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neurobagel / annotation_tool

https://annotate.neurobagel.org/
MIT License
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Annotation Tool

deployed app component test e2e test Node Nuxt Vue GitHub license Zenodo DOI


Neurobagel's annotation tool takes BIDS-style phenotypic data and corresponding data description files and gives users the ability to annotate their data using the Neurobagel data model for preparation to inject that modeled data into Neurobagel's graph database for federated querying.

The annotation tool is a Vue application, developed in JavaScript using a variety of tools including Nuxt, Cypress, and BootstrapVue.

Please refer to our official documentation for more information on how to use the annotation tool.

Quickstart | Documentation | Local Installation | Workflow | Testing | License

Quickstart

The latest (stable) version of the annotation tool is hosted at https://annotate.neurobagel.org/.

The nightly (unstable) version of the annotation tool is hosted at https://neurobagel-annotator.netlify.app/.

Local Installation

Building and running

# Install dependencies
$ npm install

# Serve with hot reload at localhost:3000
$ npm run dev

# Build for production and launch server
$ npm run build
$ npm run start

# Generate static project
$ npm run generate

Deployment

To deploy the static build on GH pages, run

npm run generate
npm run deploy

See the Nuxt documentation for more details.

Workflow

  1. Upload data table (and/or data dictionary)
  2. Link columns you want annotated with Neurobagel metadata categories
  3. Annotate the values of the those categirzed columns
  4. Download an annotated version of a BIDS-style data dictionary for your dataset

There are two means of moving forward to the next step in the annotation tool's workflow: (1) the navbar at the top right of the screen which features the page names, and (2) the next page buttons on the bottom right of each page.

Certain criteria for each page need to be be met in order to move forward. Instructions are offered above the next page button. Once the criteria have been met navbar and next page button will turn from gray to green.

Testing

The Annotation tool uses Cypress for integration, component, and unit testing. See the cypress folder for tests, custom commands, and test data.

License

The Neurobagel Annotation tool uses the MIT License.