ncbiTaxonomy: NCBI taxonomy database

In cstubben/genomes2: Genome sequencing project metadata

Description

Search the Entrez taxonomy database at NCBI

Usage

ncbiTaxonomy(term, summary=TRUE)

Arguments

term	either a valid Entrez search term or a vector of taxonomy Ids or names
summary	return results using Esummary (default) or Efetch

Details

This function uses either Esummary or Efetch to return taxonomy data from NCBI. The Efetch XML include parent ids and lineage tags not found in Esummary XML. The term may be also be a vector of taxonomy Ids (joined using a comma) or taxonomy names (joined using "OR").

Value

a data.frame

Author(s)

Chris Stubben

References

NCBI taxonomy database http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy

See Also

einfo for a list of fields in the taxonomy database.

Examples

## Not run: 
ncbiTaxonomy("Yersinia pestis")
ncbiTaxonomy("Yersinia pestis", summary=FALSE)
ncbiTaxonomy(c("Bacillus anthracis", "Yersinia pestis"))
ncbiTaxonomy("cellular organisms[Next Level]")  
# new Hantavirus species added in 2012
ncbiTaxonomy("Hantavirus[subtree] AND 2012[date] AND species[rank]") 

# can also use Lineage field with esummary
ncbiTaxonomy("Necocli virus[Lineage]")
# compare to efetch results
ncbiTaxonomy (1145238, FALSE)

## End(Not run)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.