PubMed Fetcher

pubmed-fetcher is a Python tool designed to fetch research papers from PubMed and extract relevant information into CSV files. Below are the steps to run the program:

1. If you dont already have poetry, run pip install poetry
2. Clone the repository.
3. Run : cd pubmed-fetcher
4. Run : poetry install --no-root
5. To use, use command : poetry run get-papers-list "YOUR QUERY" -f YOUR-FILE-NAME.csv -d
6. If you don't want the file to be saved then you can skip the -f parameter, in which case the output will be printed to console.
7. For help use: poetry run get-papers-list -h

Features

• Fetch PubMed IDs based on a search query.
• Retrieve detailed XML data for given PubMed IDs.
• Extract and parse required fields from PubMed XML data into CSV files.

Installation

1. Ensure you have Poetry installed. If not, you can install it using pip:

   pip install poetry

2. Clone the repository:

   git clone https://github.com/November-6/pubmed-fetcher.git

3. Change to the project directory:

   cd pubmed-fetcher

4. Install dependencies:

   poetry install --no-root

Usage

To fetch research papers from PubMed, use the command:

poetry run get-papers-list "YOUR QUERY" -f YOUR-FILE-NAME.csv -d

• Replace "YOUR QUERY" with your search query.
• Replace YOUR-FILE-NAME.csv with the desired output CSV file name.
• If you don't want the file to be saved, you can skip the -f parameter, and the output will be printed to the console.

For help, use:

poetry run get-papers-list -h

Example

To fetch papers related to "cancer research" and save the results to results.csv:

poetry run get-papers-list "cancer research" -f results.csv

To fetch papers related to "cancer research" and print the results to the console:

poetry run get-papers-list "cancer research"

Project Structure

• pubmed_fetcher.py: Contains the core functions for fetching and parsing PubMed data.
• pubmed_cli.py: Command-line interface for interacting with the tool.
• poetry.lock: Lock file generated by Poetry for managing dependencies.

License

This project is licensed under the MIT License.

Contact

For any inquiries or issues, feel free to contact me at [email protected].

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