taxonomy: Retrieving Taxonomic Information of a Query Organism

In YTLogos/myTAI: Evolutionary Transcriptomics

Description

This function takes the scientific name of a query organism and returns selected output formats of taxonomic information for the corresponding organism.

Usage

taxonomy(organism, db = "ncbi", output = "classification")

Arguments

organism	a character string specifying the scientific name of a query organism.
db	a character string specifying the database to query, e.g. db = "itis" or "ncbi".
output	a character string specifying the taxonomic information that shall be returned. Implemented are: output = "classification", "taxid", or "children".

Details

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

Author(s)

Hajk-Georg Drost

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

Examples

## Not run: 
# 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")
 

## End(Not run)

YTLogos/myTAI documentation built on May 19, 2019, 1:46 a.m.