EMO-BON Data Workflow Handbook

A comprehensive reference to our EMO-BON data workflow, covering naming conventions, workflow descriptions, URI namespace documentation, glossary terms, and DevOps guidelines.

About

This handbook provides documentation for the EMO-BON (European Marine Omics Biodiversity Observation Network) data workflow, including:

• Data management processes and workflows
• Data sources and products
• Technical infrastructure and components
• Standards and conventions
• Glossary of terms and concepts

Viewing the Book

The published book is available at: https://data.emobon.embrc.eu/data-workflow-book/

Building Locally

To build and view the book locally:

Prerequisites

• Python 3.11+
• Node.js 18+

Setup

1. Clone the repository:

git clone https://github.com/emo-bon/data-workflow-book.git
cd data-workflow-book

2. Install Python dependencies:

pip install -r requirements.txt

3. Install MyST Markdown:

npm install -g mystmd

Build

Build the book:

cd book
myst build --html

The built HTML will be in book/_build/html/.

Preview

Start a local server to preview:

cd book
myst start

Then open your browser to the URL shown (typically http://localhost:3000).

Contributing

Contributions are welcome! To contribute:

1. Fork the repository
2. Create a feature branch
3. Make your changes in the book/ directory
4. Test your changes locally
5. Submit a pull request

Structure

data-workflow-book/
├── book/                    # MyST book source
│   ├── myst.yml            # Book configuration
│   ├── index.md            # Book homepage
│   ├── 01-introduction/    # Chapter 1
│   ├── 02-data-management-flow/
│   ├── 03-data-sources/
│   ├── 04-data-products/
│   ├── 05-data-graph/
│   ├── 06-conformance/
│   ├── 07-technical-details/
│   ├── 08-addendum/
│   └── 09-data-paper/
├── .github/workflows/      # GitHub Actions
├── requirements.txt        # Python dependencies
├── CNAME                   # Custom domain
└── README.md              # This file

Technology

This book is built with:

• MyST Markdown - Modern, extensible markdown for scientific content
• GitHub Actions - Automated building and deployment
• GitHub Pages - Static site hosting

License

The content of this handbook is licensed under CC-BY-4.0.

Contact

• Email: opsci@vliz.be
• GitHub: EMO-BON organization