Vitax is a web application for exploring and working with the NCBI Taxonomy in a visual way. It provides a user-friendly interface for searching and visualizing a wide range of taxonomic information in various formats.
One of its key features is direct access to genome accessions from within the visualization, which enables a visual interface for genomic analysis based on the taxonomy.
- 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.
- Suggestions: Quickly find any taxon of interest with autocomplete suggestions as you type.
- 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 space-efficient circle packing visualiztion, where taxa are represented as circles packed hierarchically.
- Find any taxon in the visualization from a hierarchical list.
- Get metadata for any taxon right from the visualization.
- Genome Accessions: Access genome accessions for any taxon in the visualization.
- 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.
A live demo of the application is available on the website of the Research Group for Bioinformatics.
- Enter a taxon name in the search box.
- Select a taxon from the suggestions list (or press Enter to select the entered taxon if it exists). Repeat for additional taxa.
- Choose a visualization type from the display type component.
- Press "Visualize" to generate the visualization.
Vitax is built in TypeScript, uses Vite as the build tool, and DaisyUI combined with TailwindCSS for styling. D3.js is used for creating the data visualizations.
To get started with Vitax, follow the steps below to set up the project on your local machine.
Ensure you have the following installed:
- Clone the repository:
git clone https://github.com/Tjorbenn/Vitax.git
cd Vitax- Install the dependencies:
npm installThe project uses a .env file for configuration. A default .env file is included in the repository.
To override these defaults locally, create a .env.local file in the root directory or modify the .env file:
cp .env .env.localStart the development server:
npm run devThe application will be available at http://localhost:5173.
Here are some common commands used during development:
-
Linting: Check for implementation errors and potential bugs.
npm run lint
To automatically fix linting issues:
npm run lint:fix
-
Formatting: Check if code adheres to the defined formatting style.
npm run format
To automatically format code:
npm run format:fix
To build the application for production:
npm run buildYou can preview the production build locally using:
npm run previewOr you can use your own web server of choice to serve the dist directory that is created when running npm run build.
This project is licensed under the MIT License. See the LICENSE file for more information.
Tjorben – @Tjorbenn
Project Link: https://github.com/Tjorbenn/Vitax