Scholarly Research MCP Server

A powerful, consolidated research tool that helps you find and analyze academic research papers from PubMed, Google Scholar, ArXiv, and JSTOR through just 5 powerful tools.

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

Related MCP server: Academic Paper Search MCP Server

Key Features

• 5 Consolidated Tools: Powerful, multi-functional tools instead of 24 separate ones

• Multi-Source Search: PubMed, Google Scholar, ArXiv, 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

• Web research (Firecrawl): When FIRECRAWL_API_KEY is set in the environment (or a Firecrawl client is provided), the web_research tool can scrape URLs and run web search. See Configuration and copy .env.example to .env to set your key. Get an API key at firecrawl.dev.

Configuration Overview

Configuration for environment variables and API keys is documented in more detail in the docs/ folder and .env.example. At a high level, you configure API keys via environment variables and should avoid committing any secret values.

Project Structure

Core Components

src/
├── index.ts                           # Main server entry point (consolidated)
├── adapters/                          # Data source connectors
│   ├── pubmed.ts                      # PubMed API integration
│   ├── google-scholar.ts              # Google Scholar web scraping
│   ├── google-scholar-firecrawl.ts    # Firecrawl integration
│   ├── arxiv.ts                       # ArXiv 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/
├── README.md                          # Documentation index and overview
├── CONSOLIDATION_GUIDE.md             # Complete consolidation guide
├── TOOL_CONSOLIDATION.md              # Quick tool mapping reference
├── PROJECT_STRUCTURE.md               # Clean project organization
├── API_REFERENCE.md                   # Complete API documentation
├── ARCHITECTURE.md                    # Technical system design
├── DATA_MODELS.md                     # Data structure definitions
└── DEVELOPMENT.md                     # Developer setup guide

Testing

tests/
├── test-preferences.js                # Preference system tests
├── test-all-tools-simple.sh           # Bash test runner (recommended)
├── 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

Quick Start

Install in one click where the client actually supports a desktop handoff:

Cursor uses Cursor's install page to hand off to the desktop app and open the MCP install prompt. If your system does not register the Cursor URL handler, use the manual config below instead.

If Cursor adds the server but startup fails with npm error could not determine executable to run, the npm latest release is stale. In that case, clone this repo and use the local node dist/index.js command below until the refreshed npm publish is live.

VS Code uses the vscode:mcp/install deep link to open VS Code and prompt to add the MCP server to your configuration.

Other clients are documented below, but they do not currently support the same kind of reliable README click -> open desktop app -> install server flow for this project:

• Claude Desktop: supports .mcpb desktop extensions, but this repo does not currently ship a bundled .mcpb

• ChatGPT: requires a public HTTPS MCP endpoint rather than a local stdio command

• Codex: configured through codex mcp add or config.toml

• Gemini: configured through settings.json or Gemini CLI MCP commands

Claude Desktop – Copy configuration

Add this to your claude_desktop_config.json under mcpServers:

{
  "mcpServers": {
    "scholarly-research-mcp": {
      "command": "npx",
      "args": ["-y", "scholarly-research-mcp"]
    }
  }
}

Then fully restart Claude Desktop.
Config file locations:

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

• Windows: %APPDATA%/Claude/claude_desktop_config.json

• Linux: ~/.config/Claude/claude_desktop_config.json

Cursor IDE – One‑click install

If you use Cursor, you can install this MCP server with a single click:

One‑Click – Add to Cursor

This opens Cursor's install handoff page, then launches the Cursor desktop app with an MCP install prompt for npx -y scholarly-research-mcp. You’ll need Node.js and npm available on your system.

If startup fails with npm error could not determine executable to run, the currently published npm package is missing its executable metadata. Until the refreshed npm release is published, use the local clone/build path below:

git clone https://github.com/aringadre76/mcp-for-research
cd mcp-for-research
npm install
npm run build
node dist/index.js

VS Code – Copy configuration

Create .vscode/mcp.json in your project (or edit your global MCP config) and add:

{
  "servers": {
    "scholarly-research-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "scholarly-research-mcp"]
    }
  }
}

Then reload VS Code so the Copilot / MCP integration picks it up.

Claude Code – CLI

Run:

claude mcp add scholarly-research-mcp -- npx -y scholarly-research-mcp

Claude Code can also read project-scoped MCP config from a .mcp.json file in your repo if you prefer to commit the setup.

Gemini – CLI

Add this to your Gemini CLI settings file:

• User scope: ~/.gemini/settings.json

• Project scope: .gemini/settings.json

{
  "mcpServers": {
    "scholarly-research-mcp": {
      "command": "npx",
      "args": ["-y", "scholarly-research-mcp"]
    }
  }
}

Gemini CLI also supports adding MCP servers through its built-in mcp commands if you prefer not to edit JSON manually.

Codex – CLI

Run:

codex mcp add scholarly-research-mcp -- npx -y scholarly-research-mcp

Codex stores MCP configuration in ~/.codex/config.toml by default, and the Codex IDE extension shares that same MCP config.

ChatGPT – Remote connector

ChatGPT does not run local stdio MCP servers directly from a command like npx -y scholarly-research-mcp.

To use this server with ChatGPT, you need to expose it through a public HTTPS MCP endpoint, then add that endpoint in ChatGPT under Settings -> Apps & Connectors -> Create.

If you want a local desktop setup instead of deploying a remote endpoint, use Cursor, Claude Desktop, VS Code, Claude Code, Gemini CLI, or Codex instead.

Manual – Copy configuration JSON

For any MCP-compatible assistant that accepts a JSON config (similar to mcp.json), use:

{
  "mcpServers": {
    "scholarly-research-mcp": {
      "command": "npx",
      "args": ["-y", "scholarly-research-mcp"]
    }
  }
}

Paste this into the assistant’s MCP configuration and adjust paths/env vars if needed.

Requirements

• Node.js >= 18.17 (LTS recommended). Check with node -v.

• npm (comes with Node.js).

• Google Chrome or Chromium (optional) – only needed for Google Scholar scraping and ArXiv full-text extraction. If you only use PubMed, ArXiv API search, or Firecrawl-based features, no browser is required. You can point to a custom binary with PUPPETEER_EXECUTABLE_PATH or CHROME_PATH.

Local MCP Setup

1. Download the tool

   git clone https://github.com/aringadre76/mcp-for-research.git
   cd mcp-for-research

2. Install dependencies

   npm install

3. Build the tool

   npm run build

4. Configure your AI assistant

   • Find "MCP Servers" or "Tools" in your AI assistant's settings

   • Add a new MCP server

   • Set the command to: node dist/index.js

   • Set the working directory to your project folder

5. Test the setup

   npm run test:all-tools-bash

6. Connect from your AI assistant

   • Open your assistant's settings and find the section for MCP servers or tools.

   • Add a new MCP server that runs the command node dist/index.js in the mcp-for-research folder.

   • Save the configuration and ask the assistant to list or use the research_search tool to confirm it is working.

Available Tools

The server provides 5 consolidated MCP tools that replace the previous 24 individual tools:

1. research_search

Comprehensive research paper search across PubMed, Google Scholar, and ArXiv. Uses the preference-aware adapter: when Firecrawl is configured and the preference is set, Google Scholar can use Firecrawl instead of Puppeteer. JSTOR is accepted in sources but not implemented; if requested, a note is appended: "JSTOR is not implemented; results are from other sources."

Parameters: Query, sources (pubmed, google-scholar, arxiv, jstor), maxResults, startDate, endDate, journal, author, includeAbstracts, sortBy

2. paper_analysis

Get comprehensive paper information, full text, and analysis including quotes, statistics, and findings.

Combines: Paper retrieval, content extraction, and analysis tools Parameters: Identifier, analysis type, quote limits, section lengths

3. citation_manager

Generate citations in multiple formats and get citation information including counts and related papers.

Combines: Citation tools, citation counting, and related paper discovery Parameters: Identifier, action, format, related paper limits

4. research_preferences

Manage research preferences including source priorities, search settings, display options, and caching.

Combines: All preference management tools Parameters: Action, category, various preference values

5. web_research

Perform web-based research using Firecrawl for reliable content extraction and analysis.

Requires: Set FIRECRAWL_API_KEY for scrape and search. Extract, map, and crawl are not implemented; use scrape or search. Parameters: Action (scrape, search, extract, map, crawl), url, query, maxResults, formats, onlyMainContent, waitFor

Usage Examples

Search for Papers

{
  "method": "tools/call",
  "params": {
    "name": "research_search",
    "arguments": {
      "query": "machine learning",
      "sources": ["pubmed", "arxiv"],
      "maxResults": 15,
      "startDate": "2020/01/01"
    }
  }
}

Analyze a Paper

{
  "method": "tools/call",
  "params": {
    "name": "paper_analysis",
    "arguments": {
      "identifier": "12345678",
      "analysisType": "complete",
      "maxQuotes": 20
    }
  }
}

Get Citations

{
  "method": "tools/call",
  "params": {
    "name": "citation_manager",
    "arguments": {
      "identifier": "12345678",
      "action": "all",
      "format": "apa"
    }
  }
}

Migration from Previous Version

The consolidated tools are backward compatible - you can still access the same functionality, just through fewer, more powerful tools. Each consolidated tool accepts parameters that let you specify exactly what you want to do.

Troubleshooting

Common Issues

Q: The tool doesn't start A: Make sure you have Node.js >= 18.17 installed (node -v). If running from a clone, run npm install && npm run build first.

Q: My AI assistant can't find the tools A: Check that the MCP server path is correct in your AI assistant's settings. After adding the config, fully restart the assistant.

Q: Google Scholar or ArXiv full-text features fail with a Chrome error A: These features need a local Chrome or Chromium binary. Install Google Chrome, or set PUPPETEER_EXECUTABLE_PATH=/path/to/chrome. PubMed, ArXiv API search, and Firecrawl features work without a browser.

Q: Searches return no results A: Try different search terms or check if your sources are enabled in preferences.

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

Development

Running Tests

npm run test:all-tools-bash

Building

npm run build

Development Mode

npm run dev

Contributing

We welcome contributions! Please see our contributing guidelines and feel free to submit issues or pull requests.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Documentation

For comprehensive documentation, guides, and technical details, see the docs/ directory:

• Documentation Overview - Complete documentation index

• Consolidation Guide - Detailed explanation of the new approach

• Tool Reference - Quick mapping from old to new tools

• API Reference - Complete tool documentation

• Project Structure - Clean project organization

Version History

• v2.0.2: One-click install buttons, switched to puppeteer-core (no Chromium download), pinned cheerio for Node 18 compatibility, added engines field, security fix for .env in npm package

• v2.0.1: Firecrawl web research and Google Scholar integration improvements, documentation cleanup

• v2.0.0: Consolidated 24 tools into 5 powerful tools

• v1.4.x: Previous version with 24 individual tools

• v1.0.x: Initial release