sidk99 / autoanes

AutoAnes Codebase

PMC Text Extractor

A script for fetching and extracting text content from articles available in the PubMed Central (PMC) repository. Users need to provide a CSV file containing a list of PMC IDs without column headers. The extracted text content for each article is saved in a separate text file named by its PMC ID.

Instructions

1. Preparing Your CSV File

• Create a CSV file containing PMC IDs you wish to extract text from.
• Ensure the CSV doesn’t have a header, and PMC IDs are populated in the first column.

2. Configuring the Script

• Open the PMC Text Extractor script.
• 1. Find the line:

  csv_filename = "your_file.csv"

• Replace "your_file.csv" with the path and name of your CSV file containing the PMC IDs.
• 2. Find the line:

  PATH_PREFIX = "/PATH/TO/OUTPUT/FOLDER"

• Replace with the path of folder where you want to save text output for each paper.

3. Running the Script

• Setup Python enviroment with pip install -r requirements.txt
• Run the script in a Python environment. python pdf_text_extractor.py

Output

• Each output .txt file will contain the extracted text content of the corresponding PMC article.
• The file will be named using the PMC ID, TBD: store mapping of ID to name or other readable tag