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NCBITaxonomy

Wrapper around the NCBI taxonomy files

https://github.com/poisotlab/ncbitaxonomy.jl

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.9%) to scientific vocabulary

Keywords

biodiversity biodiversity-data ivado ncbi ncbi-taxonomy taxonomy verena

Keywords from Contributors

interpretability standardization hack
Last synced: 9 months ago · JSON representation

Repository

Wrapper around the NCBI taxonomy files

Basic Info
Statistics
  • Stars: 7
  • Watchers: 4
  • Forks: 2
  • Open Issues: 2
  • Releases: 14
Topics
biodiversity biodiversity-data ivado ncbi ncbi-taxonomy taxonomy verena
Created over 5 years ago · Last pushed 11 months ago
Metadata Files
Readme Contributing License Code of conduct Zenodo

README.md

NCBI taxonomy

Project Status: Active – The project has reached a stable, usable state and is being actively developed. DOI

CI codecov

Documentation

This package provides an interface to the NCBI Taxonomy. When installed, it will download the latest version of the taxonomy files from the NCBI ftp service. To update the version of the taxonomy you use, you need to build the package again.

The package is registered in the Julia registry, and can be installed with

~~~ julia import Pkg; Pkg.add("NCBITaxonomy") ~~~

in the Julia REPL, or through

~~~ julia add NCBITaxonomy ~~~

in Julia's pkg mode.

Please note that the taxonomy dump is a big download. If the NCBITAXONOMY_PATH is not set, it will be stored in the package folder under the homedir() directory, which is a bad idea. We strongly recommend editing your configuration file, or exporting the NCBITAXONOMY_PATH environment variable.

This package is developed as part of the activities of the Viral Emergence Research Initiative (VERENA) consortium, with financial support from the Institut de Valorisation des Données (IVADO) at Université de Montréal.

Owner

  • Name: the Poisot lab
  • Login: PoisotLab
  • Kind: organization
  • Location: Montréal, Canada

Quantitative and Computational Ecology

GitHub Events

Total
  • Issues event: 2
  • Member event: 10
  • Issue comment event: 2
  • Push event: 5
Last Year
  • Issues event: 2
  • Member event: 10
  • Issue comment event: 2
  • Push event: 5

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 234
  • Total Committers: 2
  • Avg Commits per committer: 117.0
  • Development Distribution Score (DDS): 0.051
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Timothée Poisot t****t@u****a 222
github-actions[bot] 4****] 12
Committer Domains (Top 20 + Academic)
umontreal.ca: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 23
  • Total pull requests: 34
  • Average time to close issues: 2 months
  • Average time to close pull requests: 12 days
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 2.3
  • Average comments per pull request: 0.5
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 16
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 6 minutes
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • tpoisot (16)
  • cjcarlson (2)
  • gottacatchenall (1)
  • sahakyanhk (1)
  • diegozea (1)
  • Rekyt (1)
  • JuliaTagBot (1)
Pull Request Authors
  • tpoisot (17)
  • github-actions[bot] (16)
  • gabrieldansereau (1)
Top Labels
Issue Labels
enhancement (15) need-triage (8) in-progress (3) bug (2) documentation (2) question (1) unreplicable (1) breaking (1)
Pull Request Labels
performance (1)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 2 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 16
juliahub.com: NCBITaxonomy

Wrapper around the NCBI taxonomy files

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2 Total
Rankings
Dependent repos count: 9.9%
Forks count: 28.1%
Average: 29.8%
Dependent packages count: 38.9%
Stargazers count: 42.3%
Last synced: 9 months ago

Dependencies

.github/workflows/CI.yml actions
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.github/workflows/CompatHelper.yml actions
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.github/workflows/Documentation.yml actions
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.github/workflows/TagBot.yml actions
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.github/workflows/benchmark.yml actions
  • actions/checkout v2 composite
  • julia-actions/julia-buildpkg latest composite
  • julia-actions/setup-julia latest composite