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

• Tools
• Environment variables
• Wiring it up
• Local run

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/