PubMed Analysis MCP Server

by Darkroaster

150 stars

557 downloads

Not rated

GitHub

About

A professional MCP server for analyzing PubMed medical literature. It helps researchers quickly gain insights into medical research dynamics by supporting advanced search syntax, keyword frequency analysis, trend tracking, publication counts, and comprehensive report generation.

Details

Author: Darkroaster
GitHub stars: 150
Downloads: 557
Categories: Search

- Literature retrieval with PubMed advanced search syntax and date filtering.
- Hotspot analysis: keyword frequency and popular research area identification.
- Trend tracking: keyword frequency changes over time.
- Publication count analysis with customizable time periods.
- Comprehensive reports: one-click generation of hotspot, trend, and statistics.

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name PubMed Analysis MCP Server

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

From the repository

Install dependencies using uv pip install -e . in the pyproject.toml directory. Configure the MCP server in mcp.json with the command uv run --directory path/to/project -m pubmearch.server, and set environment variables NCBI_USER_EMAIL and NCBI_USER_API_KEY. Use the provided tools (e.g., search_pubmed, analyze_research_keywords) via LLM prompts.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "pubmed analysis mcp server": {
            "pubmearch": {
                "command": "uv",
                "args": [
                    "pip",
                    "install",
                    "-e",
                    "."
                ]
            }
        }
    }
}

McpServers

{
    "pubmearch": {
        "command": "uv",
        "args": [
            "pip",
            "install",
            "-e",
            "."
        ]
    }
}

PubMed Analysis MCP Server

> 适用于PubMed的MCP server：这是一个刚刚开发的项目，功能仍在完善中，欢迎各位提出建议和改进！
>
> Note: This is a newly developed project with features still being refined. Suggestions and improvements are welcome!

一个专业的PubMed医学文献分析MCP服务器，帮助科研人员快速洞察医学研究动态。

A professional MCP server for analyzing PubMed medical literature to help researchers quickly gain insights into medical research dynamics.

功能特点 / Features

- 文献检索 / Literature Retrieval: 支持PubMed高级检索语法，可设置日期范围和结果数量。/ Supports PubMed advanced search syntax with date filtering.

- 热点分析 / Hotspot Analysis: 统计关键词频率，识别热门研究方向，汇总相关文献。/ Analyzes keyword frequencies to identify popular research areas.

- 趋势追踪 / Trend Tracking: 追踪关键词随时间的频率变化，揭示研究趋势演变。/ Tracks keyword changes over time to reveal evolving research trends.

- 发文统计 / Publication Count: 提供灵活的时间周期设置，分析文献数量变化。/ Analyzes publication volume changes with customizable time periods.

- 全面报告 / Comprehensive Reports: 一键生成包含热点、趋势和统计的分析报告。/ Generates complete reports with customizable parameters.

MCP工具 / MCP Tools

1. search_pubmed

搜索PubMed并保存结果。/ Search PubMed and save results.

主要参数 / Key parameters:
一般而言不需要显性设置，与大模型沟通即可。/ Generally, no need to set explicitly, communicate with large models.
- advanced_search: PubMed搜索查询（必填，与高级检索语法相同）/ PubMed search query (required, same as advanced search syntax)
- start_date: 开始日期（格式：YYYY/MM/DD）/ Start date (format: YYYY/MM/DD)
- end_date: 结束日期（格式：YYYY/MM/DD）/ End date (format: YYYY/MM/DD)
- max_results: 最大结果数（默认：1000）/ Maximum results (default: 1000)

2. list_result_files

列出可用的结果文件。/ List available result files.

3. analyze_research_keywords

分析研究热点以及研究趋势。/ Analyze research hotspots and research trends. 主要参数 / Key parameters: - top_n: 分析的关键词数量（默认：20）/ Number of keywords (default: 20)

4. analyze_publication_count

分析发文数量。/ Analyze publication counts.

5. generate_comprehensive_analysis

生成全面分析报告。/ Generate comprehensive analysis.

Trae使用示例 / Example for Trae

Between us... when I use the same model, Cursor makes me feel like I'm the one not making sense. Trae, on the other hand, just gets me. Seriously great IDE!

安装依赖 / Install Dependencies

推荐使用uv虚拟环境。/ Recommend using uv virtual environment. uv：访问uv repo

```bash

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About

Details

Jump to

Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

PubMed Analysis MCP Server

功能特点 / Features

MCP工具 / MCP Tools

1. search_pubmed

2. list_result_files

3. analyze_research_keywords

4. analyze_publication_count

5. generate_comprehensive_analysis

Trae使用示例 / Example for Trae

安装依赖 / Install Dependencies

Install

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