bio-info-pubmed 0.1.0

A tool to fetch research papers with non-academic authors from PubMed

Bio-Info

A Python tool to fetch research papers from PubMed and identify those with authors affiliated with pharmaceutical or biotech companies.

Features

• Search PubMed using the full PubMed query syntax
• Identify papers with authors affiliated with pharmaceutical or biotech companies
• Extract corresponding author emails
• Output results to CSV or console

Code Organization

The project is organized as follows:

• bio_info/: Main package directory
  • __init__.py: Package initialization
  • api.py: Module for interacting with the PubMed API
  • affiliations.py: Module for identifying non-academic authors and company affiliations
  • output.py: Module for generating and formatting CSV output
  • cli.py: Command-line interface implementation
• tests/: Test directory
  • test_bio_info.py: Unit tests for the package

Installation

This project uses Poetry for dependency management.

1. Make sure you have Python 3.8+ and Poetry installed
2. Clone the repository

git clone https://github.com/yourusername/pubmed-papers.git
cd pubmed-papers

3. Install dependencies

poetry install

Usage

After installation, you can use the get-papers-list command to search for papers:

# Basic usage, prints results to console
poetry run get-papers-list "cancer therapy"

# Save results to a CSV file
poetry run get-papers-list "artificial intelligence AND medicine" -f results.csv

# Enable debug mode
poetry run get-papers-list "COVID-19 vaccine" -d

# Limit results (default is 100)
poetry run get-papers-list "gene therapy" -m 50

Command Line Arguments

• query: PubMed search query (enclose in quotes for complex queries)
• -h, --help: Show help message and exit
• -f, --file: Specify the filename to save the results (if not provided, print to console)
• -d, --debug: Print debug information during execution
• -m, --max-results: Maximum number of results to fetch from PubMed (default: 100)

Dependencies

This project uses the following key libraries:

• Biopython: For accessing the PubMed API
• Pandas: For data manipulation and CSV handling
• Requests: For HTTP requests

Development

Running Tests

poetry run pytest

Tools Used

The following tools were used in the development of this project:

• Poetry: Dependency management
• Pytest: Testing framework
• Black: Code formatting
• MyPy: Static type checking