Summary
Wraps the NCBI E-utilities API to search and retrieve biomedical literature from PubMed directly in your MCP client. No authentication required, which keeps setup simple. Part of the Pipeworx gateway, so you can either use it standalone or connect to the full gateway for access to 250+ data sources. The ask_pipeworx tool lets you query in plain English instead of constructing API calls manually. Reach for this when you need to pull research papers, clinical studies, or medical literature into your AI workflows without leaving Claude or your editor.
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Tools
Public tool metadata for what this MCP can expose to an agent.
9 tools
pubmed_search_articlesSearch PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large res...14 params
Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large res...
Parameters* required
sortstringSort order: relevance (default), pub_date (newest first), author, or journalone of
relevance · pub_date · author · journaldefault: relevancequerystringPubMed search query (supports full NCBI syntax)
authorstringFilter by author name (e.g. "Smith J")
offsetintegerResult offset for pagination (0-based)default: 0
journalstringFilter by journal name
speciesstringFilter by speciesone of
humans · animalslanguagestringFilter by language (e.g. "english")
dateRangeobjectFilter by date range
meshTermsarrayFilter by MeSH terms
maxResultsintegerMaximum results to returndefault: 20
hasAbstractbooleanOnly include articles with abstracts
freeFullTextbooleanOnly include free full text articles
summaryCountintegerFetch brief summaries for top N results (0 = PMIDs only)default: 0
publicationTypesarrayFilter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis")
pubmed_fetch_articlesFetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.3 params
Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.
Parameters* required
pmidsarrayPubMed IDs to fetch
includeMeshbooleanInclude MeSH termsdefault: true
includeGrantsbooleanInclude grant informationdefault: false
pubmed_fetch_fulltextFetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via ELink).5 params
Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via ELink).
Parameters* required
pmidsarrayPubMed IDs to resolve to PMC full text. Provide this OR pmcids, not both. Only works for open-access articles available in PMC.
pmcidsarrayPMC IDs to fetch (e.g. ["PMC9575052"]). Provide this OR pmids, not both.
sectionsarrayFilter to specific sections by title, case-insensitive (e.g. ["Introduction", "Methods", "Results", "Discussion"])
maxSectionsintegerMaximum top-level body sections
includeReferencesbooleanInclude reference listdefault: false
pubmed_format_citationsGet formatted citations for PubMed articles in APA, MLA, BibTeX, or RIS format.2 params
Get formatted citations for PubMed articles in APA, MLA, BibTeX, or RIS format.
Parameters* required
pmidsarrayPubMed IDs to cite
stylesarrayCitation styles to generate
pubmed_find_relatedFind articles related to a source article — similar content, citing articles, or references.3 params
Find articles related to a source article — similar content, citing articles, or references.
Parameters* required
pmidstringSource PubMed ID
maxResultsintegerMaximum related articlesdefault: 10
relationshipstringRelationship type: similar (content-based), cited_by (articles citing this one), references (articles this one cites)one of
similar · cited_by · referencesdefault: similarpubmed_spell_checkSpell-check a query and get NCBI's suggested correction. Useful for refining search queries.1 params
Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.
Parameters* required
querystringPubMed search query to spell-check
pubmed_lookup_meshSearch and explore MeSH (Medical Subject Headings) vocabulary. Essential for building precise PubMed queries.3 params
Search and explore MeSH (Medical Subject Headings) vocabulary. Essential for building precise PubMed queries.
Parameters* required
termstringMeSH term to look up
maxResultsintegerMaximum resultsdefault: 10
includeDetailsbooleanFetch full MeSH records (scope notes, tree numbers, entry terms)default: true
pubmed_lookup_citationLook up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.1 params
Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.
Parameters* required
citationsarrayCitations to look up. More fields = better match accuracy.
pubmed_convert_idsConvert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.2 params
Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.
Parameters* required
idsarrayArticle identifiers to convert. All IDs must be the same type. DOIs: "10.1093/nar/gks1195", PMIDs: "23193287", PMCIDs: "PMC3531190".
idtypestringThe type of IDs being submitted. Required so the API can unambiguously resolve them.one of
pmcid · pmid · doimcp-pubmed
PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)
Part of Pipeworx — an MCP gateway connecting AI agents to 881+ live data sources.
Tools
| Tool | Description |
|---|
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"pubmed": {
"url": "https://gateway.pipeworx.io/pubmed/mcp"
}
}
}
Or connect to the full Pipeworx gateway for access to all 881+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}
Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Pubmed data" })
The gateway picks the right tool and fills the arguments automatically.
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License
MIT
Featured
Keep your Mac awake while Claude Code and 40+ AI agents run. Sleeps when they're idle.
One time payment $9 →Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →On Capafy, your Skill runs online 24/7 as an agent product, and you get paid every time someone uses it.
Start earning →