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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 can be found at https://ropensci.org/tutorials/taxize.html

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), and Tropicos.

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

**: 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...

See the newdatasource tag in the issue tracker

Tutorial

For more examples see the tutorial

Installation

Stable version from CRAN

install.packages("taxize")

Development version from GitHub

Windows users install Rtools first.

install.packages("devtools")
devtools::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 sources knows about, then we can move forth acquiring more fun taxonomic data.

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

Retrieve classifications

Classifications - think of a species, then all the taxonomic ranks up from that species, like genus, family, order, class, kingdom.

out <- classification(uids)
lapply(out, head)
#> $`315576`
#>                 name         rank     id
#> 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
#> 
#> $`492549`
#>                 name         rank     id
#> 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

Immediate children

Get immediate children of Salmo. In this case, Salmo is a genus, so this gives species within the genus.

children("Salmo", db = 'ncbi')
#> $Salmo
#>    childtaxa_id                   childtaxa_name childtaxa_rank
#> 1       1509524  Salmo marmoratus x Salmo trutta        species
#> 2       1484545 Salmo cf. cenerinus BOLD:AAB3872        species
#> 3       1483130               Salmo zrmanjaensis        species
#> 4       1483129               Salmo visovacensis        species
#> 5       1483128                Salmo rhodanensis        species
#> 6       1483127                 Salmo pellegrini        species
#> 7       1483126                     Salmo opimus        species
#> 8       1483125                Salmo macedonicus        species
#> 9       1483124                Salmo lourosensis        species
#> 10      1483123                   Salmo labecula        species
#> 11      1483122                  Salmo farioides        species
#> 12      1483121                      Salmo chilo        species
#> 13      1483120                     Salmo cettii        species
#> 14      1483119                  Salmo cenerinus        species
#> 15      1483118                   Salmo aphelios        species
#> 16      1483117                    Salmo akairos        species
#> 17      1201173               Salmo peristericus        species
#> 18      1035833                   Salmo ischchan        species
#> 19       700588                     Salmo labrax        species
#> 20       237411              Salmo obtusirostris        species
#> 21       235141              Salmo platycephalus        species
#> 22       234793                    Salmo letnica        species
#> 23        62065                  Salmo ohridanus        species
#> 24        33518                 Salmo marmoratus        species
#> 25        33516                    Salmo fibreni        species
#> 26        33515                     Salmo carpio        species
#> 27         8032                     Salmo trutta        species
#> 28         8030                      Salmo salar        species
#> 
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "ncbi"

Downstream children to a rank

Get all species in the genus Apis

downstream("Apis", db = 'itis', downto = 'Species', verbose = FALSE)
#> $Apis
#>      tsn parentname parenttsn          taxonname rankid rankname
#> 1 154396       Apis    154395     Apis mellifera    220  species
#> 2 763550       Apis    154395 Apis andreniformis    220  species
#> 3 763551       Apis    154395        Apis cerana    220  species
#> 4 763552       Apis    154395       Apis dorsata    220  species
#> 5 763553       Apis    154395        Apis florea    220  species
#> 6 763554       Apis    154395 Apis koschevnikovi    220  species
#> 7 763555       Apis    154395   Apis nigrocincta    220  species
#> 
#> attr(,"class")
#> [1] "downstream"
#> attr(,"db")
#> [1] "itis"

Upstream taxa

Get all genera up from the species Pinus contorta (this includes the genus of the species, and its co-genera within the same family).

upstream("Pinus contorta", db = 'itis', upto = 'Genus', verbose=FALSE)
#> $`Pinus contorta`
#>      tsn parentname parenttsn   taxonname rankid rankname
#> 1  18031   Pinaceae     18030       Abies    180    genus
#> 2  18033   Pinaceae     18030       Picea    180    genus
#> 3  18035   Pinaceae     18030       Pinus    180    genus
#> 4 183396   Pinaceae     18030       Tsuga    180    genus
#> 5 183405   Pinaceae     18030      Cedrus    180    genus
#> 6 183409   Pinaceae     18030       Larix    180    genus
#> 7 183418   Pinaceae     18030 Pseudotsuga    180    genus
#> 8 822529   Pinaceae     18030  Keteleeria    180    genus
#> 9 822530   Pinaceae     18030 Pseudolarix    180    genus
#> 
#> attr(,"class")
#> [1] "upstream"
#> attr(,"db")
#> [1] "itis"

Get synonyms

synonyms("Acer drummondii", db="itis")
#> $`Acer drummondii`
#>   sub_tsn                    acc_name acc_tsn
#> 1  183671 Acer rubrum var. drummondii  526853
#> 2  183671 Acer rubrum var. drummondii  526853
#> 3  183671 Acer rubrum var. drummondii  526853
#>                      acc_author                        syn_author
#> 1 (Hook. & Arn. ex Nutt.) Sarg. (Hook. & Arn. ex Nutt.) E. Murray
#> 2 (Hook. & Arn. ex Nutt.) Sarg.             Hook. & Arn. ex Nutt.
#> 3 (Hook. & Arn. ex Nutt.) Sarg.     (Hook. & Arn. ex Nutt.) Small
#>                      syn_name syn_tsn
#> 1 Acer rubrum ssp. drummondii   28730
#> 2             Acer drummondii  183671
#> 3          Rufacer drummondii  183672
#> 
#> attr(,"class")
#> [1] "synonyms"
#> attr(,"db")
#> [1] "itis"

Get taxonomic IDs from many sources

get_ids(names="Salvelinus fontinalis", db = c('itis', 'ncbi'), verbose=FALSE)
#> $itis
#> Salvelinus fontinalis 
#>              "162003" 
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=162003"
#> attr(,"class")
#> [1] "tsn"
#> 
#> $ncbi
#> Salvelinus fontinalis 
#>                "8038" 
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.ncbi.nlm.nih.gov/taxonomy/8038"
#> 
#> attr(,"class")
#> [1] "ids"

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

get_ids(names="Poa annua", db = "gbif", rows=1)
#> $gbif
#> Poa annua 
#> "2704179" 
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] TRUE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
#> 
#> attr(,"class")
#> [1] "ids"

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)

get_ids_(c("Chironomus riparius", "Pinus contorta"), db = 'nbn', rows=1:3)
#> $nbn
#> $nbn$`Chironomus riparius`
#>               guid             scientificName    rank taxonomicStatus
#> 1 NBNSYS0000027573        Chironomus riparius species        accepted
#> 2 NHMSYS0001718585      Cryptohypnus riparius species         synonym
#> 3 NHMSYS0000864966 Damaeus (Damaeus) riparius species        accepted
#> 
#> $nbn$`Pinus contorta`
#>               guid                  scientificName       rank
#> 1 NBNSYS0000004786                  Pinus contorta    species
#> 2 NHMSYS0000494848  Pinus contorta subsp. contorta subspecies
#> 3 NHMSYS0000494858 Pinus contorta subsp. murreyana subspecies
#>   taxonomicStatus
#> 1        accepted
#> 2         synonym
#> 3         synonym
#> 
#> 
#> attr(,"class")
#> [1] "ids"

Common names from scientific names

sci2comm('Helianthus annuus', db = 'itis')
#> $`Helianthus annuus`
#> [1] "common sunflower" "sunflower"        "wild sunflower"  
#> [4] "annual sunflower"

Scientific names from common names

comm2sci("black bear", db = "itis")
#> $`black bear`
#> [1] "Ursus thibetanus"            "Ursus thibetanus"           
#> [3] "Ursus americanus luteolus"   "Ursus americanus americanus"
#> [5] "Ursus americanus"            "Ursus americanus"           
#> [7] "Chiropotes satanas"

Lowest common rank among taxa

spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang")
lowest_common(spp, db = "ncbi")
#>             name        rank      id
#> 21 Boreoeutheria below-class 1437010

Coerce codes to taxonomic id classes

numeric to uid

as.uid(315567)
#> [1] "315567"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/315567"

list to uid

as.uid(list("315567", "3339", "9696"))
#> [1] "315567" "3339"   "9696"  
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found" "found" "found"
#> attr(,"multiple_matches")
#> [1] FALSE FALSE FALSE
#> attr(,"pattern_match")
#> [1] FALSE FALSE FALSE
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/315567"
#> [2] "http://www.ncbi.nlm.nih.gov/taxonomy/3339"  
#> [3] "http://www.ncbi.nlm.nih.gov/taxonomy/9696"

Coerce taxonomic id classes to a data.frame

out <- as.uid(c(315567, 3339, 9696))
(res <- data.frame(out))
#>      ids class match multiple_matches pattern_match
#> 1 315567   uid found            FALSE         FALSE
#> 2   3339   uid found            FALSE         FALSE
#> 3   9696   uid found            FALSE         FALSE
#>                                           uri
#> 1 http://www.ncbi.nlm.nih.gov/taxonomy/315567
#> 2   http://www.ncbi.nlm.nih.gov/taxonomy/3339
#> 3   http://www.ncbi.nlm.nih.gov/taxonomy/9696

Contributors

Alphebetical

Road map

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

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Version

Install

install.packages('taxize')

Monthly Downloads

5,426

Version

0.8.9

License

MIT + file LICENSE

Issues

51

Pull Requests

0

Stars

279

Forks

62

Maintainer

Scott Chamberlain

Last Published

July 11th, 2017

Functions in taxize (0.8.9)

class2tree

Convert list of classifications to a tree.
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
apg

Get APG names
apg_families

MOBOT family names
col_children

Search Catalogue of Life for for direct children of a particular taxon.
col_classification

Search Catalogue of Life for taxonomic classifications.
bold_search

Search Barcode of Life for taxonomic IDs
children

Retrieve immediate children taxa for a given taxon name or ID.
apg_lookup

Lookup in the APGIII taxonomy and replace family names
apg_orders

MOBOT order names
eol_search

Search for terms in EOL database.
eubon

EUBON taxonomy search
eubon_capabilities

EUBON capabilities
eubon_children

EUBON children
eol_invasive

Search for presence of taxonomic names in EOL invasive species databases.
eol_pages

Search for pages in EOL database using a taxonconceptID.
gbif_parse

Parse taxon names using the GBIF name parser.
genbank2uid

Get NCBI taxonomy UID from GenBankID
col_downstream

Use Catalogue of Life to get downstream taxa to a given taxonomic level.
col_search

Search Catalogue of Life for taxonomic IDs
eubon_hierarchy

EUBON hierarchy
fungorum

Index Fungorum
get_ids

Retrieve taxonomic identifiers for a given taxon name.
get_iucn

Get a IUCN Redlist taxon
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
get_tsn

Get the TSN code for a search term.
gnr_resolve

Resolve names using Global Names Resolver.
ion

ION - Index to Organism Names
itis_terms

Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
get_seqs

Retrieve gene sequences from NCBI by accession number.
get_tolid

Get the OTT id for a search term
getkey

Function to get API key.
gisd_isinvasive

Check invasive species status for a set of species from GISD database
get_genes

Retrieve gene sequences from NCBI by accession number.
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
gni_details

Search for taxonomic name details using the Global Names Index.
gni_parse

Parse scientific names using EOL's name parser.
itis_getrecord

Get full ITIS record for one or more ITIS TSN's or lsid's.
itis_hierarchy

ITIS hierarchy
itis_name

Get taxonomic names for a given taxonomic name query.
itis_acceptname

Retrieve accepted TSN and name
itis_downstream

Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
iucn_id

Get an ID for a IUCN listed taxon
iucn_status

Extractor functions for iucn-class.
iucn_getname

Get any matching IUCN species names
nbn_search

Search UK National Biodiversity Network
nbn_synonyms

Return all synonyms for a taxon name with a given id from NBN
names_list

Get a random vector of species names.
nbn_classification

Search UK National Biodiversity Network database for taxonomic classification
rank_ref

Lookup-table for IDs of taxonomic ranks
rankagg

Aggregate data by given taxonomic rank
resolve

Resolve names from different data sources
sci2comm

Get common names from scientific names.
tol_resolve

Resolve names using Open Tree of Life (OTL) resolver
tp_acceptednames

Return all accepted names for a taxon name with a given id.
plantNames

Vector of plant species (genus - specific epithet) names from ThePlantList
plantminer

Search for taxonomy data from Plantminer.com
synonyms

Retrieve synonyms from various sources given input taxonomic names or identifiers
tax_agg

Aggregate species data to given taxonomic rank
tnrs

Phylotastic Taxonomic Name Resolution Service.
eol_dataobjects

Given the identifier for a data object, return all metadata about the object
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
get_boldid

Get the BOLD (Barcode of Life) code for a search term.
get_colid

Get the Catalogue of Life ID from taxonomic names.
get_natservid

Get NatureServe taxonomic ID for a taxon name
get_nbnid

Get the UK National Biodiversity Network ID from taxonomic names.
get_ubioid

Get the uBio id for a search term
get_uid

Get the UID codes from NCBI for taxonomic names.
tp_namereferences

Return all reference records for for a taxon name with a given id.
tp_refs

Return all reference records for for a taxon name with a given id.
tnrs_sources

TNRS sources
tp_search

Search Tropicos by scientific name, common name, or Tropicos ID.
tp_summary

Return summary data a taxon name with a given id.
upstream

Retrieve the upstream taxa for a given taxon name or ID.
iplant_resolve

iPlant name resolution
ipni_search

Search for names in the International Plant Names Index (IPNI).
itis_refs

Get references related to a ITIS TSN.
itis_taxrank

Retrieve taxonomic rank name from given TSN.
itis_native

Get jurisdiction data, i.e., native or not native in a region.
ncbi_children

Search NCBI for children of a taxon
ncbi_downstream

Retrieve all taxa names downstream in hierarchy for NCBI
ncbi_getbyname

Retrieve gene sequences from NCBI by taxon name and gene names.
ncbi_search

Search for gene sequences available for taxa from NCBI.
tax_name

Get taxonomic names for a given rank
tax_rank

Get rank for a given taxonomic name.
taxize_capwords

Capitalize the first letter of a character string.
iucn_summary

Get a summary from the IUCN Red List
lowest_common

Retrieve the lowest common taxon and rank for a given taxon name or ID
ping

Ping an API used in taxize to see if it's working.
plantGenusNames

Vector of plant genus names from ThePlantList
vascan_search

Search the CANADENSYS Vascan API.
comm2sci

Get scientific names from common names.
downstream

Retrieve the downstream taxa for a given taxon name or ID.
gbif_downstream

Retrieve all taxa names downstream in hierarchy for GBIF
gbif_name_usage

Lookup details for specific names in all taxonomies in GBIF.
get_eolid

Get the EOL ID from Encyclopedia of Life from taxonomic names.
taxize_cite

Get citations and licenses for data sources used in taxize
tp_dist

Return all distribution records for for a taxon name with a given id.
tp_namedistributions

Return all distribution records for for a taxon name with a given id.
taxize-defunct

Defunct functions in taxize
tp_accnames

Return all accepted names for a taxon name with a given id.
tp_classification

Return all synonyms for a taxon name with a given id.
ubio_id

Search uBio by namebank ID.
ubio_ping

uBio ping
tpl_get

Get The Plant List csv files.
tpl_search

A light wrapper around the taxonstand fxn to call Theplantlist.org database.
ubio_classification

uBio classification
ubio_classification_search

This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
taxize-package

Taxonomic Information from Around the Web
get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.
get_wiki

Get the page name for a Wiki taxon
get_wormsid

Get Worms ID for a taxon name
gni_search

Search for taxonomic names using the Global Names Index.
gnr_datasources

Get data sources for the Global Names Resolver.
itis_kingdomnames

Get kingdom names
itis_lsid

Get TSN from LSID
ncbi_get_taxon_summary

NCBI taxon information from uids
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
phylomatic_format

Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
scrapenames

Resolve names using Global Names Recognition and Discovery.
status_codes

Get HTTP status codes
taxize_ldfast

Replacement function for ldply that should be faster in all cases.
theplantlist

Lookup-table for family, genus, and species names for ThePlantList
tp_synonyms

Return all synonyms for a taxon name with a given id.
tpl_families

Get The Plant List families.
ubio_search

This function will return NameBankIDs that match given search terms
ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.