PubMed Pharma Paper Finder

A Python command-line tool that fetches research papers from PubMed based on a user query and filters results to include only papers with at least one author affiliated with a pharmaceutical or biotech company.

Features

• Fetches papers from PubMed using the official API
• Supports PubMed's full query syntax
• Filters papers to include only those with pharmaceutical/biotech company affiliations
• Extracts key details including:
  • PubMed ID
  • Title
  • Publication Date
  • Non-academic Authors (affiliated with companies)
  • Company Affiliations
  • Corresponding Author Email (when available)
• Outputs results as CSV (to file or console)

Code Organization

The project follows a modular structure:

pubmed-pharma-paper-finder/
├── pubmed_pharma_paper_finder/
│   ├── __init__.py        # Package initialization
│   ├── core.py            # Core functionality module
│   └── cli.py             # Command-line interface
├── tests/                 # Test suite
│   └── test_mock.py       # Unit and integration tests
├── pyproject.toml         # Poetry configuration
├── README.md              # Documentation
└── LICENSE                # License information

Installation

Prerequisites

• Python 3.8 or higher
• Poetry for dependency management

Install from GitHub

# Clone the repository
git clone https://github.com/lokeshkarra/pubmed-pharma-paper-finder.git
cd pubmed-pharma-paper-finder

# Install with Poetry
poetry install

Install from Test PyPI

pip install biopython==1.85
pip install -i https://test.pypi.org/simple/ pubmed-pharma-paper-finder

‼️ Note: Requires Python 3.12+ and biopython>=1.85 ‼️

Usage

Command-Line Interface

# Basic usage
poetry run get-papers-list -e your.email@example.com "cancer AND therapy"

# Save results to a file
poetry run get-papers-list -e your.email@example.com -f results.csv "cancer AND therapy"

# Enable debug mode
poetry run get-papers-list -e your.email@example.com -d "cancer AND therapy"

# Set maximum number of results
poetry run get-papers-list -e your.email@example.com -m 200 "cancer AND therapy"

# Show help
poetry run get-papers-list -h

Options

• query: PubMed search query (supports full PubMed query syntax)
• -h, --help: Show usage instructions
• -d, --debug: Print debug information
• -f, --file: Specify a filename for saving the results (default: print to console)
• -m, --max-results: Maximum number of results to fetch (default: 100)
• -e, --email: Email address to use for NCBI API access (required)
• -k, --api-key: NCBI API key for higher rate limits (optional)

Using as a Library

You can also use the package as a library in your Python code:

from pubmed_pharma_paper_finder import PubMedPaperFinder

# Create a finder instance
finder = PubMedPaperFinder(email="your.email@example.com")

# Run a query
papers = finder.run_query("cancer AND therapy")

# Process the results
for paper in papers:
    print(f"Title: {paper['title']}")
    print(f"Company Affiliations: {paper['company_affiliations']}")

External Dependencies

• Biopython: For interacting with NCBI APIs
• Poetry: For dependency management and packaging

Testing

poetry run pytest

License

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

Development

Contributions are welcome! Please feel free to submit a Pull Request.

Development Setup

# Clone the repository
git clone https://github.com/yourusername/pubmed-pharma-paper-finder.git
cd pubmed-pharma-paper-finder

# Install development dependencies
poetry install