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

Wrapper around the NCBI taxonomy files
https://github.com/poisotlab/ncbitaxonomy.jl

biodiversity biodiversity-data ivado ncbi ncbi-taxonomy taxonomy verena

Last synced: 8 months ago
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Wrapper around the NCBI taxonomy files

• Host: GitHub
• URL: https://github.com/poisotlab/ncbitaxonomy.jl
• Owner: PoisotLab
• License: mit
• Created: 2020-11-14T00:59:09.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2025-06-30T17:10:34.000Z (12 months ago)
• Last Synced: 2025-10-05T06:46:09.745Z (8 months ago)
• Topics: biodiversity, biodiversity-data, ivado, ncbi, ncbi-taxonomy, taxonomy, verena
• Language: Julia
• Homepage: https://poisotlab.github.io/NCBITaxonomy.jl/stable/
• Size: 2.83 MB
• Stars: 7
• Watchers: 3
• Forks: 2
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Zenodo: .zenodo.json

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README

          
# NCBI taxonomy

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![DOI](https://zenodo.org/badge/312718490.svg)](https://zenodo.org/badge/latestdoi/312718490)

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![Documentation](https://github.com/PoisotLab/NCBITaxonomy.jl/workflows/Documentation/badge.svg) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://ecojulia.github.io/NCBITaxonomy.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://ecojulia.github.io/NCBITaxonomy.jl/dev)

This package provides an interface to the [NCBI Taxonomy][ncbitax]. 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.

[ncbitax]: https://www.ncbi.nlm.nih.gov/taxonomy

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](https://docs.julialang.org/en/v1/manual/environment-variables/), or

exporting the `NCBITAXONOMY_PATH` environment variable.

This package is developed as part of the activities of the Viral Emergence

Research Initiative ([VERENA][verena]) consortium, with financial support from

the Institut de Valorisation des Données ([IVADO][ivado]) at Université de

Montréal.

[verena]: https://www.viralemergence.org/

[ivado]: https://ivado.ca/en/