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PubMed MCP Server

by Xuanyu0610

PubMed MCP Server v3.0

License: MIT npm version MCP Compatible TypeScript

为 LLM Agent 提供结构化 PubMed 文献数据的 MCP 服务器。Agent 友好的响应模型,专注数据提供,分析交给 LLM。

LLM Agent <--MCP--> PubMed MCP Server <--API--> PubMed / PMC / Unpaywall

核心能力: 文献搜索 / 智能缓存 / OA 全文下载 / Agentic 响应模型


快速开始

前置要求: Node.js v18.0.0+

1. 安装

# npm 全局安装
npm install -g mcp-pubmed-llm-server

# 或从源码构建
git clone git@github.com:PancrePal-xiaoyibao/mcp-pubmed-server-pancrpal.git
cd mcp-pubmed-server-pancrpal
npm install && npm run build

2. 配置

cp .env.example .env

编辑 .env

PUBMED_API_KEY=你的NCBI_API密钥    # 可选,https://www.ncbi.nlm.nih.gov/account/settings/
PUBMED_EMAIL=你的邮箱               # 可选(建议填写)
ABSTRACT_MODE=quick                 # quick(1500字符) | deep(6000字符)
FULLTEXT_MODE=disabled              # disabled | enabled | auto

说明: API Key 和 Email 均非必填。无 Key 时匿名运行(3 次/秒),有 Key 时 10 次/秒。

3. 运行

# npm 包
mcp-pubmed-llm-server
# 或
npx mcp-pubmed-llm-server

# 源码开发
npm run dev

# 源码生产
npm run build && npm start

Related MCP server: scholar-memory

传输模式

模式

适用场景

启动方式

stdio

本地 MCP 客户端集成

npm start(默认)

Streamable HTTP

服务端远程部署

npm run start:http

stdio 模式(默认)

npm start
# 或
node dist/index.js --mode=stdio

Streamable HTTP 模式

npm run start:http
# 或
node dist/index.js --mode=streamableHttp

Docker 部署:

cd docker
cp .env.example .env   # 编辑填入配置
docker compose up -d --build

验证:

curl http://localhost:8745/health
# {"status":"ok","mode":"streamableHttp","sessions":0}

端点:

  • POST /mcp — MCP 协议消息

  • GET /mcp — SSE 事件流

  • DELETE /mcp — 关闭会话

  • GET /health — 健康检查


MCP 客户端配置

Claude Desktop / Claude Code / Cline

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": ["-y", "mcp-pubmed-llm-server"],
      "env": {
        "PUBMED_API_KEY": "你的API密钥(可选)",
        "PUBMED_EMAIL": "你的邮箱(可选)",
        "ABSTRACT_MODE": "deep",
        "FULLTEXT_MODE": "enabled"
      }
    }
  }
}

配置文件位置:

  • Claude Desktop: ~/Library/Application Support/Claude/claude_desktop_config.json (macOS)

  • Claude Code: ~/.claude/config.json

  • Cline: VS Code 设置中的 MCP Servers

Cherry Studio

stdio 模式: 同上配置,type 设为 stdio

streamableHttp 模式: type 设为 streamableHttpbaseUrl 设为 http://<服务器IP>:8745/mcp


工具列表(8 个)

文献搜索

工具

说明

关键参数

pubmed_search

文献搜索,支持 Boolean/MeSH 和分页

query, max_results, page, days_back, sort_by, format

pubmed_get_details

获取 PMID 完整信息(单个或批量)

pmids, format

pubmed_extract_info

提取论文关键信息段落

pmid, sections

pubmed_find_related

查找相关/综述文献

pmid, type, max_results

缓存管理

工具

说明

关键参数

pubmed_manage_cache

缓存统计、清理、清空

action, target

全文下载(需 FULLTEXT_MODE=enabled

工具

说明

关键参数

pubmed_detect_fulltext

检测 OA 状态和全文可用性

pmid, auto_download

pubmed_download_fulltext

下载全文 PDF(单篇或批量)

pmids, force

pubmed_system_status

系统环境和 API Key 状态检测

搜索分页

pubmed_searchpage 从 1 开始,每页最多返回 100 条。响应的 metadata.pagination 会给出当前页、总页数以及下一页页码。

{
  "query": "\"Zhang Y\"[Author]",
  "max_results": 100,
  "page": 2,
  "sort_by": "date"
}

Agentic 响应模型

每个工具返回统一的 AgentResponse<T> 结构,为 AI Agent 优化:

{
  "status": "success",
  "data": { ... },
  "metadata": {
    "tool": "pubmed_search",
    "executionMs": 1234,
    "timestamp": "2025-01-01T00:00:00.000Z",
    "pagination": { "total": 500, "returned": 20, "hasMore": true }
  },
  "suggestions": [
    {
      "tool": "pubmed_get_details",
      "reason": "Get full metadata for specific articles of interest.",
      "parameters": { "pmids": ["12345678"] }
    }
  ]
}
  • status — 成功/错误状态

  • data — 类型化的返回数据

  • metadata — 执行上下文(耗时、分页、缓存状态)

  • suggestions — Agent 下一步操作建议(工具名 + 原因 + 参数)


API Key 池配置

支持多个 NCBI API Key 轮询/主备/随机负载均衡。

在项目根目录创建 api-keys.json(参见 api-keys.json.example):

{
  "keys": [
    { "api_key": "KEY_1", "email": "user1@example.com" },
    { "api_key": "KEY_2", "email": "user2@example.com" }
  ],
  "strategy": "round-robin"
}

策略

说明

round-robin

轮询(默认)

failover

主备切换

random

随机负载均衡

优先级: api-keys.json > 环境变量 > 匿名模式

健康管理: 连续 3 次失败自动下线,60 秒冷却后恢复


项目结构

src/
├── index.ts                  # 入口点
├── config.ts                 # 配置常量 + 环境变量
├── server.ts                 # MCP Server 编排器
├── types/                    # TypeScript 类型定义
│   ├── article.ts            # Article, SearchResult, OAInfo
│   ├── responses.ts          # AgentResponse<T>, makeResponse/makeError
│   └── index.ts
├── api/
│   ├── pubmed-client.ts      # PubMed EUtilities 客户端
│   └── key-pool.ts           # API Key 号池(轮询/主备/随机)
├── cache/
│   ├── memory-cache.ts       # 内存 LRU 缓存(5 分钟,100 条上限)
│   └── file-cache.ts         # 文件持久化缓存(30 天过期)
├── services/
│   ├── fulltext.ts           # OA 检测 + PDF 下载
│   └── system.ts             # 系统环境检测
├── tools/
│   ├── definitions.ts        # MCP 工具 Schema(8 个工具)
│   └── handlers.ts           # 工具路由 + 处理逻辑
├── transport/
│   ├── stdio.ts              # stdio 传输
│   └── streamable-http.ts    # HTTP 传输(Express)
└── utils/
    └── formatter.ts          # 文章格式化(compact/standard/detailed)

故障排除

问题

解决方案

依赖缺失

npm install && npm run build

PubMed API 调用失败

检查网络;有 Key 时确认 Key 有效

Key 池全部不可用

检查 api-keys.json 中 Key 是否有效,60 秒后自动恢复

端口被占用

lsof -i :8745 查看,或设置 PORT=其他端口

Docker 健康检查失败

检查 .env 配置,docker logs pubmed-mcp


许可证

MIT License

Available Tools

5 tools
pubmed_extract_infoA
Read-onlyIdempotent

Extract specific structured sections from a PubMed article. Use when you need only certain aspects (author details, structured abstract, keywords, DOI) rather than the full record. More token-efficient than get_details for targeted extraction.

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidYesPubMed article ID.
sectionsNoWhich sections to extract.

TDQS

A4.2/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The annotations already declare readOnlyHint=true, idempotentHint=true, and openWorldHint=true, so the safety profile is covered and the description does not need to repeat it. The description adds the token-efficiency observation and the scoping of sections, but does not disclose any deeper behavioral details such as output shape, error behavior, or section-level edge cases. This is adequate but not rich.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three sentences with no filler: the purpose is front-loaded, the usage condition follows immediately, and the efficiency advantage is stated once. Every sentence contributes a distinct piece of guidance.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool has only two parameters, the schema covers both fully, and the annotations cover read-only and idempotent behavior. The description is sufficient for deciding when to call it. It falls slightly short of 5 because there is no output schema and the description does not describe the exact structure or format of the extracted sections, which would be useful for this kind of extraction tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema has 100% coverage, with clear descriptions for 'pmid' and enumerated 'sections'. The description mentions examples of sections ('author details, structured abstract, keywords, DOI) that overlap with those enum values, but adds little meaning beyond what the schema already provides. Baseline 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Extract') with a clear resource ('specific structured sections from a PubMed article') and a concrete scope ('only certain aspects...rather than the full record'). It also differentiates from pubmed_get_details by naming the token-efficiency angle, so an agent can distinguish it immediately.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It explicitly says to use this tool 'when you need only certain aspects' and contrasts it with 'the full record'. It also names the alternative tool, pubmed_get_details, and the condition under which this one is preferable ('targeted extraction'), giving an agent actionable selection criteria.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

pubmed_get_detailsA
Read-onlyIdempotent

Retrieve complete metadata for specific PubMed articles by PMID. Accepts a single PMID or array of PMIDs (up to 20). Returns full article records including abstract, authors, journal, DOI, MeSH terms. Use when you have specific PMIDs from a previous search or citation and need the full record.

ParametersJSON Schema
NameRequiredDescriptionDefault
pmidsYesSingle PMID string or array of PMIDs.
formatNoOutput format.standard

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description adds behavioral detail beyond the readOnlyHint, idempotentHint, and openWorldHint annotations: it accepts a single PMID or an array up to 20, and returns fields such as abstract, authors, journal, DOI, and MeSH terms. It does not cover error behavior or rate limits, but annotations already establish the safety profile.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences with no filler. The main purpose and input mode are front-loaded, the return content is summarized efficiently, and the usage condition completes the guidance without redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a straightforward read-only lookup tool, the description covers input shape, batch limit, return content, and when to use it. The only notable gap is that the 'format' enum semantics are not described, leaving the agent to infer what 'concise' versus 'detailed' means.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the baseline is 3. The description restates the PMID input forms and adds useful output context, but it does not explain the 'format' parameter values (concise, standard, detailed) beyond the schema's minimal 'Output format' label.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb and resource: 'Retrieve complete metadata for specific PubMed articles by PMID.' It clearly distinguishes this tool from pubmed_search, pubmed_find_related, and pubmed_extract_info by emphasizing PMID-based retrieval of full records.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly states when to use it: 'Use when you have specific PMIDs from a previous search or citation and need the full record.' It provides clear context but does not explicitly name alternatives or state when not to use it.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

pubmed_manage_cacheA
Destructive

View cache statistics or perform maintenance. Use action="stats" to check hit rates and storage usage. Use action="clean" to remove expired entries, or action="clear" to wipe a specific cache layer.

ParametersJSON Schema
NameRequiredDescriptionDefault
actionNoCache operation to perform.stats
targetNoWhich cache layer to operate on.all

TDQS

A4.3/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The annotations already flag destructiveHint=true, and the description adds meaningful nuance by specifying that 'clean' removes expired entries while 'clear' wipes a cache layer, and 'stats' is a read-only operation. This helps the agent understand the varying destructiveness of each action beyond the single annotation flag.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is compact, front-loaded with the core purpose, and uses a clean pattern of action-to-purpose mapping. Every sentence contributes necessary operational guidance with no filler or redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a two-parameter tool with enum-restricted values and a clear maintenance scope, the description covers the available actions, their effects, and the target layer concept. There is no output schema, but the described behavior is sufficient for an agent to select and invoke the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema already provides full documentation for both parameters with enum values and descriptions, so the baseline is 3. The description enriches the 'action' parameter by explaining the real-world intent of each value, but it does not add material meaning for 'target' beyond what the schema states.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly identifies a cache-management tool with specific operations: viewing statistics, cleaning expired entries, and clearing cache layers. This clearly distinguishes it from the sibling PubMed search tools, which perform content queries rather than cache maintenance.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description gives explicit guidance on which action value to use for each intended outcome: stats for hit rates/storage, clean for expired entries, clear for wiping a layer. There is no explicit 'when not to use' statement, but the distinction from sibling tools is evident and the action-level guidance is clear.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

TDQS

A4.2/5.0
Disambiguation4/5

Most tools have clearly distinct roles: search, related-article discovery, full-record retrieval, targeted extraction, and cache maintenance. However, pubmed_get_details and pubmed_extract_info both operate on specific articles and could be confused, though the descriptions clarify that get_details is for full records and extract_info is for targeted sections.

Naming Consistency5/5

All tool names follow a consistent pattern with the 'pubmed_' prefix followed by a verb phrase: search, find_related, get_details, extract_info, manage_cache. The naming convention is uniform, readable, and makes the action of each tool predictable.

Tool Count5/5

Five tools is well-scoped for a PubMed literature search and retrieval server. Each tool has a clear purpose, and the count is neither too thin nor overwhelming for the domain.

Completeness4/5

The server covers the core PubMed workflow: searching, finding related papers, retrieving full details, and extracting specific sections. Minor gaps exist such as citation formatting or advanced query helpers, but these are not essential for the primary search-and-retrieval use case.

Maintenance

ActivityMaintained
ResponsivenessNo issues

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