Scientific Paper Harvester MCP Server

A comprehensive Model Context Protocol (MCP) server that provides LLMs with real-time access to scientific papers from 6 major academic sources: arXiv, OpenAlex, PMC (PubMed Central), Europe PMC, bioRxiv/medRxiv, and CORE.

🚀 Features

Comprehensive Source Coverage

• arXiv: Computer science, physics, mathematics preprints and papers

• OpenAlex: Open catalog of scholarly papers with citation data

• PMC: PubMed Central biomedical and life science literature

• Europe PMC: European life science literature database

• bioRxiv/medRxiv: Biology and medical preprint servers

• CORE: World's largest collection of open access research papers

Advanced Capabilities

• Paper Fetching: Get latest papers from any source by category/concept

• Paper Search: Search papers by title, abstract, author, or full-text across 4 major sources

• Full-Text Extraction: Extract complete text content with intelligent fallback strategies

• Citation Analysis: Find top cited papers from OpenAlex since a specific date

• Paper Lookup: Retrieve full metadata for specific papers by ID

• Category Discovery: Browse available categories from all sources

• Smart Rate Limiting: Respectful API usage with per-source rate limiting

• DOI Resolution: Advanced DOI resolver with Unpaywall → Crossref → Semantic Scholar fallback

• Dual Interface: Both MCP protocol and CLI access

• TypeScript: Full type safety with ESM modules

📊 Coverage Statistics

• Total Sources: 6 academic databases

• Category Coverage: 100+ categories across all disciplines

• Paper Access: 200M+ papers with intelligent text extraction

• Text Extraction Success: >90% for supported paper types

• Response Time: <15 seconds average for paper fetching

🛠 Installation

📋 MCP Client Configuration

To use this server with an MCP client (like Claude Desktop), add the following to your MCP client configuration:

For published package (available on npm):

Option 1: Using npx (recommended for AI tools like Claude)

Option 2: Global installation

Then configure:

📖 Usage

CLI Interface

List Categories

Fetch Latest Papers

Fetch Top Cited Papers

Search Papers

Fetch Specific Paper Content

🔧 Available Tools

list_categories

Lists available categories/concepts from any data source.

Parameters:

• source: "arxiv" | "openalex" | "pmc" | "europepmc" | "biorxiv" | "core"

Returns:

• Array of category objects with id, name, and optional description

Examples:

fetch_latest

Fetches the latest papers from any source for a given category with metadata only (no text extraction).

Parameters:

• source: "arxiv" | "openalex" | "pmc" | "europepmc" | "biorxiv" | "core"

• category: Category ID or concept name (varies by source)

• count: Number of papers to fetch (default: 50, max: 200)

Category Examples by Source:

• arXiv: "cs.AI", "physics.gen-ph", "math.CO"

• OpenAlex: "artificial intelligence", "machine learning", "C41008148"

• PMC: "immunology", "genetics", "neuroscience"

• Europe PMC: "biology", "medicine", "cancer"

• bioRxiv/medRxiv: "biorxiv:neuroscience", "medrxiv:psychiatry"

• CORE: "computer_science", "mathematics", "physics"

Returns:

• Array of paper objects with metadata (id, title, authors, date, pdf_url)

• Text field: Empty string (text: "") - use fetch_content for full text

fetch_top_cited

Fetches the top cited papers from OpenAlex for a given concept since a specific date.

Parameters:

• concept: Concept name or OpenAlex concept ID

• since: Start date in YYYY-MM-DD format

• count: Number of papers to fetch (default: 50, max: 200)

search_papers

Searches for papers across multiple academic sources with field-specific search and sorting options.

Parameters:

• source: "arxiv" | "openalex" | "europepmc" | "core"

• query: Search query string (max 1500 characters)

• field: "all" | "title" | "abstract" | "author" | "fulltext" (default: "all")

• count: Number of results to return (default: 50, max: 200)

• sortBy: "relevance" | "date" | "citations" (default: "relevance")

Search Capabilities by Source:

• arXiv: Title, abstract, author, and general search with Boolean operators

• OpenAlex: Advanced search with relevance scoring and citation sorting

• Europe PMC: Biomedical literature with MeSH terms and full-text search

• CORE: Global academic papers with advanced query language

Example Queries:

• Keywords: "machine learning", "climate change"

• Phrases: "artificial intelligence" (use quotes for exact phrases)

• Boolean: "deep learning AND neural networks" (arXiv supports this)

• Authors: "John Smith", "Smith J"

Returns:

• Array of paper objects with metadata (id, title, authors, date, pdf_url)

• Text field: Empty string (text: "") - use fetch_content for full text

fetch_content

Fetches full metadata and text content for a specific paper by ID with complete text extraction.

Parameters:

• source: Any of the 6 supported sources

• id: Paper ID (format varies by source)

ID Formats by Source:

• arXiv: "2401.12345", "cs/0601001", "1234.5678v2"

• OpenAlex: "W2741809807" or numeric 2741809807

• PMC: "PMC8245678" or "12345678"

• Europe PMC: "PMC8245678", "12345678", or DOI

• bioRxiv/medRxiv: "10.1101/2021.01.01.425001" or "2021.01.01.425001"

• CORE: Numeric ID like "12345678"

📄 Paper Metadata Format

All tools return paper objects with the following structure:

🧠 Advanced Text Extraction

Multi-Source Strategy

Each source has specialized text extraction approaches:

• arXiv: HTML from arxiv.org/html with ar5iv.labs.arxiv.org fallback

• OpenAlex: HTML sources with DOI resolver fallback chain

• PMC: E-utilities API with XML/HTML extraction

• Europe PMC: REST API with multiple URL strategies

• bioRxiv/medRxiv: Direct HTML extraction with abstract fallback

• CORE: PDF/HTML with source URL fallback

DOI Resolution Chain

Advanced DOI resolver with multiple fallback strategies:

1. Unpaywall → Free full-text sources

2. Crossref → Publisher metadata and links

3. Semantic Scholar Academic Graph → Alternative access

Performance & Reliability

• Text Extraction Success: >90% for HTML-available papers

• Graceful Degradation: Always returns metadata even if text extraction fails

• Size Management: 6MB text limit with intelligent truncation

• Caching: 24-hour LRU cache for DOI resolution

🔄 Rate Limiting

Respectful API usage with per-source rate limiting:

• arXiv: 5 requests per minute

• OpenAlex: 10 requests per minute

• PMC: 3 requests per second

• Europe PMC: 10 requests per minute

• bioRxiv/medRxiv: 5 requests per minute

• CORE: 10 requests per minute (public), higher with API key

CORE API Configuration

For enhanced CORE access, set environment variable:

🧪 Testing

Run Test Suite

Test Coverage

• Integration Tests: All 6 sources tested end-to-end

• Performance Tests: Response time and throughput benchmarks

• Workflow Tests: Real research scenarios across multiple sources

• Unit Tests: Core components and edge cases

🏗 Architecture

Modular Driver System

• Clean separation between sources

• Consistent interface across all drivers

• Specialized text extraction per source

Advanced Features

• DOI Resolution: Multi-provider fallback chain

• Rate Limiting: Token bucket algorithm per source

• Text Processing: HTML cleaning and normalization

• Error Handling: Structured responses with actionable suggestions

• Caching: Intelligent caching for DOI resolution

Technology Stack

• TypeScript + ESM: Modern JavaScript with full type safety

• Modular Design: Clean separation of concerns

• Graceful Degradation: Always functional even with partial failures

• Response Size Management: Automatic truncation and warnings

📊 Source Comparison

🔧 Development

Build

Test Individual Sources

Performance Testing

🚨 Error Handling

Comprehensive error handling for all sources:

• Invalid paper IDs with format suggestions

• Rate limiting with retry-after information

• API timeouts and server errors

• Missing authentication (CORE API key)

• Network connectivity issues

• Text extraction failures with fallback strategies

🔍 Troubleshooting

Common Issues

• Rate limiting: Automatic retry with exponential backoff

• Missing papers: Try alternative sources for the same content

• Text extraction failures: Fallback to abstract or metadata

• CORE API limits: Set CORE_API_KEY environment variable

Performance Optimization

• Use appropriate count parameters (smaller for faster responses)

• Cache results when possible

• Use fetch_latest for discovery, fetch_content for detailed reading

📝 License

MIT

Ready to explore the world's scientific knowledge? Start with any of the 6 sources and discover papers across all academic disciplines! 🔬📚