Vitax

Visualizing the NCBI Taxonomy

Introduction

Vitax is an intuitive web application designed for scientists, researchers, and students alike who need to explore and understand the complex relationships between biological taxa. The application provides a user-friendly interface for searching and visualizing a wide range of taxonomic information in various formats.

Features

• Multiple types of relationships / taxonomic data: Investigate different types of taxonomic relationships, including:

  • Neighbors: Displays the the taxonomic neighbors of a group of target taxa.
  • Descendants: Shows the descendants of a taxon.
  • Most Recent Common Ancestor (MRCA): Shows the most recent common ancestor of a group of target taxa and their connecting lineage.

• Interactive Visualizations: Explore taxonomic relationships through a variety of interactive visualizations, including:

  • Tree: A classic hierarchical view of the taxonomic tree.
  • Graph: A network graph that shows the relationships between taxa.
  • Pack: A visualization that packs taxa into a circle.
  • When a taxon is focused via the list, the visualization briefly highlights the node with a subtle pulse effect to help locate it.

• Powerful Search: Quickly find any taxon of interest with the powerful search functionality.

• Suggestions: Get suggestions as you type to help you find the right taxon.

• Data Sources:

  • Never API: Vitax uses the Never API to provide the taxonomic relationship as well as taxonomic metadata. The Never API is a custom API developed by the Research Group for Bioinformatics of the Max-Planck-Institute for Evolutionary Biology that provides access to the taxonomic data from the NCBI Taxonomy.
  • NCBI Taxonomy: Vitax uses the NCBI Taxonomy API to add additional metadata. This includes images as well as links to external resources.
  • SemanticScholar: Vitax uses the SemanticScholar API to add publication data to taxa.

Live Demo

A live demo of the application is available on the website of the Research Group for Bioinformatics.

Getting Started

To get started with Vitax, you will need to have Node.js and npm installed on your machine.

1. Clone the repository:

git clone https://github.com/Tjorbenn/Vitax.git

2. Install the dependencies:

cd Vitax
npm install

3. Run the application:

npm run dev

4. Build the application for production:

npm run build

The application will be available at http://localhost:5173.

Usage

1. Enter a taxon name in the search box.
2. Select a taxon from the suggestions list (or press Enter to search for the entered name).
3. Choose a visualization type from the display type component.
4. The visualization will be displayed in the visualization component.

Architecture

Vitax is built in TypeScript, uses Vite as the build tool, and TailwindCSS for styling. D3.js is used for creating the data visualizations.

Built With

• TypeScript
• Vite
• DaisyUI
• TailwindCSS
• D3.js

License

This project is licensed under the MIT License. See the LICENSE file for more information.

Contact

Tjorben – @Tjorbenn

Project Link: https://github.com/Tjorbenn/Vitax