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dam2452

pubmed-mcp

by dam2452
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Python
Remote

pubmed-mcp

Polski

MCP server exposing NCBI PubMed/PMC APIs: E-utilities (search, summaries, full records, links, database info, spelling, citation matching), BioC full text, the Literature Citation Exporter, and the PMC ID Converter.

Table of contents

Related MCP server: PubMed MCP Server

Tools

Tool

Parameters

Description

search_pubmed

term: str, db: str = "pubmed", retmax: int = 20, retstart: int = 0, sort: Optional[str] = None, mindate: Optional[str] = None, maxdate: Optional[str] = None, datetype: Optional[str] = None

ESearch — matching UIDs and total count

get_summaries

db: str, ids: str, select: str = "*"

ESummary — document metadata for a list of UIDs

fetch_records

db: str, ids: str, rettype: str, retmode: "xml"|"text" = "text", max_chars: int = 20000

EFetch — full records (abstracts, FASTA, GenBank, etc.)

find_related_links

ids: str, dbfrom: str = "pubmed", db: str = "pubmed", linkname: Optional[str] = None, cmd: str = "neighbor"

ELink — related/cross-referenced records

get_database_info

db: Optional[str] = None

EInfo — list of Entrez databases, or fields/links for one database

global_query_counts

term: str

EGQuery — result counts across all Entrez databases

spelling_suggestions

db: str, term: str

ESpell — spelling-corrected search term

match_citations

citations: str

ECitMatch — batch citation-to-PMID matching

get_full_text

id: str, id_type: "pmid"|"pmcid" = "pmid", encoding: "unicode"|"ascii" = "unicode", max_chars: int = 20000

BioC — full text of a PMC Open Access article

export_citation

ids: str, db: "pubmed"|"pmc" = "pubmed", format: "citation"|"csl"|"ris"|"nbib" = "citation"

Literature Citation Exporter — formatted citation

convert_ids

ids: str, idtype: Optional["pmcid"|"pmid"|"mid"|"doi"] = None, versions: bool = False

PMC ID Converter — convert between PMID/PMCID/MID/DOI

raw_request

service: "eutils"|"bioc"|"citexport"|"idconv", path: str, params: Dict[str, Any]

Raw GET request to any of the four underlying APIs

Environment variables

Variable

Required

Description

PUBMED_MCP_EMAIL

no

Email reported to NCBI (recommended by their usage policy)

PUBMED_MCP_API_KEY

no

NCBI E-utilities API key — raises the rate limit from 3 to 10 requests/second

Wiring it up

Only requirement: uv (https://docs.astral.sh/uv/). Nothing else to install.

Claude Code

claude mcp add pubmed-mcp -- uvx --from git+https://github.com/dam2452/pubmed-mcp.git pubmed-mcp

With optional email/API key:

claude mcp add pubmed-mcp -e PUBMED_MCP_EMAIL=<value> -e PUBMED_MCP_API_KEY=<value> -- uvx --from git+https://github.com/dam2452/pubmed-mcp.git pubmed-mcp

Claude Desktop / other MCP client

{
  "mcpServers": {
    "pubmed-mcp": {
      "command": "uvx",
      "args": ["--from", "git+https://github.com/dam2452/pubmed-mcp.git", "pubmed-mcp"],
      "env": { "PUBMED_MCP_EMAIL": "<value>", "PUBMED_MCP_API_KEY": "<value>" }
    }
  }
}

After pushing a new version: uv cache clean and restart the client.

Local run

uv run --directory . pubmed-mcp

Tests (manual):

uv run --directory . --with pytest pytest test/
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