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Search web taxonomy sites and download data

README.md

taxize

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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 tutorial is can be found at http://ropensci.org/tutorials/taxize_tutorial.html

Contributors

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.

The following are URL's for API documentation, where to get API keys, and what prefix they have in function names.

Currently implemented in taxize

Souce Function prefix API Docs API key
Encylopedia of Life eol link link
Taxonomic Name Resolution Service tnrs link none
Integrated Taxonomic Information Service itis link none
Phylomatic phylomatic link none
uBio ubio link link
Global Names Resolver gnr link none
Global Names Index gni link none
IUCN Red List iucn link none
Tropicos tp link link
Plantminer plantminer link link
Theplantlist dot org tpl ** none
Catalogue of Life col link none
Global Invasive Species Database gisd *** none
National Center for Biotechnology Information ncbi none none
CANADENSYS Vascan name search API vascan link none

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

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

May be in taxize in the future...

Notes on the ITIS API

There are a lot of methods for the ITIS API. We have attempted to simplify the interface. Here are some notes:

The following are higher level functions that attempt to make interacting with the various methods easier. Some are new. The function on the left uses the functions on the right of the arrow. You can access functions on the right of the arrow as normal, but aren't shown in the main help file index to avoid cognitive load.

  • classification <- getfullhierarchyfromtsn
  • itis_downstream <- gethierarchydownfromtsn
  • itis_searchcommon <- searchbycommonnamebeginswith, searchbycommonnameendswith
  • get_tsn <- searchbycommonnamebeginswith, searchbycommonnameendswith, searchbycommonname, searchbyscientificname
  • comm2sci <- searchbycommonnamebeginswith, searchbycommonnameendswith, searchbycommonname, getscientificnamefromtsn
  • sci2comm <- searchbycommonnamebeginswith, searchbycommonnameendswith, searchbycommonname, getcommonnamesfromtsn, searchbyscientificname
  • synonyms <- getsynonymnamesfromtsn
  • itis_acceptname <- getacceptednamesfromtsn
  • itis_taxrank <- gettaxonomicranknamefromtsn, getranknames
  • itis_ping <- getdescription
  • itis_refs <- getpublicationsfromtsn
  • itis_getrecord <- getfullrecordfromtsn
  • itis_kingdomnames <- getkingdomnamefromtsn, getkingdomnames
  • itis_lsid <- getfullrecordfromlsid, getrecordfromlsid, gettsnfromlsid
  • itis_native <- getjurisdictionaloriginfromtsn, getjurisdictionoriginvalues, getjurisdictionvalues
  • itis_hierarchy <- getfullhierarchyfromtsn, gethierarchydownfromtsn, gethierarchyupfromtsn
  • itis_terms <- getitisterms, getitistermsfromcommonname, getitistermsfromscientificname

The following functions are not used in the higher level functions above, and aren't shown on the taxize index page, but are still available, e.g. FunctionName

getanymatchcount, searchforanymatch, searchforanymatchpaged, getexpertsfromtsn, getcommentdetailfromtsn, getcoremetadatafromtsn, getcoveragefromtsn, getcredibilityratingfromtsn, getcredibilityratings, getcurrencyfromtsn, getdatedatafromtsn, getlastchangedate, getothersourcesfromtsn, getparenttsnfromtsn, getglobalspeciescompletenessfromtsn, getgeographicdivisionsfromtsn, getgeographicvalues, getreviewyearfromtsn, gettaxonauthorshipfromtsn, gettaxonomicusagefromtsn, gettsnbyvernacularlanguage, getunacceptabilityreasonfromtsn, getvernacularlanguages

Quickstart

Install taxize

  • Stable version from CRAN:
install.packages("taxize")
library(taxize)
  • Or, development version from GitHub:
install.packages("devtools")
library(devtools)
install_github("taxize", "ropensci")
library(taxize)

A few examples (for more click here)

Get unique taxonomic identifier from NCBI

uids <- get_uid(c("Chironomus riparius", "Chaetopteryx"))

And retrieve classification

out <- classification(uids)
lapply(out, head)
[[1]]
                name         rank
1 cellular organisms      no rank
2          Eukaryota superkingdom
3       Opisthokonta      no rank
4            Metazoa      kingdom
5          Eumetazoa      no rank
6          Bilateria      no rank

[[2]]
                name         rank
1 cellular organisms      no rank
2          Eukaryota superkingdom
3       Opisthokonta      no rank
4            Metazoa      kingdom
5          Eumetazoa      no rank
6          Bilateria      no rank

Make a phylogeny from Phylomatic

Input the taxonomic names

taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")

Fetch the tree - the formatting of names and higher taxonmy is done within the function

tree <- phylomatic_tree(taxa=taxa, storedtree = "R20120829")

Plot

plot(tree)

Meta

Please report any issues or bugs](https://github.com/ropensci/taxize/issues).

License: CC0

This package is part of the rOpenSci project.

To cite package taxize in publications use:

To cite taxize in publications use:

  Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search
  and retrieval in R. F1000Research, 2:191. URL:
  http://f1000research.com/articles/2-191/v2.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {taxize - taxonomic search and retrieval in R},
    journal = {F1000Research},
    author = {{Scott Chamberlain} and {Eduard Szocs}},
    year = {2013},
    url = {http://f1000research.com/articles/2-191/v2},
  }

Get citation information for taxize in R doing citation(package = 'taxize')

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