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legacy_annotation_tool

https://github.com/neurobagel/legacy_annotation_tool

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary

Keywords

fair-principles linked-data
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 8
  • Open Issues: 13
  • Releases: 5
Topics
fair-principles linked-data
Created about 4 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Legacy Annotation Tool

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


NOTE: This tool is currently undergoing a major refactor - some of the instructions below may be out of date with the public version of the tool at https://annotate.neurobagel.org. Please check back soon for updated documentation!

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

```bash

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

bash 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.

Owner

  • Name: Neurobagel
  • Login: neurobagel
  • Kind: organization

Citation (CITATION.cff) 

# doc: https://citation-file-format.github.io/
# schema: https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md

cff-version: 1.2.0

title: "neurobagel_annotation_tool"

version: 0.2.0

abstract: "The Neurobagel Annotation Tool is a web app, developed in JavaScript using [VueJS](https://vuejs.org/) and [Nuxt](https://nuxt.com/)."

message: "If you use this software, please cite it as below."

repository-code: "https://github.com/neurobagel/annotation_tool.git"

contact:
  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    family-names: Urchs
    given-names: Sebastian 

authors:
  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    family-names: Urchs
    given-names: Sebastian 
    orcid: "https://orcid.org/0000-0001-5504-8579"

  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    family-names: Dai
    given-names: Alyssa
    orcid: "https://orcid.org/0000-0003-0174-6800"

  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    family-names: Armoza
    given-names: Jonathan
    orcid: "https://orcid.org/0000-0002-7193-9344"

  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    family-names: Jahanpour
    given-names: Arman    

  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    email:  nikhil.bhagwat@mcgill.ca
    family-names: Bhagwat
    given-names: Nikhil
    orcid: "https://orcid.org/0000-0001-6073-7141"

  - affiliation: "ORIGAMI lab, McGill University, Montréal, Canada"
    family-names: Poline
    given-names: Jean-Baptiste
    orcid: "https://orcid.org/0000-0002-9794-749X"    

license: MIT

GitHub Events

Total
  • Create event: 21
  • Release event: 2
  • Issues event: 9
  • Delete event: 21
  • Issue comment event: 56
  • Push event: 36
  • Pull request review event: 21
  • Pull request review comment event: 3
  • Pull request event: 46
Last Year
  • Create event: 21
  • Release event: 2
  • Issues event: 9
  • Delete event: 21
  • Issue comment event: 56
  • Push event: 36
  • Pull request review event: 21
  • Pull request review comment event: 3
  • Pull request event: 46

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 6
  • Total pull requests: 29
  • Average time to close issues: 3 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 1.83
  • Average comments per pull request: 1.93
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 24
Past Year
  • Issues: 5
  • Pull requests: 29
  • Average time to close issues: 22 days
  • Average time to close pull requests: 9 days
  • Issue authors: 2
  • Pull request authors: 4
  • Average comments per issue: 1.0
  • Average comments per pull request: 1.93
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 24
View more stats
Top Authors
Issue Authors
  • surchs (4)
  • alyssadai (1)
Pull Request Authors
  • dependabot[bot] (21)
  • surchs (3)
  • neurobagel-bot[bot] (2)
  • alyssadai (2)
Top Labels
Issue Labels
usability (1) severity:blocker (1) dependencies (1) github_actions (1) flag:blocker (1) _flag:stale (1) tests (1)
Pull Request Labels
_bot (22) dependencies (20) pr-patch (1)

Dependencies

.github/workflows/add_iss2project.yml actions
  • actions/add-to-project main composite
.github/workflows/add_pr2project.yml actions
  • actions/add-to-project main composite
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.github/workflows/cd.yaml actions
  • actions/checkout v4 composite
  • actions/setup-node v3.8.1 composite
  • peaceiris/actions-gh-pages v3 composite
.github/workflows/codespell.yml actions
  • actions/checkout v4 composite
  • codespell-project/actions-codespell v2 composite
.github/workflows/lint.yaml actions
  • actions/checkout v4 composite
.github/workflows/stale.yml actions
  • actions/stale v8 composite
.github/workflows/test_component.yml actions
  • actions/checkout v4 composite
  • cypress-io/github-action v6 composite
.github/workflows/test_e2e.yml actions
  • actions/checkout v4 composite
  • actions/setup-node v3.8.1 composite
  • cypress-io/github-action v6 composite
package-lock.json npm
  • 1361 dependencies
package.json npm
  • cy-verify-downloads ^0.1.17 development
  • cypress ^13.1.0 development
  • editorconfig ^2.0.0 development
  • eslint ^8.49.0 development
  • eslint-config-airbnb ^19.0.4 development
  • eslint-config-prettier ^9.0.0 development
  • eslint-plugin-cypress ^2.14.0 development
  • eslint-plugin-prettier ^4.2.1 development
  • eslint-plugin-vue ^9.17.0 development
  • husky ^8.0.3 development
  • lint-staged ^14.0.1 development
  • push-dir ^0.4.1 development
  • @nuxtjs/axios ^5.13.6
  • bootstrap ^4.6.1
  • bootstrap-vue ^2.23.1
  • core-js ^3.32.2
  • file-saver ^2.0.5
  • fs ^0.0.1-security
  • nuxt ^2.17.1
  • papaparse ^5.4.1
  • uuid ^9.0.0
  • vue ^2.6.14
  • vue-select ^3.20.2
  • vue-server-renderer ^2.6.14
  • vue-template-compiler ^2.6.14
  • webpack ^4.47.0