An MCP (Model Context Protocol) server and CLI toolkit for comprehensive scientific literature retrieval and analysis using PMIDs, DOIs, PMCIDs, and keyword searches.

Add this to your Claude Desktop MCP configuration:

{
  "mcpServers": {
    "artl-mcp": {
      "command": "uvx",
      "args": ["artl-mcp"]
    }
  }
}

# Install and use CLI commands
uvx artl-cli get-doi-metadata --doi "10.1038/nature12373"
uvx artl-cli search-papers-by-keyword --query "CRISPR gene editing" --max-results 5

• Keyword-based paper search with advanced filtering
• Recent publication discovery
• PubMed search with multiple output formats

• DOI/PMID/PMCID metadata extraction
• Abstract retrieval from PubMed
• Full-text access via multiple sources (PMC, Unpaywall, BioC)
• PDF text extraction and processing

• Universal identifier conversion (DOI ↔ PMID ↔ PMCID)
• Support for multiple input formats (URLs, CURIEs, raw IDs)
• Comprehensive identifier validation

• Reference analysis (papers cited BY a given paper)
• Citation analysis (papers that CITE a given paper)
• Multi-source citation data (CrossRef, OpenAlex, Semantic Scholar)
• Related paper discovery through citation networks

• MCP Mode: Returns data directly without file saving (optimal for AI assistants)
• CLI Mode: Full file saving with path reporting and content management
• Content size management - large content automatically handled appropriately
• Memory-efficient streaming for large files (PDFs, datasets)
• Cross-platform filename sanitization
• Multiple output formats (JSON, TXT, CSV, PDF) in CLI mode
• Configurable directories and temp file management in CLI mode

When running as an MCP server, you get access to 32 tools organized into categories:

MCP Mode (AI assistants): Returns data directly without file saving:

{
  "data": { /* tool-specific content */ },
  "mcp_mode": true,
  "note": "Data returned directly - use CLI for file saving"
}

CLI Mode (command line): Full file saving with path reporting:

{
  "data": { /* tool-specific content */ },
  "saved_to": "/path/to/saved/file.json"
}

• search_papers_by_keyword - Advanced keyword search with filtering
• search_recent_papers - Find recent publications
• search_pubmed_for_pmids - PubMed search returning PMIDs

• get_doi_metadata - Comprehensive DOI metadata
• get_abstract_from_pubmed_id - PubMed abstracts
• get_doi_fetcher_metadata - Enhanced metadata (requires email)
• get_unpaywall_info - Open access availability

• get_full_text_from_doi - Multi-source full text (requires email)
• extract_pdf_text - PDF text extraction
• get_pmcid_text - PMC full text
• get_full_text_from_bioc - BioC format text

• get_all_identifiers - Get all IDs for any identifier
• doi_to_pmid, pmid_to_doi - Individual conversions
• validate_identifier - Format validation

• get_paper_references - Papers cited by a given paper
• get_paper_citations - Papers citing a given paper
• get_citation_network - Comprehensive citation data
• find_related_papers - Citation-based recommendations

The artl-cli command provides access to all functionality:

# Metadata retrieval
artl-cli get-doi-metadata --doi "10.1038/nature12373"
artl-cli get-abstract-from-pubmed-id --pmid "23851394"

# Literature search
artl-cli search-papers-by-keyword --query "machine learning" --max-results 10
artl-cli search-recent-papers --query "COVID-19" --years-back 2

# Full text (requires email for some sources)
artl-cli get-full-text-from-doi --doi "10.1038/nature12373" --email "[email protected]"

# Identifier conversion
artl-cli doi-to-pmid --doi "10.1038/nature12373"
artl-cli get-all-identifiers --identifier "PMC3737249"

# Citation analysis  
artl-cli get-paper-citations --doi "10.1038/nature12373"

Several APIs require institutional email addresses:

export ARTL_EMAIL_ADDR="[email protected]"
# or create local/.env file with: [email protected]

MCP Client Configuration: Different MCP clients support configuration injection. ARTL-MCP's enhanced configuration system provides multiple methods for email setup:

• Claude Desktop: Inherits system environment variables automatically
• Goose Desktop: Requires MCP extension configuration (see USERS.md)
• Other clients: May support client-specific configuration injection

See USERS.md for comprehensive configuration instructions.

Configure where files are saved when using CLI commands:

export ARTL_OUTPUT_DIR="~/Papers"           # Default: ~/Documents/artl-mcp
export ARTL_TEMP_DIR="/tmp/my-artl-temp"    # Default: system temp + artl-mcp
export ARTL_KEEP_TEMP_FILES=true            # Default: false

Note: MCP mode returns data directly without file saving.

DOI: 10.1038/nature12373, doi:10.1038/nature12373, https://doi.org/10.1038/nature12373

PMID: 23851394, PMID:23851394, pmid:23851394

PMCID: PMC3737249, 3737249, PMC:3737249

All tools automatically detect and normalize identifier formats.

git clone https://github.com/contextualizer-ai/artl-mcp.git
cd artl-mcp
uv sync --group dev

# Run tests
make test                    # Fast development tests
make test-coverage          # Full test suite with coverage

# Code quality
make lint                   # Ruff linting
make format                 # Black formatting
make mypy                   # Type checking

• USERS.md - Comprehensive user guide with examples
• DEVELOPERS.md - Development setup and architecture