Get the UID codes from NCBI for taxonomic names.

Retrieve the Unique Identifier (UID) of a taxon from NCBI taxonomy browser.

Usage

get_uid(
  sci_com,
  ask = TRUE,
  messages = TRUE,
  rows = NA,
  modifier = NULL,
  rank_query = NULL,
  division_filter = NULL,
  rank_filter = NULL,
  key = NULL,
  sciname = NULL,
  ...
)

as.uid(x, check = TRUE)

# S3 method for class 'uid'
as.uid(x, check = TRUE)

# S3 method for class 'character'
as.uid(x, check = TRUE)

# S3 method for class 'list'
as.uid(x, check = TRUE)

# S3 method for class 'numeric'
as.uid(x, check = TRUE)

# S3 method for class 'data.frame'
as.uid(x, check = TRUE)

# S3 method for class 'uid'
as.data.frame(x, ...)

get_uid_(sci_com, messages = TRUE, rows = NA, key = NULL, sciname = NULL, ...)

Arguments

sci_com: character; scientific or common name. Or, a taxon_state object (see taxon-state)
ask: logical; should get_uid be run in interactive mode? If TRUE and more than one TSN is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches.
messages: logical; If TRUE (default) the actual taxon queried is printed on the console.
rows: numeric; Any number from 1 to infinity. If the default NA, all rows are considered. Note that this function still only gives back a uid class object with one to many identifiers. See get_uid_() to get back all, or a subset, of the raw data that you are presented during the ask process.
modifier: (character) A modifier to the sci_com given. Options include: Organism, Scientific Name, Common Name, All Names, Division, Filter, Lineage, GC, MGC, Name Tokens, Next Level, PGC, Properties, Rank, Subtree, Synonym, Text Word. These are not checked, so make sure they are entered correctly, as is.
rank_query: (character) A taxonomic rank name to modify the query sent to NCBI. See rank_ref for possible options. Though note that some data sources use atypical ranks, so inspect the data itself for options. Optional. See Querying below.
division_filter: (character) A division (aka phylum) name to filter data after retrieved from NCBI. Optional. See Filtering below.
rank_filter: (character) A taxonomic rank name to filter data after retrieved from NCBI. See rank_ref for possible options. Though note that some data sources use atypical ranks, so inspect the data itself for options. Optional. See Filtering below.
key: (character) NCBI Entrez API key. optional. See Details.
sciname: Deprecated, see sci_com
...: Ignored
x: Input to as.uid()
check: logical; Check if ID matches any existing on the DB, only used in as.uid()

Value

A vector of taxonomic identifiers as an S3 class. If a taxon is not found an NA is given. If more than one identifier is found the function asks for user input if ask = TRUE, otherwise returns NA. If ask=FALSE and rows does not equal NA, then a data.frame is given back, but not of the uid class, which you can't pass on to other functions as you normally can.

See get_id_details for further details including attributes and exceptions

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Querying

The parameter rank_query is used in the search sent to NCBI, whereas rank_filter filters data after it comes back. The parameter modifier adds modifiers to the name. For example, modifier="Organism" adds that to the name, giving e.g., Helianthus[Organism].

Filtering

The parameters division_filter and rank_filter are not used in the search to the data provider, but are used in filtering the data down to a subset that is closer to the target you want. For all these parameters, you can use regex strings since we use grep() internally to match. Filtering narrows down to the set that matches your query, and removes the rest.

Beware

NCBI does funny things sometimes. E.g., if you search on Fringella morel, a slight misspelling of the genus name, and a non-existent epithet, NCBI gives back a morel fungal species. In addition, NCBI doesn't really do fuzzy searching very well, so if there is a slight mis-spelling in your names, you likely won't get what you are expecting. The lesson: clean your names before using this function. Other data sources are better about fuzzy matching.

Authentication

See taxize-authentication for help on authentication

Note that even though you can't pass in your key to as.uid functions, we still use your Entrez API key if you have it saved as an R option or environment variable.

HTTP version

We hard code http_version = 2L to use HTTP/1.1 in HTTP requests to the Entrez API. See curl::curl_symbols('CURL_HTTP_VERSION')

Author

Eduard Szoecs, eduardszoecs@gmail.com

Examples

if (FALSE) { # \dontrun{
get_uid(c("Chironomus riparius", "Chaetopteryx"))
get_uid(c("Chironomus riparius", "aaa vva"))

# When not found
get_uid("howdy")
get_uid(c("Chironomus riparius", "howdy"))

# Narrow down results to a division or rank, or both
## By modifying the query
### w/ modifiers to the name
get_uid(sci_com = "Aratinga acuticauda", modifier = "Organism")
get_uid(sci_com = "bear", modifier = "Common Name")

### w/ rank query
get_uid(sci_com = "Pinus", rank_query = "genus")
get_uid(sci_com = "Pinus", rank_query = "subgenus")
### division query doesn't really work, for unknown reasons, so not available

## By filtering the result
## Echinacea example
### Results w/o narrowing
get_uid("Echinacea")
### w/ division
get_uid(sci_com = "Echinacea", division_filter = "eudicots")
get_uid(sci_com = "Echinacea", division_filter = "sea urchins")

## Satyrium example
### Results w/o narrowing
get_uid(sci_com = "Satyrium")
### w/ division
get_uid(sci_com = "Satyrium", division_filter = "monocots")
get_uid(sci_com = "Satyrium", division_filter = "butterflies")

## Rank example
get_uid(sci_com = "Pinus")
get_uid(sci_com = "Pinus", rank_filter = "genus")
get_uid(sci_com = "Pinus", rank_filter = "subgenus")

# Fuzzy filter on any filtering fields
## uses grep on the inside
get_uid("Satyrium", division_filter = "m")

# specify rows to limit choices available
get_uid('Dugesia') # user prompt needed
get_uid('Dugesia', rows=1) # 2 choices, so returns only 1 row, so no choices
get_uid('Dugesia', ask = FALSE) # returns NA for multiple matches

# Go to a website with more info on the taxon
res <- get_uid("Chironomus riparius")
browseURL(attr(res, "uri"))

# Convert a uid without class information to a uid class
as.uid(get_uid("Chironomus riparius")) # already a uid, returns the same
as.uid(get_uid(c("Chironomus riparius","Pinus contorta"))) # same
as.uid(315567) # numeric
as.uid(c(315567,3339,9696)) # numeric vector, length > 1
as.uid("315567") # character
as.uid(c("315567","3339","9696")) # character vector, length > 1
as.uid(list("315567","3339","9696")) # list, either numeric or character
## dont check, much faster
as.uid("315567", check=FALSE)
as.uid(315567, check=FALSE)
as.uid(c("315567","3339","9696"), check=FALSE)
as.uid(list("315567","3339","9696"), check=FALSE)

(out <- as.uid(c(315567,3339,9696)))
data.frame(out)
as.uid( data.frame(out) )

# Get all data back
get_uid_("Puma concolor")
get_uid_("Dugesia")
get_uid_("Dugesia", rows=2)
get_uid_("Dugesia", rows=1:2)
get_uid_(c("asdfadfasd","Pinus contorta"))

# use curl options
get_uid("Quercus douglasii", verbose = TRUE)
} # }