taxize allows users to search over many taxonomic data sources for species names (scientific and common) and download up and downstream taxonomic hierarchical information - among other things.

The taxize book => https://taxize.dev

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore. They follow the format of service_whatitdoes. For example, gnr_resolve uses the Global Names Resolver API to resolve species names. General functions in the package that don’t hit a specific API don’t have two words separated by an underscore, e.g., classification.

You need API keys for Encyclopedia of Life (EOL), Tropicos, IUCN, and NatureServe.

SOAP

Note that a few data sources require SOAP web services, which are difficult to support in R across all operating systems. These include: Pan-European Species directories Infrastructure and Mycobank. Data sources that use SOAP web services have been moved to taxizesoap at https://github.com/ropensci/taxizesoap.

Currently implemented in taxize

Souce Function prefix API Docs API key
Encylopedia of Life eol link link
Taxonomic Name Resolution Service tnrs "api.phylotastic.org/tnrs" none
Integrated Taxonomic Information Service itis link none
Global Names Resolver gnr link none
Global Names Index gni link none
IUCN Red List iucn link link
Tropicos tp link link
Theplantlist dot org tpl ** none
Catalogue of Life col link none
National Center for Biotechnology Information ncbi none none
CANADENSYS Vascan name search API vascan link none
International Plant Names Index (IPNI) ipni none none
Barcode of Life Data Systems (BOLD) bold link none
National Biodiversity Network (UK) nbn link none
Index Fungorum fg none none
EU BON eubon link none
Index of Names (ION) ion link none
Open Tree of Life (TOL) tol link none
World Register of Marine Species (WoRMS) worms link none
NatureServe natserv link link
Wikipedia wiki link none
Kew's Plants of the World pow none none

**: There are none! We suggest using TPL and TPLck functions in the taxonstand package. We provide two functions to get bulk data: tpl_families and tpl_get.

***: There are none! The function scrapes the web directly.

May be in taxize in the future…

See the datasources tag in the issue tracker


Installation

Stable version from CRAN

Development version from GitHub

Windows users install Rtools first.

install.packages("remotes")
remotes::install_github("ropensci/taxize")
library('taxize')

Get unique taxonomic identifier from NCBI

Alot of taxize revolves around taxonomic identifiers. Because, as you know, names can be a mess (misspelled, synonyms, etc.), it’s better to get an identifier that a particular data source knows about, then we can move forth acquiring more fun taxonomic data.

Get taxonomic IDs from many sources

You can limit to certain rows when getting ids in any get_*() functions

Furthermore, you can just back all ids if that’s your jam with the get_*_() functions (all get_*() functions with additional _ underscore at end of function name)

Screencast

Contributing

See our CONTRIBUTING document.

Contributors

Alphebetical

Road map

Check out our milestones to see what we plan to get done for each version.

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