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/
