Get Papers List

A Python program to fetch research papers from PubMed and filter those with at least one author affiliated with a pharmaceutical or biotech company.

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Features

• Fetches research papers from PubMed using a search query.
• Filters papers based on author affiliation with pharmaceutical or biotech companies.
• Extracts relevant details, including emails of authors when available.
• Outputs results in a CSV format for easy viewing and analysis.

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How the Code is Organized

The program is organized into the following components:

1. get_papers.py

• The main script that fetches papers from PubMed, filters them, and outputs the results.
• Contains functions for:
  • Fetching Paper IDs: fetch_paper_ids()
  • Fetching Paper Details: fetch_paper_details()
  • Checking Pharmaceutical/Biotech Affiliations: is_pharma_biotech()
  • Extracting Emails: extract_email()

2. Command-Line Interface

• The program is executed via the command line using poetry run get-papers-list.
• Supports the following options:
  • query: The PubMed query to search for papers.
  • -d or --debug: Enables debug mode.
  • -f or --file: Saves the results to a CSV file.

3. Dependencies

• The program uses the following libraries:
  • requests: For making HTTP requests to the PubMed API.
  • lxml: For parsing XML responses from PubMed.
  • pandas: For creating and saving the results as a CSV file.

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Installation and Execution

Prerequisites

• Python 3.8 or higher.
• Poetry (for dependency management).

Installation Steps

1. Clone the repository:

   git clone https://github.com/sanjudev1/get-papers-list.git
   cd get-papers-list