Update (Feb 2026): ChEBI 2.0 currently lacks entry-page cross-references (e.g., UniProt). Use these notebooks and watch this video for data retrieval workarounds.
About This Essential Guide
📚 Book Editions & Learning Resources
Available Editions
Portuguese Edition
2020
Additional Learning Materials
- Book slides (Jul 2024) – Use for lectures and workshops
- Workbook (July 2023) – Comprehensive exercises with detailed answers for hands-on practice
- File Archive (July 2023) – Includes the scripts, data files, text resources, and ontology files
Getting Started with Hands-On Practice
Interactive Tutorials (No Setup Required)
Try Examples Instantly at sandbox.bio
sandbox.bio lets you run all book examples directly in your browser. Whether you're on Mac, Windows, or Linux, no installation needed. Perfect for beginners or anyone who wants to test commands before setting up locally.
Try Interactive Tutorials Now →Interactive Jupyter Notebooks (includes fix for ChEBI 2.0)
Prefer a notebook environment? Access our collection of Jupyter notebooks on GitHub. These provide a structured way to walk through data and text processing workflows step-by-step.
View Notebooks on GitHub →Video Tutorials & Setup
- Video Tutorials Playlist - Watch demonstrations and explanations of all key concepts
- MobaXterm for Windows (Nov 2024) - Dedicated tutorial for Windows users to set up command-line environment
Verify Your Local Shell Environment
Download the Test Script ZIP and follow these commands to verify your shell setup has all necessary components:
wget http://labs.rd.ciencias.ulisboa.pt/book/testshell20230712.zip
unzip testshell20230712.zip
./testshell.shThis verification script ensures your environment is properly configured for all book examples and exercises.
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