Scholarly Research MCP Server

A powerful, consolidated research tool that helps you find and analyze academic research papers from PubMed, Google Scholar, and ArXiv, plus optional Firecrawl web search, through five MCP tools.

What This Tool Does

This tool helps you:

• Find research papers on any topic from multiple academic databases
• Read full papers when PubMed Central text is available (plus abstract-only for other sources)
• Get citations in common bibliographic formats
• Search within excerpts using optional text filters on PMC-derived text
• Organize research with customizable preferences

Key Features

• 5 Consolidated Tools: Powerful, multi-functional tools instead of 24 separate ones
• Multi-Source Search: PubMed, Google Scholar, and ArXiv
• 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                      

... [View full README on GitHub](https://github.com/aringadre76/mcp-for-research#readme)