taxize-package: Taxonomic Information from Around the Web

Description About Currently supported APIs Catalogue of Life (COL) Author(s)

Description

This package interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.

About

Allows users to search over many websites for species names (scientific and common) and download up- and downstream taxonomic hierarchical information - and many other things.

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 some data sources. See taxize-authentication for more information.

Currently supported APIs

API prefix SOAP?
Encyclopedia of Life (EOL) eol FALSE
Taxonomic Name Resolution Service tnrs FALSE
Integrated Taxonomic Information Service (ITIS) itis FALSE
Global Names Resolver (from EOL/GBIF) gnr FALSE
Global Names Index (from EOL/GBIF) gni FALSE
IUCN Red List iucn FALSE
Tropicos (from Missouri Botanical Garden) tp FALSE
Theplantlist.org tpl FALSE
National Center for Biotechnology Information ncbi FALSE
CANADENSYS Vascan name search API vascan FALSE
International Plant Names Index (IPNI) ipni FALSE
World Register of Marine Species (WoRMS) worms TRUE
Barcode of Life Data Systems (BOLD) bold FALSE
Pan-European Species directories Infrastructure (PESI) pesi TRUE
Mycobank myco TRUE
National Biodiversity Network (UK) nbn FALSE
Index Fungorum fg FALSE
EU BON eubon FALSE
Index of Names (ION) ion FALSE
Open Tree of Life (TOL) tol FALSE
World Register of Marine Species (WoRMS) worms FALSE
NatureServe natserv FALSE

If the source above has a TRUE in the SOAP? column, it is not available in this package. They are available from a different package called taxizesoap. See the GitHub repo for how to install https://github.com/ropensci/taxizesoap

Catalogue of Life (COL)

COL introduced rate limiting recently in 2019 - which has made the API essentially unusable - CoL+ is coming soon and we'll incorporate it here when it's stable. See https://github.com/ropensci/colpluz for the R implementation for CoL+

Author(s)

Scott Chamberlain myrmecocystus@gmail.com

Eduard Szoecs eduardszoecs@gmail.com

Zachary Foster zacharyfoster1989@gmail.com

Carl Boettiger cboettig@gmail.com

Karthik Ram karthik@ropensci.org

Ignasi Bartomeus nacho.bartomeus@gmail.com

John Baumgartner johnbb@student.unimelb.edu.au

James O'Donnell jodonnellbio@gmail.com


taxize documentation built on Sept. 19, 2020, 1:06 a.m.