GBIF Metabarcoding Data Toolkit

This is the user interface for a tool that converts OTU/ASV tables in tsv and xlsx to BIOM format. The generated BIOM files can be converted to Darwin core and published to https://www.gbif.org/. It works on top of metabarcoding-data-toolkit-backend.

Overall idea

• Web-based interface/tool that lets researchers (or other) publish a Metabarcoding dataset to GBIF
• Minimal preparation/reformatting required
• Standardise and automate important steps to ensure interoperability with other datasets
• Compliance with community standards
• Include as many immediate benefits as long as they are easily implemented
• Prioritize fast and easy publication and online visibility (and later curation, correction) as opposed to a tedious publishing process with many steps and choices

Tecnical details

In the project directory, you can run:

npm start

Runs the app in the development mode.\ Open http://localhost:3000 to view it in your browser. The page will reload when you make changes.\ You may also see any lint errors in the console.\ In development mode, the backend service is configured in the .env file through the REACT_APP_API_URL variable.

npm test

Launches the test runner in the interactive watch mode.\ See the section about running tests for more information.

npm run build

Builds the app for production to the build folder.\ It correctly bundles React in production mode and optimizes the build for the best performance. To configure the the associated backend installation, set the environment variable REACT_APP_API_URL.

Example: REACT_APP_API_URL=http://localhost:9001 npm run build

The build is minified and the filenames include the hashes.\ Your app is ready to be deployed!

Deployment

This section has moved here: https://facebook.github.io/create-react-app/docs/deployment

npm run build fails to minify

This section has moved here: https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify

Funding

The development of this tool has received funding from the European Union's Horizon Europe research and innovation programme under grant agreement No 101057437 (BioDT project, https://doi.org/10.3030/101057437)