taxizedb

Automatically converts supported taxonomic databases into SQLite for unified querying, with support for the National Center for Biotechnology Information Taxonomy, the Integrated Taxonomic Information System, World Flora Online, the Catalogue of Life, the Global Biodiversity Information Facility, and Wikidata.
https://github.com/ropensci/taxizedb

Category: Sustainable Development
Sub Category: Taxonomy and Ontology

Keywords

itis r r-package rstats taxize taxonomic-databases taxonomy

Keywords from Contributors

biodiversity biology darwincore nomenclature ecology conservation cycle routes data-access weather

Last synced: about 11 hours ago
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Repository metadata

Tools for Working with Taxonomic SQL Databases

• Host: GitHub
• URL: https://github.com/ropensci/taxizedb
• Owner: ropensci
• License: other
• Created: 2016-03-15T16:40:20.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2025-10-28T14:47:45.000Z (7 months ago)
• Last Synced: 2026-05-07T10:05:05.632Z (6 days ago)
• Topics: itis, r, r-package, rstats, taxize, taxonomic-databases, taxonomy
• Language: R
• Homepage:
• Size: 453 KB
• Stars: 33
• Watchers: 4
• Forks: 8
• Open Issues: 17
• Releases: 8
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Codemeta: codemeta.json

README.Rmd

          ---
output: github_document
editor_options: 
  chunk_output_type: console
---


taxizedb
========

```{r echo=FALSE}
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  collapse = TRUE,
  comment = "#>"
)
```

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`taxizedb` - Tools for Working with Taxonomic Databases

Docs: 

`taxizedb` is an R package for interacting with taxonomic databases. Its functionality can be divided in two parts: 1. You can download the databases to your platform 2. You can query the downloaded databases to retrieve taxonomic information.

This two step approach is different from tools which interact with web services for each query, and has a number of advantages:

* Once you download a database you can work with it offline
* Once you download a database querying it is super fast
* As long as you store your database files all the queries in your analysis will be fully reproducible

## Data sources

When you download a database with `taxizedb` it will automatically convert it to SQLite and then all query functions will interact with this SQLite database. However, not all taxonomic databases are publicly available, or can be converted to SQLite. The following databases are supported:

- [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy)
- [ITIS](https://itis.gov/)
- [World Flora Online (WFO)](https://www.worldfloraonline.org/)
- [Catalogue of Life (COL)](https://www.catalogueoflife.org/)
- [Global Biodiversity Information Facility (GBIF)](https://www.gbif.org/)
- [Wikidata](https://zenodo.org/records/1213477)

Get in touch [in the issues](https://github.com/ropensci/taxizedb/issues) with
any ideas on new data sources.

## Data sources - legacy support

[The Plant List (TPL)](https://en.wikipedia.org/wiki/The_Plant_List) has been replaced by World Flora Online. The website seems to be down so `taxizedb` can no longer facilitate new downloads. However, already downloaded database files can still be queried using `taxizedb` functions, for reproducibility.

## Package API

This package for each data sources performs the following tasks:

* Downloaded taxonomic databases `db_download_*`
* Create `dplyr` SQL backend via `dbplyr::src_dbi` - `src_*` 
* Query and get data back into a data.frame - `sql_collect`
* Manage cached database files - `tdb_cache`
* Retrieve immediate descendents of a taxon - `children`
* Retrieve the taxonomic hierarchies from local database - `classification`
* Retrieve all taxa descending from a vector of taxa - `downstream`
* Convert species names to taxon IDs - `name2taxid`
* Convert taxon IDs to species names - `taxid2name`
* Convert taxon IDs to ranks - `taxid2rank`

You can use the `src` connections with `dplyr`, etc. to do operations downstream. Or use the database connection to do raw SQL queries.

## Installation

CRAN version

```{r eval=FALSE}
install.packages("taxizedb")
```

dev version

```{r eval=FALSE}
remotes::install_github("ropensci/taxizedb")
```

## Citation

To cite taxizedb in publications use:

* Chamberlain S, Arendsee Z, Stirling T (2023). taxizedb: Tools for Working with 'Taxonomic' Databases. R package version 0.3.1. 

## Meta

* Please [report any issues, bugs or feature requests](https://github.com/ropensci/taxizedb/issues).
* License: MIT
* Get citation information for `taxizedb` in R with `citation(package = 'taxizedb')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct). By contributing to this project, you agree to abide by its terms.

[![ropensci](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

        

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Owner metadata

• Name: rOpenSci
• Login: ropensci
• Email: info@ropensci.org
• Kind: organization
• Description:
• Website: https://ropensci.org/
• Location: Berkeley, CA
• Twitter: rOpenSci
• Company:
• Icon url: https://avatars.githubusercontent.com/u/1200269?v=4
• Repositories: 307
• Last ynced at: 2023-03-10T20:30:59.242Z
• Profile URL: https://github.com/ropensci

---

GitHub Events

Total

• Release event: 1
• Pull request event: 10
• Fork event: 2
• Issues event: 3
• Watch event: 3
• Issue comment event: 4
• Push event: 7

Last Year

• Release event: 1
• Pull request event: 4
• Fork event: 1
• Issues event: 2
• Watch event: 1
• Push event: 4

---

Committers metadata

Last synced: 2 days ago

Name	Email	Commits
Scott Chamberlain	m****s@g****m	139
Tamas Stirling	s****s@g****m	79
Zebulun Arendsee	a****e@i****u	46
Carl Boettiger	c****g@g****m	16
T D James	t****1	4
Maëlle Salmon	m****n@y****e	3
Rekyt	m****e@e****r	1
Gaopeng Li	l****c@g****m	1
rOpenSci Bot	m****t@g****m	1

Committer domains:

• ens-lyon.fr: 1
• iastate.edu: 1

---

Issue and Pull Request metadata

Last synced: 4 months ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/ropensci/taxizedb

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Package metadata

• Total packages: 3
• Total downloads:
  • cran: 316 last-month
  • conda: 30,246 total
• Total docker downloads: 88,618
• Total dependent packages: 0 (may contain duplicates)
• Total dependent repositories: 10 (may contain duplicates)
• Total versions: 17
• Total maintainers: 1

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Dependencies

Score: 17.797738500031542