Data Processing Book Notebooks

This repository contains Jupyter notebooks used in the “Data and Text Processing for Health and Life Sciences” book.
The notebooks provide a step-by-step guide to data and text processing using practical shell scripting.

What You'll Learn:

• Combine simple, powerful command-line tools, like digital LEGO bricks, for biological data work
• Automate real-world biological data handling and retrieval
• Extract information from web resources efficiently
• Mine scientific literature using command-line techniques
• Work with universal, open standard formats: TSV, CSV, XML, and OWL

Note: Includes fix for new ChEBI 2.0 web interface that currently lacks detailed cross-references on entry pages.

Contents

• notebooks/ – Jupyter notebooks.
• data/ – Files with data created and used in the notebooks.
• scripts/ – Scripts created in the notebooks.

How to use in Google Colab

1. Go to Google Colab.

2. Click File > Open notebook > GitHub tab.

3. Enter your GitHub repo URL (e.g., https://github.com/lasigeBioTM/data-text-processing-notebooks) and select the notebook (e.g., notebooks/data-text-processing-notebooks-01-unix-shell.ipynb).

   Quick link method: Replace github.com with githubtocolab.com in any notebook URL, example:

   • https://github.com/lasigeBioTM/data-text-processing-notebooks/blob/main/notebooks/data-text-processing-notebooks-01-unix-shell.ipynb
   • can be replaced by:
   • https://githubtocolab.com/lasigeBioTM/data-text-processing-notebooks/blob/main/notebooks/data-text-processing-notebooks-01-unix-shell.ipynb

Viewing on GitHub

GitHub can render .ipynb files directly in the browser, so readers can view code and outputs without running them.

License

This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).