PubMed Data Extraction Script

This repository contains a Python script to search and extract PubMed records based on specific authors and topics. The extracted data is stored in a Pandas DataFrame and saved to an Excel file.

YouTube video overview of code: https://youtu.be/sGC66q45BX4

Table of Contents

• Installation
• Usage
• Customization
• Output
• License

Installation

1. Clone the repository:

   git clone https://github.com/TLDWTutorials/PubMed-Data-Extraction.git
   cd PubMed-Data-Extraction

2. Install the required dependencies:

   pip install pandas biopython

Usage

1. Update the email address to your own to avoid potential issues with Entrez:

   Entrez.email = 'your.email@example.com'

2. Customize the list of authors and topics as needed:

   authors = ['Bryan Holland', 'Mehmet Oz', 'Anthony Fauci']
   topics = ['RNA', 'cardiovascular']

3. Run the script:

   python pubmed_extraction.py

Customization

• Authors: Modify the authors list with the names of authors you want to include in the search.
• Topics: Modify the topics list with the topics you want to include in the search.
• Date Range: Adjust the date_range variable to the desired date range for your search.

Output

The script will create an Excel file named PubMed_results.xlsx containing the following columns:

• PMID
• Title
• Abstract
• Authors
• Journal
• Keywords
• URL
• Affiliations

License

This project is licensed under the MIT License.