TaxonomyTools

A suite of desktop applications for working with iNaturalist taxonomy data. This project includes two powerful tools:

• TaxonomyDict: Generate translation dictionaries from taxonomy data in TSV and StarDict formats
• TaxonomyTree: Visualize and compare taxonomic relationships with interactive family tree diagrams

🤖 AI-Generated Project

This project was intentionally generated entirely by Claude AI with zero human code editing. This was created as a learning exercise to explore the capabilities of AI-assisted software development and to demonstrate how complex, fully-functional applications can be built through AI collaboration.

Project Genesis

• 100% AI-Generated Code: Every line of code, from GUI layout to data processing algorithms
• Zero Human Editing: No manual code modifications were made by humans
• Learning Path: Developed as an exploration of Claude AI's software development capabilities
• Modern C++ & wxWidgets: Demonstrates AI's ability to work with complex frameworks and libraries

This project serves as a case study in AI-human collaboration for software development, showcasing what's possible when leveraging AI tools effectively.

Features

TaxonomyDict - Dictionary Generator

• Download & Process: Automatically download and extract iNaturalist taxonomy data
• Multi-Language Support: Generate dictionaries between any supported languages
• Scientific Names: Include scientific nomenclature in translations
• Multiple Output Formats: Export as TSV (tab-separated) or StarDict dictionary files
• Language Information: Translations include source language tags in italics for clarity
• Advanced Filtering: Filter entries to include only terms with target language translations
• Progress Tracking: Real-time progress indicators for all operations
• User-Friendly Interface: Clean, intuitive GUI with search functionality

TaxonomyTree - Family Tree Visualizer

• Interactive Visualization: Display taxonomic relationships in fan, vertical, or horizontal tree layouts
• Species Comparison: Add multiple species to compare their evolutionary relationships
• Multi-Language Display: View taxa names in primary and secondary languages simultaneously
• Common Ancestor Analysis: Automatically find and display common ancestors of selected species
• Full Tree Mode: Option to show complete taxonomic tree up to kingdom level
• Export Capabilities: Save trees as SVG vector graphics or high-resolution PNG images
• Zoom & Pan: Smooth zoom controls and drag-to-pan navigation
• Search Functionality: Quick incremental search across all taxa in selected languages

Screenshots

TaxonomyDict Interface

The main application window showing the intuitive interface with language selection, filtering options, and progress tracking.

Dictionary in Action

Example of a generated StarDict dictionary being used in GoldenDict, showing formatted translations with language tags and scientific names.

TaxonomyTree Interface

Interactive taxonomic family tree viewer showing species relationships with multi-language support and various layout options.

System Requirements

• Operating System:
  • Linux (Ubuntu 20.04+ recommended) - Built and tested
  • Windows - Cross-platform ready but untested by developer
• Dependencies:
  • wxWidgets 3.0+
  • libcurl4-openssl-dev (Linux) / libcurl (Windows)
  • libzip-dev (Linux) / libzip (Windows)
  • CMake 3.10+
  • GCC with C++20 support (Linux) / MSVC 2019+ (Windows)

Installation

Note: This project has been built and tested exclusively on Linux. While the codebase uses cross-platform libraries (wxWidgets, libcurl, libzip) and should be compatible with Windows, it has not been tested on Windows by the developer.

Dependencies (Ubuntu/Debian)

sudo apt update
sudo apt install build-essential cmake
sudo apt install libwxgtk3.0-gtk3-dev libcurl4-openssl-dev libzip-dev

Building from Source

git clone <repository-url>
cd TaxonomyTools
mkdir build && cd build
cmake ..
make

This will build both applications.

Running the Applications

# Launch the dictionary generator
./build/TaxonomyDict

# Launch the tree visualizer
./build/TaxonomyTree

You can also build individual applications:

# Build only TaxonomyDict
cmake -DBUILD_TAXONOMY_TREE=OFF ..
make

# Build only TaxonomyTree
cmake -DBUILD_TAXONOMY_DICT=OFF ..
make

User Guide

TaxonomyDict User Guide

1. Getting Started

Download Taxonomy Data

1. Enter Data URL: Paste the iNaturalist taxonomy data URL in the download field
   • Default URL: https://www.inaturalist.org/taxa/inaturalist-taxonomy.zip
2. Click "Download": Choose where to save the ZIP file
3. Wait for Download: Progress bar shows download status
4. Load Archive: Use "Load Existing Archive" to process the downloaded file

Load Existing Archive

• Click "Load Existing Archive": Browse and select a previously downloaded taxonomy ZIP file
• Processing: The application extracts and indexes the taxonomy data
• Language Detection: Available languages are automatically detected and populated

2. Dictionary Configuration

Source Language Selection

• Choose Source Language: Select from the dropdown list of available languages
• Scientific Names: Use "Scientific Name" as source for scientific → vernacular dictionaries
• Search Functionality: Type to quickly find languages in the list

Target Languages Selection

• Multiple Selection: Check one or more target languages from the list
• Search Support: Type to filter and find languages quickly
• Mix and Match: Combine multiple vernacular languages with scientific names

Advanced Options

• Include Scientific Names: ☑️ Add scientific nomenclature to all entries
• Filter Only Targets: ☑️ Include only terms that have translations in selected target languages
  • Unchecked: Include all source terms (some may only have scientific names)
  • Checked: Include only terms with actual target language translations

3. Dictionary Generation

Output Configuration

1. Set Output Directory: Click "Browse" to choose where dictionaries will be saved
2. File Naming: Files are automatically named as taxonomy_[source-language]_dictionary

Generate Dictionary

1. Click "Generate Dictionary": Starts the generation process
2. Progress Tracking: Monitor progress through the status bar and progress indicator
3. Output Files: Two formats are generated simultaneously:
   • TSV File: taxonomy_[source]_dictionary.tsv - Tab-separated format
   • StarDict Files: .dict, .idx, .ifo - StarDict dictionary format

4. Dictionary Formats

TSV Format

• Structure: Source Term[TAB]Translations
• Translations: Multiple translations separated by <br> tags
• Language Tags: Each translation includes language in italics: translation <i>(language)</i>
• URLs: Reference URLs separated with double line breaks for visual clarity

StarDict Format

• Compatible: Works with StarDict, GoldenDict, and other dictionary applications
• Metadata: Includes source/target language information in dictionary properties
• HTML Formatting: Supports rich text formatting with language tags

5. Example Usage Scenarios

English → Multiple Languages

• Source: English
• Targets: Spanish, French, German
• Include Scientific: ☑️
• Result: English terms with translations in all selected languages plus scientific names

Scientific → Vernacular

• Source: Scientific Name
• Targets: English, Spanish
• Filter Only Targets: ☑️
• Result: Only scientific names that have vernacular translations in English or Spanish

Comprehensive Dictionary

• Source: English
• Targets: All available languages
• Include Scientific: ☑️
• Filter Only Targets: ☐
• Result: Complete dictionary with all available translations

6. Language Information Display

Translations are formatted with clear language indicators:

• Format: translation <i>(language)</i>
• Example: Wolf <i>(English)</i>, Lobo <i>(Spanish)</i>, Loup <i>(French)</i>
• Scientific Names: Clearly marked as <i>(Scientific Name)</i>
• URLs: Separated for easy identification of reference links

7. Performance Tips

• Large Datasets: Processing complete taxonomy data may take several minutes
• Filtered Results: Use "Filter Only Targets" for faster processing and smaller files
• Language Selection: Limit target languages for faster generation if not all are needed
• Progress Monitoring: All operations show real-time progress and can be monitored

8. File Management

Generated Files

• TSV: Human-readable, spreadsheet-compatible format
• StarDict: Professional dictionary application format
• Metadata: Dictionary properties include language information and generation date

File Locations

• Default Output: User-selected directory
• Naming Convention: Consistent naming based on source language
• File Sizes: Vary based on language coverage and filtering options

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TaxonomyTree User Guide

1. Getting Started

Download or Load Taxonomy Data

1. Download Data: Use File → Download Taxonomy Data (Ctrl+D)
   • Downloads the latest iNaturalist taxonomy archive
   • Shows progress during download
2. Load Archive: Use File → Load Archive (Ctrl+O)
   • Browse and select a taxonomy ZIP file
   • Wait for processing and language detection

2. Language Configuration

Primary Language Selection

• Choose Primary: Select the main display language from the dropdown
• Autocomplete: Type to quickly find languages
• Search Index: Changes rebuild the search index for the selected language

Secondary Language (Optional)

• Add Secondary: Select an additional language for bilingual display
• None Option: Select "(None)" to show only primary language
• Dual Display: Both languages appear on tree nodes when secondary is selected

3. Finding and Adding Species

Search Taxa

1. Type Search Term: Enter at least 3 characters in the search box
2. View Results: Search results appear automatically with scientific names in parentheses
3. Add to Compare List: Double-click any result to add it to the comparison list

Compare List Management

• View Selected: All selected species appear in the compare list
• Remove Species: Double-click any item in the compare list to remove it
• Clear All: Click "Clear List" button to remove all species at once

4. Tree Visualization

Layout Options

• Fan Layout (Ctrl+1): Circular/radial tree spreading from center
• Vertical Layout (Ctrl+2): Traditional top-to-bottom tree
• Horizontal Layout (Ctrl+3): Left-to-right tree layout

Display Options

• Show Boxes (Ctrl+B): Toggle rectangular boxes around node labels
• Show Full Tree (Ctrl+F): Display complete ancestry up to kingdom level
  • Unchecked: Shows only common ancestor relationships
  • Checked: Extends tree to include all taxonomic levels to kingdom

Navigation Controls

• Zoom In (Ctrl+= or Ctrl+Numpad+): Increase tree size
• Zoom Out (Ctrl+- or Ctrl+Numpad-): Decrease tree size
• Reset Zoom (Ctrl+0 or Ctrl+Numpad0): Return to 100% zoom
• Mouse Wheel: Hold Ctrl and scroll to zoom
• Drag to Pan: Click and drag to move the tree view
• Scroll Bars: Use scrollbars for precise navigation

5. Exporting Trees

Export to SVG

1. Select: File → Export to SVG (Ctrl+S) (NOTE: Fan layout cannot be exported to SVG, it reverts to 300 dpi PNG)
2. Choose Location: Select save location and filename
3. Vector Format: Produces scalable vector graphics perfect for publications

Export to PNG

1. Select: File → Export to PNG (Ctrl+P)
2. Set DPI: Enter desired resolution (70-600 DPI)
   • 150 DPI: Standard screen resolution
   • 300 DPI: Print quality
   • 600 DPI: High-quality publications
3. Raster Format: Produces pixel-based images at specified resolution

6. Understanding the Tree Display

Node Information

• Primary Name: Displayed in the selected primary language
• Secondary Name: Shown below in secondary language (if selected)
• Scientific Names: Always available when hovering or in scientific name mode
• Taxonomic Rank: Indicated by node position and styling

Tree Structure

• Common Ancestors: Automatically calculated and displayed
• Branch Lines: Connect related taxa showing evolutionary relationships
• Terminal Nodes: Selected species appear at the tree endpoints
• Internal Nodes: Common ancestors and intermediate taxonomic ranks

7. Example Usage Scenarios

Compare Similar Species

• Purpose: Understand how closely related different species are
• Example: Compare Wolf, Dog, Fox to see Canidae family relationships
• Result: Visual tree showing common ancestors and divergence points

Multi-Language Learning

• Purpose: Learn species names in multiple languages
• Example: Primary=English, Secondary=Spanish
• Result: See both English and Spanish names on all nodes

Full Taxonomic Context

• Purpose: Understand complete classification hierarchy
• Example: Add any species, enable "Show Full Tree"
• Result: Complete tree from Kingdom to Species

Publication Graphics

• Purpose: Create high-quality figures for papers
• Example: Configure tree, export as SVG at high DPI
• Result: Publication-ready vector graphics with perfect scaling

8. Performance Tips

• Language Indexing: Initial language selection may take a few seconds for large datasets
• Search Response: Search results appear with slight delay for smooth typing
• Tree Complexity: More species = more complex tree calculations
• Export Quality: Higher DPI = larger file sizes and longer export times
• Full Tree Mode: Enabling full tree significantly increases tree size and complexity

9. Keyboard Shortcuts

File Operations

• Ctrl+D: Download taxonomy data
• Ctrl+O: Load archive
• Ctrl+S: Export to SVG
• Ctrl+P: Export to PNG
• Ctrl+Q: Exit application

View Controls

• Ctrl+1: Fan layout
• Ctrl+2: Vertical layout
• Ctrl+3: Horizontal layout
• Ctrl+B: Toggle boxes
• Ctrl+F: Toggle full tree

Zoom Controls

• Ctrl+=: Zoom in
• Ctrl+-: Zoom out
• Ctrl+0: Reset zoom
• Ctrl+Wheel: Smooth zoom

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Technical Details

Architecture

Common Components

• GUI Framework: wxWidgets for cross-platform desktop interface
• Threading: Multi-threaded design for responsive UI during operations
• Data Processing: CSV parsing with efficient memory management
• Network: libcurl for reliable data downloading
• Compression: libzip for archive handling

TaxonomyDict Specifics

• Dictionary Formats: TSV and StarDict generation engines
• Text Processing: HTML markup and formatting for rich text display
• Multi-target Support: Efficient handling of multiple target languages

TaxonomyTree Specifics

• Tree Algorithms: Efficient common ancestor finding and tree construction
• Search Indexing: Fast multi-language search with autocomplete
• Rendering Engine: Custom vector graphics rendering for tree layouts
• Export Formats: SVG vector and PNG raster image generation
• Zoom & Pan: Smooth interactive navigation with hardware acceleration

Data Sources

• Primary: iNaturalist taxonomy database
• Format: CSV files within ZIP archives
• Languages: 50+ supported vernacular languages
• Coverage: Comprehensive taxonomic data across biological kingdoms

Dictionary Quality

• Source Accuracy: Data sourced from iNaturalist's curated taxonomy
• Language Tags: Clear identification of translation languages
• Reference Links: Direct links to iNaturalist species pages
• Formatting: HTML-compatible markup for rich text display

Contributing

As this is an AI-generated project showcasing Claude AI capabilities, contributions should focus on:

• Testing and bug reports
• Documentation improvements
• Feature suggestions
• Use case examples

License

This project is licensed under the MIT License - see the LICENSE file for details.

This unique project demonstrates AI-generated software capabilities through AI-human collaboration:

• AI Prompting & Direction: Darau, Blė
• Icon Design: Darau, Blė
• Code Generation & Implementation: Claude AI (Anthropic)

Acknowledgments

• iNaturalist: For providing comprehensive taxonomy data
• Claude AI: For generating 90% of the codebase
• wxWidgets Community: For the excellent cross-platform GUI framework
• Open Source Community: For the foundational libraries used

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This README and 90% of the project were generated by Claude AI as part of an exploration into AI-assisted software development capabilities.

Copyright to AI prompting: Darau, Blė.