Exatool

Exatool is written in python and is able to retrieve the full text of an article (when free). Its purpose is to allow a better understanding of the material used by the scientific community using a keyword research. Python scripts to visualize the data are also available. The development is still ongoing and currently limited to the PubMed database of research articles.

If you have questions, find bugs, or have ideas of features you would like to propose, do not hesitate to reach out at mattgitqna@gmail.com

If you do not enjoy using a terminal, fear not ! You can use a neat GUI through the webapp version of exatool accessible here : https://exatools.streamlit.app/

You can download a rudimentary graphic interface for exatool here : https://github.com/ZeepReactorr/exatools/releases/download/release_1.0/exatool_WINDOWS_1.0_setup.exe
Be aware that it will be slower than if you used a terminal :).

Prerequisite

To run the programs smoothly, you need to have installed the following packages :

• bs4
• requests
• PyPDF2
• BytesIO
• numpy
• matplotlib

All those packages can be installed with pip install <package_name> from the terminal

Installation

To install the Exatool program, run the following command line in your terminal :

git clone https://github.com/ZeepReactorr/exatools

Usage

To run the program, enter the following command line in your terminal, filling the gaps with the required parameters :

python ~/PATH/TO/exatool.py ~/PATH/TO/OUTPUT_DIR 'Pubmed URL' keyword_1 keyword_2... keyword_n

The program will keep the progression updated in the console. The ouptut graphical plot will be saved in the output directory you indicated as well as the intermediary files. Be careful that the date range in your Pubmed query and indicated date range variable match, if they don't, the plot will not be correct.
Make sure that the URL is between quotes, as the command will return an error otherwise.

Example of prompt :

python C:/PATH/TO/exatool.py C:/PATH/TO/OUTPUT/DIRECTORY 'https://pubmed.ncbi.nlm.nih.gov/?term=prokaryote+sequencing&filter=simsearch2.ffrft' Illumina Nanopore

This will count the respective occurency of Nanopore or Illumina sequencing for articles related to Prokaryote sequencing throughout pubmed and automatically generate a graph displaying just that.

The reviews are filtered out. Only research papers with methods are taken into account.

Credit

If you found this tool useful during your research, please cite :

BETTIATI M. (2024). Exatools [Python]. https://github.com/ZeepReactorr/exatools (Original work published 2024)