PubMed Research Paper Fetcher

Fetch research papers from PubMed API and filter authors affiliated with pharmaceutical/biotech companies.

---

📌 Features

✅ Fetches research papers using PubMed API
✅ Filters authors affiliated with pharma/biotech companies
✅ Saves results as CSV file
✅ Supports CLI arguments for flexibility
✅ Uses Poetry for dependency management

---

📦 Project Structure

pubmedapitask/
│── researchpapers/
│   ├── __init__.py
│   ├── main.py              # CLI script for fetching and processing papers
│   ├── pubmedapi.py         # Fetches data from PubMed API
│   ├── data_processing.py   # Extracts and filters authors from XML data
│── .gitignore
│── pyproject.toml           # Poetry dependencies and setup
│── README.md                # Documentation

---

🛠 Installation & Setup

1️⃣ Clone the Repository

git clone https://github.com/ShreyasDankhade/pubmedapitask.git
cd pubmedapitask

2️⃣ Install Poetry (If Not Installed)

pip install poetry

3️⃣ Install Dependencies

poetry install

4️⃣ Install Required Modules

Before running the project, ensure all dependencies are installed:

pip install -r requirements.txt

🚀 Usage

Run the script via Poetry:

Fetch papers and print output

poetry run get-papers-list "cancer immunotherapy"

Fetch papers and save as CSV

poetry run get-papers-list "diabetes research" -f research_results.csv

Enable Debug Mode

poetry run get-papers-list "genetic engineering" -d

---

🔧 Command-Line Arguments

Option	Description
query	(Required) Search term for fetching research papers
-f, --file	Specify filename to save results as a CSV
-d, --debug	Enable debug mode for detailed logs

---

⚙️ Running Inside Poetry Shell

If poetry run doesn't work, enter the Poetry virtual environment first:

poetry shell
get-papers-list "cancer immunotherapy" -f output.csv

---

📜 Example Output

PubmedID,Title,Publication Date,Authors with Pharma/Biotech Affiliations
123456, "Breakthrough in Cancer Research", 2024-03, "Dr. John Doe, Dr. Emily Smith"
789101, "Genetic Engineering in Medicine", 2023-11, "Dr. Alex Brown"

---

🔄 Updating the Project

To update dependencies:

poetry update

To pull latest changes from GitHub:

git pull origin main
poetry install

---

🔍 Troubleshooting

1️⃣ "ModuleNotFoundError"

If Poetry cannot find modules:

poetry install
poetry run get-papers-list "cancer research"

2️⃣ "get-papers-list: command not found"

Manually run the script:

poetry run python researchpapers/main.py "cancer research"

---

📌 Technologies Used

• Python 3.9+
• Poetry (Dependency Management)
• Requests (HTTP Requests)
• Pandas (Data Processing)
• XML Parsing (PubMed Data Extraction)

---

📧 Contact

For questions or support, contact Shreyas Dankhade at shreyasdankhade75@gmail.com.

---