pypubmech

A Python package for fetching and processing PubMed articles with comprehensive metadata extraction and MeSH term support.

Features

• Search PubMed articles by keyword or MeSH terms
• Extract comprehensive article metadata including:
  • Title, Abstract, Authors
  • Volume, Issue, Journal
  • Citations and Links
  • MeSH terms
• Export results to CSV
• Compare different sets of PMIDs

Installation

pip install pypubmech

Quick Start

from pypubmech import PubMedClient

# Initialize client
client = PubMedClient(email="your.email@example.com")

# Search by keyword
pmids = client.search_by_keyword("cancer", 100)

# Fetch metadata
client.fetch_article_metadata()

# Export to CSV
client.export_to_csv("cancer_articles.csv")

MeSH Search Example

# Search using MeSH terms
mesh_query = "Neoplasms[MeSH] AND Genetics[MeSH]"
pmids = client.search_by_mesh(mesh_query)
client.fetch_article_metadata()
client.export_to_csv("cancer_genetics.csv")

Development

Setup

1. Clone the repository:

git clone https://github.com/yourusername/pypubmech.git
cd pypubmech

2. Create a virtual environment:

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install development dependencies:

pip install -e ".[dev]"

Running Tests

pytest tests/

Contributing

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

License

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