Pubmed MCP Server

Name: Pubmed MCP Server
Author: cyanheads

作者：cyanheads版本 2.12.0i★ –i电脑或云端

注册名称io.github.cyanheads/pubmed-mcp-server

安装

概览

作者提供的说明（英文原文）

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

PopNx MCP 的三大支柱

这三项永远不会合并成一个分数：意见、测量和人气是不同的东西。

用户评价i暂无评价评价功能将在后续阶段与账户功能一起开放
我们的基础检查i3 项中通过 3 项依据公开信息检查；尚未扫描代码
使用情况i正在增长↓ 3189/周 · ★ –

它能帮你做什么

我们还没有为它写通俗的介绍。下面是我们从注册中心读取到的事实。

连接方式: 电脑或云端
传输方式: stdio, Streamable HTTP
分类: 诊所与健康

安装

选择你使用的 AI 应用，然后复制设置。

安装之前

基础检查：3 项中通过 3 项
在作者的服务器上运行：你向它提出的内容会经过他们的服务器。
可以做 12 件事（工具） pubmed_search_articles, pubmed_fetch_articles, pubmed_fetch_fulltext, pubmed_format_citations …
需要你自己填写： MCP_LOG_LEVEL, NCBI_API_KEY, NCBI_ADMIN_EMAIL, UNPAYWALL_EMAIL

你需要

在云端运行无需安装任何东西，通过互联网连接
npm已安装 Node.js（用于 npx 命令）

你用的是哪个应用？

ClaudeClaude CodeCursorVS CodeChatGPT

在上方选择你的应用。我们会记住它，下次按钮会显示“安装到 …”。

适用于网页版、桌面版和手机版 Claude：

打开 Settings → Connectors
点击 Add custom connector
粘贴下面的地址，然后点击 Add
如果要求登录，请登录作者的服务

https://pubmed.caseyjhand.com/mcp

或者在你的电脑上运行

打开 Claude Desktop → Settings → Developer → Edit Config，把下面的内容粘贴到 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"
      }
    }
  }
}

在终端中运行这条命令

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

或者在你的电脑上运行

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

运行前请先填写空着的值。

在 Cursor 中打开

或者自己复制设置

粘贴到项目中的 .cursor/mcp.json，或 ~/.cursor/mcp.json

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

或者在你的电脑上运行

在 Cursor 中打开

或者自己复制设置

粘贴到项目中的 .cursor/mcp.json，或 ~/.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"
      }
    }
  }
}

浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。

在 VS Code 中打开

或者自己复制设置

粘贴到项目中的 .vscode/mcp.json

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

或者在你的电脑上运行

在 VS Code 中打开

或者自己复制设置

粘贴到项目中的 .vscode/mcp.json

{
  "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"
      }
    }
  }
}

浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。

ChatGPT 只能连接互联网上的服务器：

打开网页版 ChatGPT → Settings → Connectors (Apps)
点击 Create 或 Add（部分套餐需要先在 Advanced 中开启 Developer mode）
粘贴下面的地址，起个名字，然后保存
如果要求登录，请登录作者的服务

https://pubmed.caseyjhand.com/mcp

菜单名称可能因套餐和版本不同而略有差异。

你的选择通过 Cookie 保存在这台设备上，无需账户。

需要你填写的值

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.

这些设置是根据作者在注册中心的条目生成的。如果 README 的写法不同，请以 README 为准。

它能做什么

工具名称和描述与服务器在 2026年11月6日报告的完全一致。这些内容由作者撰写，不是我们写的；我们以纯文本形式显示。

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

基础检查i

我们检查的是任何人都能看到的信息；我们没有阅读代码。不适用的检查项不计入总数。 · 检查于 2026年11月8日

✓ 通过
作者与仓库一致
注册名称已通过 GitHub 账户 cyanheads 验证，该账户拥有此仓库
… 尚未检查
仍在维护
我们还没有从 GitHub 读取这个仓库
… 尚未检查
有许可证
我们还没有从 GitHub 读取这个仓库
✓ 通过
端点有响应
在 222 毫秒内响应（HTTP 200）
– 不适用
使用 OAuth 登录
无需登录
✓ 通过
工具描述中没有隐藏指令
已读取 12 个工具描述，未发现针对 AI 的隐藏指令

与“诊所与健康”中的其他服务器比较i

星标数多于此分类中其他 1028 个服务器的 0%
发布到注册中心的时间比此分类中其他 1028 个服务器的 83% 更新
基础检查结果等于或优于此分类中其他 1028 个服务器的 100%

与注册中心里这个分类中所有活跃的服务器比较。只有当发布者拥有该仓库时，星标数才计入。

常见问题

Pubmed MCP Server 安全吗？

它在 3 项适用的基础检查中通过了 3 项。我们没有阅读代码。在添加密钥或令牌之前，请先看看这个服务器要求哪些权限，并使用只具备所需权限的密钥。

它需要哪些密钥或代码？

注册中心没有列出必需的密钥，不过有些服务器会在首次使用时要求你登录。

它在我的电脑上运行还是在云端？

两种方式都可以：安装在你的电脑上，或者连接云端版本。

它还在维护吗？

GitHub 仓库最后更新于–，最新版本（2.12.0）于5天前进入注册中心。

哪些应用可以使用它？

支持 MCP 的应用，例如 Claude Desktop、Claude Code、Cursor 和 VS Code。它通过 URL 连接，所以接受远程 MCP 服务器的应用也可以使用，例如开启开发者模式的 ChatGPT。

有什么可以替代它？

同一分类中有：Mirobody, FHIR MCP Server, Google Health MCP

替代选择

同一分类中其他作者的服务器，按星标数排序。

如何看卡片：↓ 每周下载量i★ GitHub 星标i三大支柱：评价 · 检查 · 使用情况i更新 = 最新版本发布到注册中心的时间i

Mirobody

Lab results to LOINC codes and UCUM units, symptoms and diagnoses to ICPC-3. Offline, no API key.

作者：thetahealth正在增长↓ 290/周★ 1408昨天更新

在你的电脑上运行✓ thetahealth.ai

安装

FHIR MCP Server

MCP server providing seamless access to FHIR APIs for AI tools and healthcare applications

作者：wso2正在增长↓ 823/周★ 13710天前更新

在你的电脑上运行

安装

Google Health MCP

Privacy-first unofficial Google Health API v4 MCP server for health, sleep, activity, HR agents

作者：davidmosiah正在增长↓ 1024/周★ 794个月前更新

在你的电脑上运行

安装

作者的 README

打开 README

按原文从作者的仓库复制。PopNx MCP 没有审查或背书其内容。HTML、图片和脚本已被移除。链接会离开本站。

@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

只显示了开头部分；其余内容请在仓库中阅读

Pubmed MCP Server

概览

PopNx MCP 的三大支柱

它能帮你做什么

安装

安装之前

或者在你的电脑上运行

或者在你的电脑上运行

或者在你的电脑上运行

或者在你的电脑上运行

需要你填写的值

它能做什么

基础检查i

作者与仓库一致

仍在维护

有许可证

端点有响应

使用 OAuth 登录

工具描述中没有隐藏指令

与“诊所与健康”中的其他服务器比较i

常见问题

替代选择

Mirobody

FHIR MCP Server

Google Health MCP

作者的 README

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