We are developing taxize as a package to allow 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 Encyclopedia of Life (EOL), the Universal Biological
Indexer and Organizer (uBio), Tropicos, and Plantminer.
Currently supported APIs are:
llc{
API prefix SOAP?
Encyclopedia of Life (EOL) eol FALSE
Integrated Taxonomic Information Service (ITIS) itis FALSE
Phylomatic phylomatic FALSE
uBio ubio 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
Plantminer plantminer FALSE
Theplantlist.org tpl FALSE
Catalogue of Life col FALSE
Global Invasive Species Database gisd 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
}
If the source above has a TRUE in the SOAP? column, it is not available if you
installed this package from CRAN. They are available from a different package called taxizesoap.
See the Github repo for how to install https://github.com/ropensci/taxizesoap