Scholar MCP Server

A Model Context Protocol (MCP) server that gives AI agents comprehensive access to scientific literature. It acts as middleware between LLMs and academic databases — Scopus, OpenAlex, and Unpaywall — providing automated paper discovery, author analytics, metadata extraction, citation tracking, and multimodal PDF rendering.

Features

• Multi-Source Paper Discovery

  • Scopus — Primary metadata engine with support for advanced Boolean syntax (requires API key).
  • OpenAlex — Open-access-first search with full abstract reconstruction.
  • Unpaywall — Native title search and DOI-to-PDF resolution across global OA repositories.

• Author Analytics & Disambiguation

  • Rapid author name autocomplete via OpenAlex for disambiguation.
  • Deep author profiles: h-index, i10-index, ORCID, institutional history, and top research concepts.
  • Scopus Author Retrieval for precise Elsevier-sourced citation metrics.
  • Chronologically sorted publication lists per author.

• Citation Tracking

  • Forward citations (who cited this paper) and backward references (who this paper cites) via OpenAlex.

• Full-Text Extraction

  • High-fidelity text extraction from OA PDFs using PyMuPDF with accurate multi-column layout handling.
  • HTML fallback extraction via BeautifulSoup for non-PDF resources.
  • All-in-one DOI → Unpaywall → PDF → text pipeline in a single tool call.

• Multimodal Vision Rendering

  • Renders PDF pages as PNG images for direct consumption by Vision-capable LLMs.
  • Ideal for analyzing charts, tables, equations, and layouts that text extraction cannot capture.

• Citation & Writing Automation

  • Automated BibTeX generation for LaTeX workflows via CrossRef.
  • High-precision citation formatting (APA, IEEE, Chicago, etc.) using CrossRef content negotiation.

• Landscaping & Discovery

  • Explore research topics, domains, and trending concepts via OpenAlex.
  • Efficient batch metadata retrieval for up to 50 DOIs in a single session.

• Graceful Paywall Handling

  • Injects meta-instructions to the LLM agent requesting manual document uploads when encountering closed-access content.

Architecture

graph TD
    A[LLM Agent] -->|MCP Protocol| B(Scholar MCP Server)
    B --> C{Database Router}
    C -->|Primary| D[Scopus API]
    C -->|Fallback| E[OpenAlex API]
    C -->|DOI Resolver| F[Unpaywall API]
    C -->|Citations| P[CrossRef API]
    
    D --> G{Access Check}
    E --> G
    F --> G
    P --> G
    
    G -->|Open Access| H[PDF Buffer Download]
    G -->|Closed Access| I[Human-in-the-Loop Prompt]
    H --> J[PyMuPDF Text Extractor]
    H --> K[PyMuPDF Vision Renderer]
    J --> L[Return Context to LLM]
    K --> L
    I --> L
    B --> M{Author Router}
    M -->|Profile| N[OpenAlex Authors API]
    M -->|Metrics| O[Scopus Author API]
    N --> L
    O --> L

Installation

Prerequisites

• Python 3.10+
• Elsevier Developer API Key (for Scopus features)

Setup

# Clone the repository
git clone https://github.com/mlintangmz2765/Scholar-MCP.git
cd Scholar-MCP

# Create and activate virtual environment
python -m venv venv
# Windows
.\venv\Scripts\activate
# Unix/macOS
source venv/bin/activate

# Install in editable mode
pip install -e .

# Configure environment
cp .env.example .env

Environment Variables

Variable	Required	Description
SCOPUS_API_KEY	Yes	Elsevier API key for Scopus search and author retrieval.
SCOPUS_INST_TOKEN	No	Institutional token for full abstract access via Scopus.
CONTACT_EMAIL	Yes	Email for OpenAlex/Unpaywall polite-pool API routing.

Configuration

Configure your MCP client (Claude Desktop, Cursor, Gemini CLI, etc.) by pointing to the virtual environment Python binary and server.py:

{
  "mcpServers": {
    "scholar-academic-mcp": {
      "command": "/absolute/path/to/Scholar-MCP/venv/bin/python",
      "args": [
        "/absolute/path/to/Scholar-MCP/server.py"
      ],
      "env": {
        "SCOPUS_API_KEY": "your_scopus_api_key",
        "SCOPUS_INST_TOKEN": "your_optional_inst_token",
        "CONTACT_EMAIL": "your_email@domain.com"
      }
    }
  }
}

Note: On Windows, use venv/Scripts/python.exe instead of venv/bin/python.

Tools

The server registers 18 tools across 7 categories:

Paper Discovery

Tool	Signature	Description
search_papers_tool	(query, limit=5, use_scopus=True, sort_by="relevance")	Search papers via Scopus (Boolean syntax) or OpenAlex. Sort by cited_by_count or publication_year.
get_paper_details_tool	(paper_id)	Fetch full metadata and abstract by Scopus ID, DOI, or OpenAlex ID (with automatic routing).
search_titles_unpaywall_tool	(query, is_oa=None)	Search Unpaywall's database directly by title. Set is_oa=True for strictly OA results.
get_related_works_tool	(paper_id, limit=10)	Find related/similar papers using OpenAlex's bibliographic coupling.

Author Analytics

Tool	Signature	Description
autocomplete_authors_tool	(name, limit=5)	Rapidly disambiguate author names and resolve OpenAlex Author IDs.
search_authors_tool	(name, institution=None, limit=5)	Deep author profiles: h-index, i10-index, ORCID, affiliations, concepts.
search_author_by_orcid_tool	(orcid)	Look up an author directly by ORCID (raw or URL format).
retrieve_author_works_tool	(author_id, limit=15)	Chronologically sorted publications for a given OpenAlex author.
get_author_profile_scopus_tool	(author_id)	Fetch precise Scopus-sourced h-index, citation counts, and affiliation.

Citation Tracking

Tool	Signature	Description
get_citations_tool	(paper_id, direction="references")	Retrieve forward citations or backward references via OpenAlex.

Full-Text & PDF

Tool	Signature	Description
get_full_text_tool	(url, start_page=None, end_page=None)	Extract text from an OA PDF or HTML page. Supports page range selection.
get_full_text_visual_tool	(url, max_pages=3)	Render PDF pages as images for Vision-capable LLMs.
fetch_pdf_text_unpaywall_tool	(doi)	All-in-one: resolve DOI via Unpaywall → download PDF → extract text.

Citation & Writing

Tool	Signature	Description
get_bibtex_tool	(doi)	Generate a BibTeX entry for LaTeX via CrossRef content negotiation.
format_citation_tool	(doi, style="apa")	Format citation in APA, IEEE, Chicago, Harvard, Vancouver, MLA, or Turabian.

Open Access Resolution

Tool	Signature	Description
get_unpaywall_link_tool	(doi)	Resolve a DOI to all available OA locations via Unpaywall.

Research Discovery

Tool	Signature	Description
search_topics_tool	(query, limit=10)	Browse research topics/concepts. Returns fields, domains, and publication volume.
batch_lookup_tool	(dois: list[str])	Batch-fetch metadata for multiple DOIs in a single call (max 50).

Reliability & Production Parity

Scholar MCP is built for stability and precision in production research workflows, emphasizing data integrity and fault tolerance:

• Strict Schema Validation
  • Powered by Pydantic models to enforce strict data contracts for all API responses.
  • Ensures agents receive structured, predictable data even if upstream schemas drift.
• Resilient Network Layer
  • Intelligent Retries: Integrated tenacity decorators with exponential backoff for transient HTTP errors (429, 5xx).
  • Fault-Tolerant Concurrency: Batch operations use asyncio.gather with localized exception handling, ensuring a single DOI failure doesn't compromise the entire session.
• Production-Grade Observability
  • Structured standard-error (stderr) logging provides deep visibility into the request lifecycle without polluting the MCP JSON-RPC transport.
• Deterministic Verification
  • Comprehensive pytest suite utilizing respx for deterministic API mocking and edge-case simulation without network dependencies.

Project Structure

Scholar-MCP/
├── .github/workflows/ # GitHub Actions (CI & Releases)
├── scripts/           # Automation & Validation scripts
├── tests/             # Pytest suite (respx mocked)
├── server.py          # FastMCP tool entry point
├── api.py             # API Clients (Scopus, OpenAlex, Unpaywall, CrossRef)
├── extractor.py       # PDF/HTML Extraction & Rendering
├── models.py          # Pydantic Data Validation
├── server.json        # MCP Registry Manifest
├── pyproject.toml     # Python packaging configuration
├── requirements.txt   # Dependencies
├── VERSION            # Version tracking (v1.0.0)
├── LICENSE            # MIT License
├── README.md          # Documentation
├── .env.example       # Template for API keys
└── .gitignore         # Git exclusion rules

Troubleshooting

Symptom	Cause	Resolution
HTTP 401 from Scopus	Standard API keys lack META_ABS view access.	Set SCOPUS_INST_TOKEN or use OpenAlex as fallback.
HTTP 403 on PDF download	Publisher anti-bot protection (Cloudflare, DataDome).	Provide the PDF manually to the LLM.
Empty Unpaywall results	Paper is behind a strict paywall with no OA copies.	Request the PDF from the author via ResearchGate or institutional access.
SCOPUS_API_KEY is not set	Missing environment variable.	Ensure .env is configured or pass via MCP client env block.

Contributing

1. Fork the repository.
2. Create a feature branch (git checkout -b feature/my-feature).
3. Commit your changes (git commit -m 'feat: add new capability').
4. Push to the branch (git push origin feature/my-feature).
5. Open a Pull Request.

Please ensure all code follows PEP 8 conventions.

License

MIT License. See LICENSE for details.

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Disclaimer: Automated querying of publisher APIs must comply with the respective Terms of Service of Elsevier, OpenAlex, and Unpaywall. Do not distribute API keys. Adhere to all applicable rate limits.

mcp-name: io.github.mlintangmz2765/scholar