PubMed MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_API_KEY | No | Optional NCBI API key to increase rate limit from 3 req/s to 10 req/s. Obtain from NCBI account settings. |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| searchA | Search PubMed with MeSH support, structured filters, pagination, and selectable output verbosity. output_mode=minimal returns id/title/url/full_text_available only (legacy-compatible); compact (default) adds authors/journal/year/doi/pmcid; full additionally includes abstract/mesh_terms/publication_types. |
| fetchA | Retrieve abstract for a single PMID (OpenAI MCP compliant). Accepts exactly one PMID. For multiple PMIDs, use fetch_batch. |
| fetch_batchA | Retrieve abstracts for multiple PMIDs in a single batch request. Returns structured data per PMID. Set include_abstract=false to omit the abstract field (e.g., when you only need full author lists). |
| get_full_textA | Retrieve full text of articles from PubMed Central (PMC) by PMC ID. Supports section filtering to reduce token usage. |
| countA | Get only the count of search results for query adjustment and optimization. Fast — retrieves no actual data. Useful for refining search strategies. |
| find_similar_articlesA | Find similar articles for a given PMID using MeSH terms and title-based similarity. Useful for literature review and related research discovery. |
| export_to_risA | Export PubMed articles to RIS format for citation managers (EndNote/Zotero/Mendeley). Returns compact RIS with minimal metadata — citation managers auto-fetch the rest via PMID. |
| get_citation_countsA | Get citation counts for PMIDs. Default source is iCite (counts only, includes citations from outside PubMed). Set citing_source='pubmed' for elink-based PubMed-internal citations and to retrieve citing PMIDs (useful for backward snowballing). |
| convert_idsA | Convert between PMID, PMCID, and DOI identifiers using NCBI ID Converter API. |
| batch_processA | Run multiple operations against the same set of PMIDs in one call. Helpful for systematic-review style workflows. operations is an array drawn from: 'abstract', 'citations', 'similar', 'ris_export', 'full_text'. Respects NCBI rate limits via max_concurrency (default 3). |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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