🔍 Research Paper Fetching using PubMed API

This project is a Python-based CLI tool that allows users to search for research papers from the PubMed database based on a user-specified query. It filters the results to include only papers with at least one author affiliated with a pharmaceutical or biotech company and saves the output to a CSV file.

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🔑 Key Features

♦️ User-Specified Query – Search for papers using any keyword or topic.
♦️ PubMed API Integration – Fetch research papers directly from PubMed using Entrez.
♦️ Author Affiliation Filtering – Filters papers based on pharma/biotech-related affiliations.
♦️ Structured CSV Output – Saves results to a CSV file with key details.
♦️ Command-Line Support – Supports options like --debug , --help and --file.

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🛠️ Technologies stack and Libraries Used

• Python 3.9+ – Download
• Biopython – For fetching data from the PubMed API using Entrez → Biopython Documentation
• Pandas – For handling and processing data → Pandas Documentation
• Poetry – For managing project dependencies → Poetry Documentation
• argparse – For handling command-line arguments → argparse Documentation
• ChatGPT – Used for generating code, debugging, and improving documentation → ChatGPT
• Git - For version control → Git Documentation

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📥Installation and Setup Process:

1. Clone the Repository

Open your terminal and run:

git clone https://github.com/your-username/research-paper-by-using-pubmed-api.git
cd research-paper-by-using-pubmed-api

2. Install Poetry

Open your terminal and run:

pip install poetry

3. Initialize the Project with Poetry

Set up the environment using Poetry:

poetry install

4. Set Up Python Environment (if needed)

If you have multiple Python versions installed:

poetry env use python3.10

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##🧑‍🔧Configuration: Make sure to set your email in the script to comply with PubMed API guidelines:

Entrez.email = "your-email@example.com"

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💡How to Use:

1. Basic Search

poetry run get-papers-list "cancer"

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2. Save Output to a CSV File

To save the output to a CSV file:

poetry run get-papers-list "AI in medicine" -m 20 -f results.csv

3. Enable Debug Mode

To debug and print detailed output:

poetry run get-papers-list "drug discovery" -d

4.help or Display usage instructions.

To Display usage instructions:

poetry run get-papers-list "cancer" -h or --help

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🔗 Project Structure

Edit
├── fetch_pubmed.py        # Main script for fetching and processing papers
├── pyproject.toml         # Poetry project configuration file
├── README.md              # Project documentation
├── .gitignore             # Ignore unnecessary files
└── results.csv            # Output file (if specified)

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📝 Example CSV Output

Pubmed ID	Title	Publication Date	Non-academic Authors	Company Affiliations	Corresponding Author Email
12345678	AI in Drug Discovery	2025	John Doe, Jane Smith	XYZ Pharma, ABC Biotech	mkaif0262@gmail.com

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🔧 Troubleshooting:

**1. Permission Denied for Poetry Commands

Try running commands with sudo:

sudo poetry install

2. Encoding Issues:

If you get encoding errors, convert files to UTF-8:

iconv -f WINDOWS-1252 -t UTF-8 README.md > README-converted.md

✅ Requirements

1. Functional Requirements

• Adherence to the problem statement – The program should strictly follow the problem statement and deliver the expected output.
• Ability to fetch and filter results correctly – The program should accurately fetch research papers and filter them based on pharma/biotech affiliations.

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2. Non-functional Requirements

• Typed Python – Use type hints consistently for all functions and variables.
• Performance – Optimize API calls and processing to minimize execution time.
• Readability – Ensure clear and maintainable code with meaningful variable names, comments, and docstrings.
• Organization – Maintain logical separation of concerns using modular functions and classes.
• Robustness – Include error handling for invalid queries, API failures, and missing data to prevent crashes and improve user experience.