This function takes the scientific name of a query organism and returns selected output formats of taxonomic information for the corresponding organism.
taxonomy(organism, db = "ncbi", output = "classification")a character string specifying the scientific name of a query organism.
a character string specifying the database to query, e.g. db = "itis" or "ncbi".
a character string specifying the taxonomic information that shall be returned.
Implemented are: output = "classification", "taxid", or "children".
This function is based on the powerful package taxize and implements the customized retrieval of taxonomic information for a query organism.
The following data bases can be selected to retrieve taxonomic information:
db = "itis" : Integrated Taxonomic Information Service
db = "ncbi" : National Center for Biotechnology Information
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
if (FALSE) {
# 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")
}