MCP Servers

pubmed-mcp

MCP server for accessing NCBI PubMed/PMC databases, enabling search, retrieval of summaries and full records, citation export, and ID conversion through various APIs.

README

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.

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/

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