PubMed Paper Fetcher

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

Features

• Search PubMed using their full query syntax
• Identify authors with non-academic affiliations
• Export results to CSV with detailed paper information
• Command-line interface with multiple options
• Type-hinted Python code for better maintainability

Installation

Prerequisites

• Python 3.13 or higher
• Poetry for dependency management

Setup

1. Clone the repository:

git clone https://github.com/BiTsY2K/PubMedFetcher.git
cd pubmedfetcher

2. Install dependencies using Poetry:

poetry install

This will install all required dependencies:

• requests (>=2.32.3)
• pandas (>=2.2.3)
• logging (>=0.4.9.6)

Usage

The tool can be used via the command line using the get-papers-list command installed by Poetry.

Basic Usage

poetry run get-papers-list "<your-search-query>"

Command Line Options

• -h, --help: Display usage instructions
• -d, --debug: Print debug information during execution
• -f, --file FILENAME: Specify output file path (CSV format)
  • If not provided, results will be printed to console

Examples

1. Basic search with output to console:

poetry run get-papers-list "cancer immunotherapy"

2. Search with file output:

poetry run get-papers-list "CRISPR" -f results.csv

3. Search with debug information:

poetry run get-papers-list "antibody development" -d -f results.csv

Output Format

The tool generates a CSV file with the following columns:

• PubmedID: Unique identifier for the paper
• Title: Title of the paper
• Publication Date: Date the paper was published
• Non-academic Author(s): Names of authors affiliated with non-academic institutions
• Company Affiliation(s): Names of pharmaceutical/biotech companies
• Corresponding Author Email: Email address of the corresponding author

Project Structure

pubmedfetcher/
├── pubmedfetcher/
│   ├── pubmed_fetcher/
│   │   ├── __init__.py
│   │   ├── main.py
│   │   └── modules.py
│   ├── __init__.py
│   ├── types.py
│   └── tests/
│       ├── __init__.py
│       └── test_fetcher.py
├── LICENSE.md
├── README.md
├── poetry.lock
├── pyproject.toml
└── test_data.xml

Tools and Resources Used

1. Development Tools:

   • Poetry for dependency management
   • GitHub for version control
   • Python's type hints for static typing

2. Key Libraries:

   • requests: For API communication
   • pandas: For data manipulation and CSV export
   • logging: For debug information and error tracking

Useful Links

Official Documentation

• PubMed E-utilities Documentation
• PubMed API Reference
• NCBI Help Manual

Development Tools

• Poetry Documentation
• Python Type Hints Guide
• Pandas Documentation
• Requests Library Documentation

Contributing

1. Fork the repository
2. Create a feature branch
3. Commit your changes
4. Push to the branch
5. Create a Pull Request

License

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

Author

ROHIT RAI ([email protected])