oa_pmc_extr

This repository automatically requests and extracts Full Text from Open Access PMC for use in non-commercial research.

Installation

oa_pmc_extr has a number of dependencies on other Python packages, it is recommended to install it in an isolated environment.

git clone https://github.com/biomedicalinformaticsgroup/oa_pmc_extr.git

pip install ./oa_pmc_extr

After installation, you can remove the file if you want using:

rm -rf oa_pmc_extr

You can also uninstall oa_pmc_extr using:

pip uninstall oa_pmc_extr

Get started

The only function available in this repository is called 'pmc_oa_generation'. It only takes one argument 'PATH', which is the directory you want to save the output in. It has the default value './' meaning the current directory.

from oa_pmc_extr import pmc_oa_generation
pmc_oa_generation(PATH)

The funtion is extracting the files from /pub/pmc/oa_bulk API using ftp requests from the oa_comm, oa_noncomm, and oa_other sets.

The result

The function will generate a pre-made directory called pmc_oabulk_output. Within pmc_oabulk_output there are three subdirectories called parsed_files, unzip_files, and zip_files. All of the subdirectories contains 2 directories, txt and xml. The files contained in these directories are obtained from the PMC API for all 3 licenses type (commercial, non commercial, and other).

• zip_files contains the raw files obtained directly from the API. There are .gz files containing the PMC files in .txt or .xml, the filelists containing metadata about the PMC files saved as .txt and .csv.
• unzip_files contains the uncompressed PMC files from the .gz files. These are saved in a pre-made directory made by PMC. They look like 'PMC000xxxxxx'.
• parsed_files contains the same structure as unzip_files but the file were loaded and clean to remove the information outside the full text.