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klados

A curation tool to edit test cases for the Phyloref curation workflow

https://github.com/phyloref/klados

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 6 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 (7.0%) to scientific vocabulary
Last synced: 8 months ago · JSON representation ·

Repository

A curation tool to edit test cases for the Phyloref curation workflow

Basic Info
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 1
  • Open Issues: 64
  • Releases: 17
Created over 8 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

Klados

DOI

Klados allows users to curate phyloreferences side-by-side with the phylogenies they were originally defined on. The curated phylogenies are stored in the Phyx format, which can be downloaded as an OWL 2 ontology in the JSON-LD format. Phyx files can be incorporated into the Clade Ontology.

Citing Klados

You can currently cite Klados as:

Vaidya G, Becker A, Cellinese N, Lapp H (2023) Klados: a tool for authoring, testing and curating phyloreferences. GitHub: https://github.com/phyloref/klados DOI: 10.5281/zenodo.7103131

Project setup

npm install

Compiles and hot-reloads for development

npm run serve

Compiles and minifies for production

npm run build

This will store compiled files into the docs/ folder, allowing it to be immediately published on Github Pages.

Run your tests

npm run test

Lints and fixes files

npm run lint

Customize configuration

See Configuration Reference.

Owner

  • Name: Phyloreferencing
  • Login: phyloref
  • Kind: organization

Computable, persistent, and portable semantics for clades on the Tree of Life

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: "Klados: a tool for authoring, testing and curating phyloreferences"
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - orcid: 'https://orcid.org/0000-0003-0587-0454'
    given-names: Gaurav
    family-names: Vaidya
    affiliation: >-
      Renaissance Computing Institute, University of North
      Carolina, Chapel Hill, NC, USA
  - given-names: Anna
    family-names: Becker
    affiliation: >-
      Florida Museum of Natural History, University of
      Florida, Gainesville, FL, United States of America
  - given-names: Nico
    family-names: Cellinese
    orcid: 'https://orcid.org/0000-0002-7157-9414'
    affiliation: >-
      Florida Museum of Natural History and Informatics
      Institute, University of Florida, Gainesville, FL, USA
  - given-names: Hilmar
    family-names: Lapp
    orcid: 'https://orcid.org/0000-0001-9107-0714'
    affiliation: >-
      Department of Biostatistics and Bioinformatics, Duke
      University, Durham, NC, USA
doi: 10.5281/zenodo.7103131
identifiers:
  - type: doi
    value: 10.5281/zenodo.7103131
    description: Source code archived to Zenodo
repository-code: 'https://github.com/phyloref/klados'
url: 'https://phyloref.org/klados/'
repository: 'https://zenodo.org/record/7103132'
abstract: >-
  Tool for curating phyloreferences side-by-side with the phylogenies they were originally defined on. Phyloreferences
  and their accompanying phylogenies are stored in the Phyx format, which can be downloaded as an OWL 2 ontology in the
  JSON-LD format.
license: MIT

GitHub Events

Total
  • Create event: 21
  • Release event: 2
  • Issues event: 30
  • Delete event: 20
  • Issue comment event: 30
  • Push event: 87
  • Pull request review comment event: 12
  • Pull request review event: 35
  • Pull request event: 45
Last Year
  • Create event: 21
  • Release event: 2
  • Issues event: 30
  • Delete event: 20
  • Issue comment event: 30
  • Push event: 87
  • Pull request review comment event: 12
  • Pull request review event: 35
  • Pull request event: 45

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 17
  • Total pull requests: 25
  • Average time to close issues: over 2 years
  • Average time to close pull requests: 3 months
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 2.41
  • Average comments per pull request: 0.88
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 5
  • Pull requests: 22
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 1 month
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.2
  • Average comments per pull request: 0.45
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 9
View more stats
Top Authors
Issue Authors
  • gaurav (28)
  • hlapp (2)
Pull Request Authors
  • gaurav (24)
  • dependabot[bot] (12)
Top Labels
Issue Labels
programming only (8) bug (7) difficulty: easy (6) difficulty: moderate (6) documentation (3) discussion needed (2) user interface (2) testing (1) enhancement (1) priority: low (1) priority: high (1)
Pull Request Labels
dependencies (11) javascript (5)

Dependencies

package-lock.json npm
  • 1445 dependencies
package.json npm
  • @babel/cli ^7.10.5 development
  • @babel/core ^7.10.5 development
  • @babel/preset-env ^7.10.4 development
  • @vue/cli-plugin-babel ^3.12.1 development
  • @vue/cli-plugin-eslint ^3.12.1 development
  • @vue/cli-service ^3.12.1 development
  • @vue/test-utils ^1.0.3 development
  • babel-core ^7.0.0-bridge.0 development
  • babel-eslint ^10.1.0 development
  • babel-jest ^24.9.0 development
  • eslint ^5.16.0 development
  • eslint-config-airbnb-base ^13.2.0 development
  • eslint-plugin-import ^2.22.0 development
  • eslint-plugin-json ^1.4.0 development
  • eslint-plugin-mocha ^5.3.0 development
  • eslint-plugin-vue ^5.2.3 development
  • jest ^24.9.0 development
  • vue-jest ^3.0.6 development
  • vue-template-compiler ^2.6.11 development
  • @babel/plugin-transform-modules-commonjs ^7.10.4
  • @fortawesome/fontawesome-svg-core ^1.2.29
  • @fortawesome/free-solid-svg-icons ^5.13.1
  • @fortawesome/vue-fontawesome ^0.1.10
  • @phyloref/phyx ^1.0.1
  • bootstrap ^4.5.0
  • bootstrap-vue ^2.15.0
  • filesaver.js-npm ^1.0.1
  • jquery ^3.5.1
  • lodash ^4.17.19
  • newick-js ^1.1.1
  • popper.js ^1.16.1
  • vue ^2.6.11
  • vue-resize ^0.4.5
  • vuex ^3.5.1
  • x-hub-signature ^1.2.0
.github/workflows/deploy-to-github-pages.yml actions
  • JamesIves/github-pages-deploy-action v4 composite
  • actions/checkout v2 composite
.github/workflows/test-backend.yml actions
  • fjogeleit/http-request-action v1 composite