Pubmed MCP Server

Name: Pubmed MCP Server
Author: cyanheads

by cyanheadsversion 2.12.0i★ –iComputer or cloud

Registry nameio.github.cyanheads/pubmed-mcp-server

Install

Overview

Description from the maker (original English)

Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi3 of 3 passedChecked from public information; code not scanned yet
UsageiGrowing↓ 3.2K/wk · ★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Computer or cloud
Transport: stdio, Streamable HTTP
Category: Clinics & health

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 3 of 3 passed
Runs on the maker’s server: what you ask it goes through their server.
Can do 12 things (tools) pubmed_search_articles, pubmed_fetch_articles, pubmed_fetch_fulltext, pubmed_format_citations …
You fill in yourself: MCP_LOG_LEVEL, NCBI_API_KEY, NCBI_ADMIN_EMAIL, UNPAYWALL_EMAIL

You need

Runs in the cloudNothing to install; it connects over the internet
npmNode.js installed (for the npx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Works in Claude on the web, desktop and mobile:

Open Settings → Connectors
Press Add custom connector
Paste the address below and press Add
If it asks you to sign in, sign in with the maker

https://pubmed.caseyjhand.com/mcp

Or run it on your computer

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value",
        "NCBI_API_KEY": "your-value",
        "NCBI_ADMIN_EMAIL": "your-value",
        "UNPAYWALL_EMAIL": "your-value"
      }
    }
  }
}

Run this in your terminal

claude mcp add --transport http pubmed https://pubmed.caseyjhand.com/mcp

Or run it on your computer

claude mcp add pubmed --env MCP_LOG_LEVEL=your-value --env NCBI_API_KEY=your-value --env NCBI_ADMIN_EMAIL=your-value --env UNPAYWALL_EMAIL=your-value -- npx -y @cyanheads/pubmed-mcp-server

Fill in the empty values before running it.

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "pubmed": {
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

Or run it on your computer

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value",
        "NCBI_API_KEY": "your-value",
        "NCBI_ADMIN_EMAIL": "your-value",
        "UNPAYWALL_EMAIL": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "pubmed": {
      "type": "http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

Or run it on your computer

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "pubmed": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value",
        "NCBI_API_KEY": "your-value",
        "NCBI_ADMIN_EMAIL": "your-value",
        "UNPAYWALL_EMAIL": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

ChatGPT connects only to servers on the internet:

Open ChatGPT on the web → Settings → Connectors (Apps)
Press Create or Add (some plans need Developer mode under Advanced first)
Paste the address below, give it a name and save
If it asks you to sign in, sign in with the maker

https://pubmed.caseyjhand.com/mcp

Menu names can differ slightly by plan and over time.

Your choice stays on this device in a cookie; no account needed.

Values you fill in

MCP_LOG_LEVEL env
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').
NCBI_API_KEY env
NCBI API key for higher rate limits (10 req/s vs 3 req/s).
NCBI_ADMIN_EMAIL env
Contact email sent with NCBI requests (recommended by NCBI).
UNPAYWALL_EMAIL env
Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Tool names and descriptions exactly as the server reported them on Nov 6, 2026. The maker wrote them, not us; we show them as plain text.

pubmed_search_articles
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 result
pubmed_fetch_articles
Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, linked retraction, erratum, and comment notices, and databank accessions such as trial registration IDs; grants and the members of a collective author
pubmed_fetch_fulltext
Fetch full-text articles from PubMed Central as structured sections — the body, then back matter such as acknowledgments, declarations, and appendices — with tables and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for its open
pubmed_format_citations
Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array. Retractions, errata, and expressions of concern NCBI links to an article come back in `notices`; Vancouver and APA also
pubmed_find_related
Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.
pubmed_spell_check
Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled. Corrections are applied in place, so field tags, operators, spaci
pubmed_lookup_mesh
Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.
pubmed_lookup_citation
Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least
pubmed_convert_ids
Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.
pubmed_fetch_citation_metrics
Fetch NIH iCite citation metrics for PubMed articles: the Relative Citation Ratio (RCR), NIH percentile, citation count, citations per year, expected and field citation rates, the Approximate Potential to Translate (APT), the human, animal, and molecular/cellular shares of each a
pubmed_europepmc_search
Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical
pubmed_europepmc_fetch
Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as `records: [{ source, epmcId }]`, an array even for one record. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncat

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 8, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account cyanheads, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
✓ Pass
Endpoint responds
Responded in 222 ms (HTTP 200)
– Not applicable
Sign-in with OAuth
No sign-in needed
✓ Pass
No hidden instructions in tool descriptions
Read 12 tool descriptions and found no hidden instructions to the AI

Compared with others in Clinics & healthi

More stars than 0% of the other 1028 servers in this category
Published to the registry more recently than 83% of the other 1028 servers in this category
Basic checks equal to or better than 100% of the other 1028 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is Pubmed MCP Server safe?

It passed 3 of 3 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

Either way works: install it on your computer or connect to the cloud version.

Is it still maintained?

The GitHub repo last changed –, and the latest version (2.12.0) reached the registry 5 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. It connects by URL, so apps that accept remote MCP servers work too, such as ChatGPT in developer mode.

What can I use instead?

In the same category: Mirobody, FHIR MCP Server, Google Health MCP

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

@cyanheads/pubmed-mcp-server Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP. 12 Tools • 1 Resource • 1 Prompt

Public Hosted Server: https://pubmed.caseyjhand.com/mcp

Overview

Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fetch metadata and full text, resolve identifiers and partial citations, format references, and ground queries in MeSH vocabulary. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above. Ships the pubmed-guide agent skill (skill://pubmed-guide/SKILL.md), which MCP clients read for PubMed query syntax, DOI-to-PMID routes outside PMC, reference-list resolution, citation counts, and full-text misses.

Tools

Tool	Description
`pubmed_search_articles`	Search PubMed with full query syntax, structured filters, date ranges, and optional summaries
`pubmed_fetch_articles`	Fetch article metadata by PMID: abstract, authors, journal, MeSH terms, databank accessions such as trial registration IDs, grants, a collective author's investigators on request, linked retraction and correction notices
`pubmed_fetch_fulltext`	Fetch full text by PMID, PMCID, or DOI, falling back from PMC to Europe PMC to Unpaywall
`pubmed_europepmc_search`	Search Europe PMC for preprints, patents, Agricola, and open-access records PubMed doesn't carry
`pubmed_europepmc_fetch`	Fetch complete Europe PMC records, including the untruncated abstract, as `records: [{ source, epmcId }]`
`pubmed_fetch_citation_metrics`	Fetch NIH iCite citation metrics by PMID: Relative Citation Ratio, NIH percentile, citation counts and rates
`pubmed_format_citations`	Format citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM), with linked retraction and correction notices
`pubmed_find_related`	Find similar articles, citing articles, or references for a PMID
`pubmed_spell_check`	Correct a misspelled PubMed query via NCBI ESpell
`pubmed_lookup_mesh`	Look up MeSH headings with tree numbers, scope notes, and entry terms
`pubmed_lookup_citation`	Resolve partial references, up to 25 at a time, to PMIDs via ECitMatch
`pubmed_convert_ids`	Convert between DOI, PMID, and PMCID via the PMC ID Converter

Resources

Resource	Description
`pubmed://database/info`	PubMed database metadata via EInfo (field list, record count, last update)

Prompts

Prompt	Description
`research_plan`	Generate a structured four-phase biomedical research plan

Capability reference

`pubmed_search_articles` tool

Full PubMed query syntax plus filters (author, journal, MeSH, publication type, language, species, abstract, free full text) and publication/modification/Entrez date ranges
query is optional: with an author, journal, MeSH, or publication-type filter, the filters alone make the search (a journal's output over a date range, for example)
Up to 1,000 results per page and offsets up to 9,998, or maxResults: 0 for the match count alone; summaryCount adds briefs for up to 50 hits. A larger page size is served at the cap with a notice naming where to continue
Reports totalCount, the effectiveQuery PubMed ran, and the appliedFilters
Rejects blank filter values, impossible dates, and reversed date ranges before PubMed is called

`pubmed_fetch_articles` tool

Up to 200 PMIDs per call; misses are listed in unavailablePmids
Abstract, authors, journal, DOI, publication types, linked retraction/erratum/comment notices, and links; MeSH terms on by default, grants via includeGrants, and the members of a collective author (its InvestigatorList, thousands on some consortium trials) via includeInvestigators
A retracted, corrected, or questioned article opens with the same notice block as pubmed_format_citations, directly under its title
dataBanks lists the record's trial registrations and data deposits (ClinicalTrials.gov NCT IDs, GenBank and PDB accessions, Dryad DOIs) verbatim; search pubmed_search_articles for [si] to find other records citing one
recordType separates journal articles from Bookshelf chapters and books; opt-in maxResponseCharacters defers overflow to deferred.ids

`pubmed_fetch_fulltext` tool

pmcids, pmids, and dois in any mix, up to 50 distinct identifiers per call: the first 10 are fetched and the rest returned in overLimit for a follow-up call. Each is tried against PMC, then Europe PMC, then Unpaywall (needs UNPAYWALL_EMAIL); an article several of them name is fetched and returned once, and viaSource names the tier that answered
source: "pmc" returns sections (the body, then back matter such as acknowledgments, declarations, and appendices), tables, and figures; source: "unpaywall" returns a best-effort HTML or PDF text body
Europe PMC full text is fetched for records Europe PMC marks open access, preprints included; articles carry the licenses their PMC JATS states
Misses carry a typed reason and triedTiers; sections, maxSections, maxCharacters, overflowMode, and maxResponseCharacters bound the response, truncation reports what was cut, and sectionCap names the sections maxSections cut

`pubmed_europepmc_search` tool

Adds preprints (PPR), patents (PAT), and Agricola (AGR) to MED and PMC; defaults to MED, PMC, PPR
Cursor pagination via cursorMark / nextCursorMark, up to 100 per page; a larger page size is served at the cap with a notice naming where to continue. Abstracts arrive as 400-character snippets
Optional sort of comma-separated asc|desc keys; relevance is the default order, and a sort Europe PMC cannot use fails as europepmc_invalid_input
Hits carry license and hasFullTextXml
Not registered when EUROPEPMC_ENABLED=false

`pubmed_europepmc_fetch` tool

Up to 25 records per call as records: [{ source, epmcId }], each pair copied from a search hit, with the full abstract, license, and hasFullTextXml; unresolved ids land in notFound; opt-in maxResponseCharacters defers overflow to deferred.records
Not registered when EUROPEPMC_ENABLED=false

`pubmed_fetch_citation_metrics` tool

Up to 1,000 PMIDs per call; the first 200 distinct are fetched and the rest returned in overLimit, PMIDs NIH iCite has no record for in unavailablePmids
Relative Citation Ratio (with a provisional flag), NIH percentile, citation count and rates, Approximate Potential to Translate, MeSH category shares, and clinical citations
iCite does not flag retractions; check pubmed_fetch_articles for notices
Source: NIH iCite

`pubmed_format_citations` tool

Up to 50 PMIDs per call, in any mix of apa, mla, bibtex, ris, and vancouver
Bookshelf records cite as edited books, each chapter dated by its own last revision or contribution date; PMIDs that can't be fetched are reported as unavailable
Vancouver writes page ranges in elided Citing Medicine form (1637-1645 → 1637-45); BibTeX issn and RIS SN carry the journal's linking ISSN, and RIS TI drops its trailing period
Retractions, errata, and expressions of concern NCBI links to an article come back as notices and are shown ahead of its citations; Vancouver adds a Retraction in: / Erratum in: note and APA a retraction parenthetical

`pubmed_find_related` tool

similar, cited_by, or references, up to 50 per page with offset pagination. A larger page size is served at the cap with a notice naming where to continue
Falls back to Europe PMC, then OpenAlex, and names the provider that answered; fails as all_providers_failed if none can

`pubmed_spell_check` tool

Returns original, corrected, and hasSuggestion; corrections land in place, so field tags, operators, spacing, and gene symbols stay as written, and a single letter such as an author initial is never swapped for another
Values of indexed field tags (aged[mh], zhang y[au], free full text[sb]) are kept as written; free-text fields ([tiab], [ti], [tw]) are still corrected
Run it after a zero-hit or thin search, then retry pubmed_search_articles with corrected

`pubmed_lookup_mesh` tool

Descriptors by name or free-text term, with an exact heading match pinned first (the descriptor, for a drug-class heading); up to 50 per page, continued via nextOffset. A larger page size is served at the cap with a notice naming where to continue
Records carry their MeSH unique ID (meshId, e.g. D000072657) beside the Entrez UID; includeDetails (default on) adds tree numbers, scope notes, and entry terms

`pubmed_lookup_citation` tool

Up to 25 partial citations per call; a journal or a four-digit year is required, and volume, first page, and author sharpen the match
Each is matched independently and comes back matched, not_found, or ambiguous, with recovery detail

`pubmed_convert_ids` tool

Up to 50 ids per call, all of one declared idType (doi, pmid, pmcid); only PMC-indexed articles resolve
One success or error row per id, in order, so a partial batch never fails

`pubmed://database/info` resource

Live EInfo call for the pubmed database, returned as application/json
count, lastUpdate, and fields[], whose names are the search tags pubmed_search_articles accepts

`research_plan` prompt

Arguments: title, goal, and keywords required; organism and includeAgentPrompts optional
Returns a four-phase

Only the beginning is shown; read the rest in the repo

Pubmed MCP Server

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

Or run it on your computer

Or run it on your computer

Or run it on your computer

Or run it on your computer

Values you fill in

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Clinics & healthi

Common questions

Alternatives

Mirobody

FHIR MCP Server

Google Health MCP

README from the maker

Overview

Tools

Resources

Prompts

Capability reference

pubmed_search_articles tool

pubmed_fetch_articles tool

pubmed_fetch_fulltext tool

pubmed_europepmc_search tool

pubmed_europepmc_fetch tool

pubmed_fetch_citation_metrics tool

pubmed_format_citations tool

pubmed_find_related tool

pubmed_spell_check tool

pubmed_lookup_mesh tool

pubmed_lookup_citation tool

pubmed_convert_ids tool

pubmed://database/info resource

research_plan prompt

`pubmed_search_articles` tool

`pubmed_fetch_articles` tool

`pubmed_fetch_fulltext` tool

`pubmed_europepmc_search` tool

`pubmed_europepmc_fetch` tool

`pubmed_fetch_citation_metrics` tool

`pubmed_format_citations` tool

`pubmed_find_related` tool

`pubmed_spell_check` tool

`pubmed_lookup_mesh` tool

`pubmed_lookup_citation` tool

`pubmed_convert_ids` tool

`pubmed://database/info` resource

`research_plan` prompt