This vignette will introduce users to the retrieval of taxonomic
information with myTAI. The taxonomy()
function (formerly) implemented in myTAI relies on the
powerful package taxize. More specifically,
the taxonomic information retrieval has been customized for the
myTAI standard and for organism specific information
retrieval.
While the previous taxonomy() function has been
deprecated since taxize() was pulled from
CRAN, users can nevertheless follow the taxonomy pipeline by installing
the taxize package and copy the old taxonomy
function.
# install taxize from CRAN
install.packages("taxize")
# if taxize is not available again
install.packages("remotes")
remotes::install_github("ropensci/taxize")Copy the taxonomy function:
open for the taxonomy function
Click on the copy icon to copy the function.
#' @title Retrieving Taxonomic Information of a Query Organism
#' @description This function takes the scientific name of a query organism
#' and returns selected output formats of taxonomic information for the corresponding organism.
#' @param organism a character string specifying the scientific name of a query organism.
#' @param db a character string specifying the database to query, e.g. \code{db} = \code{"itis"} or \code{"ncbi"}.
#' @param output a character string specifying the taxonomic information that shall be returned.
#' Implemented are: \code{output} = \code{"classification"}, \code{"taxid"}, or \code{"children"}.
#' @details This function is based on the powerful package \pkg{taxize} and implements
#' the customized retrieval of taxonomic information for a query organism.
#'
#' The following data bases can be selected to retrieve taxonomic information:
#'
#' \itemize{
#' \item \code{db = "itis"} : Integrated Taxonomic Information Service
#' \item \code{db = "ncbi"} : National Center for Biotechnology Information
#' }
#'
#'
#'
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' # retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
#' # from NCBI Taxonomy
#' taxonomy("Arabidopsis thaliana",db = "ncbi")
#'
#' # the same can be applied to database : "itis"
#' taxonomy("Arabidopsis thaliana",db = "itis")
#'
#' # retrieving the taxonomic hierarchy of "Arabidopsis"
#' taxonomy("Arabidopsis",db = "ncbi") # analogous : db = "ncbi" or "itis"
#'
#' # or just "Arabidopsis"
#' taxonomy("Arabidopsis",db = "ncbi")
#'
#' # retrieving the taxonomy id of the query organism and in the correspondning database
#' # taxonomy("Arabidopsis thaliana",db = "ncbi", output = "taxid")
#'
#' # the same can be applied to databases : "ncbi" and "itis"
#' taxonomy("Arabidopsis thaliana",db = "ncbi", output = "taxid")
#' taxonomy("Arabidopsis thaliana",db = "itis", output = "taxid")
#'
#'
#' # retrieve children taxa of the query organism stored in the correspondning database
#' taxonomy("Arabidopsis",db = "ncbi", output = "children")
#'
#' # the same can be applied to databases : "ncbi" and "itis"
#' taxonomy("Arabidopsis thaliana",db = "ncbi", output = "children")
#' taxonomy("Arabidopsis thaliana",db = "itis", output = "children")
#'
#' }
#' @references
#'
#' Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search and retrieval in R. F1000Research,
#' 2:191. URL: http://f1000research.com/articles/2-191/v2.
#'
#' Scott Chamberlain, Eduard Szocs, Carl Boettiger, Karthik Ram, Ignasi Bartomeus, and John Baumgartner
#' (2014) taxize: Taxonomic information from around the web. R package version 0.3.0.
#' https://github.com/ropensci/taxize
#' @export
taxonomy <- function(organism, db = "ncbi", output = "classification"){
if (!is.element(output,c("classification","taxid","children")))
stop ("The output '",output,"' is not supported by this function.")
if (!is.element(db,c("ncbi","itis")))
stop ("Database '",db,"' is not supported by this function.")
name <- id <- NULL
if (db == "ncbi")
tax_hierarchy <- as.data.frame(taxize::classification(taxize::get_uid(organism), db = "ncbi")[[1]])
else if (db == "itis")
tax_hierarchy <- as.data.frame(taxize::classification(taxize::get_tsn(organism), db = "itis")[[1]])
# tryCatch({colnames(tax_hierarchy) <- c("name","rank","id")},stop("The connection to ",db," did not work properly. Please check your internet connection or maybe the API did change.", call. = FALSE))
if(output == "classification"){
return(tax_hierarchy)
}
if(output == "taxid"){
return(dplyr::select(dplyr::filter(tax_hierarchy, name == organism),id))
}
if(output == "children"){
return(as.data.frame(taxize::children(organism, db = db)[[1]]))
}
}The taxonomy() function implemented in
myTAI can be used to classify genomes according to
phylogenetic classification into Phylostrata (Phylostratigraphy) or to
retrieve species specific taxonomic information when performing
Divergence Stratigraphy (see Introduction for details).
For larger taxonomy queries it may be useful to create an NCBI Account and set up an ENTREZ API KEY.
# install.packages(c("taxize", "usethis"))
taxize::use_entrez()
# Create your key from your (brand-new) account's.
# After generating your key set it as ENTREZ_KEY in .Renviron.
# ENTREZ_KEY='youractualkeynotthisstring'
# For that, use usethis::edit_r_environ()
usethis::edit_r_environ()Taxonomic Information Retrieval
The taxonomy() function to retrieve taxonomic
information.
retrieve taxonomy hierarchy
In the following example we will obtain the taxonomic hierarchy of
Arabidopsis thaliana from NCBI Taxonomy.
# retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
# from NCBI Taxonomy
taxonomy( organism = "Arabidopsis thaliana",
db = "ncbi",
output = "classification" ) name rank id
1 cellular organisms no rank 131567
2 Eukaryota superkingdom 2759
3 Viridiplantae kingdom 33090
4 Streptophyta phylum 35493
5 Streptophytina no rank 131221
6 Embryophyta no rank 3193
7 Tracheophyta no rank 58023
8 Euphyllophyta no rank 78536
9 Spermatophyta no rank 58024
10 Magnoliophyta no rank 3398
11 Mesangiospermae no rank 1437183
12 eudicotyledons no rank 71240
13 Gunneridae no rank 91827
14 Pentapetalae no rank 1437201
15 rosids subclass 71275
16 malvids no rank 91836
17 Brassicales order 3699
18 Brassicaceae family 3700
19 Camelineae tribe 980083
20 Arabidopsis genus 3701
21 Arabidopsis thaliana species 3702The organism argument takes the scientific name of a
query organism, the db argument specifies that database
from which the corresponding taxonomic information shall be retrieved,
e.g. ncbi (NCBI Taxonomy) and itis (Integrated
Taxonomic Information System) and the output argument
specifies the type of taxonomic information that shall be returned for
the query organism, e.g. classification,
taxid, or children.
The output of classification is a
data.frame storing the taxonomic hierarchy of
Arabidopsis thaliana starting with
cellular organisms up to Arabidopsis thaliana.
The first column stores the taxonomic name, the second column the
taxonomic rank, and the third column the NCBI Taxonomy id for
corresponding taxa.
Analogous classification information can be obtained
from different databases.
# retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
# from the Integrated Taxonomic Information System
taxonomy( organism = "Arabidopsis thaliana",
db = "itis",
output = "classification" ) name rank id
1 Plantae Kingdom 202422
2 Viridiplantae Subkingdom 954898
3 Streptophyta Infrakingdom 846494
4 Embryophyta Superdivision 954900
5 Tracheophyta Division 846496
6 Spermatophytina Subdivision 846504
7 Magnoliopsida Class 18063
8 Rosanae Superorder 846548
9 Brassicales Order 822943
10 Brassicaceae Family 22669
11 Arabidopsis Genus 23040The output argument allows you to directly access
taxonomy ids for a query organism or species.
retrieve taxonomy ID from ncbi
# retrieving the taxonomy id of the query organism from NCBI Taxonomy
taxonomy( organism = "Arabidopsis thaliana",
db = "ncbi",
output = "taxid" ) id
1 3702retrieve taxonomy ID from itis
# retrieving the taxonomy id of the query organism from Integrated Taxonomic Information Service
taxonomy( organism = "Arabidopsis",
db = "itis",
output = "taxid" ) id
1 23040So far, the following data bases can be accesses to retrieve taxonomic information:
-
db = "itis": Integrated Taxonomic Information Service -
db = "ncbi": National Center for Biotechnology Information
Retrieve Children Nodes
Another output supported by taxonomy() is
children that returns the immediate children taxa for a
query organism. This feature is useful to determine species
relationships for quantifying recent evolutionary conservation with
Divergence Stratigraphy.
retrieve children nodes from ncbi
# retrieve children taxa of the query organism stored in the correspondning database
taxonomy( organism = "Arabidopsis",
db = "ncbi",
output = "children" ) childtaxa_id childtaxa_name childtaxa_rank
1 1547872 Arabidopsis umezawana species
2 1328956 (Arabidopsis thaliana x Arabidopsis arenosa) x Arabidopsis suecica species
3 1240361 Arabidopsis thaliana x Arabidopsis arenosa species
4 869750 Arabidopsis thaliana x Arabidopsis lyrata species
5 412662 Arabidopsis pedemontana species
6 378006 Arabidopsis arenosa x Arabidopsis thaliana species
7 347883 Arabidopsis arenicola species
8 302551 Arabidopsis petrogena species
9 97980 Arabidopsis croatica species
10 97979 Arabidopsis cebennensis species
11 81970 Arabidopsis halleri species
12 59690 Arabidopsis kamchatica species
13 59689 Arabidopsis lyrata species
14 45251 Arabidopsis neglecta species
15 45249 Arabidopsis suecica species
16 38785 Arabidopsis arenosa species
17 3702 Arabidopsis thaliana speciesretrieve children nodes from itis
# retrieve children taxa of the query organism stored in the correspondning database
taxonomy( organism = "Arabidopsis",
db = "itis",
output = "children" ) parentname parenttsn rankname taxonname tsn
1 Arabidopsis 23040 Species Arabidopsis thaliana 23041
2 Arabidopsis 23040 Species Arabidopsis arenicola 823113
3 Arabidopsis 23040 Species Arabidopsis arenosa 823130
4 Arabidopsis 23040 Species Arabidopsis lyrata 823171These results allow us to choose subject organisms for
Divergence
Stratigraphy.