📄 PubMed Paper Fetcher CLI

A command-line tool to fetch research papers from PubMed based on a user query and identify papers with at least one author affiliated with a pharmaceutical or biotech company.

The results can be printed to the console or saved to a CSV file.

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✨ Features

✅ Fetches papers from PubMed API using full query syntax
✅ Filters papers to detect non-academic authors and company affiliations (pharma/biotech)
✅ Outputs to console or CSV file
✅ Optional debug mode to show API flow and intermediate data
✅ Built with Poetry for dependency management & packaging

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📂 Project Structure

pubmed-cli-tool/
│
├── pubmed\_cli/               # Core package
│   ├── fetcher.py            # PubMed API calls (Entrez E-utilities)
│   ├── filters.py            # Logic for parsing & identifying pharma/biotech authors
│   ├── utils.py              # CSV saving utilities
│   └── **init**.py
│
├── scripts/                  # CLI entry point
│   ├── cli.py                # Main CLI logic (argparse)
│   └── **init**.py
│
├── tests/                    # Pytest test suite
│   ├── test\_cli.py
│   ├── test\_fetcher.py
│   └── test\_filter.py
│
├── dist/                     # (auto-generated) build artifacts for TestPyPI/PyPI
├── pyproject.toml            # Poetry config (dependencies, CLI command)
├── README.md                 # Documentation
└── ...

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🔧 Installation (Developers)

Clone the repo & install dependencies:

git clone https://github.com/<your-username>/pubmed-cli-tool.git
cd pubmed-cli-tool
poetry install

Run tests to verify everything works:

poetry run pytest

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🚀 Usage

Run the CLI command:

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

Options:

-d, --debug           Enable debug output
-f, --file <name>     Save results to CSV (instead of printing to console)
-h, --help            Show help message

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📌 Examples

1️⃣ Print to console:

poetry run get-papers-list "cancer immunotherapy" --debug

2️⃣ Save to CSV:

poetry run get-papers-list "cancer immunotherapy" -f results.csv

This generates results.csv with columns:

• PubmedID
• Title
• Publication Date
• Non-academic Authors
• Company Affiliations
• Corresponding Author Email

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🔍 How It Detects Pharma/Biotech Authors

• Affiliations containing university, college, institute, hospital = academic
• Affiliations containing pharma, biotech, inc, ltd, corp, therapeutics = industry

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🛠 Tools & Libraries

• Poetry – Dependency management & packaging
• Biopython – PubMed API access (via Bio.Entrez)
• Requests – API calls
• argparse – CLI parsing
• pytest – Testing framework

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📦 Future Improvements

• ML-based affiliation classification
• More robust handling of missing metadata
• Better CSV formatting options
• Continuous integration tests

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📥 Install from TestPyPI

The package is live on TestPyPI for preview.

pip install -i https://test.pypi.org/simple/pubmed-paper-fetcher-cl

Then run:

get-papers-list "CRISPR" --debug

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