📚 My PubMed Package

A Python CLI & library to search PubMed, filter pharmaceutical/biotech papers, and export results to CSV.

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🚀 Features

✅ Search PubMed with a query (full syntax supported).
✅ Fetch research papers and extract metadata.
✅ Identify pharmaceutical/biotech-affiliated authors using heuristics.
✅ Save results to CSV or print them in the terminal.
✅ Command-line interface (CLI) for easy execution.
✅ Python module for programmatic use.
✅ Lightweight & easy to install (only depends on requests).

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🛠 Installation

Install from PyPI

You can install the package directly from PyPI using:

pip install my-pubmed-package

This installs both the Python library and the CLI tool (get-papers-list).

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🎮 CLI Usage

After installation, you can run the CLI tool:

get-papers-list "machine learning in drug discovery" -d -f results.csv

Command Options

Option	Description
query	(Required) The PubMed search query. Full syntax supported.
-d, --debug	Enable verbose debug logs.
-f <filename>, --file <filename>	Save output to CSV. If omitted, prints results to the console.
-h, --help	Display help message.

Example:

get-papers-list "cancer immunotherapy" -d -f papers.csv

✅ Fetches 50 papers
✅ Filters those with pharma/biotech affiliations
✅ Saves the output in papers.csv

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📄 Example Output

CSV File (results.csv) Example:

PubmedID,Title,Publication Date,Non-academic Author(s),Company Affiliation(s),Corresponding Author Email
39941149,"Discovery of TRPV4-Targeting Small Molecules",2025-Feb-06,"Yu Wang","State Key Laboratory of Pathogen and Biosecurity","coen.vanhasselt@lacdr.leidenuniv.nl"
39935140,"Disorganization of Small-World Functional Networks",2025-Feb,"","Department of Radiology, Tongde Hospital of Zhejiang Province",""
39930345,"C-H Aminoalkylation of 5-Membered Heterocycles",2025-Feb-11,"Cyndi Qixin He; Marion H Emmert","Process Research and Development, Merck & Co., Inc.","parthapatrim.roy@gcu.ac.in"

Terminal Output Example (if no -f is provided):

--- Pharma/Biotech Papers ---
PubmedID: 39941149
Title: Discovery of TRPV4-Targeting Small Molecules
Publication Date: 2025-Feb-06
Non-academic Author(s): Yu Wang
Company Affiliation(s): State Key Laboratory of Pathogen and Biosecurity
Corresponding Author Email: coen.vanhasselt@lacdr.leidenuniv.nl
--------------------------------------------------

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🖥 Programmatic Usage

You can also use my-pubmed-package as a Python module:

from my_pubmed_package.pubmed_module import search_pubmed_ids, fetch_pubmed_details_bulk

# Search PubMed for PMIDs
pmids = search_pubmed_ids("heart attack therapy", retmax=10, verbose=True)

# Fetch metadata
articles = fetch_pubmed_details_bulk(pmids, verbose=True)

# Print first result
print(articles[0])

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🔄 Updating the Package

To update to the latest version:

pip install --upgrade my-pubmed-package

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🛠 Troubleshooting

1️⃣ get-papers-list: command not found

If the CLI is not recognized, try running it with:

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

OR:

python -m my_pubmed_package.cli "cancer immunotherapy" -d -f results.csv

2️⃣ No PMIDs found

Try using broader search queries or visit PubMed to refine.

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📜 License

This project is licensed under the MIT License.

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🎉 Thank You!

If you find this package useful, star it on GitHub and share it with others! 🚀