authors": ["Smith John", "Johnson Anne", "Brown Robert"],
      "journal": "New England Journal of Medicine",
      "journal_abbr": "N Engl J Med",
      "pub_date": "2024 Jan 15",
      "abstract": "Full abstract text here...",
      "doi": "10.1056/NEJMoa2401234",
      "pmcid": "PMC1234567",
      "url": "https://pubmed.ncbi.nlm.nih.gov/12345678/"
    }
  ],
  "count": 1
}

4. pubmed_summary

Get article summary information from PubMed using ESummary API. Returns concise metadata including title, authors, publication date, journal details, volume, issue, pages, and other bibliographic information (without full abstract text).

Parameters:

  • pmids (required): One or more PubMed IDs (PMIDs) separated by commas, e.g., "12345678" or "12345678,87654321"

Example prompt:

Get summaries for PubMed articles 12345678, 87654321, and 11223344

Response format:

{
  "summaries": [
    {
      "pmid": "12345678",
      "title": "Advances in cancer immunotherapy",
      "authors": ["Smith J", "Johnson A", "Brown R"],
      "last_author": "Brown Robert",
      "source": "N Engl J Med",
      "full_journal_name": "The New England journal of medicine",
      "pub_date": "2024 01",
      "epub_date": "2024 01 10",
      "volume": "390",
      "issue": "2",
      "pages": "123-135",
      "doi": "10.1056/NEJMoa2401234",
      "pmcid": "PMC1234567",
      "issn": "0028-4793",
      "pub_types": ["Journal Article", "Review"],
      "languages": ["eng"],
      "has_abstract": true,
      "url": "https://pubmed.ncbi.nlm.nih.gov/12345678/"
    }
  ],
  "count": 1
}

Notes

  1. API key safety: Do not commit the .env file
  2. Rate limits: PubMed API key usage is rate-limited
  3. Network: Requires stable internet access to PubMed
  4. SSE connectivity: Ensure firewalls allow HTTP on the SSE port

Troubleshooting

Issue: Cannot reach PubMed

  • Verify the API key is correct and active
  • Check network connectivity

Issue: SSE server fails to start

  • Confirm the port is free
  • Ensure environment variables are set correctly
  • Inspect logs for details

Issue: MCP client cannot connect

  • Confirm the server is running
  • Check the URL config (http://localhost:8080/sse)
  • Ensure transport is set to sse

License

MIT License

Resources

  • https://pubmed.ncbi.nlm.nih.gov/
  • https://www.ncbi.nlm.nih.gov/books/NBK25501/
  • https://modelcontextprotocol.io/
  • https://github.com/mark3labs/mcp-go
Quick Setup
Installation guide for this server

Installation Command (package not published)

git clone https://github.com/Morii0603/PubMed-MCP
Manual Installation: Please check the README for detailed setup instructions and any additional dependencies required.

Cursor configuration (mcp.json)

{ "mcpServers": { "morii0603-pubmed-mcp": { "command": "git", "args": [ "clone", "https://github.com/Morii0603/PubMed-MCP" ] } } }