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@phyloref/phyx

Phyloreference Exchange (Phyx) library in JavaScript

https://github.com/phyloref/phyx.js

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
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary

Keywords

nodejs phyloreferencing

Keywords from Contributors

mesh sequences interactive hacking network-simulation
Last synced: 4 months ago · JSON representation ·

Repository

Phyloreference Exchange (Phyx) library in JavaScript

Basic Info
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 31
  • Releases: 5
Topics
nodejs phyloreferencing
Created almost 7 years ago · Last pushed 5 months ago
Metadata Files
Readme Changelog License Citation

README.md

phyx.js

Build Status DOI NPM Version

The Phyloreference Exchange (PHYX) format is a JSON representation that can be used to store and transfer definitions of phyloreferences. This library provides classes to help interpret some parts of these files, and for transforming an entire Phyx file into a JSON-LD representation that can be reasoned over with an OWL 2 DL reasoner. See the Phyloreference Curation Tool or the Clade Ontology for examples of its usage.

Usage

You can install phyx.js using npm:

shell $ npm install @phyloref/phyx

Tutorials demonstrating the use of phyx.js are available.

Citation

phyx.js should be cited by citing our publication documenting the Phyx format and phyx.js.

Vaidya G, Cellinese N, Lapp H. 2022. A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx) PeerJ 10:e12618 doi:10.7717/peerj.12618

Funding

Funded by the US National Science Foundation through collaborative grants DBI-1458484 and DBI-1458604. See Funding for details.

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: phyx.js
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - family-names: Vaidya
    given-names: Gaurav
    orcid: 'https://orcid.org/0000-0003-0587-0454'
  - family-names: Lapp
    given-names: Hilmar
    orcid: 'https://orcid.org/0000-0001-9107-0714'
identifiers:
  - type: doi
    value: 10.5281/zenodo.5576556
    description: >-
      This DOI will always resolve to the latest version of
      phyx.js.
  - type: doi
    value: 10.5281/zenodo.15086850
    description: The versioned DOI for version 1.2.0 of phyx.js.
repository-code: 'https://github.com/phyloref/phyx.js'
url: 'https://github.com/phyloref/phyx.js'
repository-artifact: 'https://www.npmjs.com/package/@phyloref/phyx'
license: MIT
version: v1.2.0
date-released: '2025-03-26'
preferred-citation:
  authors:
    - family-names: Vaidya
      given-names: Gaurav
      orcid: 'https://orcid.org/0000-0003-0587-0454'
    - family-names: Cellinese
      given-names: Nico
      orcid: 'https://orcid.org/0000-0002-7157-9414'
    - family-names: Lapp
      given-names: Hilmar
      orcid: 'https://orcid.org/0000-0001-9107-0714'
  title: >-
    A new phylogenetic data standard for computable clade definitions: the
    Phyloreference Exchange Format (Phyx)
  type: article
  doi: 10.7717/peerj.12618
  date-released: '2022-02-15'

GitHub Events

Total
  • Create event: 6
  • Release event: 1
  • Issues event: 3
  • Delete event: 4
  • Issue comment event: 2
  • Push event: 18
  • Pull request review event: 4
  • Pull request event: 6
Last Year
  • Create event: 6
  • Release event: 1
  • Issues event: 3
  • Delete event: 4
  • Issue comment event: 2
  • Push event: 18
  • Pull request review event: 4
  • Pull request event: 6

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 652
  • Total Committers: 4
  • Avg Commits per committer: 163.0
  • Development Distribution Score (DDS): 0.284
Past Year
  • Commits: 30
  • Committers: 1
  • Avg Commits per committer: 30.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Gaurav Vaidya g****v@g****m 467
Gaurav Vaidya g****v@r****g 180
dependabot[bot] 4****] 4
Hilmar Lapp h****p@d****t 1
Committer Domains (Top 20 + Academic)
drycafe.net: 1 renci.org: 1 ggvaidya.com: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time
  • Total issues: 45
  • Total pull requests: 75
  • Average time to close issues: about 1 year
  • Average time to close pull requests: about 2 months
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 1.18
  • Average comments per pull request: 0.81
  • Merged pull requests: 58
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: 3 months
  • Average time to close pull requests: 6 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gaurav (42)
  • hlapp (3)
Pull Request Authors
  • gaurav (74)
  • dependabot[bot] (6)
  • hlapp (1)
Top Labels
Issue Labels
programming only (10) Phyx context issues (3) enhancement (1) testing (1)
Pull Request Labels
dependencies (6)

Packages

  • Total packages: 1
  • Total downloads:
    • npm 25 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 3
  • Total versions: 14
  • Total maintainers: 2
npmjs.org: @phyloref/phyx

Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files

  • Versions: 14
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 25 Last month
Rankings
Dependent repos count: 6.4%
Forks count: 15.5%
Average: 17.3%
Stargazers count: 21.1%
Dependent packages count: 21.1%
Downloads: 22.5%
Maintainers (2)
hlapp mrvaidya
Last synced: 5 months ago

Dependencies

package-lock.json npm
  • 466 dependencies
package.json npm
  • ajv ^6.12.2 development
  • chai ^4.2.0 development
  • esdoc ^1.1.0 development
  • esdoc-node ^1.0.5 development
  • esdoc-standard-plugin ^1.0.0 development
  • eslint ^5.16.0 development
  • eslint-config-airbnb-base ^13.2.0 development
  • eslint-plugin-import ^2.22.1 development
  • eslint-plugin-json-format ^2.0.1 development
  • eslint-plugin-mocha ^5.3.0 development
  • mocha ^5.2.0 development
  • nodejs-file-downloader ^4.1.1 development
  • yargs ^15.3.1 development
  • jsonld ^5.0.0
  • lodash ^4.17.20
  • moment ^2.27.0
  • newick-js ^1.1.1
  • retus ^1.1.1
  • yargs ^15.4.1
every-topology-testing/validate-trees.py/requirements.txt pypi
  • dendropy * test
.github/workflows/tests.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-node v1 composite