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scholarly-research-mcp

v1.4.2

Published

MCP server for scholarly research across PubMed, JSTOR, and Google Scholar

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Links

Git

Maintainers

arin_gadrearin_gadre

Keywords

mcpresearchscholarlypubmedjstorgoogle-scholar

Readme

Scholarly Research Tool

A powerful tool that helps you find and analyze academic research papers from PubMed, Google Scholar, and JSTOR.

NPM GitHub License

What This Tool Does

This tool helps you:

  • Find research papers on any topic from multiple academic databases
  • Read full papers when available (not just abstracts)
  • Extract key information like quotes, statistics, and findings
  • Get citations in the format you need for your work
  • Search within papers to find specific information
  • Organize research with customizable preferences

Project Structure

This tool is organized into several key components:

Core Components

src/
├── index.ts                           # Main server entry point
├── adapters/                          # Data source connectors
│   ├── pubmed.ts                      # PubMed API integration
│   ├── google-scholar.ts              # Google Scholar web scraping
│   ├── google-scholar-firecrawl.ts    # Firecrawl integration
│   ├── unified-search.ts              # Basic multi-source search
│   ├── enhanced-unified-search.ts     # Advanced multi-source search
│   └── preference-aware-unified-search.ts # User preference integration
├── preferences/                       # User preference management
│   └── user-preferences.ts            # Preference storage and retrieval
└── models/                            # Data structures and interfaces
    ├── paper.ts                       # Paper data models
    ├── search.ts                      # Search parameter models
    └── preferences.ts                 # Preference models

Documentation

docs/
├── ARCHITECTURE.md                    # Technical system design
├── API_REFERENCE.md                   # Complete API documentation
├── DATA_MODELS.md                     # Data structure definitions
├── DEVELOPMENT.md                     # Developer setup guide
└── TROUBLESHOOTING.md                 # Problem-solving guide

Testing

tests/
├── test-preferences.js                # Preference system tests
├── test-all-tools-simple.sh           # Bash test runner
├── test_all_tools.py                  # Python test runner
└── test-all-tools.js                  # JavaScript test runner

Configuration

├── package.json                       # Project dependencies and scripts
├── tsconfig.json                      # TypeScript configuration
├── .env.example                       # Environment variables template
└── README.md                          # This file

Key Features

  • 24 MCP Tools: Complete set of research tools
  • Multi-Source Search: PubMed, Google Scholar, and JSTOR
  • User Preferences: Customizable search and display settings
  • Content Extraction: Full-text paper access and analysis
  • Citation Management: Multiple citation format support
  • Error Handling: Robust fallback mechanisms

Quick Start

Option 1: Use Through AI Assistants (Easiest - No Setup Required)

If you're not comfortable with technical setup, you can use this tool through AI assistants like:

  • Claude (Anthropic)
  • ChatGPT (OpenAI)
  • Cursor (Code editor with AI)

These assistants can use this tool to help you find research papers without any setup on your part.

Option 2: Set Up MCP on Your Computer (For Advanced Users)

This option lets you use the tool directly with AI assistants on your computer. It's like giving your AI assistant a special tool to find research papers.

Setting Up MCP (Model Context Protocol)

MCP is like a "language" that lets AI assistants talk to tools on your computer. Think of it like installing a special app that your AI assistant can use.

What You Need

  • A computer (Windows, Mac, or Linux)
  • An AI assistant that supports MCP (like Claude Desktop, Cursor, or others)
  • Basic computer skills (downloading files, running programs)

Step-by-Step Setup

Step 1: Install Node.js

Node.js is like the "engine" that runs the research tool.

For Windows:

  1. Go to nodejs.org
  2. Click the big green "LTS" button to download
  3. Run the downloaded file and follow the installation steps
  4. Restart your computer

For Mac:

  1. Go to nodejs.org
  2. Click the big green "LTS" button to download
  3. Open the downloaded file and follow the installation steps

For Linux:

sudo apt update
sudo apt install nodejs npm

Check if it worked:

  • Open Command Prompt (Windows) or Terminal (Mac/Linux)
  • Type: node --version
  • You should see a version number like "v18.17.0"

Step 2: Install the Research Tool

This downloads the research tool to your computer.

  1. Open Command Prompt (Windows) or Terminal (Mac/Linux)
  2. Type this command and press Enter:
    npm install -g scholarly-research-mcp
  3. Wait for it to finish (it might take a few minutes)
  4. You'll see a success message when it's done

Step 3: Set Up Your AI Assistant

Now you need to tell your AI assistant where to find the research tool.

For Claude Desktop:

  1. Open Claude Desktop
  2. Go to Settings (gear icon)
  3. Find "MCP Servers" or "Tools"
  4. Click "Add Server"
  5. Choose "Custom"
  6. Set the path to: scholarly-research-mcp
  7. Save and restart Claude

For Cursor:

  1. Open Cursor
  2. Press Ctrl+Shift+P (Windows/Linux) or Cmd+Shift+P (Mac)
  3. Type "MCP" and select "MCP: Add Server"
  4. Choose "Custom"
  5. Set the path to: scholarly-research-mcp
  6. Restart Cursor

For Other AI Assistants: Look for settings related to "MCP", "Tools", "Servers", or "Custom Tools" in your AI assistant's settings.

Step 4: Test It Out

  1. Restart your AI assistant
  2. Ask it: "Can you help me find research papers about climate change?"
  3. If it works, you'll see the AI assistant using the research tool to find papers for you!

Troubleshooting Setup

Problem: "Node.js is not recognized"

  • Solution: Restart your computer after installing Node.js

Problem: "npm is not recognized"

  • Solution: Restart your computer after installing Node.js

Problem: "Permission denied" when installing

  • Windows: Run Command Prompt as Administrator
  • Mac/Linux: Add sudo before the command:
    sudo npm install -g scholarly-research-mcp

Problem: AI assistant can't find the tool

  • Make sure you typed the path exactly: scholarly-research-mcp
  • Try restarting your AI assistant
  • Check if the tool installed correctly by typing: scholarly-research-mcp --version

What Happens After Setup

Once everything is working:

  • Your AI assistant will have access to 24 research tools
  • You can ask it to find papers, get citations, extract content, and more
  • The tool will remember your preferences and settings
  • You can search across PubMed, Google Scholar, and JSTOR

Getting Help with Setup

If you're stuck:

  1. Check the error message - it usually tells you what's wrong
  2. Make sure Node.js is installed - type node --version to check
  3. Try restarting your computer - this fixes many setup issues
  4. Ask for help - open an issue on GitHub with your error message

How to Use

Basic Search

Tell the tool what you're looking for:

  • "Find papers about climate change"
  • "Search for research on machine learning in healthcare"
  • "Get papers about COVID-19 vaccines published in 2023"

Get Paper Details

Once you find a paper you're interested in:

  • Get the full abstract and author information
  • Read the complete paper text (when available)
  • Extract specific sections like Introduction, Methods, Results
  • Find quotes and statistics for your research

Save Your Preferences

The tool remembers your settings:

  • Which databases to search (PubMed, Google Scholar, JSTOR)
  • How many results you want to see
  • How you want results displayed
  • Your preferred search order

What You Can Search

PubMed (Medical and Life Sciences)

  • Medical research papers
  • Biology and chemistry studies
  • Clinical trials and reviews
  • Free access to many papers

Google Scholar (All Academic Fields)

  • Papers from all academic disciplines
  • Books and theses
  • Citation information
  • Related research suggestions

JSTOR (Humanities and Social Sciences)

  • History and literature papers
  • Social science research
  • Economics and political science
  • Arts and culture studies

Examples of What You Can Do

For Students

  • Find sources for your research papers
  • Get proper citations in APA, MLA, or other formats
  • Extract key quotes and statistics
  • Understand complex research through section breakdowns

For Researchers

  • Discover related work in your field
  • Find supporting evidence for your arguments
  • Track citation counts and impact
  • Access full-text papers when available

For Writers and Journalists

  • Fact-check claims with academic sources
  • Find expert opinions and research
  • Build comprehensive bibliographies
  • Access primary research sources

Getting Help

If Something Doesn't Work

  1. Check your internet connection - The tool needs internet to search databases
  2. Try different search terms - Sometimes specific terms work better than general ones
  3. Check if papers are available - Not all papers have free full-text access
  4. Contact support - Open an issue on GitHub if you need help

Common Questions

Q: Why can't I read the full paper? A: Some papers require subscriptions or institutional access. The tool shows you what's available for free.

Q: How do I cite a paper I found? A: Use the citation tools to get the paper in the format you need (APA, MLA, etc.).

Q: Can I save my search results? A: Yes! The tool remembers your preferences and can export results for you.

For Developers

If you're a developer and want to contribute or integrate this tool:

# Get the code
git clone https://github.com/aringadre76/mcp-for-research.git
cd mcp-for-research

# Set it up
npm install
npm run build

# Run tests
npm run test:all-tools-bash

Support

  • GitHub Issues: Report problems or request features
  • Documentation: See PROJECT_STRUCTURE.md for technical details
  • Contributing: Help improve the tool for everyone

License

This tool is free to use under the MIT License.