pubmearch

# PubMed Analysis MCP Server > **MCP server for PubMed**: This is a newly developed project with features still being refined. Suggestions and improvements are welcome! > > **Note**: This is a newly developed project with features still being refined. Suggestions and improvements are welcome! A professional MCP server for analyzing PubMed medical literature to help researchers quickly gain insights into medical research dynamics. A professional MCP server for analyzing PubMed medical literature to help researchers quickly gain insights into medical research dynamics. ## Features / Features - **Literature Retrieval**: Supports PubMed advanced search syntax with date filtering. / Supports PubMed advanced search syntax with date filtering. - **Hotspot Analysis**: Analyzes keyword frequencies to identify popular research areas. / Analyzes keyword frequencies to identify popular research areas. - **Trend Tracking**: Tracks keyword changes over time to reveal evolving research trends. / Tracks keyword changes over time to reveal evolving research trends. - **Publication Count**: Analyzes publication volume changes with customizable time periods. / Analyzes publication volume changes with customizable time periods. - **Comprehensive Reports**: Generates complete reports with customizable parameters. / Generates complete reports with customizable parameters. ## MCP Tools / MCP Tools ### 1. search_pubmed Search PubMed and save results. / Search PubMed and save results. Key parameters / Key parameters: Generally, no need to set explicitly, communicate with large models. / Generally, no need to set explicitly, communicate with large models. - `advanced_search`: PubMed search query (required, same as advanced search syntax) / PubMed search query (required, same as advanced search syntax) - `start_date`: Start date (format: YYYY/MM/DD) / Start date (format: YYYY/MM/DD) - `end_date`: End date (format: YYYY/MM/DD) / End date (format: YYYY/MM/DD) - `max_results`: Maximum results (default: 1000) / Maximum results (default: 1000) ### 2. list_result_files List available result files. / List available result files. ### 3. analyze_research_keywords Analyze research hotspots and research trends. / Analyze research hotspots and research trends. Key parameters / Key parameters: - `top_n`: Number of keywords (default: 20) / Number of keywords (default: 20) ### 4. analyze_publication_count Analyze publication counts. / Analyze publication counts. ### 5. generate_comprehensive_analysis Generate comprehensive analysis. / Generate comprehensive analysis. ## Trae Example / 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!* ### Install Dependencies / Install Dependencies Recommend using uv virtual environment. / Recommend using uv virtual environment. uv：[访问uv repo](https://github.com/astral-sh/uv) ```bash # pyproject.toml 目录下： uv pip install -e . ``` ### Write mcp.json Merge the following configuration in mcp.json (for Windows): ```json {   "mcpServers": {     "pubmearch": {       "command": "cmd",       "args": [         "/c",         "uv",         "run",         "--directory",         "path/to/project/root/directory", // The folder where the pubmearch folder is located         "-m",         "pubmearch.server"       ],       "env": {         "NCBI_USER_EMAIL": "youremailaddress@email.com",         "NCBI_USER_API_KEY": "your_api_key"       }     }   } } ``` ### Get PubMed API key / Get PubMed API key 1. Log in to PubMed. / Log in to PubMed. 2. Click on your profile picture and select " Account Settings". / Click on your profile picture and select " Account Settings". 3. Scroll down to the "API Keys" section and click "Create API Key". / Scroll down to the "API Keys" section and click "Create API Key". ### LLM prompt (Agent mode) **Use advanced search syntax**. / **Use advanced search syntax**. - Help me analyze the research hotspots on prostate cancer immunotherapy in the past three months. The advanced search query is ((prostat*[Title/Abstract]) AND (cancer[Title/Abstract])) AND (immu*[Title/Abstract]). - 帮我分析一下近三个月前列腺癌免疫治疗的研究热点，检索词为((prostat*[Title/Abstract]) AND (cancer[Title/Abstract])) AND (immu*[Title/Abstract]). ## Notes / Notes - Follow NCBI usage policies. / Follow NCBI usage policies. - Results saved in `pubmearch/results` directory, logs in `pubmed_server.log`. / Results saved in `pubmearch/results` directory, logs in `pubmed_server.log`. - I am busy with my studies, the project may be delayed. / I am busy with my studies, the project may be delayed. ## Contributions / Contributions Contributions are welcome via Issues or Pull Requests. / Contributions are welcome via Issues or Pull Requests. ## License / License [MIT](https://github.com/Darkroaster/pubmearch/blob/main/LICENSE)