Biotope Tutorials

Welcome to the Biotope tutorials! This guide will help you understand how to work with Biotope for metadata annotation.

Workflow Overview

Biotope supports multiple workflows for managing your data and metadata:

Git-Integrated Workflow (Recommended)

graph LR
    subgraph "biotope init workflow"
        direction TB
        A[Start] --> B[Initialize Project]
        B --> C[Set Project Metadata]
        C --> D[Configure Validation]
    end

    subgraph "biotope add/get workflow"
        direction TB
        E[Add or Download Files] --> F[Calculate SHA256 Hash]
        F --> G[Create Basic Metadata]
        G --> H[Stage in Git]

        subgraph "Enhanced Metadata"
            direction TB
            H --> I[Interactive Annotation]
            I --> J[Pre-filled with Project Metadata]
            J --> K[Complete Metadata]
        end

        K --> L[Commit Changes]
        L --> M[Share with Team]
    end

Workflow Description

The enhanced biotope workflow now includes project-level metadata management:

1. Initialize Project: Use biotope init to set up your project with optional project metadata
2. Set Project Metadata: Configure project-level metadata (description, URL, creator, license, citation) for annotation pre-filling
3. Add or Download Files: Add local files with biotope add or download remote files with biotope get
4. Calculate SHA256 Hash: Generate checksums for data integrity
5. Create Basic Metadata: Automatically generate initial Croissant ML metadata
6. Stage in Git: Prepare metadata changes for version control
7. Enhanced Metadata: Use biotope annotate to add detailed metadata with project metadata pre-fill
8. Commit Changes: Save metadata changes with Git
9. Share with Team: Use standard Git workflows for collaboration

Getting Started

For Local Files (Recommended)

To get started with local files, use the Git-integrated workflow:

# Initialize project with project metadata
biotope init

# Add local data files
biotope add data/raw/experiment.csv

# Annotate with project metadata pre-fill
biotope annotate interactive --staged

# Commit changes
biotope commit -m "Add experiment dataset"

For Downloaded Files

To get started with downloaded files, use the download workflow:

# Initialize project (if not already done)
biotope init

# Download and stage files
biotope get https://example.com/data/file.csv

# Check status
biotope status

# Annotate with project metadata pre-fill
biotope annotate interactive --staged

# Commit changes
biotope commit -m "Add downloaded dataset"

Project Metadata Management

Set up project-level metadata for consistent annotation:

# Set project metadata during init or later
biotope config set-project-metadata

# View current project metadata
biotope config show-project-metadata

# Use in annotation (automatically pre-filled)
biotope annotate interactive --staged

Tutorials

For detailed information about each workflow, please refer to the specific tutorial pages:

• Adding Files: Learn how to add local files to your biotope project
• Downloading Files: Learn how to download and annotate files from URLs
• Annotating Data: Learn how to create detailed metadata for your data with project metadata pre-fill