imclab / taxize

Search web taxonomy sites and download data

taxize

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 here

Contributors

• Scott Chamberlain
• Eduard Szöcs
• Carl Boettiger
• Karthik Ram
• Ignasi Bartomeus
• John Baumgartner

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	here	here
Taxonomic Name Resolution Service	tnrs	here	none
Integrated Taxonomic Information Service	itis	here	none
Phylomatic	phylomatic	here	none
uBio	ubio	here	here
Global Names Resolver	gnr	here	none
Global Names Index	gni	here	none
IUCN Red List	iucn	here	none
Tropicos	tp	here	here
Plantminer	plantminer	here	here
Theplantlist dot org	tpl	**	none
Catalogue of Life	col	here	none
Global Invasive Species Database	gisd	***	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...

• Tree of Life web project
  • Their website
  • API docs
  • to be function prefix: tol
• Freshwaterecology - The Taxa and Autecology Database for Freshwater Organisms
  • Their website
  • API docs: There are none! The function scraps the web directly.
  • to be function prefix: fresh
  • Note: Currently only the macro-invertebrate database is supported!
• USDA Plants
• NatureServe
• Lichen Taxon dictionary
• MycoBank

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

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"))

Retrieving data for species ' Chironomus riparius '

Retrieving data for species ' Chaetopteryx '

And retrieve classification

out <- classification(uids)
lapply(out, head)

[[1]]
              ScientificName         Rank     UID
1         cellular organisms      no rank  131567
2                  Eukaryota superkingdom    2759
3               Opisthokonta      no rank   33154
4                    Metazoa      kingdom   33208
5                  Eumetazoa      no rank    6072
6                  Bilateria      no rank   33213

[[2]]
       ScientificName         Rank     UID
1  cellular organisms      no rank  131567
2           Eukaryota superkingdom    2759
3        Opisthokonta      no rank   33154
4             Metazoa      kingdom   33208
5           Eumetazoa      no rank    6072
6           Bilateria      no rank   33213

Make a phylogeny from Phylomatic

Input the taxonomic names

taxa <- c("Poa annua", "Abies procera", "Helianthus annuus")

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

tree <- phylomatic_tree(taxa=taxa, get = 'POST', informat='newick', method = "phylomatic", storedtree = "R20120829", taxaformat = "slashpath", outformat = "newick", clean = "true")

Plot

plot(tree)

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')